cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3469913.v1
title: Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

description: Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 in HeLa cells was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects.
DOI: 10.6084/m9.figshare.3469874
title: Reduced stability and intracellular transport of dsRNA contribute to poor RNAi response in lepidopteran insects

description: RNA interference (RNAi) has become a widely used reverse genetic tool to study gene function in eukaryotic organisms and is being developed as a technology for insect pest management. The efficiency of RNAi varies among organisms. Insects from different orders also display differential efficiency of RNAi, ranging from highly efficient (coleopterans) to very low efficient (lepidopterans). We investigated the reasons for varying RNAi efficiency between lepidopteran and coleopteran cell lines and also between the Colorado potato beetle<i>, Leptinotarsa decemlineata</i> and tobacco budworm<i>, Heliothis virescens</i>. The dsRNA either injected or fed was degraded faster in <i>H. virescens</i> than in <i>L. decemlineata</i>. Both lepidopteran and coleopteran cell lines and tissues efficiently took up the dsRNA. Interestingly, the dsRNA administered to coleopteran cell lines and tissues was taken up and processed to siRNA whereas the dsRNA was taken up by lepidopteran cell lines and tissues but no siRNA was detected in the total RNA isolated from these cell lines and tissues. The data included in this paper showed that the degradation and intracellular transport of dsRNA are the major factors responsible for reduced RNAi efficiency in lepidopteran insects.
DOI: 10.6084/m9.figshare.3469874.v2
title: Reduced stability and intracellular transport of dsRNA contribute to poor RNAi response in lepidopteran insects

description: RNA interference (RNAi) has become a widely used reverse genetic tool to study gene function in eukaryotic organisms and is being developed as a technology for insect pest management. The efficiency of RNAi varies among organisms. Insects from different orders also display differential efficiency of RNAi, ranging from highly efficient (coleopterans) to very low efficient (lepidopterans). We investigated the reasons for varying RNAi efficiency between lepidopteran and coleopteran cell lines and also between the Colorado potato beetle<i>, Leptinotarsa decemlineata</i> and tobacco budworm<i>, Heliothis virescens</i>. The dsRNA either injected or fed was degraded faster in <i>H. virescens</i> than in <i>L. decemlineata</i>. Both lepidopteran and coleopteran cell lines and tissues efficiently took up the dsRNA. Interestingly, the dsRNA administered to coleopteran cell lines and tissues was taken up and processed to siRNA whereas the dsRNA was taken up by lepidopteran cell lines and tissues but no siRNA was detected in the total RNA isolated from these cell lines and tissues. The data included in this paper showed that the degradation and intracellular transport of dsRNA are the major factors responsible for reduced RNAi efficiency in lepidopteran insects.
DOI: 10.6084/m9.figshare.3469874.v1
title: Reduced stability and intracellular transport of dsRNA contribute to poor RNAi response in lepidopteran insects

description: RNA interference (RNAi) has become a widely used reverse genetic tool to study gene function in eukaryotic organisms and is being developed as a technology for insect pest management. The efficiency of RNAi varies among organisms. Insects from different orders also display differential efficiency of RNAi, ranging from highly efficient (coleopterans) to very low efficient (lepidopterans). We investigated the reasons for varying RNAi efficiency between lepidopteran and coleopteran cell lines and also between the Colorado potato beetle<i>, Leptinotarsa decemlineata</i> and tobacco budworm<i>, Heliothis virescens</i>. The dsRNA either injected or fed was degraded faster in <i>H. virescens</i> than in <i>L. decemlineata</i>. Both lepidopteran and coleopteran cell lines and tissues efficiently took up the dsRNA. Interestingly, the dsRNA administered to coleopteran cell lines and tissues was taken up and processed to siRNA whereas the dsRNA was taken up by lepidopteran cell lines and tissues but no siRNA was detected in the total RNA isolated from these cell lines and tissues. The data included in this paper showed that the degradation and intracellular transport of dsRNA are the major factors responsible for reduced RNAi efficiency in lepidopteran insects.
DOI: 10.6084/m9.figshare.3469829
title: Regions of variable DNA methylation in human placenta associated with newborn neurobehavior

description: The placenta regulates the <i>in utero</i> environment and functionally impacts fetal development. Candidate gene studies identified variation in placental DNA methylation is associated with newborn neurologic and behavioral outcomes including movement quality, lethargic behavior, attention, and arousal. We sought to identify novel regions of variable DNA methylation associated with newborn attention, lethargy, quality of movement, and arousal by performing an epigenome-wide association study in 335 infants from a US birth cohort. Methylation status was quantified using the Illumina HumanMethylation450 BeadChip array and associations to newborn outcomes assessed by the NICU Network Neurobehavioral Scales (NNNS) were identified while incorporating established bioinformatics algorithms to control for confounding by cell type composition. Methylation of CpGs within <i>FHIT</i> (cg15970800) and <i>ANKRD11</i> (cg16710656) demonstrated genome-wide significance (<i>P</i> &lt; 1.8 × 10<sup>−7</sup>) in specific associations with infant attention. CpGs whose differential methylation was associated with all 4 neurobehavioral outcomes were common to 50 genes involved in biological processes relating to cellular adhesion and nervous system development. Comprehensive methylation profiling identified relationships between methylation of <i>FHIT</i> and <i>ANKRD11</i>, which have been previously linked to neurodevelopment and behavioral outcomes in genetic association studies. Subtle changes in DNA methylation of these genes within the placenta may impact normal variation of a newborn's ability to alter and track visual and auditory stimuli. Gene ontology analysis suggested that those genes with variable methylation related to these outcomes are over-represented in biological pathways involved in brain development and placental physiology, supportive of our hypothesis for a key role of the placenta in neurobehavioral outcomes.
DOI: 10.6084/m9.figshare.3469829.v2
title: Regions of variable DNA methylation in human placenta associated with newborn neurobehavior

description: The placenta regulates the <i>in utero</i> environment and functionally impacts fetal development. Candidate gene studies identified variation in placental DNA methylation is associated with newborn neurologic and behavioral outcomes including movement quality, lethargic behavior, attention, and arousal. We sought to identify novel regions of variable DNA methylation associated with newborn attention, lethargy, quality of movement, and arousal by performing an epigenome-wide association study in 335 infants from a US birth cohort. Methylation status was quantified using the Illumina HumanMethylation450 BeadChip array and associations to newborn outcomes assessed by the NICU Network Neurobehavioral Scales (NNNS) were identified while incorporating established bioinformatics algorithms to control for confounding by cell type composition. Methylation of CpGs within <i>FHIT</i> (cg15970800) and <i>ANKRD11</i> (cg16710656) demonstrated genome-wide significance (<i>P</i> &lt; 1.8 × 10<sup>−7</sup>) in specific associations with infant attention. CpGs whose differential methylation was associated with all 4 neurobehavioral outcomes were common to 50 genes involved in biological processes relating to cellular adhesion and nervous system development. Comprehensive methylation profiling identified relationships between methylation of <i>FHIT</i> and <i>ANKRD11</i>, which have been previously linked to neurodevelopment and behavioral outcomes in genetic association studies. Subtle changes in DNA methylation of these genes within the placenta may impact normal variation of a newborn's ability to alter and track visual and auditory stimuli. Gene ontology analysis suggested that those genes with variable methylation related to these outcomes are over-represented in biological pathways involved in brain development and placental physiology, supportive of our hypothesis for a key role of the placenta in neurobehavioral outcomes.
DOI: 10.6084/m9.figshare.3469829.v1
title: Regions of Variable DNA Methylation in Human Placenta Associated with Newborn Neurobehavior

description: The placenta regulates the <i>in utero</i> environment and functionally impacts fetal development. Candidate gene studies identified variation in placental DNA methylation is associated with newborn neurologic and behavioral outcomes including movement quality, lethargic behavior, attention, and arousal. We sought to identify novel regions of variable DNA methylation associated with newborn attention, lethargy, quality of movement, and arousal by performing an epigenome-wide association study in 335 infants from a US birth cohort. Methylation status was quantified using the Illumina HumanMethylation450 BeadChip array and associations to newborn outcomes assessed by the NICU Network Neurobehavioral Scales (NNNS) were identified while incorporating established bioinformatics algorithms to control for confounding by cell type composition. Methylation of CpGs within <i>FHIT</i> (cg15970800) and <i>ANKRD11</i> (cg16710656) demonstrated genome-wide significance (<i>P</i>&lt;1.8×10<sup>−7</sup>) in specific associations with infant attention. CpGs whose differential methylation was associated with all four neurobehavioral outcomes were common to 50 genes involved in biological processes relating to cellular adhesion and nervous system development. Comprehensive methylation profiling identified relationships between methylation of <i>FHIT</i> and <i>ANKRD11</i>, which have been previously linked to neurodevelopment and behavioral outcomes in genetic association studies. Subtle changes in DNA methylation of these genes within the placenta may impact normal variation of a newborn's ability to alter and track visual and sound stimuli. Gene ontology analysis suggested that those genes with variable methylation related to these outcomes are over-represented in biological pathways involved in brain development and placental physiology, supportive of our hypothesis for a key role of the placenta in neurobehavioral outcomes.
DOI: 10.6084/m9.figshare.3469817
title: Do cocar ao catálogo: a representação bibliográfica da autoria indígena no Brasil

description: O presente trabalho possui como temática principal a representaçãobibliográfica do conhecimento indígena registrado, especificamente sobre arepresentação da autoria indígena nos registros bibliográficos. Enquantorecursos informacionais, são analisados aqueles que compõem ou poderãocompor os acervos de bibliotecas e unidades de informação, considerando-seaqui os materiais bibliográficos publicados. Tem como objetivo geral discorrersobre a representação bibliográfica de obras elaboradas por povos indígenasbrasileiros. O foco está na representação da autoria de obras com carátercoletivo, ou seja, de obras emanadas do conhecimento da comunidadeindígena como um povo e não da autoria individual indígena. Trata-se de umapesquisa exploratória, que pode ser compreendida em três momentos distintos:1) pesquisa bibliográfica, que contempla o levantamento bibliográfico; 2) coletade dados por entrevista, recorrendo aos autores indígenas brasileiros paraapresentar a visão dos indígenas sobre as questões autorais; 3) pesquisadocumental, que busca analisar e exemplificar a representação bibliográfica daautoria indígena. O levantamento bibliográfico forneceu a base para realizaçãoda entrevista e coleta de dados dos materiais publicados. A entrevista foirealizada com quatro autores indígenas de diferentes povos, seguindo umroteiro semi-estruturado. Para a análise dos materiais bibliográficos recorreu-seà duas listas compiladas por Freire (2005) e Santos (2014). Em tais listas foipossível verificar a diversidade de tipos de materiais e temáticas produzidospelos povos indígenas, de criação individual e produção coletiva. A análise dosdados apresenta alguns exemplos de livros publicados, evidenciando questõesreferentes ao conceito de autoria apresentado nos livros e nas entrevistas comos fundamentos apresentados no referencial teórico. Por fim, apresenta-se umaproposta para a representação da autoria indígena, com base nos dadosanalisados e nos estudos teóricos acerca da Organização e Representação doConhecimento. Conclui-se que pensar em políticas de representaçãobibliográfica que contemplem a representação da autoria indígena é, nãosomente desejável, quanto um compromisso com os povos originários, a fim degarantir o reconhecimento do valor de seus saberes ancestrais e ao seu direitoà auto representação social, respeitando sua origem e identidade cultural.Observa-se também que o registro da autoria de povos indígenas narepresentação bibliográfica além de evidenciar o reconhecimento desses povoscomo os detentores e criadores de seus conhecimentos, trata-se também deum resgate e fortalecimento da própria identidade do povo brasileiro.
DOI: 10.6084/m9.figshare.3469817.v3
title: Do cocar ao catálogo: a representação bibliográfica da autoria indígena no Brasil

description: O presente trabalho possui como temática principal a representaçãobibliográfica do conhecimento indígena registrado, especificamente sobre arepresentação da autoria indígena nos registros bibliográficos. Enquantorecursos informacionais, são analisados aqueles que compõem ou poderãocompor os acervos de bibliotecas e unidades de informação, considerando-seaqui os materiais bibliográficos publicados. Tem como objetivo geral discorrersobre a representação bibliográfica de obras elaboradas por povos indígenasbrasileiros. O foco está na representação da autoria de obras com carátercoletivo, ou seja, de obras emanadas do conhecimento da comunidadeindígena como um povo e não da autoria individual indígena. Trata-se de umapesquisa exploratória, que pode ser compreendida em três momentos distintos:1) pesquisa bibliográfica, que contempla o levantamento bibliográfico; 2) coletade dados por entrevista, recorrendo aos autores indígenas brasileiros paraapresentar a visão dos indígenas sobre as questões autorais; 3) pesquisadocumental, que busca analisar e exemplificar a representação bibliográfica daautoria indígena. O levantamento bibliográfico forneceu a base para realizaçãoda entrevista e coleta de dados dos materiais publicados. A entrevista foirealizada com quatro autores indígenas de diferentes povos, seguindo umroteiro semi-estruturado. Para a análise dos materiais bibliográficos recorreu-seà duas listas compiladas por Freire (2005) e Santos (2014). Em tais listas foipossível verificar a diversidade de tipos de materiais e temáticas produzidospelos povos indígenas, de criação individual e produção coletiva. A análise dosdados apresenta alguns exemplos de livros publicados, evidenciando questõesreferentes ao conceito de autoria apresentado nos livros e nas entrevistas comos fundamentos apresentados no referencial teórico. Por fim, apresenta-se umaproposta para a representação da autoria indígena, com base nos dadosanalisados e nos estudos teóricos acerca da Organização e Representação doConhecimento. Conclui-se que pensar em políticas de representaçãobibliográfica que contemplem a representação da autoria indígena é, nãosomente desejável, quanto um compromisso com os povos originários, a fim degarantir o reconhecimento do valor de seus saberes ancestrais e ao seu direitoà auto representação social, respeitando sua origem e identidade cultural.Observa-se também que o registro da autoria de povos indígenas narepresentação bibliográfica além de evidenciar o reconhecimento desses povoscomo os detentores e criadores de seus conhecimentos, trata-se também deum resgate e fortalecimento da própria identidade do povo brasileiro.
DOI: 10.6084/m9.figshare.3469805
title: DFT study of the reaction between TBD, 4-methyl benzylalcohol, and two molecule of 1-O-methyl-2,3-O-isopropylidene-4,6-O-carbonate-α-ᴅ-mannopyranose (ring-opening polymerization propagation step via a secondary alcohol chain)

description: Data to support article: Polymers from Sugars and CO<sub>2</sub>: Synthesis and Polymerization of a ᴅ-Mannose-Based Cyclic Carbonate DOI: 10.6084/m9.figshare.3469805 <br> Authors: Georgina L. Gregory, <sup>[a] [b]</sup> Liliana M. Jenisch,<sup>[a]</sup> Bethan Charles, <sup>[a] [b]</sup> Gabriele Kociok-Köhn<sup>[c] </sup>and Antoine Buchard<sup>[a] </sup>*<sup><br></sup> <sup>[a] Department of Chemistry, University of Bath, Bath BA2 7AY, UK<br>[b] EPSRC Centre for Doctoral Training in Sustainable Chemical Technologies, University of Bath, Bath BA2 7AY, UK<br>[c] Chemical Characterisation and Analysis Facility (CCAF), University of Bath, Bath BA2 7AY, UK</sup>DFT study: - DFT optimized geometries and computed free enthalpies of local minima (intermediates) and local maxima (transition states) were used to investigate the mechanism of the reaction between TBD, 4-methylbenzyl alcohol and 2 molecule of D-mannose based monomer<b> 1 </b>(1-O-methyl-2,3-O-isopropylidene-4,6-O-carbonate-α-ᴅ-mannopyranose)<b><sub> </sub></b>to account for the propagation step of ring-opening polymerization<b>, </b>via a secondary alcohol chain intermediate.<b><sub><br></sub></b> Protocols: <br>rwB97XD/6-311++G(d,p)/6-31+G(d)cpcm=dichloromethane/T=298.15K<br> Content: - Gaussian09 rev D.01 output files- ROP_propagation from a secondary alcohol.pdf, illustrating the calculations made and summarizing the free enthalpies computed.
DOI: 10.6084/m9.figshare.3469805.v1
title: DFT study of the reaction between TBD, 4-methyl benzylalcohol, and two molecule of 1-O-methyl-2,3-O-isopropylidene-4,6-O-carbonate-α-ᴅ-mannopyranose (ring-opening polymerization propagation step via a secondary alcohol chain)

description: Data to support article: Polymers from Sugars and CO<sub>2</sub>: Synthesis and Polymerization of a ᴅ-Mannose-Based Cyclic Carbonate DOI: 10.6084/m9.figshare.3469805 <br> Authors: Georgina L. Gregory, <sup>[a] [b]</sup> Liliana M. Jenisch,<sup>[a]</sup> Bethan Charles, <sup>[a] [b]</sup> Gabriele Kociok-Köhn<sup>[c] </sup>and Antoine Buchard<sup>[a] </sup>*<sup><br></sup> <sup>[a] Department of Chemistry, University of Bath, Bath BA2 7AY, UK<br>[b] EPSRC Centre for Doctoral Training in Sustainable Chemical Technologies, University of Bath, Bath BA2 7AY, UK<br>[c] Chemical Characterisation and Analysis Facility (CCAF), University of Bath, Bath BA2 7AY, UK</sup>DFT study: - DFT optimized geometries and computed free enthalpies of local minima (intermediates) and local maxima (transition states) were used to investigate the mechanism of the reaction between TBD, 4-methylbenzyl alcohol and 2 molecule of D-mannose based monomer<b> 1 </b>(1-O-methyl-2,3-O-isopropylidene-4,6-O-carbonate-α-ᴅ-mannopyranose)<b><sub> </sub></b>to account for the propagation step of ring-opening polymerization<b>, </b>via a secondary alcohol chain intermediate.<b><sub><br></sub></b> Protocols: <br>rwB97XD/6-311++G(d,p)/6-31+G(d)cpcm=dichloromethane/T=298.15K<br> Content: - Gaussian09 rev D.01 output files- ROP_propagation from a secondary alcohol.pdf, illustrating the calculations made and summarizing the free enthalpies computed.
DOI: 10.6084/m9.figshare.3469784
title: Metabolomic analyses reveal that anti-aging metabolites are depleted by palmitate but increased by oleate <i>in vivo</i>

description: Recently, we reported that saturated and unsaturated fatty acids trigger autophagy through distinct signal transduction pathways. Saturated fatty acids like palmitate (PA) induce autophagic responses that rely on phosphatidylinositol 3-kinase, catalytic subunit type 3 (PIK3C3, best known as VPS34) and beclin 1 (BECN1). Conversely, unsaturated fatty acids like oleate (OL) promote non-canonical, PIK3C3- and BECN1-independent autophagy. Here, we explored the metabolic effects of autophagy-inducing doses of PA and OL in mice. Mass spectrometry coupled to principal component analysis revealed that PA and OL induce well distinguishable changes in circulating metabolites as well as in the metabolic profile of the liver, heart, and skeletal muscle. Importantly, PA (but not OL) causes the depletion of multiple autophagy-inhibitory amino acids in the liver. Conversely, OL (but not PA) increased the hepatic levels of nicotinamide adenine dinucleotide (NAD), an obligate co-factor for autophagy-stimulatory enzymes of the sirtuin family. Moreover, PA (but not OL) raised the concentrations of acyl-carnitines in the heart, a phenomenon that perhaps is linked to its cardiotoxicity. PA also depleted the liver from spermine and spermidine, 2 polyamines have been ascribed with lifespan-extending activity. The metabolic changes imposed by unsaturated and saturated fatty acids may contribute to their health-promoting and health-deteriorating effects, respectively.
DOI: 10.6084/m9.figshare.3469784.v1
title: Metabolomic analyses reveal that anti-aging metabolites are depleted by palmitate but increased by oleate <i>in vivo</i>

description: Recently, we reported that saturated and unsaturated fatty acids trigger autophagy through distinct signal transduction pathways. Saturated fatty acids like palmitate (PA) induce autophagic responses that rely on phosphatidylinositol 3-kinase, catalytic subunit type 3 (PIK3C3, best known as VPS34) and beclin 1 (BECN1). Conversely, unsaturated fatty acids like oleate (OL) promote non-canonical, PIK3C3- and BECN1-independent autophagy. Here, we explored the metabolic effects of autophagy-inducing doses of PA and OL in mice. Mass spectrometry coupled to principal component analysis revealed that PA and OL induce well distinguishable changes in circulating metabolites as well as in the metabolic profile of the liver, heart, and skeletal muscle. Importantly, PA (but not OL) causes the depletion of multiple autophagy-inhibitory amino acids in the liver. Conversely, OL (but not PA) increased the hepatic levels of nicotinamide adenine dinucleotide (NAD), an obligate co-factor for autophagy-stimulatory enzymes of the sirtuin family. Moreover, PA (but not OL) raised the concentrations of acyl-carnitines in the heart, a phenomenon that perhaps is linked to its cardiotoxicity. PA also depleted the liver from spermine and spermidine, 2 polyamines have been ascribed with lifespan-extending activity. The metabolic changes imposed by unsaturated and saturated fatty acids may contribute to their health-promoting and health-deteriorating effects, respectively.