cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1246749
title: DNA end resection is needed for the repair of complex lesions in G1-phase human cells

description: ABSTRACTRepair of DNA double strand breaks (DSBs) is influenced by the chemical complexity of the lesion. Clustered lesions (complex DSBs) are generally considered more difficult to repair and responsible for early and late cellular effects after exposure to genotoxic agents. Resection is commonly used by the cells as part of the homologous recombination (HR) pathway in S- and G2-phase. In contrast, DNA resection in G1-phase may lead to an error-prone microhomology-mediated end joining. We induced DNA lesions with a wide range of complexity by irradiation of mammalian cells with X-rays or accelerated ions of different velocity and mass. We found replication protein A (RPA) foci indicating DSB resection both in S/G2- and G1-cells, and the fraction of resection-positive cells correlates with the severity of lesion complexity throughout the cell cycle. Besides RPA, Ataxia telangiectasia and Rad3-related (ATR) was recruited to complex DSBs both in S/G2- and G1-cells. Resection of complex DSBs is driven by meiotic recombination 11 homolog A (MRE11), CTBP-interacting protein (CtIP), and exonuclease 1 (EXO1) but seems not controlled by the Ku heterodimer or by phosphorylation of H2AX. Reduced resection capacity by CtIP depletion increased cell killing and the fraction of unrepaired DSBs after exposure to densely ionizing heavy ions, but not to X-rays. We conclude that in mammalian cells resection is essential for repair of complex DSBs in all phases of the cell-cycle and targeting this process sensitizes mammalian cells to cytotoxic agents inducing clustered breaks, such as in heavy-ion cancer therapy.
DOI: 10.6084/m9.figshare.1246794.v2
title: Floristic survey of Restinga Forests in southern Bahia reveals the effect of geography on community composition

description: The Restinga forests of southern Bahia are found over coastal sandy Quaternary sediments. Their flora is poorly known and the present study aimed to assess their floristic composition. We surveyed four sites at Maraú and Itacaré municipalities and identified 302 angiosperm species belonging to 184 genera of 75 families. The species richest families were Fabaceae (35 species), Myrtaceae (25), Rubiaceae (21), Sapotaceae (13), Bromeliaceae (12), Annonaceae (11), Erythroxylaceae (10), Melastomataceae (9), and Apocynaceae (8). Local flora includes elements with distribution restricted to Mata Atlântica domain, disjunct between Amazon and Mata Atlântica domains, and those occupying moist forests and dry vegetation of central Brazil. We also tested the hypothesis that floristic composition of the Restinga forests is influenced by geographically close wet forests through cluster and principal component analyzes with eleven Restinga forest and nine wet forest of Mata Atlântica domain sites. The results support five main groups, most of them include both Restinga forest sites and adjacent wet forests, thus corroborating the hypothesis that geographical proximity to floristic stock of wet forests have great influence in floristic composition of Restinga forests. This is the supplementary material cited on the paper.
DOI: 10.6084/m9.figshare.1246795.v1
title: AMIANTO . EL COMERCIO DE LA MUERTE

description: Análisis del documental LA TRAMA DEL AMIANTO
DOI: 10.6084/m9.figshare.1246794.v1
title: Supplementary-material

description: Suplementary material from the article "Floristic survey of Restinga Forests in southern Bahia reveals the effect of geography on community composition" by Fernandes & Queiroz
DOI: 10.6084/m9.figshare.1246749.v1
title: DNA end resection is needed for the repair of complex lesions in G1-phase human cells

description: ABSTRACTRepair of DNA double strand breaks (DSBs) is influenced by the chemical complexity of the lesion. Clustered lesions (complex DSBs) are generally considered more difficult to repair and responsible for early and late cellular effects after exposure to genotoxic agents. Resection is commonly used by the cells as part of the homologous recombination (HR) pathway in S- and G2-phase. In contrast, DNA resection in G1-phase may lead to an error-prone microhomology-mediated end joining. We induced DNA lesions with a wide range of complexity by irradiation of mammalian cells with X-rays or accelerated ions of different velocity and mass. We found replication protein A (RPA) foci indicating DSB resection both in S/G2- and G1-cells, and the fraction of resection-positive cells correlates with the severity of lesion complexity throughout the cell cycle. Besides RPA, Ataxia telangiectasia and Rad3-related (ATR) was recruited to complex DSBs both in S/G2- and G1-cells. Resection of complex DSBs is driven by meiotic recombination 11 homolog A (MRE11), CTBP-interacting protein (CtIP), and exonuclease 1 (EXO1) but seems not controlled by the Ku heterodimer or by phosphorylation of H2AX. Reduced resection capacity by CtIP depletion increased cell killing and the fraction of unrepaired DSBs after exposure to densely ionizing heavy ions, but not to X-rays. We conclude that in mammalian cells resection is essential for repair of complex DSBs in all phases of the cell-cycle and targeting this process sensitizes mammalian cells to cytotoxic agents inducing clustered breaks, such as in heavy-ion cancer therapy.
DOI: 10.6084/m9.figshare.1246745
title: Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons

description: In the mammalian genome, each histone family contains multiple replication-dependent paralogs, which are found in clusters where their transcription is thought to be coupled to the cell cycle. Here, we wanted to interrogate the transcriptional regulation of these paralogs during retinal development and aging. We employed deep sequencing, quantitative PCR, <i>in situ</i> hybridization (ISH), and microarray analysis, which revealed that replication-dependent histone genes were not only transcribed in progenitor cells but also in differentiating neurons. Specifically, by ISH analysis we found that different histone genes were actively transcribed in a subset of neurons between postnatal day 7 and 14. Interestingly, within a histone family, not all paralogs were transcribed at the same level during retinal development. For example, expression of <i>Hist1h1b</i> was higher embryonically, while that of <i>Hist1h1c</i> was higher postnatally. Finally, expression of replication-dependent histone genes was also observed in the aging retina. Moreover, transcription of replication-dependent histones was independent of rapamycin-mediated mTOR pathway inactivation. Overall, our data suggest the existence of variant nucleosomes produced by the differential expression of the replication-dependent histone genes across retinal development. Also, the expression of a subset of replication-dependent histone isotypes in senescent neurons warrants re-examining these genes as “replication-dependent.” Thus, our findings underscore the importance of understanding the transcriptional regulation of replication-dependent histone genes in the maintenance and functioning of neurons.
DOI: 10.6084/m9.figshare.1246743
title: Indole-3-carbinol and its N-alkoxy derivatives preferentially target ER<b>α</b>-positive breast cancer cells

description: Indole-3-carbinol (I3C) is a natural anti-carcinogenic compound found at high concentrations in <i>Brassica</i> vegetables. I3C was recently reported to inhibit neutrophil elastase (NE) activity, while consequently limiting the proteolytic processing of full length cyclin E into pro-tumorigenic low molecular weight cyclin E (LMW-E). In this study, we hypothesized that inhibition of NE activity and resultant LMW-E generation is critical to the anti-tumor effects of I3C. LMW-E was predominately expressed by ERα-negative breast cancer cell lines. However, ERα-positive cell lines demonstrated the greatest sensitivity to the anti-tumor effects of I3C and its more potent N-alkoxy derivatives. We found that I3C was incapable of inhibiting NE activity or the generation of LMW-E. Therefore, this pathway did not contribute to the anti-tumor activity of I3C. Gene expression analyzes identified ligand-activated aryl hydrocarbon receptor (AhR), which mediated sensitivity to the anti-tumor effects of I3C in ERα-positive MCF-7 cells. In this model system, the reactive oxygen species (ROS)-induced upregulation of ATF-3 and pro-apoptotic BH3-only proteins (e.g. NOXA) contributed to the sensitivity of ERα-positive breast cancer cells to the anti-tumor effects of I3C. Overexpression of ERα in MDA-MB-231 cells, which normally lack ERα expression, increased sensitivity to the anti-tumor effects of I3C, demonstrating a direct role for ERα in mediating the sensitivity of breast cancer cell lines to I3C. Our results suggest that ERα signaling amplified the pro-apoptotic effect of I3C-induced AhR signaling in luminal breast cancer cell lines, which was mediated in part through oxidative stress induced upregulation of ATF-3 and downstream BH3-only proteins.
DOI: 10.6084/m9.figshare.1246742
title: Comparison of whole blood and PBMC gene expression

description: PBMC and whole blood gene expression analysis from Advanced Heart Failure patients undergoing Mechanical Circulatory Support Device implantation obtained simultaneously.
DOI: 10.6084/m9.figshare.1246742.v1
title: Comparison of whole blood and PBMC gene expression

description: PBMC and whole blood gene expression analysis from Advanced Heart Failure patients undergoing Mechanical Circulatory Support Device implantation obtained simultaneously.
DOI: 10.6084/m9.figshare.1246741
title: Drosophila medulla full connectome

description: This is the drosophila medulla connectome (directed graph, Pajek format) built from the supplementary table 1 from http://www.nature.com/nature/journal/v500/n7461/full/nature12450.html 379 Nodes (neurons), 3193 links, connection strenghts are the number of synapses per neuron pair. I will post the code (bash script) I used to generate the connectome later so that people can double check.
DOI: 10.6084/m9.figshare.1246745.v2
title: Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons

description: In the mammalian genome, each histone family contains multiple replication-dependent paralogs, which are found in clusters where their transcription is thought to be coupled to the cell cycle. Here, we wanted to interrogate the transcriptional regulation of these paralogs during retinal development and aging. We employed deep sequencing, quantitative PCR, <i>in situ</i> hybridization (ISH), and microarray analysis, which revealed that replication-dependent histone genes were not only transcribed in progenitor cells but also in differentiating neurons. Specifically, by ISH analysis we found that different histone genes were actively transcribed in a subset of neurons between postnatal day 7 and 14. Interestingly, within a histone family, not all paralogs were transcribed at the same level during retinal development. For example, expression of <i>Hist1h1b</i> was higher embryonically, while that of <i>Hist1h1c</i> was higher postnatally. Finally, expression of replication-dependent histone genes was also observed in the aging retina. Moreover, transcription of replication-dependent histones was independent of rapamycin-mediated mTOR pathway inactivation. Overall, our data suggest the existence of variant nucleosomes produced by the differential expression of the replication-dependent histone genes across retinal development. Also, the expression of a subset of replication-dependent histone isotypes in senescent neurons warrants re-examining these genes as “replication-dependent.” Thus, our findings underscore the importance of understanding the transcriptional regulation of replication-dependent histone genes in the maintenance and functioning of neurons.
DOI: 10.6084/m9.figshare.1246745.v1
title: Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons

description: In the mammalian genome, each histone family contains multiple replication-dependent paralogs, which are found in clusters where their transcription is thought to be coupled to the cell cycle. Here, we wanted to interrogate the transcriptional regulation of these paralogs during retinal development and aging. We employed deep sequencing, quantitative PCR, <i>in situ</i> hybridization (ISH), and microarray analysis, which revealed that replication-dependent histone genes were not only transcribed in progenitor cells but also in differentiating neurons. Specifically, by ISH analysis we found that different histone genes were actively transcribed in a subset of neurons between postnatal day 7 and 14. Interestingly, within a histone family, not all paralogs were transcribed at the same level during retinal development. For example, expression of <i>Hist1h1b</i> was higher embryonically, while that of <i>Hist1h1c</i> was higher postnatally. Finally, expression of replication-dependent histone genes was also observed in the aging retina. Moreover, transcription of replication-dependent histones was independent of rapamycin-mediated mTOR pathway inactivation. Overall, our data suggest the existence of variant nucleosomes produced by the differential expression of the replication-dependent histone genes across retinal development. Also, the expression of a subset of replication-dependent histone isotypes in senescent neurons warrants re-examining these genes as “replication-dependent.” Thus, our findings underscore the importance of understanding the transcriptional regulation of replication-dependent histone genes in the maintenance and functioning of neurons.
DOI: 10.6084/m9.figshare.1246737
title: Microbes We Eat Data

description: These are all of the data files associated with "The Microbes We Eat" Lang et al. manuscript, published in PeerJ in 2014.
DOI: 10.6084/m9.figshare.1246741.v2
title: Drosophila medulla full connectome

description: This is the drosophila medulla connectome (directed graph, Pajek format) built from the supplementary table 1 from http://www.nature.com/nature/journal/v500/n7461/full/nature12450.html 379 Nodes (neurons), 3193 links, connection strenghts are the number of synapses per neuron pair. I will post the code (bash script) I used to generate the connectome later so that people can double check.
DOI: 10.6084/m9.figshare.1246743.v1
title: Indole-3-carbinol and its N-alkoxy derivatives preferentially target ER<b>α</b>-positive breast cancer cells

description: Indole-3-carbinol (I3C) is a natural anti-carcinogenic compound found at high concentrations in <i>Brassica</i> vegetables. I3C was recently reported to inhibit neutrophil elastase (NE) activity, while consequently limiting the proteolytic processing of full length cyclin E into pro-tumorigenic low molecular weight cyclin E (LMW-E). In this study, we hypothesized that inhibition of NE activity and resultant LMW-E generation is critical to the anti-tumor effects of I3C. LMW-E was predominately expressed by ERα-negative breast cancer cell lines. However, ERα-positive cell lines demonstrated the greatest sensitivity to the anti-tumor effects of I3C and its more potent N-alkoxy derivatives. We found that I3C was incapable of inhibiting NE activity or the generation of LMW-E. Therefore, this pathway did not contribute to the anti-tumor activity of I3C. Gene expression analyzes identified ligand-activated aryl hydrocarbon receptor (AhR), which mediated sensitivity to the anti-tumor effects of I3C in ERα-positive MCF-7 cells. In this model system, the reactive oxygen species (ROS)-induced upregulation of ATF-3 and pro-apoptotic BH3-only proteins (e.g. NOXA) contributed to the sensitivity of ERα-positive breast cancer cells to the anti-tumor effects of I3C. Overexpression of ERα in MDA-MB-231 cells, which normally lack ERα expression, increased sensitivity to the anti-tumor effects of I3C, demonstrating a direct role for ERα in mediating the sensitivity of breast cancer cell lines to I3C. Our results suggest that ERα signaling amplified the pro-apoptotic effect of I3C-induced AhR signaling in luminal breast cancer cell lines, which was mediated in part through oxidative stress induced upregulation of ATF-3 and downstream BH3-only proteins.
DOI: 10.6084/m9.figshare.1246741.v1
title: Drosophila medulla full connectome

description: This is the drosophila medulla connectome (directed graph, Pajek format) built from the supplementary table 1 from http://www.nature.com/nature/journal/v500/n7461/full/nature12450.html 379 Nodes (neurons), 3318 links, connection strenghts are the number of synapses per neuron pair. I will post the code (bash script) I used to generate the connectome later so that people can double check.
DOI: 10.6084/m9.figshare.1246737.v1
title: Microbes We Eat Data

description: These are all of the data files associated with "The Microbes We Eat" Lang et al. manuscript, published in PeerJ in 2014.
DOI: 10.6084/m9.figshare.1246725
title: Clinical Research: A Globalized Network

description: These files relate to data extracted from ClinicalTrials.gov. In the database file, data for individual clinical trials are included, and attributes include study identifier, study type, trial dates, interventions, sample size, countries in which the study was conducted, etc. The Edges file contains geographic data derived from the clinical trials data set that can be used to generate networks to illustrate geographic connectivity through clinical research, using open access software such as Gephi. The Gephi file includes networks for all countries worldwide, as well as regional networks for each major grographic region. The figures are network diagrams generated by Gephi showing geographic connectivity among individual countries through common participation in multinational clinical trials. The thickness of the connecting lines (edges) reflects the strength of a connection.
DOI: 10.6084/m9.figshare.1246707
title: 48 h incubation of HeLa cells in medium only (a control)

description: HeLa cells were incubated for 48 h in full medium (10% FBS, DMEM, 1% NEAA). The medium was then removed and cells were washed three times with warm 1 x PBS. The cells were then fixed and processed for TEM. Three different cell sections were imaged by TEM (10 images).
DOI: 10.6084/m9.figshare.1246726
title: The fate of surface cell layers of <i>Daucus carota</i> (L.) embryos raised in suspension culture

description: The ultrastructure and fate of surface cells covering mature somatic embryos of <i>Daucus carota</i> grown in suspension culture were analyzed and new information obtained concerning somatic embryogenesis in these conditions. Our studies showed that during some developmental stages, these embryos were covered irregularly and discontinuously by cells with a typical protodermal phenotype characterized by a cuticle on the outer cell wall. We observed that cells with cuticles were peeled off from the surface of mature embryos. Before peeling off, these cells underwent programmed cell death, which was confirmed by the TdT-mediated dUTP nick end labeling method. Transmission electron microscopy revealed advanced processes of autophagy in these cells.
DOI: 10.6084/m9.figshare.1246728
title: Evaluation of the DNA barcoding approach to develop a reference data-set for the threatened flora of Sicily

description: The Mediterranean Basin is one of the most significantly altered World Biodiversity Hotspots with extensive habitat loss and fast genetic population erosion, for which urgent biodiversity reconnaissance and preservation actions are required. In particular, Sicily has about 600 taxa classified as threatened or near-threatened. The correct recognition and identification of such biodiversity is required for supporting further activities. The objective of this work is to assess the ability of the DNA barcoding approach to identify different taxonomic groups from a collection of the most threatened plant taxa, throughout natural Sicilian populations. The evaluation of the DNA barcoding core markers, <i>rbc</i>L and <i>mat</i>K, was carried out on 30 taxa belonging to 13 families. DNA barcode fragments were recovered from all taxa (100%). The <i>rbc</i>L gene was recovered from 97% of the taxa and <i>mat</i>K gene from 73%. In this test, 19 taxa overall (63%) were totally resolved at the specific or subspecific level, by at least one of the core markers. Fourteen of the 17 most threatened taxa (EN, CR) included in this work were totally discriminated. The <i>mat</i>K and <i>rbc</i>L locus, respectively, resolved 64% and 48% of the taxa successfully sequenced. The <i>mat</i>K gene expressed the highest genetic distance (K2P value), from 0.4% to 8.6%, against a range of 0.1–2% of <i>rbc</i>L gene. However, the <i>rbc</i>L gene appeared a good compromise between PCR, sequencing success and species-level resolution. Cryptic groups suggest the implementation of additional barcoding markers or different primer combinations, particularly for <i>mat</i>K, in order to increase the performances. However, this preliminary result confirms the potential of the barcoding approach for quick identification of unknown and heterogeneous plant groups to generate a dedicated reference data-set of the threatened Sicilian flora for a wide range of applications.
DOI: 10.6084/m9.figshare.1246726.v2
title: The fate of surface cell layers of <i>Daucus carota</i> (L.) embryos raised in suspension culture

description: The ultrastructure and fate of surface cells covering mature somatic embryos of <i>Daucus carota</i> grown in suspension culture were analyzed and new information obtained concerning somatic embryogenesis in these conditions. Our studies showed that during some developmental stages, these embryos were covered irregularly and discontinuously by cells with a typical protodermal phenotype characterized by a cuticle on the outer cell wall. We observed that cells with cuticles were peeled off from the surface of mature embryos. Before peeling off, these cells underwent programmed cell death, which was confirmed by the TdT-mediated dUTP nick end labeling method. Transmission electron microscopy revealed advanced processes of autophagy in these cells.