cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1312986.v3
title: Alteration of <i>Arabidopsis SLAC1</i> promoter and its association with natural variation in drought tolerance

description: Natural variation for drought tolerance is a major issue in adaptation and geographic distribution of terrestrial plants. Despite the importance, little is known about the genes and molecular mechanisms that determine its naturally occurring diversity. We analyzed the intraspecific drought tolerance variation between 2 accessions of <i>Arabidopsis thaliana</i>, Columbia (Col)-0 and Wassilewskija (Ws)-2. Measurement of weight loss in detached seedlings demonstrated a clear difference between drought-tolerant Col-0 and drought-sensitive Ws-2. They also differed in their stomatal response under drought condition. Using a quantitative genetic approach, we found a significant quantitative locus on chromosome 1. Surveying in the locus, we extrapolated that the <i>SLAC1</i> gene, which is associated with stomatal closure, was likely responsible for the difference of drought tolerance. Comparison of their nucleotide and amino acid sequences revealed that there were few differences in regions encoding <i>SLAC1</i> protein but was a large deletion in <i>SLAC1</i> promoter of Ws-2. Histochemical GUS staining showed that the <i>SLAC1</i> expressed dominantly in guard cells of Col-0, but did less in guard cells of Ws-2. Quantitative PCR analysis also showed that transcript level of <i>SLAC1</i> in guard cells was higher in Col-0 than in Ws-2. The <i>SLAC1</i> transcription analyses indicate low accumulation of <i>SLAC1</i> in guard cells of Ws-2. When taken together, our results suggest that the low drought tolerance of Ws-2 was associated with the deletion of the promoter region of Ws-2 <i>SLAC1</i>.
DOI: 10.6084/m9.figshare.1312958.v1
title: Ubiquitin-H2AX fusions render 53BP1 recruitment to DNA damage sites independent of RNF8 or RNF168

description: The mammalian E3 ubiquitin ligases RNF8 and RNF168 facilitate recruitment of the DNA damage response protein 53BP1 to sites of DNA double-strand breaks (DSBs). The mechanism involves recruitment of RNF8, followed by recruitment of RNF168, which ubiquitinates histones H2A/H2AX on K15. 53BP1 then binds to nucleosomes at sites of DNA DSBs by recognizing, in addition to methyl marks, histone H2A/H2AX ubiquitinated on K15. We report here that expressing H2AX fusion proteins with N-terminal bulky moieties can rescue 53BP1 recruitment to sites of DNA DSBs in cells lacking RNF8 or RNF168 or in cells treated with proteasome inhibitors, in which histone ubiquitination at sites of DNA DSBs is compromised. The rescue required S139 at the C-terminus of the H2AX fusion protein and was occasionally accompanied by partial rescue of ubiquitination at sites of DNA DSBs. We conclude that recruitment of 53BP1 to sites of DNA DSBs is possible in the absence of RNF8 or RNF168, but still dependent on chromatin ubiquitination.
DOI: 10.6084/m9.figshare.1312963.v3
title: Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells

description: Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. <i>Mycoplasmas spp</i>., including <i>Mycoplasma hyorhinis,</i> efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the <i>M. hyorhinis</i> CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, ∼11% of GATC sites overlap with CGs (e.g., CGAT<sup>m</sup>CG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.
DOI: 10.6084/m9.figshare.1312986.v5
title: Alteration of <i>Arabidopsis SLAC1</i> promoter and its association with natural variation in drought tolerance

description: Natural variation for drought tolerance is a major issue in adaptation and geographic distribution of terrestrial plants. Despite the importance, little is known about the genes and molecular mechanisms that determine its naturally occurring diversity. We analyzed the intraspecific drought tolerance variation between 2 accessions of <i>Arabidopsis thaliana</i>, Columbia (Col)-0 and Wassilewskija (Ws)-2. Measurement of weight loss in detached seedlings demonstrated a clear difference between drought-tolerant Col-0 and drought-sensitive Ws-2. They also differed in their stomatal response under drought condition. Using a quantitative genetic approach, we found a significant quantitative locus on chromosome 1. Surveying in the locus, we extrapolated that the <i>SLAC1</i> gene, which is associated with stomatal closure, was likely responsible for the difference of drought tolerance. Comparison of their nucleotide and amino acid sequences revealed that there were few differences in regions encoding <i>SLAC1</i> protein but was a large deletion in <i>SLAC1</i> promoter of Ws-2. Histochemical GUS staining showed that the <i>SLAC1</i> expressed dominantly in guard cells of Col-0, but did less in guard cells of Ws-2. Quantitative PCR analysis also showed that transcript level of <i>SLAC1</i> in guard cells was higher in Col-0 than in Ws-2. The <i>SLAC1</i> transcription analyses indicate low accumulation of <i>SLAC1</i> in guard cells of Ws-2. When taken together, our results suggest that the low drought tolerance of Ws-2 was associated with the deletion of the promoter region of Ws-2 <i>SLAC1</i>.
DOI: 10.6084/m9.figshare.1312958.v2
title: Ubiquitin-H2AX fusions render 53BP1 recruitment to DNA damage sites independent of RNF8 or RNF168

description: The mammalian E3 ubiquitin ligases RNF8 and RNF168 facilitate recruitment of the DNA damage response protein 53BP1 to sites of DNA double-strand breaks (DSBs). The mechanism involves recruitment of RNF8, followed by recruitment of RNF168, which ubiquitinates histones H2A/H2AX on K15. 53BP1 then binds to nucleosomes at sites of DNA DSBs by recognizing, in addition to methyl marks, histone H2A/H2AX ubiquitinated on K15. We report here that expressing H2AX fusion proteins with N-terminal bulky moieties can rescue 53BP1 recruitment to sites of DNA DSBs in cells lacking RNF8 or RNF168 or in cells treated with proteasome inhibitors, in which histone ubiquitination at sites of DNA DSBs is compromised. The rescue required S139 at the C-terminus of the H2AX fusion protein and was occasionally accompanied by partial rescue of ubiquitination at sites of DNA DSBs. We conclude that recruitment of 53BP1 to sites of DNA DSBs is possible in the absence of RNF8 or RNF168, but still dependent on chromatin ubiquitination.
DOI: 10.6084/m9.figshare.1312963.v4
title: Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells

description: Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. <i>Mycoplasmas spp</i>., including <i>Mycoplasma hyorhinis,</i> efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the <i>M. hyorhinis</i> CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, ∼11% of GATC sites overlap with CGs (e.g., CGAT<sup>m</sup>CG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.
DOI: 10.6084/m9.figshare.1312910
title: Data: A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings

description: Data for publication: A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings, Plos One 2014, by Charleston Noble, Adam N. Nilsson, Camilla Freitag, Jason P. Beech, Jonas O. Tegenfeldt, Tobias Ambjornsson
DOI: 10.6084/m9.figshare.1312986.v4
title: Alteration of <i>Arabidopsis SLAC1</i> promoter and its association with natural variation in drought tolerance

description: Natural variation for drought tolerance is a major issue in adaptation and geographic distribution of terrestrial plants. Despite the importance, little is known about the genes and molecular mechanisms that determine its naturally occurring diversity. We analyzed the intraspecific drought tolerance variation between 2 accessions of <i>Arabidopsis thaliana</i>, Columbia (Col)-0 and Wassilewskija (Ws)-2. Measurement of weight loss in detached seedlings demonstrated a clear difference between drought-tolerant Col-0 and drought-sensitive Ws-2. They also differed in their stomatal response under drought condition. Using a quantitative genetic approach, we found a significant quantitative locus on chromosome 1. Surveying in the locus, we extrapolated that the <i>SLAC1</i> gene, which is associated with stomatal closure, was likely responsible for the difference of drought tolerance. Comparison of their nucleotide and amino acid sequences revealed that there were few differences in regions encoding <i>SLAC1</i> protein but was a large deletion in <i>SLAC1</i> promoter of Ws-2. Histochemical GUS staining showed that the <i>SLAC1</i> expressed dominantly in guard cells of Col-0, but did less in guard cells of Ws-2. Quantitative PCR analysis also showed that transcript level of <i>SLAC1</i> in guard cells was higher in Col-0 than in Ws-2. The <i>SLAC1</i> transcription analyses indicate low accumulation of <i>SLAC1</i> in guard cells of Ws-2. When taken together, our results suggest that the low drought tolerance of Ws-2 was associated with the deletion of the promoter region of Ws-2 <i>SLAC1</i>.
DOI: 10.6084/m9.figshare.1312907
title: ERP_study_data

description: We distinguish two evaluative systems which evoke automatic and reflective emotions. Automatic emotions are direct reactions to stimuli whereas reflective emotions are always based on verbalized (and often abstract) criteria of evaluation. We conducted an electroencephalography (EEG) study in which 25 women were required to read and respond to emotional words which engaged either the automatic or reflective system. Stimulus words were emotional (positive or negative) and neutral. We found an effect of valence on an early response with dipolar fronto-occipital topography; positive words evoked a higher amplitude response than negative words. We also found that to pographically specific differences in the amplitude of the late positive complex were related to the system involved in processing. Emotional stimuli engaging the automatic system were associated with significantly higher amplitudes in the left-parietal region; the response to neutral words was similar regardless of the system engaged. A different pattern of effects was observed in the central region, neutral stimuli engaging the reflective system evoked a higher amplitudes response whereas there was no system effect for emotional stimuli. These differences could not be reduced to effects of differences between the arousing properties and concreteness of the words used as stimuli.
DOI: 10.6084/m9.figshare.1312963.v5
title: Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells

description: Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. <i>Mycoplasmas spp</i>., including <i>Mycoplasma hyorhinis,</i> efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the <i>M. hyorhinis</i> CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, ∼11% of GATC sites overlap with CGs (e.g., CGAT<sup>m</sup>CG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.
DOI: 10.6084/m9.figshare.1312963.v6
title: Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells

description: Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. <i>Mycoplasmas spp</i>., including <i>Mycoplasma hyorhinis,</i> efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the <i>M. hyorhinis</i> CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, ∼11% of GATC sites overlap with CGs (e.g., CGAT<sup>m</sup>CG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.
DOI: 10.6084/m9.figshare.1312907.v1
title: ERP_study_data

description: We distinguish two evaluative systems which evoke automatic and reflective emotions. Automatic emotions are direct reactions to stimuli whereas reflective emotions are always based on verbalized (and often abstract) criteria of evaluation. We conducted an electroencephalography (EEG) study in which 25 women were required to read and respond to emotional words which engaged either the automatic or reflective system. Stimulus words were emotional (positive or negative) and neutral. We found an effect of valence on an early response with dipolar fronto-occipital topography; positive words evoked a higher amplitude response than negative words. We also found that to pographically specific differences in the amplitude of the late positive complex were related to the system involved in processing. Emotional stimuli engaging the automatic system were associated with significantly higher amplitudes in the left-parietal region; the response to neutral words was similar regardless of the system engaged. A different pattern of effects was observed in the central region, neutral stimuli engaging the reflective system evoked a higher amplitudes response whereas there was no system effect for emotional stimuli. These differences could not be reduced to effects of differences between the arousing properties and concreteness of the words used as stimuli.
DOI: 10.6084/m9.figshare.1312910.v1
title: Data: A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings

description: Data for publication: A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings, Plos One 2014, by Charleston Noble, Adam N. Nilsson, Camilla Freitag, Jason P. Beech, Jonas O. Tegenfeldt, Tobias Ambjornsson
DOI: 10.6084/m9.figshare.1312900
title: Human RNA and DNA sets in FASTA format

description: Human RNA and DNA sets in FASTA format used to generate Figure 6 of Lee, E.S., Akef, A. and Palazzo A.F., "The Consensus 5' Splice Site Motif Inhibits mRNA Nuclear Export" PLOS ONE 2015 in press.
DOI: 10.6084/m9.figshare.1312895
title: Data - Altered Resting-State Functional Connectivity of the Frontal-Striatal Reward System in Social Anxiety Disorder

description: Behavioral and fMRI data
DOI: 10.6084/m9.figshare.1312896
title: Facilitating biodiversity science through Virtual Research Environments

description: This talk was delivered during the Canadian Biodiversity Science and Information workshop on 19 Feb 2015.
DOI: 10.6084/m9.figshare.1312900.v1
title: Data used to generate Figure 6 in Lee et al., PLOS ONE 2015

description: Human RNA and DNA sets in FASTA format used to generate Figure 6 of Lee et al., PLOS ONE 2015.
DOI: 10.6084/m9.figshare.1312875
title: Life history data for Rhizoglyphus robini

description: Data are for individual life history of the bulb mite (Rhizoglyphus robini). Growth measurements, survival, and offspring data were collected daily and for both sexes until death of individuals. Mites were fed ad libitum oats and kept in unlit incubators at 24°C and &gt;70%. Data were collected between August 2012 and May 2013. Data file is in Microsoft excel format that includes a sheet with raw data and a detailed metafile sheet.
DOI: 10.6084/m9.figshare.1312839
title: SYK inhibitors

description: SYK inhibitors screened by chooseLD. Presentation at SIGBIO41, 20th March 2015, Hokkaido Univesrsity
DOI: 10.6084/m9.figshare.1312838
title: SYk inhibitors

description: This is a supplementary data set of the paper, Hideaki Umeyama, Mitsuo Iwadate, Y-h. Taguchi In silico Spleen Tyrosine Kinase Inhibitor Screening by ChooseLD IPSJ Transactions on Bioinformatics<br>Vol. 8 (2015) pp. 14-20
DOI: 10.6084/m9.figshare.1312837
title: Informatics

description: This fileset contains data relevant to AMIA 2015 submission titled: Process Mining of Growing Adoption of Genomic Precision Medicine Testing Using Commercial Claims and Encounters Database To facilitate comparison and execution on other datasets, we used R Markdown format designed for reproducible science that combines the analysis code with the resulting analytical report (see this fileset for code [*.Rmd] and output reports [*.docx]).
DOI: 10.6084/m9.figshare.1312838.v1
title: SYk inhibitors

description: This is a supplementary data set of the paper, Hideaki Umeyama, Mitsuo Iwadate, Y-h. Taguchi In silico Spleen Tyrosine Kinase Inhibitor Screening by ChooseLD IPSJ Transactions on Bioinformatics<br>Vol. 8 (2015) pp. 14-20
DOI: 10.6084/m9.figshare.1312839.v2
title: SYK inhibitors

description: SYK inhibitors screened by chooseLD. Presentation at SIGBIO41, 20th March 2015, Hokkaido Univesrsity
DOI: 10.6084/m9.figshare.1311757
title: ELectronic Health Record

description: EHR Adoption
DOI: 10.6084/m9.figshare.1312839.v1
title: SYK inhibitors

description: SYK inhibitors screened by chooseLD. Presentation at SIGBIO41, 20th March 2015, Hokkaido Univesrsity
DOI: 10.6084/m9.figshare.1312837.v1
title: Informatics

description: This fileset contains data relevant to AMIA 2015 submission titled: Process Mining of Growing Adoption of Genomic Precision Medicine Testing Using Commercial Claims and Encounters Database To facilitate comparison and execution on other datasets, we used R Markdown format designed for reproducible science that combines the analysis code with the resulting analytical report (see this fileset for code [*.Rmd] and output reports [*.docx]).