cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1245030.v3
title: Progress towards structural understanding of infectious sheep PrP-amyloid

description: The still elusive structural difference of non-infectious and infectious amyloid of the mammalian prion protein (PrP) is a major pending milestone in understanding protein-mediated infectivity in neurodegenerative diseases. Preparations of PrP-amyloid proven to be infectious have never been investigated with a high-resolution technique. All available models to date have been based on low-resolution data. Here, we establish protocols for the preparation of infectious samples of full-length recombinant (rec) PrP-amyloid in NMR-sufficient amounts by spontaneous fibrillation and seeded fibril growth from brain extract. We link biological and structural data of infectious recPrP-amyloid, derived from bioassays, atomic force microscopy, and solid-state NMR spectroscopy. Our data indicate a semi-mobile N‑terminus, some residues with secondary chemical shifts typical of α‑helical secondary structure in the middle part between ∼115 to ∼155, and a distinct β‑sheet core C‑terminal of residue ∼155. These findings are not in agreement with all current models for PrP-amyloid. We also provide evidence that samples seeded from brain extract may not differ in the overall arrangement of secondary structure elements, but rather in the flexibility of protein segments outside the β-core region. Taken together, our protocols provide an essential basis for the high-resolution characterization of non-infectious and infectious PrP-amyloid in the near future.
DOI: 10.6084/m9.figshare.1245026
title: Variation of Height due to limitations of Competition and Trade-off

description: This data was collected on two separate days; October 14,2014 and October 21, 2014 from 2:30pm to 5:30pm by a group of four students (Sangavi, Gracy, Gabrielle and Anna-lisa) at the grasslands found East of Stong pond at York University Keele Campus. The temperature was forecasted at around 25°C on the first day and 15°C on the second day. In the grassland, the transect tape which was around 30 metres was laid down in a straight line and starting at 0m, every 5 metres onwards a measurement was made. The transect tape had to be moved several times to get the 30 replicates for each day.At each 5m mark(5m,10m,etc.) a seperate transect tape was used to measure 3 different plant species that were found within 1 metre of the measured point. The three species included S. canadensis , C. vulgare and A. prenanthoides. On October 14,2014, the transect was laid in the inner grassland and on October 21, 2014, the transect was laid on the outer grassland. The plant height was measured in metres to keep it consistent with the distance between plants. There was 30 replicates measured each day, for a total of 60 transects over the course of both days.
DOI: 10.6084/m9.figshare.1245030.v2
title: Progress towards structural understanding of infectious sheep PrP-amyloid

description: The still elusive structural difference of non-infectious and infectious amyloid of the mammalian prion protein (PrP) is a major pending milestone in understanding protein-mediated infectivity in neurodegenerative diseases. Preparations of PrP-amyloid proven to be infectious have never been investigated with a high-resolution technique. All available models to date have been based on low-resolution data. Here, we establish protocols for the preparation of infectious samples of full-length recombinant (rec) PrP-amyloid in NMR-sufficient amounts by spontaneous fibrillation and seeded fibril growth from brain extract. We link biological and structural data of infectious recPrP-amyloid, derived from bioassays, atomic force microscopy, and solid-state NMR spectroscopy. Our data indicate a semi-mobile N‑terminus, some residues with secondary chemical shifts typical of α‑helical secondary structure in the middle part between ∼115 to ∼155, and a distinct β‑sheet core C‑terminal of residue ∼155. These findings are not in agreement with all current models for PrP-amyloid. We also provide evidence that samples seeded from brain extract may not differ in the overall arrangement of secondary structure elements, but rather in the flexibility of protein segments outside the β-core region. Taken together, our protocols provide an essential basis for the high-resolution characterization of non-infectious and infectious PrP-amyloid in the near future.
DOI: 10.6084/m9.figshare.1245027.v2
title: Fetal lung and placental methylation is associated with in utero nicotine exposure

description: In utero smoke exposure has been shown to have detrimental effects on lung function and to be associated with persistent wheezing and asthma in children. One potential mechanism of IUS effects could be alterations in DNA methylation, which may have life-long implications. The goal of this study was to examine the association between DNA methylation and nicotine exposure in fetal lung and placental tissue in early development; nicotine exposure in this analysis represents a likely surrogate for in-utero smoke. We performed an epigenome-wide analysis of DNA methylation in fetal lung tissue (n = 85, 41 smoke exposed (48%), 44 controls) and the corresponding placental tissue samples (n = 80, 39 smoke exposed (49%), 41 controls) using the Illumina HumanMethylation450 BeadChip array. Differential methylation analyses were conducted to evaluate the variation associated with nicotine exposure. The most significant CpG sites in the fetal lung analysis mapped to the <i>PKP3</i> (<i>P</i> = 2.94 × 10<sup>−03</sup>), <i>ANKRD33B</i> (<i>P</i> = 3.12 × 10<sup>−03</sup>), <i>CNTD2</i> (<i>P</i> = 4.9 × 10<sup>−03</sup>) and <i>DPP10</i> (<i>P</i> = 5.43 × 10<sup>−03</sup>) genes. In the placental methylome, the most significant CpG sites mapped to the <i>GTF2H2C</i> and <i>GTF2H2D</i> genes (<i>P</i> = 2.87 × 10<sup>−06</sup> − 3.48 × 10<sup>−05</sup>). One hundred and one unique CpG sites with <i>P</i>-values &lt; 0.05 were concordant between lung and placental tissue analyses. Gene Set Enrichment Analysis demonstrated enrichment of specific disorders, such as asthma and immune disorders. Our findings demonstrate an association between in utero nicotine exposure and variable DNA methylation in fetal lung and placental tissues, suggesting a role for DNA methylation variation in the fetal origins of chronic diseases.
DOI: 10.6084/m9.figshare.1245029.v3
title: <b>TGF-β induces global changes in DNA methylation during the epithelial-to-mesenchymal transition in ovarian cancer cells</b>

description: A key step in the process of metastasis is the epithelial-to-mesenchymal transition (EMT). We hypothesized that epigenetic mechanisms play a key role in EMT and to test this hypothesis we analyzed global and gene-specific changes in DNA methylation during TGF-β-induced EMT in ovarian cancer cells. Epigenetic profiling using the Infinium HumanMethylation450 BeadChip (HM450) revealed extensive (<i>P</i> &lt; 0.01) methylation changes after TGF-β stimulation (468 and 390 CpG sites altered at 48 and 120 h post cytokine treatment, respectively). The majority of gene-specific TGF-β-induced methylation changes occurred in CpG islands located in or near promoters (193 and 494 genes hypermethylated at 48 and 120 h after TGF-β stimulation, respectively). Furthermore, methylation changes were sustained for the duration of TGF-β treatment and reversible after the cytokine removal. Pathway analysis of the hypermethylated loci identified functional networks strongly associated with EMT and cancer progression, including cellular movement, cell cycle, organ morphology, cellular development, and cell death and survival. Altered methylation and corresponding expression of specific genes during TGF-β-induced EMT included <i>CDH1</i> (E-cadherin) and <i>COL1A1</i> (collagen 1A1). Furthermore, TGF-β induced both expression and activity of DNA methyltransferases (DNMT) -1, -3A, and -3B, and treatment with the DNMT inhibitor SGI-110 prevented TGF-β-induced EMT. These results demonstrate that dynamic changes in the DNA methylome are implicated in TGF-β-induced EMT and metastasis. We suggest that targeting DNMTs may inhibit this process by reversing the EMT genes silenced by DNA methylation in cancer.
DOI: 10.6084/m9.figshare.1245011
title: Impacts of Distance from a Body of Water on Insect Abundance and Plant Species Richness

description: Insect abundance and plant richness were measured at the grassland east of Stong pond (43.770960, -79.506432) at York University. The experiment was conducted on October 14, 2014 on a clear, sunny day with a temperature of 22°C and on October 21, 2014 which was a colder, rainy day with a temperature of 7°C and an overcast sky. The researchers on this team were Reema Patel, Melanie de Sousa, Gurnit Atwal and Silvio Pacciti. A transect tape (~30m, or 100 inches) was laid out from the edge of the grassland going inwards towards the pond. Since one tape was not sufficient, two transect tapes were used and the total length was summed. The length from the grassland to the pond was measured to be about 60 metres, and this length was divided into 3 equal sections (~20m each), classified as closest to the pond, intermediate distance, and furthest from the pond. A sweep net that was 15 inches in diameter with a nylon mesh was used to sweep along a straight line along the 3 distances with the transect tape as a guide. At the end of each 20m mark, the sweeper would count how many insects were collected inside the net. A total of 20 sweeps were made in different portions of the grassland (10 each day), these sections were determined by moving from a starting point randomly selected, to 5m to the left. For each replicate, the transect was laid out again so the sweeper would know how far to sweep and when to tally the amount of insects collected. The insects were released one by one as each one was accounted for. For each sweep that was made, a 1m by 1m quadrat was laid out at the beginning and end of each section to measure plant richness. The measurements obtained from both the beginning and end of each section were averaged and recorded.
DOI: 10.6084/m9.figshare.1245026.v1
title: Variation of Height due to limitations of Competition and Trade-off

description: This data was collected on two separate days; October 14,2014 and October 21, 2014 from 2:30pm to 5:30pm by a group of four students (Sangavi, Gracy, Gabrielle and Anna-lisa) at the grasslands found East of Stong pond at York University Keele Campus. The temperature was forecasted at around 25°C on the first day and 15°C on the second day. In the grassland, the transect tape which was around 30 metres was laid down in a straight line and starting at 0m, every 5 metres onwards a measurement was made. The transect tape had to be moved several times to get the 30 replicates for each day.At each 5m mark(5m,10m,etc.) a seperate transect tape was used to measure 3 different plant species that were found within 1 metre of the measured point. The three species included S. canadensis , C. vulgare and A. prenanthoides. On October 14,2014, the transect was laid in the inner grassland and on October 21, 2014, the transect was laid on the outer grassland. The plant height was measured in metres to keep it consistent with the distance between plants. There was 30 replicates measured each day, for a total of 60 transects over the course of both days.
DOI: 10.6084/m9.figshare.1245021
title: AlignFS: A tool for identifying protein-coding sequence and correcting frame-shifts - RefSeq BLAST databases

description: These are the RefSeq BLAST databases associated with the AlignFS program.
DOI: 10.6084/m9.figshare.1245029.v2
title: <b>TGF-β induces global changes in DNA methylation during the epithelial-to-mesenchymal transition in ovarian cancer cells</b>

description: A key step in the process of metastasis is the epithelial-to-mesenchymal transition (EMT). We hypothesized that epigenetic mechanisms play a key role in EMT and to test this hypothesis we analyzed global and gene-specific changes in DNA methylation during TGF-β-induced EMT in ovarian cancer cells. Epigenetic profiling using the Infinium HumanMethylation450 BeadChip (HM450) revealed extensive (<i>P</i> &lt; 0.01) methylation changes after TGF-β stimulation (468 and 390 CpG sites altered at 48 and 120 h post cytokine treatment, respectively). The majority of gene-specific TGF-β-induced methylation changes occurred in CpG islands located in or near promoters (193 and 494 genes hypermethylated at 48 and 120 h after TGF-β stimulation, respectively). Furthermore, methylation changes were sustained for the duration of TGF-β treatment and reversible after the cytokine removal. Pathway analysis of the hypermethylated loci identified functional networks strongly associated with EMT and cancer progression, including cellular movement, cell cycle, organ morphology, cellular development, and cell death and survival. Altered methylation and corresponding expression of specific genes during TGF-β-induced EMT included <i>CDH1</i> (E-cadherin) and <i>COL1A1</i> (collagen 1A1). Furthermore, TGF-β induced both expression and activity of DNA methyltransferases (DNMT) -1, -3A, and -3B, and treatment with the DNMT inhibitor SGI-110 prevented TGF-β-induced EMT. These results demonstrate that dynamic changes in the DNA methylome are implicated in TGF-β-induced EMT and metastasis. We suggest that targeting DNMTs may inhibit this process by reversing the EMT genes silenced by DNA methylation in cancer.
DOI: 10.6084/m9.figshare.1244999
title: Interactions between insect abundance and plant richness in relation to distances to a pond

description: On October 14th and October 21st, observations of insect abundance and plant richness were collected and recorded at the Grassland East of Stong College. The first day the temperature was about 18°C and sunny whereas the second day was windy and cloudy with a temperature of 5°C. Each day a measuring tape of 60m was laid down from the pond to the outer area of the grassland. The 60m distance was divided evenly (20m) into three parts; closest to the pond, midway to the pond, and farthest away from the pond. Sweep nets were used to count the abundance of insects within each area and quadrats were used to record the average plant richness in each area. Ten random samples were collected in each of the specific areas on the 10 different transecting lines throughout the grassland area for each day. This gave a total of 20 samples for the experiment.
DOI: 10.6084/m9.figshare.1244997
title: Effect of tall-grass invasion on the flowering-related functional pattern of submediterranean hay-meadows

description: Several studies demonstrated that abandonment changes the functional composition of grasslands; nevertheless, little is known about the effects of grassland abandonment on the flowering-related functional pattern. We hypothesized that invasion by tall grasses affects this pattern. We counted the number of flowering shoots per species at five times during the growing season, in 80 plots placed in mown and in abandoned grasslands (central Apennines), and assessed the differences in the trait composition of flowering species between the two treatments. The selected traits were linked to resource acquisition and stress tolerance strategies. Our results indicated that abiotic environmental control is prevalent in determining the phenological pattern in both conditions and in accordance with the phenological “mid-domain hypothesis”. We demonstrated that when the dominant species is a tall grass with competitive behaviour, the magnitude of this phenomenon is amplified due to the abiotic changes yielded by the tall grass invasion. Indeed, in the central and late phases of the growing season (when invasive tall grasses are growing and blooming), abandoned grasslands were marked by a set of traits devoted to stress tolerance or underlying a long reproductive cycle or linked to competition for light.
DOI: 10.6084/m9.figshare.1244993
title: Wing stroke kinematics and its independent components in Drosophila melanogaster

description: This dataset includes preprocessed kinematic data (Signals.mat), the MATLAB code for the computational analysis described in the accompanying paper (MATLAB_code.zip), and the results of the analysis (Components.mat). Using a high-speed computer vision system, we recorded the wing motion of tethered flying fruit flies for up to 12 000 consecutive wing strokes at a sampling rate of 6250 Hz. We then decomposed the joint motion pattern of both wings into components that had the minimal mutual information (a measure of statistical dependence). In 100 flight segments measured from 10 individual flies, we identified 7 distinct types of frequently occurring least-dependent components, each defining a kinematic pattern (a specific deformation of the wing stroke and the sequence of its activation from cycle to cycle). Two of these stroke deformations can be associated with the control of yaw torque and total flight force, respectively. A third deformation involves a change in the downstroke-to-upstroke duration ratio, which is expected to alter the pitch torque. A fourth kinematic pattern consists in the alteration of stroke amplitude with a period of 2 wingbeat cycles, extending for dozens of cycles. Our analysis indicates that these four elementary kinematic patterns can be activated mutually independently, and occur both in isolation and in linear superposition. The results strengthen the available evidence for independent control of yaw torque, pitch torque, and total flight force. Our computational method facilitates systematic identification of novel patterns in large kinematic datasets. For details of the experimental procedure, data preprocessing and computational analysis, see: Chakraborty S, Bartussek J, Fry SN, Zapotocky M (2015) Independently Controlled Wing Stroke Patterns in the Fruit Fly Drosophila melanogaster. PLOS ONE 10(2): e0116813. doi:10.1371/journal.pone.0116813.
DOI: 10.6084/m9.figshare.1244999.v2
title: Interactions between insect abundance and plant richness in relation to distances to a pond

description: On October 14th and October 21st, observations of insect abundance and plant richness were collected and recorded at the Grassland East of Stong College. The first day the temperature was about 18°C and sunny whereas the second day was windy and cloudy with a temperature of 5°C. Each day a measuring tape of 60m was laid down from the pond to the outer area of the grassland. The 60m distance was divided evenly (20m) into three parts; closest to the pond, midway to the pond, and farthest away from the pond. Sweep nets were used to count the abundance of insects within each area and quadrats were used to record the average plant richness in each area. Ten random samples were collected in each of the specific areas on the 10 different transecting lines throughout the grassland area for each day. This gave a total of 20 samples for the experiment.
DOI: 10.6084/m9.figshare.1244993.v1
title: Wing stroke kinematics and its independent components in Drosophila melanogaster

description: This dataset includes preprocessed kinematic data (Signals.mat), the MATLAB code for the computational analysis described in the accompanying paper (MATLAB_code.zip), and the results of the analysis (Components.mat). Using a high-speed computer vision system, we recorded the wing motion of tethered flying fruit flies for up to 12 000 consecutive wing strokes at a sampling rate of 6250 Hz. We then decomposed the joint motion pattern of both wings into components that had the minimal mutual information (a measure of statistical dependence). In 100 flight segments measured from 10 individual flies, we identified 7 distinct types of frequently occurring least-dependent components, each defining a kinematic pattern (a specific deformation of the wing stroke and the sequence of its activation from cycle to cycle). Two of these stroke deformations can be associated with the control of yaw torque and total flight force, respectively. A third deformation involves a change in the downstroke-to-upstroke duration ratio, which is expected to alter the pitch torque. A fourth kinematic pattern consists in the alteration of stroke amplitude with a period of 2 wingbeat cycles, extending for dozens of cycles. Our analysis indicates that these four elementary kinematic patterns can be activated mutually independently, and occur both in isolation and in linear superposition. The results strengthen the available evidence for independent control of yaw torque, pitch torque, and total flight force. Our computational method facilitates systematic identification of novel patterns in large kinematic datasets. For details of the experimental procedure, data preprocessing and computational analysis, see: Chakraborty S, Bartussek J, Fry SN, Zapotocky M (2015) Independently Controlled Wing Stroke Patterns in the Fruit Fly Drosophila melanogaster. PLOS ONE 10(2): e0116813. doi:10.1371/journal.pone.0116813.
DOI: 10.6084/m9.figshare.1244999.v1
title: Interactions between insect abuncane and plant richness in relation to distances to a pond

description: On October 14th and October 21st, observations of insect abundance and plant richness were collected and recorded at the Grassland East of Stong College. The first day the temperature was about 18°C and sunny whereas the second day was windy and cloudy with a temperature of 5°C. Each day a measuring tape of 60m was laid down from the pond to the outer area of the grassland. The 60m distance was divided evenly (20m) into three parts; closest to the pond, midway to the pond, and farthest away from the pond. Sweep nets were used to count the abundance of insects within each area and quadrats were used to record the average plant richness in each area. Ten random samples were collected in each of the specific areas on the 10 different transecting lines throughout the grassland area for each day. This gave a total of 20 samples for the experiment.
DOI: 10.6084/m9.figshare.1245021.v1
title: AlignFS refseq BLAST databases

description: These are the RefSeq BLAST databases associated with the AlignFS program.
DOI: 10.6084/m9.figshare.1245021.v3
title: AlignFS: A tool for identifying protein-coding sequence and correcting frame-shifts - RefSeq BLAST databases

description: These are the RefSeq BLAST databases associated with the AlignFS program.
DOI: 10.6084/m9.figshare.1244997.v1
title: Effect of tall-grass invasion on the flowering-related functional pattern of submediterranean hay-meadows

description: Several studies demonstrated that abandonment changes the functional composition of grasslands; nevertheless little is known about the effects of grassland abandonment on the flowering-related functional pattern. We hypothesised that invasion by tall grasses affects this pattern. We counted the number of flowering shoots per species at five times during the growing season, in 80 plots placed in mown and in abandoned grasslands (central Apennines), and assessed the differences in the trait composition of flowering species between the two treatments using Czekanowski similarity index, multi-response permutation procedures, and indicator species analysis. The selected traits were linked to resource acquisition and stress tolerance strategies. Our results indicated that abiotic environmental control is prevalent in determining the phenological pattern in both conditions and in accordance with the phenological “mid-domain hypothesis”. We demonstrated that when the dominant species is a tall grass with competitive behaviour, the magnitude of this phenomenon is amplified due to the abiotic changes yielded by the tall grass invasion. Indeed, in the central and late phases of the growing season (when invasive tall grasses are growing and blooming), abandoned grasslands were marked by a set of traits devoted to stress tolerance or underlying a long reproductive cycle (i.e. rhizomes, heavy seeds, summer green, persistent green, and succulent leaves), or linked to competition for light (upright growth form).
DOI: 10.6084/m9.figshare.1245021.v2
title: AlignFS refseq BLAST databases

description: These are the RefSeq BLAST databases associated with the AlignFS program.