cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30437783
title: Expression of G-quadruplex coordinates BRCA1, CDH1, and RASSF1 via DNA methylation in mouse breast cancer cells

description: G-quadruplex (G4) structures are enriched in key genomic regions and regulate gene expression and chromosomal stability. However, their role in de novo DNA methylation remains unclear. DNA methyltransferase 3A (DNMT3A) and DNA methyltransferase 3B (DNMT3B) are vital for cancer initiation and progression. This study investigated the role of G4 structures in regulating DNMT3A and DNMT3B expression and their epigenetic function in breast cancer. G4 structures in DNMT3A and DNMT3B were identified using Quadruplex forming G-Rich Sequences Mapper, circular dichroism, and gel mobility shift assays. The effects of the G4 stabilizer pyridostatin on breast cancer 4T1 cell proliferation, migration, DNMT3A and DNMT3B expression, and promoter methylation of Breast Cancer 1 (BRCA1), E-cadherin (CDH1), and Ras Association Domain Family Member 1 (RASSF1) were evaluated. G4-forming sequences were found in the core promoter regions of DNMT3A and DNMT3B. They formed parallel G4 structures in vitro. Pyridostatin enhanced G4 stability, inhibited 4T1 cell proliferation and migration, downregulated DNMT3A and DNMT3B expression, reduced promoter methylation of BRCA1 and RASSF1, and altered target gene expression. Promoter G4 structures actively regulate gene expression by modulating de novo DNA methylation, suggesting that targeting G4s may represent a novel therapeutic strategy for breast cancer. Specific regions of DNA are capable of folding into a distinctive structure called a G-quadruplex (G4). These structures act like switches, controlling whether genes are turned on or off and helping to maintain chromosome stability. However, the role of these factors in the DNA methylation process remains unclear. Two key enzymes, DNA methyltransferase 3A (DNMT3A) and DNA methyltransferase 3B (DNMT3B), are responsible for these modifications, and their activity has been associated with cancer development. In this study, the effects of G4 structures on the expression of DNMT3A and DNMT3B, and consequently on breast cancer-related genes, were examined. G4 structures were detected in the regulatory regions of both DNMT3A and DNMT3B. When these G4 structures were stabilized using a chemical compound, the activities of the enzymes were altered, resulting in changes in the expression of breast cancer-related genes. These results indicate that gene expression and DNA methylation can be regulated by G4 structures in DNA, and it is suggested that targeting these structures may provide a novel strategy for breast cancer treatment.
DOI: 10.6084/m9.figshare.30437783.v1
title: Expression of G-quadruplex coordinates BRCA1, CDH1, and RASSF1 via DNA methylation in mouse breast cancer cells

description: G-quadruplex (G4) structures are enriched in key genomic regions and regulate gene expression and chromosomal stability. However, their role in de novo DNA methylation remains unclear. DNA methyltransferase 3A (DNMT3A) and DNA methyltransferase 3B (DNMT3B) are vital for cancer initiation and progression. This study investigated the role of G4 structures in regulating DNMT3A and DNMT3B expression and their epigenetic function in breast cancer. G4 structures in DNMT3A and DNMT3B were identified using Quadruplex forming G-Rich Sequences Mapper, circular dichroism, and gel mobility shift assays. The effects of the G4 stabilizer pyridostatin on breast cancer 4T1 cell proliferation, migration, DNMT3A and DNMT3B expression, and promoter methylation of Breast Cancer 1 (BRCA1), E-cadherin (CDH1), and Ras Association Domain Family Member 1 (RASSF1) were evaluated. G4-forming sequences were found in the core promoter regions of DNMT3A and DNMT3B. They formed parallel G4 structures in vitro. Pyridostatin enhanced G4 stability, inhibited 4T1 cell proliferation and migration, downregulated DNMT3A and DNMT3B expression, reduced promoter methylation of BRCA1 and RASSF1, and altered target gene expression. Promoter G4 structures actively regulate gene expression by modulating de novo DNA methylation, suggesting that targeting G4s may represent a novel therapeutic strategy for breast cancer. Specific regions of DNA are capable of folding into a distinctive structure called a G-quadruplex (G4). These structures act like switches, controlling whether genes are turned on or off and helping to maintain chromosome stability. However, the role of these factors in the DNA methylation process remains unclear. Two key enzymes, DNA methyltransferase 3A (DNMT3A) and DNA methyltransferase 3B (DNMT3B), are responsible for these modifications, and their activity has been associated with cancer development. In this study, the effects of G4 structures on the expression of DNMT3A and DNMT3B, and consequently on breast cancer-related genes, were examined. G4 structures were detected in the regulatory regions of both DNMT3A and DNMT3B. When these G4 structures were stabilized using a chemical compound, the activities of the enzymes were altered, resulting in changes in the expression of breast cancer-related genes. These results indicate that gene expression and DNA methylation can be regulated by G4 structures in DNA, and it is suggested that targeting these structures may provide a novel strategy for breast cancer treatment.
DOI: 10.5061/dryad.8cp33
title: Data from: Alternative mating tactics in the yellow dung fly: resolving mechanisms of small-male advantage off pasture

description: Recent work suggests the yellow dung fly mating system may include
 alternative patroller-competitor mating tactics in which large males
 compete for gravid females on dung, whereas small, non-competitive males
 search for females at foraging sites. Small males obtain most matings off
 pasture, yet the behavioural mechanism(s) giving rise to this pattern are
 unknown. We investigated the male and female behaviours that determine
 mating success in this environment by conducting field mating experiments
 and found small males to benefit from several attributes specific to the
 off-pasture mating environment. First, small males from foraging sites
 exhibited higher mating propensity, indicating that large males away from
 dung may be depleted of energy and/or sperm. Second, small males were more
 discriminating, being significantly less likely to attempt with non-gravid
 females, which are absent on dung but common off pasture. Third,
 non-gravid females were generally more likely to actively struggle and
 reject mating attempts; however, such behaviours occurred
 disproportionately more often with large males. Female Scathophaga
 stercoraria thus appear to preferentially mate with small males when off
 pasture. These findings challenge assumptions about male-female
 interactions in systems with alternative mating tactics and reveal hidden
 processes that may influence selection patterns in the field.
description: all
 dataThese data were obtained
 using experimental matings conducted in Plexiglas chambers in the field.
 Male mating attempts were recorded (Attempt/No attempt), latency to
 attempt (min), outcome of attempt (Copulation/Rejection), capture success
 (Yes/No), female resistance (Yes/No), female resistance duration (sec),
 and male displacement when faced with resistance (Yes/No). Raw measures of
 body size are also included in reticle units (at 32x mag). Finally, female
 egg development was recorded as either nongravid or gravid (meaning female
 clutch visually appeared mature).AMTs in the YDF
 data.xlsx
DOI: 10.6084/m9.figshare.30713092
title: Genome-wide methylation changes upon Caco-2 cells exposure to undigested and digested titanium dioxide nanoparticles

description: Titanium dioxide nanoparticles (TiO<sub>2</sub>NPs) are relevant nanomaterials (NMs) for biomedicine and industry, which raise concerns about its effects on human health, particularly through ingestion. Several studies found that exposure to NMs can lead to DNA methylation changes. DNA methylation regulates gene expression, playing a vital role in development and disease, with aberrant methylation linked to cancer and other health conditions. We aimed at identifying DNA methylation changes in intestinal cells exposed to three TiO<sub>2</sub>NPs (NM-102, NM-103, NM-105), either digested or undigested. Their cellular effects were investigated by functional pathway and gene ontology (GO) analysis. 48, 41, 55 differentially methylated genes (DMG) were identified after exposure to undigested NM-102, NM-103, NM-105; 71, 65, 55 DMG in the digested counterparts. Undigested TiO<sub>2</sub>NPs affected many G-proteins/adenylate cyclase-related pathways (PKA, glucagon, GPER1, CREB1, ADORA2B); the digested had lower impact. Cancer-related pathways were shared. Enriched molecular functions were mainly transcription-related; different biological processes were enriched if TiO<sub>2</sub>NPs were digested or not. TiO<sub>2</sub>NPs exposure causes DNA methylation changes that have a functional impact on intestinal cells, which differs with its physicochemical properties and digestion. NM-105 caused hypermethylation, unlike the other TiO<sub>2</sub>NPs. This study highlights DNA methylation relevance in assessing NMs’ toxicity. Titanium dioxide nanoparticles (TiO<sub>2</sub>NP) are widely present in our daily lives, including in food as a white pigment to make it better-looking and appealing. Although there are many toxicological studies on TiO<sub>2</sub>NP, few have focused on its effects on DNA methylation, which is a mechanism for regulating gene expression, and consequently, cellular functions. In this study, human intestinal cells were exposed to three different types of TiO<sub>2</sub>NP, before and after simulated digestion. Our results indicate that the physical-chemical characteristics of TiO<sub>2</sub>NP influence its effects and demonstrate the impact of digestion, relevant in the context of oral exposure. Moreover, they highlight the biological impact of TiO<sub>2</sub>NP on intestinal cells through DNA methylation changes and, consequently, the relevance of studying these changes when assessing the adverse effects of nanomaterials on human health.
DOI: 10.6084/m9.figshare.30713092.v1
title: Genome-wide methylation changes upon Caco-2 cells exposure to undigested and digested titanium dioxide nanoparticles

description: Titanium dioxide nanoparticles (TiO<sub>2</sub>NPs) are relevant nanomaterials (NMs) for biomedicine and industry, which raise concerns about its effects on human health, particularly through ingestion. Several studies found that exposure to NMs can lead to DNA methylation changes. DNA methylation regulates gene expression, playing a vital role in development and disease, with aberrant methylation linked to cancer and other health conditions. We aimed at identifying DNA methylation changes in intestinal cells exposed to three TiO<sub>2</sub>NPs (NM-102, NM-103, NM-105), either digested or undigested. Their cellular effects were investigated by functional pathway and gene ontology (GO) analysis. 48, 41, 55 differentially methylated genes (DMG) were identified after exposure to undigested NM-102, NM-103, NM-105; 71, 65, 55 DMG in the digested counterparts. Undigested TiO<sub>2</sub>NPs affected many G-proteins/adenylate cyclase-related pathways (PKA, glucagon, GPER1, CREB1, ADORA2B); the digested had lower impact. Cancer-related pathways were shared. Enriched molecular functions were mainly transcription-related; different biological processes were enriched if TiO<sub>2</sub>NPs were digested or not. TiO<sub>2</sub>NPs exposure causes DNA methylation changes that have a functional impact on intestinal cells, which differs with its physicochemical properties and digestion. NM-105 caused hypermethylation, unlike the other TiO<sub>2</sub>NPs. This study highlights DNA methylation relevance in assessing NMs’ toxicity. Titanium dioxide nanoparticles (TiO<sub>2</sub>NP) are widely present in our daily lives, including in food as a white pigment to make it better-looking and appealing. Although there are many toxicological studies on TiO<sub>2</sub>NP, few have focused on its effects on DNA methylation, which is a mechanism for regulating gene expression, and consequently, cellular functions. In this study, human intestinal cells were exposed to three different types of TiO<sub>2</sub>NP, before and after simulated digestion. Our results indicate that the physical-chemical characteristics of TiO<sub>2</sub>NP influence its effects and demonstrate the impact of digestion, relevant in the context of oral exposure. Moreover, they highlight the biological impact of TiO<sub>2</sub>NP on intestinal cells through DNA methylation changes and, consequently, the relevance of studying these changes when assessing the adverse effects of nanomaterials on human health.
DOI: 10.5061/dryad.35r23
title: Data from: Polyploid formation shapes flowering plant diversity

description: Polyploidy, or whole genome duplication, has been an important feature of
 eukaryotic evolution. This is especially true in flowering plants, where
 all extant angiosperms have descended from polyploid species. Here we
 present a broad comparative analysis of the effect of polyploidy on
 flowering plant diversity. We examine the widely held hypothesis that
 polyploid flowering plants generate more diversity than their diploid
 counterparts, by fitting stochastic birth/death models to observed ploidal
 frequency data from 60 extant angiosperm genera. Our results suggest the
 opposite, that diploids speciate at higher rates than polyploids, through
 a combination of simple diploid speciation and tetraploidy. Importantly,
 the estimated diploid advantage stemmed primarily from a higher rate of
 polyploidization in diploids than polyploids. Our model is also able to
 account for the empirically observed correlation between polyploidy and
 species richness without assuming that polyploids have a speciation
 advantage over diploids.
description: Ploidal
 DistributionsIn this table, we
 provide the chromosome count data for each genus and the observed or
 assumed age.online_tableA1.csvParameter EstimatesIn this table, we provide the parameter estimates under both models, and the goodness-of-fit results for the Simple Ratchet model. The column headers follow the naming convention: model.parameter for the estimates, model.parameter.upper for the upper limit of the 95% credible interval, and model.parameter.lower for the lower limit of the 95% credible interval.online_tableA2.csvSummary StatisticsThe ABC-SMC model-fitting algorithm used the following nine metrics. The values for each metrics for the 60 genera are provided. The ABC-SMC algorithm, in particular the box-cox correction and PLS regression, performs best on continuous metrics, which is why we did not use the number of species in each ploidal class as metrics. Despite the reduced performance of categorical metrics, we included the highest observed ploidal level because it was highly informative for parameter inference. (1) Total genus size (2) Proportion diploids (3) Proportion tetraploids (4) Proportion species &gt; = 4n (5) Proportion species &gt; = 6n (6) Highest ploidal level observed (7) Proportion highest observed ploidal level (8) Average ploidy level (9) Variance in ploidy level.online_tableA4.csv
DOI: 10.5061/dryad.55hr85m
title: Data from: A prospective study of serum metabolites and risk of ischemic stroke

description: Objective: To identify promising blood-based biomarkers and novel
 etiological pathways of disease risk, we applied an untargeted serum
 metabolomics profiling in a community-based prospective study of ischemic
 stroke (IS). Methods: In 3,904 men and women from the Atherosclerosis Risk
 In Communities (ARIC) study, Cox proportional hazard models were used to
 estimate the association of incident IS with the standardized level of 245
 fasting serum metabolites individually, adjusting for age, sex, race,
 field center, batch, diabetes, hypertension, current smoking status, body
 mass index, and estimated glomerular filtration rate. Validation of
 results was carried out in an independent sample of 114 IS cases and 112
 healthy controls. Results: Serum levels of two long-chain dicarboxylic
 acids, tetradecanedioate and hexadecanedioate, were strongly correlated
 (r=0.88) and were associated with incident IS after adjusting for
 covariates (Hazard Ratio [95% Confidence Interval (CI)] = 1.11 [1.06-1.16]
 and 1.12 [1.07-1.17], respectively; p&lt;0.0001). Analyses by IS
 subtypes suggested that these associations were specific to cardioembolic
 stroke (CES). Associations of tetradecanedioate and hexadecanedioate with
 IS were independently confirmed (Odds Ratio [95% CI] = 1.76 [1.21; 2.56]
 and 1.60 [1.11; 2.32], respectively). Conclusion: Two serum long-chain
 dicarboxylic acids, metabolic products of ω-oxidation of fatty acids, were
 associated with IS and CES independently of known risk factors. Pathways
 related to intracellular hexadecanedioate synthesis or those involved in
 its clearance from the circulation may mediate IS risk. These results
 highlight the potential of metabolomics to discover novel circulating
 biomarkers for stroke and to unravel novel pathways for IS and its
 subtypes.
description: Supplemental
 InformationSupplemental files
 associated with manuscriptSupplement
 10-22-2018.docx
DOI: 10.5061/dryad.ct74m
title: Data from: Density drives polyandry and relatedness influences paternal success in the Pacific gooseneck barnacle, Pollicipes elegans

description: Background: Polyandry is a common mating strategy in animals, increasing
 female fitness through direct (material) and indirect (genetic) benefits.
 Most theories about the benefits of polyandry come from studies of
 terrestrial animals, which have relatively complex mating systems and
 behaviors; less is known about the potential benefits of polyandry in
 sessile marine animals, for which potential mates may be scarce and
 females have less control over pre-copulatory mate choice. Here, we used
 microsatellite markers to examine multiple paternity in natural
 aggregations of the Pacific gooseneck barnacle Pollicipes elegans, testing
 the effect of density on paternity and mate relatedness on male
 reproductive success. Results: We found that multiple paternity was very
 common (79% of broods), with up to five fathers contributing to a brood,
 though power was relatively low to detect more than four fathers. Density
 had a significant and positive linear effect on the number of fathers
 siring a brood, though this relationship leveled off at high numbers of
 fathers, which may reflect a lack of power and/or an upper limit to
 polyandry in this species. Significant skew in male reproductive
 contribution in multiply-sired broods was observed and we found a positive
 and significant relationship between the proportion of offspring sired and
 the genetic similarity between mates, suggesting that genetic
 compatibility may influence reproductive success in this species.
 Conclusions: To our knowledge, this is the first study to show high levels
 of multiple paternity in a barnacle, and overall, patterns of paternity in
 P. elegans appear to be driven primarily by mate availability. Evidence of
 paternity bias for males with higher relatedness suggests some form of
 post-copulatory sexual selection is taking place, but more work is needed
 to determine whether it operates during or post-fertilization. Overall,
 our results suggest that while polyandry in P. elegans is driven by mate
 availability, it may also provide a mechanism for females to ensure
 fertilization by compatible gametes and increase reproductive success in
 this sessile species.
description: Genotype data for
 Barnacle paternity study of Pollicipes elegans-- BMC Evol.
 BioThis spreadsheet
 contains two tabs. The first contains the larval genotype data for each of
 the 14 broods (C1- C22) used for the paternity analyses. The mother's
 genotype is the first row of each brood's dataset. Each subsequent
 row (emb1-embX) is the genotype of each embryo sampled for that brood.
 Pole1-Pole44 are the microsatellite markers used. The Second tab contains
 the adult genotype data from 3 barnacle aggregations used for analysis of
 relatedness and fine-scale population structure. Data are arranged by
 aggregation (1-3) for 8 microsatellite markers.Genotype data for Barnacle
 paternity_Plough et al 2014 BMC Evol.
 Bio.xlsx
DOI: 10.5061/dryad.h2j2466
title: Data from: Cytoskeleton structure and total methylation of mouse cardiac and lung tissue during space flight

description: The purpose of this work was to evaluate the protein and mRNA expression
 levels of multiple cytoskeletal proteins in the cardiac and lung tissue of
 mice that were euthanized onboard the United States Orbital Segment of the
 International Space Station 37 days after the start of the SpaceX-4
 mission (September 2014, USA). The results showed no changes in the
 cytoskeletal protein content in the cardiac and lung tissue of the mice,
 but there were significant changes in the mRNA expression levels of the
 associated genes, which may be due to an increase in total genome
 methylation. The mRNA expression levels of DNA methylases, the cytosine
 demethylases Tet1 and Tet3, histone acetylase and histone deacetylase did
 not change, and the mRNA expression level of cytosine demethylase Tet2 was
 significantly decreased.
description: Data
 SetThis file provides
 information about experimental design and minimal data set, data used to
 build graphs.
DOI: 10.5061/dryad.5b2k6
title: Data from: Genetic differences in the response to landscape fragmentation by a habitat generalist, the bobcat, and a habitat specialist, the ocelot

description: The ecology of a species strongly influences genetic variation and
 population structure. This interaction has important conservation
 implications because taxa with low dispersal capability and inability to
 use different habitats are more susceptible to anthropogenic stressors.
 Ocelots (Leopardus pardalisalbescens) and bobcats (Lynx rufus texensis)
 are sympatric in Texas and northeastern Mexico; however, their ecology and
 conservation status are markedly different. We used 10 microsatellite loci
 and a 397-bp segment of the mitochondrial control region to examine how
 historical and ecological differences in these two species have influenced
 current patterns of genetic diversity in a landscape heavily altered by
 anthropogenic activities. Substantially higher genetic diversity
 (heterozygosity and haplotype diversity) and population connectivity was
 observed for bobcats in comparison to ocelots. The level of divergence
 among proximate ocelot populations (&lt;30 km) was greater than
 between bobcat populations separated by &gt;100 km. Ocelot populations
 in the US have never recovered from reductions experienced during the
 twentieth century, and their low genetic variation and substantial
 isolation are exacerbated by strong preference for dense native thornshrub
 and avoidance of open habitat. In contrast, despite continued legal
 harvesting and frequent road-related mortality, bobcats have maintained
 wide distribution, high abundance, and population connectivity. Our study
 illustrates that sympatric species with a similar niche can still have
 sufficient ecological differences to alter their response to anthropogenic
 change. Sensitive species, such as the ocelot, require additional
 conservation actions to sustain populations. Ecological differences among
 species occupying a similar guild are important to consider when
 developing conservation plans.
description: Microsatellite data for
 ocelots and bobcatsIndividuals sampled in
 southern Texas and Northern Mexico. See Janecka et al. 2016 Conservation
 Genetics publication for information on sampling locations, methods, and
 other descriptions of data.Gentypes are for microsatellite
 lociBobcat
 and ocelot microsat data for Dryad.xlsx