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opencc-zeroDec 2018View details →

Data from: Developmental Dieldrin exposure alters DNA methylation at genes related to dopaminergic neuron development and Parkinson's disease in mouse midbrain

Human and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson's disease (PD). Despite previous work showing a link between developmental dieldrin exposure and increased neuronal susceptibility to MPTP toxicity in male C57BL/6 mice, the mechanism mediating this effect has not been identified. Here, we tested the hypothesis that developmental exposure to dieldrin increases neuronal susceptibility via genome-wide changes in DNA methylation. Starting at 8 weeks of age and prior to mating, female C57BL/6 mice were exposed to 0.3 mg/kg dieldrin by feeding (every 3 days) throughout breeding, gestation, and lactation. At 12 weeks of age, pups were sacrificed and ventral mesencephalon, containing primarily substantia nigra, were microdissected. DNA was isolated and dieldrin-related changes in DNA methylation were assessed via reduced representation bisulfite sequencing (RRBS). We identified significant, sex-specific differentially methylated CpGs (DMCs) and regions (DMRs) by developmental dieldrin exposure (FDRNr4a2 and Lmx1b genes, which are involved in dopaminergic neuron development and maintenance. Developmental dieldrin exposure had distinct effects on the male and female epigenome. Together, our data suggest that developmental dieldrin exposure establishes sex-specific poised epigenetic states early in life. These poised epigenomes may mediate sensitivity to subsequent toxic stimuli and contribute to the development of late-life neurodegenerative disease, including PD.

opencc-zeroDec 2016View details →

Data from: Diversity and preserved shell coloration patterns of Miocene Conidae (Neogastropoda) from an exposure of the Gatun Formation, Colon Province, Panama

Extant members of the neogastropod family Conidae (cone snails) are renowned for their often dazzling shell coloration patterns and venomous feeding habits. Many cone snail species have also been described from the fossil record, but to date have been little used to understand the evolutionary history of extant clades. The cone snail fauna of the Miocene Gatun Formation of Colón Province, Panama is especially important for understanding the temporal and biogeographic history of tropical American Conidae. Intensive, focused collecting from an exposure of the lower Gatun Formation (deposited ca. 11-10 Ma) resulted in the discovery of nearly 900 specimens of Conidae. Remarkably, many of these well-preserved specimens exhibit revealed coloration patterns when exposed to ultraviolet light. The fluorescing coloration patterns were used in conjunction with other features of shell morphology to differentiate species and, in most cases, evaluate their potential relationships to members of the extant tropical American fauna. Nine species are fully described from this locality, one of which is recognized as new: Conus (Stephanoconus) woodringi n. sp. At least one, and perhaps more, Conidae species are also present at the study locality. The diversity of this Conidae fauna is considered moderate relative to other recently analyzed tropical American fossil assemblages. The phylogenetic diversity of the assemblage, however, is noteworthy: six of the ten species can be confidently assigned to six different clades of extant Conidae, providing potentially useful calibration points for future phylogenetic studies.

opencc-zeroDec 2019View details →

Occupational exposure to silica and risk of heart disease: a systematic review with meta-analysis

Objective To search for evidence of the relationship between occupational silica exposure and heart disease. Design A systematic review and meta-analysis. Background Growing evidences suggest a connection between occupational silica exposure and heart disease; however, the link between them is less clear. Data sources PubMed, ScienceDirect, Springer and EMBASE were searched for articles published between 1 January 1995 and 20 June 2019. Articles that investigated the effects of occupational silica exposure on heart disease risk were considered. Study selection We included cohort studies, including prospective, retrospective and retro-prospective studies. Data extraction and synthesis We extracted data by using a piloted data collection form and conducted random-effects meta-analysis and exposure-response analyses. The meta-relative risk (meta-RR), a measure of the average ratio of heart disease rates for those with and without silica exposure, was used as an inverse variance-weighted average of relative risks from the individual studies. The Newcastle-Ottawa Quality assessment Scale about cohort studies was used for study quality assessment. Outcome measure We calculated heart disease risks of pulmonary heart disease, ischaemic heart disease and other heart diseases. Results Twenty cohort articles were included. Results suggest a significant increase of overall heart disease risk (meta-RR = 1.08, 95% CI = 1.03, 1.13). Stronger evidences of association with pulmonary heart disease were found through both categories of heart disease risk estimate (meta-RR = 1.24, 95% CI = 1.08, 1.43) and exposure-response analyses (meta-RR = 1.39, 95% CI = 1.19, 1.62). Moreover, our subgroup analyses revealed that the statistical heterogeneity among studies could be attributed mainly to the diversities of reference group, occupation and study quality score. Conclusions Silica-exposed workers have increased risk of overall heart disease, especially pulmonary heart disease. While further research is needed to better clarify the relationship between occupational silica exposure and ischaemic heart disease.

opencc-zeroDec 2019View details →

Phenology-dependent cold exposure and thermal performance of Ostrinia nubilalis ecotypes

Background: Understanding adaptation involves establishing connections between selective agents and beneficial population responses. However, relatively little attention has been paid to seasonal adaptation, in part, because it requires complex and integrative knowledge about seasonally fluctuating environmental factors, the effects of variable phenology on exposure to those factors, and evidence for temporal specialization. In the European corn borer moth, Ostrinia nubilalis , sympatric pheromone strains exploit the same host plant ( Zea mays ) but may genetically differ in phenology and be reproductively "isolated by time." Z strain populations in eastern North America have been shown to have a prolonged larval diapause and produce one annual mating flight (July), whereas E strain populations complete an earlier (June) and a later (August) mating flight by shortening diapause duration. Here, we find evidence consistent with seasonal "adaptation by time" between these ecotypes. Results: We use 12 years of field observation of adult seasonal abundance to estimate phenology of ecotype life cycles and to quantify life-stage specific climatic conditions. We find that the observed reduction of diapause duration in the E strain leads their non-diapausing, active life stages to experience a ~4˚C colder environment compared to the equivalent life stages in the Z strain. For a representative pair of populations under controlled laboratory conditions, we compare life-stage specific cold tolerance and find non-diapausing, active life stages in the E strain have as much as a 60% greater capacity to survive rapid cold shock. Enhanced cold hardiness appears unrelated to life-stage specific changes in the temperature at which tissues freeze. Conclusions: Our results suggest that isolation by time and adaptation by time may both contribute to population divergence, and they argue for expanded study in this species of allochronic populations in nature experiencing the full spectrum of seasonal environments. Cyclical selective pressures are inherent properties of seasonal habitats. Diverse fluctuating selective agents across each year (temperature, predation, competition, precipitation, etc.) may therefore be underappreciated drivers of biological diversity.

opencc-zeroMar 2020View details →

Paternal exposure to a common herbicide alters the behavior and serotonergic system of zebrafish offspring

Increasingly, studies are revealing that endocrine disrupting chemicals (EDCs) can alter animal behavior. Early life exposure to EDCs may permanently alter phenotypes through to adulthood. In addition, the effects of EDCs may not be isolated to a single generation − offspring may indirectly be impacted, via non-genetic processes. Here, we analyzed the effects of paternal atrazine exposure on behavioral traits (distance moved, exploration, bottom-dwelling time, latency to enter the top zone, and interaction with a mirror) and whole-brain mRNA of genes involved in the serotonergic system regulation (slc6a4a, slc6a4b, htr1Aa, htr1B, htr2B) of zebrafish (Danio rerio). F0 male zebrafish were exposed to atrazine at 0.3, 3 or 30 part per billion (ppb) during early juvenile development, the behavior of F1 progeny was tested at adulthood, and the effect of 0.3 ppb atrazine treatment on mRNA transcription was quantified. Paternal exposure to atrazine significantly reduced interactions with a mirror (a proxy for aggression) and altered the latency to enter the top zone of a tank in unexposed F1 offspring. Bottom-dwelling time (a proxy for anxiety) also appeared to be somewhat affected, and activity (distance moved) was reduced in the context of aggression. slc6a4a and htr1Aa mRNA transcript levels were found to correlate positively with anxiety levels in controls, but we found that this relationship was disrupted in the 0.3 ppb atrazine treatment group. Overall, paternal atrazine exposure resulted in alterations across a variety of behavioral traits and showed signs of serotonergic system dysregulation, demonstrating intergenerational effects. Further research is needed to explore transgenerational effects on behavior and possible mechanisms underpinning behavioral effects.

opencc-byAug 2020View details →

Soil Exposure at Umstead Park

This soil exposure was the main subject of an on-site photocapture project to allow NC State DELTA's NMD team to further explore the use of photogrammetry in classroom media. This model shows This model is part of an effort in the NC State DELTA NMD team to further our media creation efforts and bring even better content to classrooms in exciting new ways. You can find out more about the DELTA department at https://delta.ncsu.edu/. This model was captured by a team composed of Matthew Castro, Stephen Waddell, Rhett Hissam, Michael Castro, and Derek DeStefano working to get multiple photograph sets for processing. The model was generated and processed by Matthew Castro and Stephen Waddell. Source: Objaverse 1.0 / Sketchfab

opencc-zeroMay 2014View details →

Datasets for article: The emotional and attentional impact of exposure to one’s own body in bulimia nervosa: A physiological view

The data of the article titled: The emotional and attentional impact of exposure to one’s own body in bulimia nervosa: A physiological view submitted to PLOS ONE

opencc-zeroFeb 2015View details →

dataset for article: Ortega-Roldan, B., Rodriguez-Ruiz, S., Perakakis, P., Fernandez-Santaella, M.C., Vila, J. (2014). The emotional and attentional impact of exposure to one’s own body in bulimia nervosa: A physiological view. PLoS ONE 9(7): e102595

dataset for article: Ortega-Roldan, B., Rodriguez-Ruiz, S., Perakakis, P., Fernandez-Santaella, M.C., Vila, J. (2014). The emotional and attentional impact of exposure to one’s own body in bulimia nervosa: A physiological view. PLoS ONE 9(7): e102595

Heat Stress Exposure Maps - Urban Planning Scenario 2026 - 2045: Berlin, Germany

Berlin heat stress exposure map: average number of heatwave days per year versus socio economic data - urban planning scenario (2026-2045). Heat stress exposure maps for Berlin representing the average number of heatwave days per year versus socio economic data per statistical unit.  The average number of heatwave days per year has been modeled over the reference period 2026-2045 using the present land use / cover situation for the city but combined with urban planning projects information until 2030. Hence, the urban morphology has been updated accordingly. Scenario: Urban planning scenario (situation LULC today + integrated urban planning projects 2030) Exposure mapping variable: Total population 2030 Population density inhabitants per hectare 2030

Heat Stress Exposure Maps - Base Scenario 1986 - 2005: Almada, Portugal

Average number of heatwave days per year versus socio economic data - base scenario Heat stress exposure maps for the city of Almada representing the average number of heatwave days per year versus socio economic data per statistical unit.  The average number of heatwave days per year has been modelled over the reference period 1986-2005 using the present land use / cover situation for the city. Exposure mapping variable include the following: Total population 2011 Population density inhabitants per hectare 2011 Number of inhabitants aged 0 to 19 years 2011 Number of inhabitants aged 20 to 65 years 2011 Number of inhabitants aged +65 years 2011 Number of childcare centres 2014 Number of hospitals 2014 Number of schools 2014 Number of schools and universities 2014 Number of universities 2014 Number of resthomes 2014

Heat Stress Exposure Maps - Urban Planning Scenario 2026 - 2045: Antwerp, Belgium

Antwerp heat stress exposure map: average number of heatwave days per year versus socio economic data - urban planning scenario (2026-2045) Heat stress exposure maps for Antwerp representing the average number of heatwave days per year versus socio economic data per statistical unit.  The average number of heatwave days per year has been modeled over the reference period 2026-2045 using the present land use / cover situation for the city but combined with urban planning projects information until 2030. Hence, the urban morphology has been updated accordingly. Exposure mapping variable include: * Total population 2030 * Population density inhabitants per hectare 2030

Heat Stress Exposure Maps - Urban Planning Scenario 2026 - 2045: Almada, Portugal

Almada heat stress exposure map: average number of heatwave days per year versus socio economic data - urban planning scenario (2026-2045) Heat stress exposure maps for the city of Almada representing the average number of heatwave days per year versus socio economic data per statistical unit.  The average number of heatwave days per year has been modeled over the reference period 2026-2045 using the present land use / cover situation for the city but combined with urban planning projects information until 2030. Hence, the urban morphology has been updated accordingly. Exposure mapping variable include: * Total population 2011 * Population density inhabitants per hectare 2011

Heat Stress Exposure Maps - Base Scenario 1986 - 2005: Antwerp, Belgium

Average number of heatwave days per year versus socio economic data - base scenario (1986-2005) Heat stress exposure maps for the city of Antwerp representing the average number of heatwave days per year versus socio economic data per statistical unit.  The average number of heatwave days per year has been modelled over the reference period 1986-2005 using the present land use / cover situation for the city. Exposure mapping variable include the following: Total population 2014 Population density inhabitants per hectare 2014 Number of inhabitants aged 0 to 4 years 2014 Number of inhabitants aged 0 to 17 years 2014 Number of inhabitants aged 18 to 65 years 2014 Number of inhabitants aged +65 years 2014 Number of schools 2014 Number of childcare centers 2014 Number of hospitals 2014 Number of elderly stay facilities 2014

Heat Stress Exposure Maps - Base Scenario 1986 - 2005: Berlin, Germany (Map-2 & Map-3)

Heat Stress Exposure Maps - Base Scenario 1986 - 2005: Berlin, Germany Map-2 & Map-3 (zip.file) ref. to DOI: 10.5281/zenodo.45015

Heat Stress Exposure Maps - Base Scenario 1986 - 2005: Berlin, Germany

Average number of heatwave days per year versus socio economic data - base scenario (1986-2005) Heat stress exposure maps for the city of Berlin representing the average number of heatwave days per year versus socio economic data per statistical unit.  The average number of heatwave days per year has been modelled over the reference period 1986-2005 using the present land use / cover situation for the city. Exposure mapping variable include the following: Total population 2013 Population density inhabitants per hectare 2013 Number of inhabitants aged 0 to 17 years 2013 Number of inhabitants aged 18 to 65 years 2013 Number of inhabitants aged +65 years 2013 Number of schools 2014 Number of childcare centers 2014 Number of hospitals 2014 Number of elderly stay facilities 2014

opencc-by-4.0Jan 2017View details →

Topological Overlap Matrices for DNA Methylation data of Gestational Diabetes Cohort with BMI and Exposure Status

DNA methylation in placenta was measured with the Infinium HumanMethylation450 BeadChip (Illumina, Inc) microarray, in a sample of 28 women, 20 of whom had a gestational diabetes (GD)-affected pregnancy and 8 who did not. We used GD status as our exposure variable, assuming that this has widespread effects on DNA methylation and on its correlation patterns. Our response, Y, is the standardized body mass index (BMI) in the offspring at the age of 5. For the 10,000 most variable probes, we provide 3 topological overlap matrices (TOM), which are used in our analysis (note that each of the following TOM matrices are a 10,000 by 10,000 symmetric matrix with row names and column names corresponding to the CpG probe IDs: <ol> <li>TOM_Methylation_All_10k.rds: based on all 28 subjects, </li> <li>TOM_Methylation_E0_10k.rds: based on the 8 subjects without a GD-affected pregnancy</li> <li>TOM_Methylation_E1_10k.rds: based on the 20 subjects with a GD-affected pregnancy </li> </ol> The BMI (phenotype) and GD status (exposure) are given in the following dataset: <ol> <li>BMI_and_Exposure_Status.rds: 28 x 2 matrix of the phenotype and exposure. each row is a subject.</li> </ol> Using our ECLUST method (preprint available at http://sahirbhatnagar.com/slides/manuscript1_SB_v4.pdf), we derive 77 clusters, and here we provide the 1st principal component of each cluster: <ol> <li>Cluster_Summary_1stPC.rds: 28 x 77 matrix, where each row is a subject, in the same order as the BMI_and_Exposure_Status.rds data</li> <li>Cluster_CpGs_names.rds: a list of length 77, where each element of the list contains the list of CpG probe IDs contained in each of the clusters</li> </ol> To read in the data use the readRDS function, e.g.: TOM_All <- readRDS(file = "TOM_Methylation_All_10k.rds")

opencc-by-4.0Jul 2017View details →

Sample1-4 response before and after exposure

Sample 1-4 response before and after exposure. Sample type and dimensions given in schematic. Tests based on RTCA DO-160 C. Before and after exposure to: Low temperature −55 ◦C and high 70 ◦C,three hour hold. Thermal shock, ramp rate of 5 ◦C/min between low and high temperature. Altitude: pressure held at 11.6 kPa abs.

opencc-zeroNov 2023View details →

Data for: Feeding frequency does not interact with BPA exposure to influence metabolism of behaviour in zebrafish (Danio rerio)

Resource limitation can constrain energy (ATP) production, and thereby affect locomotion and behaviour such as exploration of novel environments and boldness. Consequently, ecological processes such as dispersal and interactions within and between species may be influenced by food availability. Energy metabolism, and behaviour are regulated by endocrine signaling, and may therefore be impacted by endocrine disrupting compounds (EDCs) such as bisphenol A (BPA) derived from plastic manufacture and pollution. It is important to determine the impacts of these novel environmental contexts to understand how human activity alters individual physiology and behaviour and thereby populations. Our aim was to determine whether BPA exposure interacts with feeding frequency to alter metabolism and behaviour. In a fully factorial experiment, we show that low feeding frequency reduced zebrafish (Danio rerio) mass, condition, resting metabolic rates, total distance moved and speed in a novel arena, as well as anxiety indicated by the number of times fish returned to a dark shelter. However, feeding frequency did not significantly affect maximal metabolic rates, aerobic scope, swimming performance, latency to leave a shelter, or metabolic enzyme activities (citrate synthase and lactate dehydrogenase). Natural or anthropogenic fluctuation in food resources can therefore impact energetics and movement of animals with repercussions for ecological processes such as dispersal. BPA exposure reduced LDH activity and body mass, but did not interact with feeding frequency. Hence, behaviour of adult fish is relatively insensitive to disruption by BPA. However, alteration of LDH activity by BPA could disrupt lactate metabolism and signalling and together with reduction in body mass could affect size-dependent reproductive output. BPA released by plastic manufacture and pollution can thereby impact conservation and management of natural resources.

opencc-by-4.0Nov 2023View details →

Long-term changes in pituitary gene expression following developmental exposure to environmental contaminants (BPS, BDE-47, or TBBPA) in male mice.

Experimental DesignIn this study we evaluate the long-term gene expression changes in pituitary in male mice exposed developmentally to one of three known endocrine disrupting chemicals: bisphenol-S (BPS), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), and 3,3',5,5'-tetrabromobisphenol A (TBBPA).  Male mice were exposed to chemical treatment through their mothers' during pregnancy (umbilical blood flow) and nursing, from pregnancy day 8 through weaning at postnatal day 21 (PND21). Each chemical exposure was calculated to equal 0.2mg/kg bw/day. The details of exposure protocol are described elsewhere (Kim et al, 2015). The male pups were allowed to grow untreated until adulthood at PND140. At PND140, male mice were euthanized, then their pituitaries removed, snap frozen in liquid nitrogen, and then stored at -80°C. The data-files described below represent major steps of our analysis:1. FASTQ files for mouse pituitary RNA-seq data.Male mouse pituitary RNA was isolated using a Trizol protocol, checked for purity and concentration and then processed for mRNA sequencing using the Illumina TruSeq kit and protocol (TruSeq Stranded mRNA LP, Cat # 20020594 and TruSeq RNA Sg Idx SetB, Cat # 20020493, Illumina, San Diego, CA) following the manufacturer's recommended procedures. High throughput sequencing was conducted using the NextSeq500 sequencing system. cDNA libraries were single-end sequenced in 76 cycles using a NSQ 500/550 Hi Output KT v2.5 (Cat #20024906 Illumina, San-Diego, CA) in one multiplex run (N=3/exposure group).  Read filtering, trimming, and de-multiplexing were performed using the BaseSpace cloud service by Illumina (<a href="https://basespace.illumina.com/home/index">https://basespace.illumina.com/home/index</a>, RRID:SCR_011881). Processed reads were mapped to the mouse reference genome (MM10) using the RNA-Seq Alignment v. 1.1.1. software with Bowtie 2. Each FASTQ file is a compressed file representing data from one sequencing flow cell lane for each sample (4 files per sample). Sample identifiers are coded for treatment: X = Vehicle control, R = TBBPA, C = BDE-47, E = BPS. 2. Differential expression data.Aligned reads were used to assemble transcripts and analyze differential expression using Cufflinks Assembly & DE v. 2.1.0. package. Reads aligned to known annotated regions for both control and exposed groups were used to calculate log2 FPKM ratios.  Differentially expressed genes were identified as genes altered with false discovery rate significance ≤ 0.05 (FDR, q ≤ 0.05).  Data on all exposure groups are shown in different sheets of the same file - Differential_expression.xlsx.3. Enrichment of biological categories associated with DEGs induced by chemical exposures. All differentially expressed genes were uploaded to Metascape for the analysis of enriched biological categories using default settings. Results of Metascape analysis are shown in two MS Excel files per exposure group, one showing negatively enriched categories and one positively enriched categories. The title of each file consists of three parts connected via underscore sign: the name of the chemical, the direction of enrichment, and the name of analysis - metascape (e.g., BDE-47_negative_metascape.xlsx).4. Pathway analysis for chemical exposures.All differentially expressed genes were uploaded to Ingenuity Pathway Analysis and enriched canonical pathways were identified  using default settings . Altered molecular or disease pathways, their p-values, and associated differentially expressed genes are provided for each exposure. Data for all exposure groups are shown in different sheets of the same file - IPA_pathway_analysis.xlsx.References:Kim B, Colon E, Chawla S, Vandenberg LN, Suvorov A. Endocrine disruptors alter social behaviors and indirectly influence social hierarchies via changes in body weight. Environ Health. 2015 Aug 5;14:64. doi: 10.1186/s12940-015-0051-6. PMID: 26242739; PMCID: PMC4524022.