A CROSS-SECTIONAL ANALYSIS OF CHILDREN'S NEURODEVELOPMENT AND THEIR GUT MICROBIOTA AT THREE YEARS OF AGE IN RURAL CHINA
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA692605 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13478800_1.fastq.gz | Fastqsanger.gz | |||
| SRR13478800_2.fastq.gz | Fastqsanger.gz | |||
| SRR13478801_1.fastq.gz | Fastqsanger.gz | |||
| SRR13478801_2.fastq.gz | Fastqsanger.gz | |||
| SRR13478802_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 94 |
Similar Datasets
Project description:We investigated cross-sectional associations between children's neurodevelopment and their gut microbiota composition. Study children (36 months of age) lived in rural China (n = 46). Neurodevelopment was assessed using the Bayley Scales of Infant Development, 2nd Edition, yielding the Mental Developmental Index (MDI) and Psychomotor Developmental Index (PDI). Children's gut microbiota was assessed using 16S rRNA gene profiling. Microbial diversity was characterized using alpha diversity patterns. Additionally, 3 coabundance factors were determined for the 25 most abundant taxa. Multivariable linear regression models were constructed to examine the relationships between Bayley scores (MDI and PDI) and children's gut microbiota. In adjusted models, MDI and PDI scores were not associated with alpha diversity indices. However, in adjusted models, MDI and PDI scores were positively associated with the first coabundance factor, which captured positive loadings for the genera Faecalibacterium, Sutterella, and Clostridium cluster XIVa. For an interquartile range increase in the first coabundance factor, MDI scores increased by 3.9 points [95% confidence interval (CI): 0, 7.7], while PDI scores increased by 8.6 points (95% CI 3.1, 14). Our results highlight the potential for gut microbial compositional characteristics to be important correlates of children's Bayley Scales performance at 36 months of age.
| S-EPMC8016964 | biostudies-literature
Project description:Forty-six percent of the world's population resides in rural areas, the majority of whom belong to vulnerable and low-income groups. They mainly use cheap solid fuels for cooking and heating, which release a large amount of PM2.5 and cause adverse effects to human health. PM2.5 exhibits urban-rural differences in its health risk to the respiratory system. However, the majority of research on this issue has focused on respiratory diseases induced by atmospheric PM2.5 in urban areas, while rural areas have been ignored for a long time, especially the pathogenesis of respiratory diseases. This is not helpful for promoting environmental equity to aid low-income and vulnerable groups under PM2.5 pollution. Thus, this study focuses on rural atmospheric PM2.5 in terms of its chemical components, toxicological effects, respiratory disease types, and pathogenesis, represented by PM2.5 from rural areas in the Sichuan Basin, China (Rural SC-PM2.5). In this study, organic carbon is the most significant component of Rural SC-PM2.5. Rural SC-PM2.5 significantly induces cytotoxicity, oxidative stress, and inflammatory response. Based on multiomics, bioinformatics, and molecular biology, Rural SC-PM2.5 inhibits ribonucleotide reductase regulatory subunit M2 (RRM2) to disrupt the cell cycle, impede DNA replication, and ultimately inhibit lung cell proliferation. Furthermore, this study supplements and supports the epidemic investigation. Through an analysis of the transcriptome and human disease database, it is found that Rural SC-PM2.5 may mainly involve pulmonary hypertension, sarcoidosis, and interstitial lung diseases; in particular, congenital diseases may be ignored by epidemiological surveys in rural areas, including tracheoesophageal fistula, submucous cleft of the hard palate, and congenital hypoplasia of the lung. This study contributes to a greater scientific understanding of the health risks posed by rural PM2.5, elucidates the pathogenesis of respiratory diseases, clarifies the types of respiratory diseases, and promotes environmental equity.
2024-12-08 | GSE246730 | GEO
Project description:Atmospheric particulate matter (PM) is a recognized risk factor for the global burden of disease in human populations. We are presenting here the application of toxicogenomics in the evaluation of the toxic effects of organic content of atmospheric particle matter (PM), from urban and rural environments (city of Barcelona and village of La Pobla, NE Spain), using the developing zebrafish embryo. The main goal is to identify the metabolic pathways involved in the adverse effects observed in zebrafish embryos exposed to PM organic content from urban and rural environments, also allowing the selection of genes of interest that are differentially expressed. The relevance of particle size to the PM toxicity is also addressed. Indeed, the zebrafish embryos were exposed to PM of aerodynamic diameter larger than 7.2 μm and smaller than 0.5 μm (PM10 and PM0.5, respectively). PM0.5 concentrated biological and toxic activities linked to organic substances. Transcriptomic analyses showed strong induction of the AhR signalling pathway (a.k.a. dioxin-like activity) for embryos exposed to both rural and urban extracts, correlating with the concentrations of PAHs. Urban extracts, with strong contribution of traffic emissions, specifically de-regulated oxidative stress-related genes, as well as pancreatic and eye-lens specific genes, two organs known to be affected by air pollution in humans. Exposure to rural extracts, with high contribution of wood burning emissions, affected genes implicated in basic cellular functions, in agreement with their strong embryotoxicity. Extracts from rural and urban samples elicited both common and specific transcriptome responses, suggesting different potentially adverse outcomes depending on PM source and composition. The authors thank the financial support of the Spanish Ministry (project TEA-PARTICLE, grant number CGL2011-29621) and the Portuguese Foundation for Science and Technology for the doctoral grant of Sofia R. Mesquita (SFRH/BD/80710/2011) funded by the Program POPH-QREN through the Portuguese Ministry of Education and Science and the European Social Fund, and support through project PEst-C/MAR/LA0015/2013. The PM filter samples used in the present study were PM10 and PM0.5 from the urban site - total of 4 samples from 2 sampling months; and PM0.5 from the rural site - total of 2 samples from 2 sampling months (PM10 samples from the rural site were not tested due to their very low concentration in organic compounds, and insignificant biological activity, previously measured). Sampling occurred during the cold periods of the year 2012/2013. The organic fraction of PM samples was extracted by sonication using a mixture of dichloromethane:methanol. Then, the extracts were filtered, evaporated and re-dissolved in Dimethyl sulfoxide (DMSO). Zebrafish fertilized eggs were exposed to PM organic extracts (0.2% DMSO) from the urban and rural sites from 24 to 120h post-fertilization. Total RNA was isolated from whole embryos (pools of 20 individuals), using Trizol reagent protocol (Invitrogen Life Technologies, Carlsberg, CA). The microarray study was performed using the Agilent Two-colour D. rerio Oligo Microarray v3 platform, following the Agilent Microarray â?? Based Gene Expression Analysis protocol. Three biological replicates were performed for each PM sample and controls. Biological replicates, a technical replicate and a self-to-self, were simultaneously amplified and labelled using Cyanine 3 (Cy3) and Cyanine 5 (Cy5) dye. After cRNA purification (RNeasy Kit, Quiagen GmbH, Hilden, Germany), the cRNA concentration and labelling were quantified in the NanoDrop spectrophotometer, obtaining incorporation rates in the range of 15-20pmol of cyanide dye/µl cRNA and yield values > 0.825ug, as recommended. cRNA was fragmented and hybridized in 4x44K arrays, for 17h at 65oC. After the hybridization the array slides were washed, and immediately scanned using Microarray Scanner Agilent G2505C system. Data was extracted using Agilent Feature Extraction Software v10.5.1.1, and the quality of microarray data was evaluated using the Quality Control report provided by Agilent Software. Based on the microarray data analysis, 22 primers were selected and designed using Primer Express 2.0 software (Applied Biosystems, Foster City, CA). Genes were quantified by real-time PCR to validate the microarray data, and a subset of 13 genes were further selected by their robust behaviour in the validation assays, allowing to differentiate the toxic potential of PM from urban and rural sources.
2015-10-26 | E-GEOD-53522 | biostudies-arrayexpress
Project description:BackgroundRice is an important dietary source for methylmercury; however, rice does not contain the same beneficial nutrients as fish. Our main objective was to assess associations of prenatal methylmercury exposure through rice ingestion with child neurodevelopment in rural China.MethodsEligible peripartum women were enrolled (n = 391), provided peripartum hair samples, and children's neurodevelopment was assessed at 12 months (n = 264, 68%) and 36 months (n = 190, 48%) using the Bayley Scales of Infant Development, 2nd Edition, including the Mental Developmental Index (MDI) and the Psychomotor Developmental Index (PDI). Associations between prenatal methylmercury exposure during the third trimester [log2 maternal hair total mercury (THg)] and child's neurodevelopment were assessed using linear mixed models for repeated measures.ResultsIn adjusted models, a doubling in maternal hair THg corresponded to a 1.3-point decrement in the MDI score [95% confidence interval (CI): - 2.6, - 0.14], and a 1.2-point decrement in the PDI score (95% CI: - 2.6, 0.14). Overall, adverse associations between maternal hair THg and MDI scores attenuated over time. However, associations were robust and stable over time among children whose primary caregiver was their parent(s). During the study follow-up, an increasing proportion of children were raised by grandparents (12 months: 9% versus 36 months: 27%), a trend associated with rural-to-urban parental migration for work.ConclusionsFor young children living in rural China, a biomarker of prenatal methylmercury exposure was associated with decrements in cognitive function assessed between 12 and 36 months of age. Changes in the family structure over the study follow-up time interval potentially impacted children's sensitivity to prenatal methylmercury exposure.
| S-EPMC8082930 | biostudies-literature
Project description:Atmospheric particulate matter (PM) is a recognized risk factor for the global burden of disease in human populations. We are presenting here the application of toxicogenomics in the evaluation of the toxic effects of organic content of atmospheric particle matter (PM), from urban and rural environments (city of Barcelona and village of La Pobla, NE Spain), using the developing zebrafish embryo. The main goal is to identify the metabolic pathways involved in the adverse effects observed in zebrafish embryos exposed to PM organic content from urban and rural environments, also allowing the selection of genes of interest that are differentially expressed. The relevance of particle size to the PM toxicity is also addressed. Indeed, the zebrafish embryos were exposed to PM of aerodynamic diameter larger than 7.2 μm and smaller than 0.5 μm (PM10 and PM0.5, respectively). PM0.5 concentrated biological and toxic activities linked to organic substances. Transcriptomic analyses showed strong induction of the AhR signalling pathway (a.k.a. dioxin-like activity) for embryos exposed to both rural and urban extracts, correlating with the concentrations of PAHs. Urban extracts, with strong contribution of traffic emissions, specifically de-regulated oxidative stress-related genes, as well as pancreatic and eye-lens specific genes, two organs known to be affected by air pollution in humans. Exposure to rural extracts, with high contribution of wood burning emissions, affected genes implicated in basic cellular functions, in agreement with their strong embryotoxicity. Extracts from rural and urban samples elicited both common and specific transcriptome responses, suggesting different potentially adverse outcomes depending on PM source and composition. The authors thank the financial support of the Spanish Ministry (project TEA-PARTICLE, grant number CGL2011-29621) and the Portuguese Foundation for Science and Technology for the doctoral grant of Sofia R. Mesquita (SFRH/BD/80710/2011) funded by the Program POPH-QREN through the Portuguese Ministry of Education and Science and the European Social Fund, and support through project PEst-C/MAR/LA0015/2013.
2015-10-26 | GSE53522 | GEO
Project description:The molecular basis of evolutionary change is assumed to be genetic variation. However, growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may also be involved in evolutionary change. An important first step in evaluating this hypothesis is to test for the presence of epigenetic variation between natural populations living under different environmental conditions. In the current study we explored variation between populations of Darwin’s finches living in adjacent “urban” and “rural” environments on Santa Cruz Island in the Galápagos. We tested for morphological, genetic, and epigenetic differences between the urban and rural populations of each of two species of ground finches, Geospiza fortis and G. fuliginosa. Using data collected from more than 1000 birds, we found significant morphological differences between populations of G. fortis, but not G. fuliginosa. We did not find genetic differences between populations of either species, based on comparisons of copy number variation (CNV). In contrast, we did find epigenetic differences between the urban and rural populations of both species, based on DNA methylation analysis. We explored genomic features and gene associations of the differentially methylated regions (DMR), as well as their possible functional significance. In summary, our study documents local population epigenetic variation within species of Darwin’s finches.
2017-01-07 | GSE87825 | GEO
Project description:Epigenetic variation has the potential to control environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the responsiveness of epigenetic variation, which should be even more important when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories. The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2 and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. Observations suggest there is no effect of geographic distance or any consistent pattern of DMRs between urban and rural lakes. Environmental factors may influence epigenetic response.
2019-09-27 | GSE133502 | GEO
Project description:The Study Of Urban and Rural Crohn disease Evolution (SOURCE, n=380) characterized exposures, diet, and host and microbial factors in rural and urban Chinese controls and newly diagnosed Crohn Disease (CD), and in treatment-naïve Israeli CD and controls. We considered diet-omics domains simultaneously to detect complex interactions in the gut to prioritize potential beneficial and pathogenic factors.
2024-02-15 | GSE233900 | GEO
Project description:BackgroundOver the recent decades, residential lifestyle and household environment have changed substantially with rapid development of industrialization and urbanization in China. Whether the prevalence of respiratory diseases changed is still lack of evidence. The objective of this study is to assess potential changes in children's respiratory disease prevalence and associated household environmental factors in Wuhan over a 25-year time interval.MethodsTwo cross-sectional studies in the Period 1 (1993 to 1996) and Period 2 (2017 to 2018) were compared in this research. Elementary school children in period 1 (N=2,517) and in period 2 (N=3,152) were recruited in Wuhan, China. The respiratory health condition, home environmental factors, and family socioeconomic status of each subject were acquired through questionnaire survey using the same protocols in both periods. We used the Chi-square test to analyze the difference of household environmental factors (focused on three indoor air quality determinants) and children's respiratory health condition between two periods. Logistic regression models were used to assess the impacts of household environmental determinants on children's respiratory diseases and symptoms between the two studies, by adjusting a set of covariates.ResultsThe three indoor air quality determinants have reduced substantially in prevalence from period 1 to period 2: environment tobacco smoke (ETS) from 86.6% to 45.9%, household coal use from 47.6% to 4.9%, and kitchen smoke from 58.9% to 7.3%. The prevalence of certain respiratory symptoms in children significantly decreased, such as cough with colds (51.1% to 41.6%) and phlegm with colds (22.3% to 17.7%). The prevalence of asthma was 2.5% and 2.4% and that of bronchitis was 27.1% and 29.8% in both periods. Coal use was a risk factor for asthma in period 1 (OR =2.34, 95% CI: 1.30-4.23), while it was not significantly associated with prevalence of asthma in period 2 (OR =0.60, 95% CI: 0.08-4.51).ConclusionsHousehold indoor air quality determinants and respiratory health condition of children in Wuhan has been improved over the last 25 years. At present, kitchen smoke is an important factor affecting the prevalence of wheeze whatever child has a cold or not and reducing exposure to ETS could be beneficial to protect children to be less likely to develop bronchitis.
| S-EPMC8339747 | biostudies-literature
Project description:BackgroundAttention-deficit/hyperactivity disorder (ADHD) is one of the most common neurodevelopmental disorders in childhood and is caused by both genetic and environmental factors. As genetic factors are nonmodifiable, environmental factors have attracted increasing attention.ObjectiveTo investigate the relationships between urinary chlorpyrifos (CPF) levels, blood micronutrient levels, and ADHD prevalence in children living in rural areas of China.MethodsThis cross-sectional study collected data on CPF exposure (according to urinary levels), blood micronutrient levels, and ADHD prevalence in children aged 1-6 years in rural China. The CPF levels were determined by mass spectrometry. Blood levels of micronutrients, including zinc, iron, calcium, copper, magnesium, and vitamin D, were measured by professional detection kits. ADHD was diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition. Descriptive statistics and univariate analysis were conducted using SPSS 21.0, and path analysis was conducted using Mplus 8.0.ResultsOf the 738 children who met the eligibility criteria, 673 children (673/738, 91.2%) were included in the final analysis. Baseline questionnaires and urine samples were collected from all 673 subjects. A total of 672 children provided blood samples for micronutrient testing, and 651 completed the ADHD assessment. Approximately one-fifth of children (144/673, 21.4%) had detectable levels of CPF in their urine, and 6.9% (45/651) were diagnosed with ADHD. Path analysis showed that the total effect of CPF exposure on ADHD risk was 0.166 (P < 0.05), with a direct effect of 0.197 (P < 0.05) and an indirect effect of -0.031 (P < 0.05) via vitamin D. The mediating effect of urinary CPF levels on ADHD risk via vitamin D was 18.67%.ConclusionHigher levels of CPF exposure are associated with higher risk of ADHD. Additionally, increasing vitamin D levels may have a beneficial effect on the relationship between CPF exposure and ADHD risk. Our findings highlight the importance of modifying environmental factors to reduce ADHD risk and provide insight into future ADHD interventions.
| S-EPMC9616114 | biostudies-literature