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ABSTRACT: Wildfire disturbance

PROVIDER: PRJNA1158506 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR30595200_1.fastq.gz	Fastqsanger.gz
	SRR30595200_2.fastq.gz	Fastqsanger.gz
	SRR30595300_1.fastq.gz	Fastqsanger.gz
	SRR30595300_2.fastq.gz	Fastqsanger.gz
	SRR30595201_1.fastq.gz	Fastqsanger.gz

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Project description:Wildfire disturbance

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Functional Variant Discovery Identifies SPRY2 as a Genetic Mechanism Linking Wood Smoke with Asthma

Project description:Climate change is impacting human health through a historic rise in wildfire smoke across the United States and the world. Whereas the deleterious effects of wildfire smoke and associated air pollution on asthma outcomes are well-established epidemiologically, genetic risks and molecular mechanisms of how wildfire smoke affects asthma are unknown. This knowledge gap hinders the identification of high-risk individuals and the creation of targeted therapies or recommendations to protect these individuals. Here, we employ a genetic approach to identify common variant (minor allele frequency > 0.05) exposure-conditional genetic risk variants that localize with genomic responses to wood smoke particles (WSP), a model of wildfire smoke exposure, and associate with asthma in the Genetic Epidemiology Research on Aging (GERA) cohort. Our novel approach used nascent transcriptional signatures derived from WSP-exposed Beas-2B airway epithelial cells to reduce the genome sequence for discovery and allow a permutation-based statistical approach to identify 52 candidate SNPs. We applied biologic and bioinformatic filters to prioritize variants for direct testing of allele-dependent transcriptional regulatory function in plasmid reporters. The rs3861144 variant identified by this approach controls WSP responses of airway epithelial cells to SPRY2, which we showed is involved in mechanical injury repair in cell culture. Our results demonstrate that wildfire particulates contribute to asthma risk at the molecular level, and we have identified mechanistic targets and genetic variant candidates to apply for clinical risk prediction and development of targeted therapies for high-risk individuals.

2024-12-02 | GSE283113 | GEO

Project description:Changes in assembly processes in soil bacterial communities following a wildfire disturbance

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Effects of Smoldering Eucalyptus Wood Smoke Extract on Primary Human Brain Microvascular Endothelial Cells (HBMEC) and Immortalized Human Cerebral Microvascular Endothelial Cell Line (hCMEC/D3)

Project description:Increase in frequency and size of wildfire raises a significant public health concern due to rapid climate change. Epidemiological studies have shown that wildfire smoke exposure can increase the risk of neurological disorders. Our study aims to understand how wildfire smoke particles affect brain endothelial cells using both primary human brain microvascular endothelial cells (HBMEC) and an immortalized human cerebral microvascular endothelial cell line (hCMEC/D3). HBMEC and hCMEC/D3 were exposed to different levels of smoldering eucalyptus smoke particles (10, 30, 50 ug/mL) for 24 hr. Supernatants were collected for LDH and ELISA array, cell lysates were collected for RNAseq, and cells were fixed and stained for tight junction marker (Zonula Occludens-1, ZO-1) via ICC. Our study found that treatment to smoldering eucalyptus particles can increase inflammatory cytokine production dose-dependently in HBMECs and hCMEC/D3. Moreover, RNAseq analyses resulted in dose-dependent changes in HBMEC and hCMEC/D3 from wood smoke treatment that could be mediated via AhR and Nrf2 pathways.

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Project description:Wildfire experiments-2025

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Analysis of CAL165 cells transcriptome using RNASeq

Project description:Total RNA extracted from the head and neck cell line CAL165 were purified using miRNeasy minikit (Qiagen). RNA libraries were then generated with the NEB next small library prep set for SOLID (New England Biolabs) and sequenced on the Applied Biosystems SOLiD 5500 wildfire system following the manufacturer's instructions.

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Project description:The molecular mechanisms governing heart development provide an important framework to understand congenital heart disease. The embryonic vertebrate heart tube develops an atrioventricular canal that divides the atrial and ventricular chambers, forms atrioventricular conduction tissue and organizes valve development. To better understand the molecular mechanism underlying atrioventricular canal versus chamber myocardium expression, a double-reporter transgenic mouse line was generated in which the expression of EGFP (green fluorescent protein) and Katushka (red fluorescent protein) are selectively expressed in the atrioventricular canal and in the chamber myocardium, respectively. We assessed the genome-wide H3K27ac pattern in isolated embryonic AV canal and in chamber cardiomyocytes, respectively. EGFP and Katushka-positive cells were purified by FACS and fixed. ChIP was performed with the truemicro ChIP (Diagenode) according to the manufacturer’s protocol using the H3K27ac antibody (abcam ab4729). Chipped DNA were subjected to library preparation using the 5500 Series SOLiD™ Systems ample preparation kit (Applied Biosystems) according to manufactures recommendations and sequenced using the 5500 wildfire system (SOLiD).

2014-03-06 | E-GEOD-55611 | biostudies-arrayexpress

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2017-06-07 | GSE89509 | GEO

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