Mining Gene Expression Data for Pollutants (Dioxin, Toluene, Formaldehyde) and Low Dose of Gamma-Irradiation

Abstract

General and specific effects of molecular genetic responses to adverse environmental factors are not well understood. This study examines genome-wide gene expression profiles of Drosophila melanogaster in response to ionizing radiation, formaldehyde, toluene, and 2,3,7,8-tetrachlorodibenzo-p-dioxin. We performed RNA-seq analysis on 25,415 transcripts to measure the change in gene expression in males and females separately. An analysis of the genes unique to each treatment yielded a list of genes as a gene expression signature. In the case of radiation exposure, both sexes exhibited a reproducible increase in their expression of the transcription factors sugarbabe and tramtrack. The influence of dioxin up-regulated metabolic genes, such as anachronism, CG16727, and several genes with unknown function. Toluene activated a gene involved in the response to the toxins, Cyp12d1-p; the transcription factor Fer3’s gene; the metabolic genes CG2065, CG30427, and CG34447; and the genes Spn28Da and Spn3, which are responsible for reproduction and immunity. All significantly differentially expressed genes, including those shared among the stressors, can be divided into gene groups using Gene Ontology Biological Process identifiers. These gene groups are related to defense response, biological regulation, the cell cycle, metabolic process, and circadian rhythms. KEGG molecular pathway analysis revealed alteration of the Notch signaling pathway, TGF-beta signaling pathway, proteasome, basal transcription factors, nucleotide excision repair, Jak-STAT signaling pathway, circadian rhythm, Hippo signaling pathway, mTOR signaling pathway, ribosome, mismatch repair, RNA polymerase, mRNA surveillance pathway, Hedgehog signaling pathway, and DNA replication genes. Females and, to a lesser extent, males actively metabolize xenobiotics by the action of cytochrome P450 when under the influence of dioxin and toluene. Finally, in this work we obtained gene expression signatures pollutants (dioxin, toluene), low dose of gamma-irradiation and common molecular pathways for different kind of stressors.

Inhalation toxicity of indoor air pollutants in Drosophila melanogaster using integrated transcriptomics and computational behavior analyses

“…The microarray analysis showed that inhalation of both toluene (1,000 μg/m 3 ) and formaldehyde (100 μg/m 3 ) for 24 h was sufficient to induce genome-wide gene expression changes in Drosophila . The GO and pathway analyses for DEGs identified GO terms or pathways similar to those previously reported in a murine model including GO terms of immune response, xenobiotic metabolism, neurological system process, and pathways related to the cellular stress response such as NF-κb, PI3K, and p38 MAPK pathways151617181920. This indicated that the inhalation of toluene and formaldehyde induced similar cellular responses in Drosophila compared to those in mammals.…”

The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions

“…Sample preparation and RNA sequencing were carried out by previously used protocol with modifications [6, 7]. The Illumina TruSeq™ RNA Sample Preparation Kit (Low-Throughput protocol) was used to prepare samples for mRNA sequencing libraries.…”

Self-oscillating Water Chemiluminescence Modes and Reactive Oxygen Species Generation Induced by Laser Irradiation; Effect of the Exclusion Zone Created by Nafion

“…A search for latent correlations in the time series of data, related to the chemiluminescence intensity, was performed by the method of detrended fluctuation analysis (DFA) [39] with a modification [40]. In this method, the fluctuation function Fd(l) is plotted in accordance with equation:…”

“…The wavelet transform of the time series {Xi}of the luminescence intensity values makes it possible to reveal the amplitude-frequency and phase-frequency characteristics of signals locally with time [40]. The result of the wavelet transform represents the expansion of the time series {Xi} over the basis of soliton-like functions (the so-called Morlet basis): …”