scholarly journals Meta-Analysis of Oxidative Transcriptomes in Insects

Antioxidants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 345
Author(s):  
Hidemasa Bono
Keyword(s):  
Oxidative Stress ◽  
Stress Response ◽  
Meta Analysis ◽  
Adherens Junction ◽  
Enrichment Analysis ◽  
Oxidative Stress Response ◽  
Insect Species ◽  
Rna Seq ◽  
Manual Curation ◽  
Analysis Workflow

Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data of Drosophila melanogaster were found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data of Caenorhabditis elegans were curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response.

scholarly journals Meta-Analysis of Oxidative Transcriptomes in Insects

2021 ◽  
Author(s):  
Hidemasa Bono
Keyword(s):  
Oxidative Stress ◽  
Stress Response ◽  
Meta Analysis ◽  
Adherens Junction ◽  
Enrichment Analysis ◽  
Oxidative Stress Response ◽  
Insect Species ◽  
Rna Seq ◽  
Manual Curation ◽  
Analysis Workflow

AbstractData accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data of Drosophila melanogaster were found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data of Caenorhabditis elegans were curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response.

scholarly journals Understanding genetic changes underlying the molybdate resistance and the glutathione production inSaccharomyces cerevisiaewine strains using an evolution-based strategy

2016 ◽  
Author(s):  
Francesco Mezzetti ◽  
Justin C. Fay ◽  
Paolo Giudici ◽  
Luciana De Vero
Keyword(s):  
Oxidative Stress ◽  
Stress Response ◽  
Oxidative Stress Response ◽  
Selection Strategy ◽  
Rna Seq ◽  
Genetic Changes ◽  
Over Expression ◽  
Sexual Recombination ◽  
Wine Strain ◽  
The Relationship

AbstractIn this work we have investigated the genetic changes underlying the high glutathione (GSH) production showed by the evolvedSaccharomyces cerevisiaestrain UMCC 2581, selected in a molybdate-enriched environment after sexual recombination of the parental wine strain UMCC 855. To reach our goal, we first generated strains with the desired phenotype, and then we mapped changes underlying adaptation to molybdate by using a whole-genome sequencing. Moreover, we carried out the RNA-seq that allowed an accurate measurement of gene expression and an effective comparison between the transcriptional profiles of parental and evolved strains, in order to investigate the relationship between genotype and high GSH production phenotype.Among all genes evaluated only two genes,MED2andRIM15both related to oxidative stress response, presented new mutations in the UMCC 2581 strain sequence and were potentially related to the evolved phenotype.Regarding the expression of high GSH production phenotype, it included over-expression of amino acids permeases and precursor biosynthetic enzymes rather than the two GSH metabolic enzymes, whereas GSH production and metabolism, transporter activity, vacuolar detoxification and oxidative stress response enzymes were probably added resulting in the molybdate resistance phenotype. This work provides an example of a combination of an evolution-based strategy to successful obtain yeast strain with desired phenotype and inverse engineering approach to genetic characterize the evolved strain. The obtained genetic information could be useful for further optimization of the evolved strains and for providing an even more rapid approach to identify new strains, with a high GSH production, through a marked-assisted selection strategy.

scholarly journals Identification of Four Oxidative Stress-Responsive MicroRNAs, miR-34a-5p, miR-1915-3p, miR-638, and miR-150-3p, in Hepatocellular Carcinoma

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Yong Wan ◽  
Ruixia Cui ◽  
Jingxian Gu ◽  
Xing Zhang ◽  
Xiaohong Xiang ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Hepatocellular Carcinoma ◽  
Stress Response ◽  
Clinical Investigation ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Oxidative Stress Response ◽  
Rank Aggregation ◽  
Integrated Analysis ◽  
Pathway Enrichment Analysis

Increasing evidence suggests that oxidative stress plays an essential role during carcinogenesis. However, the underlying mechanism between oxidative stress and carcinogenesis remains unknown. Recently, microRNAs (miRNAs) are revealed to be involved in oxidative stress response and carcinogenesis. This study aims to identify miRNAs in hepatocellular carcinoma (HCC) cells which might involve in oxidative stress response. An integrated analysis of miRNA expression signature was performed by employing robust rank aggregation (RRA) method, and four miRNAs (miR-34a-5p, miR-1915-3p, miR-638, and miR-150-3p) were identified as the oxidative stress-responsive miRNAs. Pathway enrichment analysis suggested that these four miRNAs played an important role in antiapoptosis process. Our data also revealed miR-34a-5p and miR-1915-3p, but not miR-150-3p and miR-638, were regulated by p53 in HCC cell lines under oxidative stress. In addition, clinical investigation revealed that these four miRNAs might be involved in oxidative stress response by targeting oxidative stress-related genes in HCC tissues. Kaplan-Meier analysis showed that these four miRNAs were associated with patients’ overall survival. In conclusion, we identified four oxidative stress-responsive miRNAs, which were regulated by p53-dependent (miR-34a-5p and miR-1915-3p) and p53-independent pathway (miR-150-3p and miR-638). These four miRNAs may offer new strategy for HCC diagnosis and prognosis.

scholarly journals RNase E cleavage shapes the transcriptome ofRhodobacter sphaeroidesand strongly impacts phototrophic growth

2018 ◽  
Vol 1 (4) ◽  
pp. e201800080 ◽  
Author(s):  
Konrad U Förstner ◽  
Carina M Reuscher ◽  
Kerstin Haberzettl ◽  
Lennart Weber ◽  
Gabriele Klug
Keyword(s):  
Oxidative Stress ◽  
Stress Response ◽  
Oxidative Stress Response ◽  
Cleavage Sites ◽  
Rnase E ◽  
Rna Seq ◽  
Rapid Changes ◽  
Photosynthetic Complexes ◽  
Phototrophic Growth

Bacteria adapt to changing environmental conditions by rapid changes in their transcriptome. This is achieved not only by adjusting rates of transcription but also by processing and degradation of RNAs. We applied TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) for the transcriptome-wide identification of RNase E cleavage sites and of 5′ RNA ends, which are enriched when RNase E activity is reduced inRhodobacter sphaeroides. These results reveal the importance of RNase E for the maturation and turnover of mRNAs, rRNAs, and sRNAs in this guanine-cytosine-rich α-proteobacterium, some of the latter have well-described functions in the oxidative stress response. In agreement with this, a role of RNase E in the oxidative stress response is demonstrated. A remarkably strong phenotype of a mutant with reduced RNase E activity was observed regarding the formation of photosynthetic complexes and phototrophic growth, whereas there was no effect on chemotrophic growth.

scholarly journals Transcriptome analysis of Xanthomonas oryzae pv. oryzicola exposed to H2O2 reveals horizontal gene transfer contributes to its oxidative stress response

2019 ◽  
Author(s):  
Yuan Fang ◽  
Haoye Wang ◽  
Xia Liu ◽  
Yuchun Rao ◽  
Xin Dedong ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Time Series ◽  
Stress Response ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Oxidative Stress Response ◽  
Xanthomonas Oryzae ◽  
Gene Location ◽  
Rna Seq

AbstractXanthomonas oryzae pv. oryzicola (Xoc) is the causal agent of bacterial leaf streak in rice. It is known as one of the most severe seed-born bacterial diseases of rice, molecular role governing its interaction with rice is mostly still unexplored. To successfully invade rice, the survival of the Xoc is mandotarory following generating a specific response to its host’s oxidative stress condition. However, the response network of Xoc is still unknown. To address this question, we performed a time-series RNA-seq analysis on the Xoc response to H2O2. Overall, our RNA sequence analysis of Xoc revealed a significant global gene expression profile when it exposed to H2O2. The response of key genes was also noted that soxR triggers and regulates the Xoc oxidative stress response in the early stage of infection, gene expression kinetics among the time-series samples, namely for TonB-dependent receptors and the suf and pst operons. Moreover, a hypothetical protein (XOC_2868) showed significant differential expression following its mutant endorsed RNA-seq findings by clearly displaying a greater H2O2 sensitivity and decreased pathogenicity than the wild-type. Gene location and phylogeny analysis strongly suggests that this gene may have been horizontally transferred from a Burkholderiaceae ancestor. Our study not only provides a first glance of Xoc’s global response against oxidative stress, but it also reveals the impact of horizontal gene transfer in the evolutionary history of Xoc.

scholarly journals Effect of Oral Vitamin E on Oxidative Stress in Diabetic Kidney Disease：A Protocol of Systematic Review and Meta-Analysis

2021 ◽  
Author(s):  
Renhong Wan ◽  
Pengwei Miao ◽  
Yue Ji ◽  
Yihua Fan ◽  
Xiaohan Liu ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Diabetic Nephropathy ◽  
Vitamin E ◽  
Stress Response ◽  
Data Extraction ◽  
Meta Analysis ◽  
Oxidative Stress Response ◽  
Cochrane Library ◽  
Oral Vitamin ◽  
History Of Use

Abstract BackgroundThe occurrence and progression of diabetic nephropathy is closely related to oxidative stress response. Vitamin E, as a lipid soluble antioxidant, has a long history of use. It may improve oxidative stress response to some extent, but there is no relevant support of evidence-based medicine. The purpose of this study was to systematically evaluate the effect of oral vitamin E on oxidative stress response in patients with diabetic nephropathy.MethodsA computer was used for retrieving data from English database (PubMed, Embase, Web of Science, the Cochrane Library) and Chinese database (CNKI, Wangfang, VIP, CBMDISC) between the creation time to October 2020, a randomized controlled clinical study on oral vitamin E treatment of diabetic nephropathy. Two investigators conducted data extraction and literature quality evaluation for the included studies, and a Meta- analysis on the included articles was conducted using RevMan5.3 software.ConclusionsThis study will summarize up-to-date high-quality RCTs to assess the antioxidant effects of oral vitamin E on diabetic nephropathy. The findings of this study will help to determine whether oral vitamin E is effective and safe in patients with diabetic nephropathy.Systematic review registration: PROSPERO CRD42020213945

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