scholarly journals Transcriptome analysis of chloride intracellular channel knockdown in Drosophila identifies oxidation-reduction function as possible mechanism of altered sensitivity to ethanol sedation

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0246224
Author(s):  
Rory M. Weston ◽  
Rebecca E. Schmitt ◽  
Mike Grotewiel ◽  
Michael F. Miles
Keyword(s):  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Reduction Process ◽  
Major Influence ◽  
Biological Processes ◽  
Ethanol Sensitivity ◽  
Substantial Impact ◽  
Reduction Processes ◽  
Oxidation Reduction ◽  
Acute Ethanol

Chloride intracellular channels (CLICs) are a unique family of evolutionarily conserved metamorphic proteins, switching between stable conformations based on redox conditions. CLICs have been implicated in a wide variety biological processes including ion channel activity, apoptosis, membrane trafficking, and enzymatic oxidoreductase activity. Understanding the molecular mechanisms by which CLICs engage in these activities is an area of active research. Here, the sole Drosophila melanogaster ortholog, Clic, was targeted for RNAi knockdown to identify genes and biological processes associated with Clic expression. Clic knockdown had a substantial impact on global transcription, altering expression of over 7% of transcribed Drosophila genes. Overrepresentation analysis of differentially expressed genes identified enrichment of Gene Ontology terms including Cytoplasmic Translation, Oxidation-Reduction Process, Heme Binding, Membrane, Cell Junction, and Nucleolus. The top term, Cytoplasmic Translation, was enriched almost exclusively with downregulated genes. Drosophila Clic and vertebrate ortholog Clic4 have previously been tied to ethanol sensitivity and ethanol-regulated expression. Clic knockdown-responsive genes from the present study were found to overlap significantly with gene sets from 4 independently published studies related to ethanol exposure and sensitivity in Drosophila. Bioinformatic analysis of genes shared between these studies revealed an enrichment of genes related to amino acid metabolism, protein processing, oxidation-reduction processes, and lipid particles among others. To determine whether the modulation of ethanol sensitivity by Clic may be related to co-regulated oxidation-reduction processes, we evaluated the effect of hyperoxia on ethanol sedation in Clic knockdown flies. Consistent with previous findings, Clic knockdown reduced acute ethanol sedation sensitivity in flies housed under normoxia. However, this effect was reversed by exposure to hyperoxia, suggesting a common set of molecular-genetic mechanism may modulate each of these processes. This study suggests that Drosophila Clic has a major influence on regulation of oxidative stress signaling and that this function overlaps with the molecular mechanisms of acute ethanol sensitivity in the fly.

scholarly journals Transcriptome Analysis of Chloride Intracellular Channel Knockdown in Drosophila Identifies Oxidation-Reduction Function as Possible Mechanism of Altered Sensitivity to Ethanol Sedation

2021 ◽  
Author(s):  
Rory M. Weston ◽  
Rebecca E. Schmitt ◽  
Mike Grotewiel ◽  
Michael F. Miles
Keyword(s):  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Reduction Process ◽  
Major Influence ◽  
Biological Processes ◽  
Ethanol Sensitivity ◽  
Substantial Impact ◽  
Reduction Processes ◽  
Oxidation Reduction ◽  
Acute Ethanol

AbstractChloride intracellular channels (CLICs) are a unique family of evolutionarily conserved metamorphic proteins, switching between stable conformations based on redox conditions. CLICs have been implicated in a wide variety biological processes including ion channel activity, apoptosis, membrane trafficking, and enzymatic oxidoreductase activity. Understanding the molecular mechanisms by which CLICs engage in these activities is an area of active research. Here, the sole Drosophila melanogaster ortholog, Clic, was targeted for RNAi knockdown to identify genes and biological processes associated with Clic expression. Clic knockdown had a substantial impact on global transcription, altering expression of over 9% of transcribed Drosophila genes. Overrepresentation analysis of differentially expressed genes identified enrichment of 23 Gene Ontology terms including Cytoplasmic Translation, Oxidation-Reduction Process, Heme Binding, Membrane, Cell Junction, and Nucleolus. The top term, Cytoplasmic Translation, was enriched almost exclusively with downregulated genes. Drosophila Clic and vertebrate ortholog Clic4 have previously been tied to ethanol sensitivity and ethanol-regulated expression. Clic knockdown-responsive genes from the present study were found to overlap significantly with gene sets from 4 independently published studies related to ethanol exposure and sensitivity in Drosophila. Bioinformatic analysis of genes shared between these studies revealed an enrichment of genes related to amino acid metabolism, protein processing, oxidation-reduction processes, and lipid particles among others. To determine whether the modulation of ethanol sensitivity by Clic may be related to co-regulated oxidation-reduction processes, we evaluated the effect of hyperoxia on ethanol sedation in Clic knockdown flies. Consistent with previous findings, Clic knockdown reduced acute ethanol sedation sensitivity in flies housed under nomoxia. However, this effect was reversed by exposure to hyperoxia, suggesting a common set of molecular-genetic mechanism may modulate each of these processes. This study suggests that Drosophila Clic has a major influence on regulation of oxidative stress signaling and that this function overlaps with the molecular mechanisms of acute ethanol sensitivity in the fly.

scholarly journals Proteomic Analysis of Rapeseed Root Response to Waterlogging Stress

Plants ◽  
2018 ◽  
Vol 7 (3) ◽  
pp. 71 ◽  
Author(s):  
Jinsong Xu ◽  
Xing Qiao ◽  
Zhitao Tian ◽  
Xuekun Zhang ◽  
Xiling Zou ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Yangtze River Basin ◽  
Reduction Process ◽  
Absolute Quantification ◽  
Brassica Napus L ◽  
Waterlogging Stress ◽  
Oxidation Reduction ◽  
Root Response ◽  
Isobaric Tags

The overall health of a plant is constantly affected by the changing and hostile environment. Due to climate change and the farming pattern of rice (Oryza sativa) and rapeseed (Brassica napus L.), stress from waterlogging poses a serious threat to productivity assurance and the yield of rapeseed in China’s Yangtze River basin. In order to improve our understanding of the complex mechanisms behind waterlogging stress and identify waterlogging-responsive proteins, we firstly conducted iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomic analysis of rapeseed roots under waterlogging treatments, for both a tolerant cultivar ZS9 and sensitive cultivar GH01. A total of 7736 proteins were identified by iTRAQ, of which several hundred showed different expression levels, including 233, 365, and 326 after waterlogging stress for 4H, 8H, and 12H in ZS9, respectively, and 143, 175, and 374 after waterlogging stress for 4H, 8H, and 12H in GH01, respectively. For proteins repeatedly identified at different time points, gene ontology (GO) cluster analysis suggested that the responsive proteins of the two cultivars were both enriched in the biological process of DNA-dependent transcription and the oxidation–reduction process, and response to various stress and hormone stimulus, while different distribution frequencies in the two cultivars was investigated. Moreover, overlap proteins with similar or opposite tendencies of fold change between ZS9 and GH01 were observed and clustered based on the different expression ratios, suggesting the two genotype cultivars exhibited diversiform molecular mechanisms or regulation pathways in their waterlogging stress response. The following qRT-PCR (quantitative real-time polymerase chain reaction) results verified the candidate proteins at transcription levels, which were prepared for further research. In conclusion, proteins detected in this study might perform different functions in waterlogging responses and would provide information conducive to better understanding adaptive mechanisms under environmental stresses.

Electrochemical Behavior of (Zn, Mn)-Al Nitrated Hydrotalcites

2012 ◽  
Vol 15 (4) ◽  
pp. 301-306 ◽  
Author(s):  
Alvaro Sampieri ◽  
Jorge Vázquez-Arenas ◽  
Ignacio González ◽  
Geolar Fetter ◽  
Heriberto Pfeiffer ◽  
...  
Keyword(s):  
Electrochemical Behavior ◽  
Lamellar Structure ◽  
Oxidation Process ◽  
Reduction Process ◽  
The Other ◽  
Oxidation Processes ◽  
Reduction Processes ◽  
Oxidation Reduction ◽  
Alkaline Conditions ◽  
Continuous Oxidation

The electrochemical behavior of synthetic binary, Zn-Al and Mn-Al, and ternary (Zn-Mn)-Al hydrotalcites (HT) was studied by cyclic voltammetry in alkaline conditions (pH≡12). The Zn-Al HT characterization revealed two irreversible and continuous oxidation processes: i) Zn0|Zn2+ and ii) Zn0|ZnO. On the other hand, the binary HT containing Mn presented a reversible behavior for the oxidation-reduction process Mn4+|Mn3+. The same oxidation-reduction processes were observed in the ternary HT. However, variations in the reduction-oxidation process were detected by XRD for the ternary HT as a result of spinel formation. These results could also be influenced due to a higher accessibility of manganese in HT since the morphology of hydrotalcite (lamellar structure) provides a regular distribution of Mn atoms interacting with Zn atoms through hydroxyl bridges.

Differential transcriptome profiling of the diapause and cold-responsive genes in unfed adult Dermacentor silvarum Olenev (Acari: Ixodidae) 

2020 ◽  
Vol 25 (2) ◽  
pp. 193-213
Author(s):  
Zhijun Yu ◽  
Tingwei Pei ◽  
Meng Zhang ◽  
Tongxuan Wang ◽  
Qingying Jia ◽  
...  
Keyword(s):  
Reduction Process ◽  
Transcriptome Profiling ◽  
Northern China ◽  
Biological Processes ◽  
Transcriptome Profile ◽  
Kegg Pathway Analysis ◽  
Oxidation Reduction ◽  
Transcriptomic Sequencing ◽  
Summer Diapause ◽  
And Control

The tick Dermacentor silvarum mainly overwinters in northern China as an unfed adult entering diapause; however, little is known about the involvement of genes and pathways in summer diapause and overwintering adults of this species. Hence, we investigated the differential transcriptome profile of D. silvarum ticks’ diapause and cold-responsive genes and pathways during its summer diapause, overwintering, and questing/active stages. Through transcriptomic sequencing, a total of 136,740 unigenes were assembled, and 1,549, 2,196, and 2,125 differentially expressed genes (DEG) were identified in active and diapause, diapause and overwintering, and active and overwintering ticks, respectively. Between active and diapause ticks, 875 genes were up-regulated, while 674 genes were found down-regulated in diapause ticks. When compared with active ticks, overwintering ticks had 993 up-regulated genes and 1,132 down-regulated genes. Comparison between diapause and overwintering ticks revealed 745 up-regulated and 1,451 down-regulated genes in overwintering ticks. Gene Ontology analysis revealed that, among the active, diapause, and overwintering ticks, most of the DEGs in molecular function were enriched in catalytic activity and hydrolase activity. In the cellular component, most DEGs were assigned to the integral component of the cell membrane , whereas the oxidation-reduction process was the most enriched among biological processes. In addition, the lysosome pathway was the most enriched pathway identified in KEGG pathway analysis. The above results deepened our understanding of the mechanism underlying diapause and overwintering adaptation of ticks, which is important for integrative prevention and control of ticks and tick-borne diseases. 

scholarly journals Antioxidant Effects and Potential Molecular Mechanism of Action of Limonium aureum Extract Based on Systematic Network Pharmacology

2022 ◽  
Vol 8 ◽  
Author(s):  
Zhen Yang ◽  
Yanan Mo ◽  
Feng Cheng ◽  
Hongjuan Zhang ◽  
Ruofeng Shang ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Signaling Pathways ◽  
Molecular Mechanisms ◽  
Reduction Process ◽  
Wild Plant ◽  
Network Pharmacology ◽  
Mrna Levels ◽  
Biological Processes ◽  
Antioxidant Effects

Oxidative stress is the redox imbalance state of organisms that involves in a variety of biological processes of diseases. Limonium aureum (L.) Hill. is an excellent wild plant resource in northern China, which has potential application value for treating oxidative stress. However, there are few studies that focused on the antioxidant effect and related mechanism of L. aureum. Thus, the present study combining systematic network pharmacology and molecular biology aimed to investigate the antioxidant effects of L. aureum and explore its underlying anti-oxidation mechanisms. First, the antioxidant activity of L. aureum extracts was confirmed by in vitro and intracellular antioxidant assays. Then, a total of 11 bioactive compounds, 102 predicted targets, and 70 antioxidant-related targets were obtained from open source databases. For elucidating the molecular mechanisms of L. aureum, the PPI network and integrated visualization network based on bioinformatics assays were constructed to preliminarily understand the active compounds and related targets. The subsequent enrichment analysis results showed that L. aureum mainly affect the biological processes involving oxidation-reduction process, response to drug, etc., and the interference with these biological processes might be due to the simultaneous influence on multiple signaling pathways, including the HIF-1 and ERBB signaling pathways. Moreover, the mRNA levels of predicted hub genes were measured by qRT-PCR to verify the regulatory effect of L. aureum on them. Collectively, this finding lays a foundation for further elucidating the anti-oxidative damage mechanism of L. aureum and promotes the development of therapeutic drugs for oxidative stress.

scholarly journals Transcriptomic Analysis of Methyl Jasmonate Treatment Reveals Gene Networks Involved in Drought Tolerance at the Early Developmental Stage in Pearl Millet (Pennisetum Glaucum L. Br)

2021 ◽  
Author(s):  
Adama Ndiaye ◽  
Amadou Oury Diallo ◽  
Ndèye Coura Fall ◽  
Rose Diambogne Diouf ◽  
Diaga Diouf ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Methyl Jasmonate ◽  
Pearl Millet ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Reduction Process ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Stage Of Development ◽  
Oxidation Reduction

Abstract Water deficit stress at the early stage of development is one of the main factors limiting pearl millet production. A practice to cope with would be to apply hormones to stimulate plant growth and development. Exogenous methyl jasmonate (MeJA) can improve drought tolerance by modulating key pathways, therefore, we assumed that can occur in pearl millet during the early stage of development. To decipher the molecular mechanisms controlling these pathways, RNAseq was conducted in two pearl millet genotypes, drought-sensitive SosatC88 and drought-tolerant Souna3, in response to 200 µM of MeJA. Transcriptomic analysis between the MeJA-treated and non-treated plants revealed 3270 differentially expressed genes (DEGs) in SosatC88 and 127 DEGs in Souna3. Gene ontology (GO) classification assigned most regulated DEGs in SosatC88 to heme binding, oxidation-reduction process, response to oxidative stress and membrane, and in Souna3 to terpene synthase activity, lyase activity, magnesium ion binding, and thylakoid. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis reveals that DEGs in SosatC88 are related to the oxidation-reduction process, the biosynthesis of other secondary metabolites, the signal transduction, and the metabolism of terpenoids, while in Souna3, DEGs are related to the metabolism of terpenoids and the energy metabolism. Two genes encoding a diterpenoid biosynthesis-related and a Glutathione S transferase T3 were contra-regulated between SosatC88 and Souna3. Additionally, five random genes differentially expressed by RNAseq were validated using qPCR. These insights into the molecular mechanisms of pearl millet genotype tolerance at the early stage of development contribute to the understanding of the role of hormones in adaptation to drought-prone environments.

scholarly journals Molecular regulation of Snai2 in development and disease

2019 ◽  
Vol 132 (23) ◽  
Author(s):  
Wenhui Zhou ◽  
Kayla M. Gross ◽  
Charlotte Kuperwasser
Keyword(s):  
Transcription Factor ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Epithelial To Mesenchymal Transition ◽  
Zinc Finger Protein ◽  
Main Role ◽  
Biological Processes ◽  
Developmental Defects ◽  
Mesenchymal Transition ◽  
Damage Repair

ABSTRACT The transcription factor Snai2, encoded by the SNAI2 gene, is an evolutionarily conserved C2H2 zinc finger protein that orchestrates biological processes critical to tissue development and tumorigenesis. Initially characterized as a prototypical epithelial-to-mesenchymal transition (EMT) transcription factor, Snai2 has been shown more recently to participate in a wider variety of biological processes, including tumor metastasis, stem and/or progenitor cell biology, cellular differentiation, vascular remodeling and DNA damage repair. The main role of Snai2 in controlling such processes involves facilitating the epigenetic regulation of transcriptional programs, and, as such, its dysregulation manifests in developmental defects, disruption of tissue homeostasis, and other disease conditions. Here, we discuss our current understanding of the molecular mechanisms regulating Snai2 expression, abundance and activity. In addition, we outline how these mechanisms contribute to disease phenotypes or how they may impact rational therapeutic targeting of Snai2 dysregulation in human disease.

scholarly journals Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

2021 ◽  
Author(s):  
Zhilin Yuan ◽  
Irina S. Druzhinina ◽  
John G. Gibbons ◽  
Zhenhui Zhong ◽  
Yves Van de Peer ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Genomic Island ◽  
Population Genomics ◽  
Growth Yield ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Mechanisms ◽  
Melanin Biosynthesis ◽  
Two Populations

AbstractUnderstanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila–S. salsa symbiosis.

scholarly journals Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types

2021 ◽  
Vol 7 (3) ◽  
pp. eabd9036
Author(s):  
Sara Saez-Atienzar ◽  
Sara Bandres-Ciga ◽  
Rebekah G. Langston ◽  
Jonggeol J. Kim ◽  
Shing Wan Choi ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Polygenic Risk Score ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Data Driven Approach ◽  
Single Nucleus ◽  
Lateral Sclerosis

Despite the considerable progress in unraveling the genetic causes of amyotrophic lateral sclerosis (ALS), we do not fully understand the molecular mechanisms underlying the disease. We analyzed genome-wide data involving 78,500 individuals using a polygenic risk score approach to identify the biological pathways and cell types involved in ALS. This data-driven approach identified multiple aspects of the biology underlying the disease that resolved into broader themes, namely, neuron projection morphogenesis, membrane trafficking, and signal transduction mediated by ribonucleotides. We also found that genomic risk in ALS maps consistently to GABAergic interneurons and oligodendrocytes, as confirmed in human single-nucleus RNA-seq data. Using two-sample Mendelian randomization, we nominated six differentially expressed genes (ATG16L2, ACSL5, MAP1LC3A, MAPKAPK3, PLXNB2, and SCFD1) within the significant pathways as relevant to ALS. We conclude that the disparate genetic etiologies of this fatal neurological disease converge on a smaller number of final common pathways and cell types.

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