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. 

Modelling of Chromium Hexavalent Reduction by Ferrous Ion in a Batch Stirred Tank

2009 ◽  
Vol 4 (1) ◽  
Author(s):  
Mohamed Kheireddine Aroua ◽  
Chun Ming Chew ◽  
Mohamed Azlan Hussain
Keyword(s):  
Reduction Process ◽  
Stirred Tank ◽  
Quasi Equilibrium ◽  
Time Data ◽  
Equilibrium Conditions ◽  
Oxidation Reduction ◽  
Oxidation Reduction Potential ◽  
On Line ◽  
And Control ◽  
Non Equilibrium

In this paper mathematical models are proposed to simulate the dynamic behaviour of the reduction of Cr(VI) with Fe(II) in a batch stirred tank. Two approaches have been adopted to represent systems in non-equilibrium and quasi-equilibrium conditions. The models derived reflect the changes of the relevant reactant species concentration based on the Oxidation Reduction Potential (ORP) of the system. An automated pilot plant has been designed and commissioned to carry out on-line/real time data acquisition and control for this Cr(VI) reduction process experimentally. Both the quasi-equilibrium and non-equilibrium models were validated experimentally. Simulated and on-line results indicate distinctive ORP profiles pattern for these two processes. The ORP profiles for non-equilibrium processes show a distinctive pattern which indicates the complete reduction of Cr(VI) in the batch sample.

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 Identification of Key Candidate Genes Involved in the Progression of Idiopathic Pulmonary Fibrosis

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1123
Author(s):  
Yu Cui ◽  
Jie Ji ◽  
Jiwei Hou ◽  
Yi Tan ◽  
Xiaodong Han
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Candidate Genes ◽  
Expression Profiles ◽  
Biological Processes ◽  
Protein Protein Interaction ◽  
Novel Treatments ◽  
Kegg Pathway Analysis ◽  
Cell Components ◽  
Upregulated Genes

Idiopathic pulmonary fibrosis (IPF) is a lethal, agnogenic interstitial lung disease with limited therapeutic options. To investigate vital genes involved in the development of IPF, we integrated and compared four expression profiles (GSE110147, GSE53845, GSE24206, and GSE10667), including 87 IPF samples and 40 normal samples. By reanalyzing these datasets, we managed to identify 62 upregulated genes and 20 downregulated genes in IPF samples compared with normal samples. Differentially expressed genes (DEGs) were analyzed by gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to illustrate relevant pathways of IPF, biological processes, molecular function, and cell components. The DEGs were then subjected to protein–protein interaction (PPI) for network analysis, serving to find 11 key candidate genes (ANXA3, STX11, THBS2, MMP1, MMP9, MMP7, MMP10, SPP1, COL1A1, ITGB8, IGF1). The result of RT-qPCR and immunohistochemical staining verified our finding as well. In summary, we identified 11 key candidate genes related to the process of IPF, which may contribute to novel treatments of IPF.

scholarly journals Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

2021 ◽  
Author(s):  
Xiaoping Huang ◽  
Hongyu Zhang ◽  
Qiang Wang ◽  
Rong Guo ◽  
Lingxia Wei ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Leaf Senescence ◽  
Flag Leaf ◽  
Reduction Process ◽  
Sequencing Analysis ◽  
Biological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Non Coding Rnas ◽  
Systematic Identification

Abstract Key message This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. Abstract LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation–reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

scholarly journals Association between EFHD2 gene polymorphisms and schizophrenia among the Han population in northern China

2020 ◽  
Vol 48 (6) ◽  
pp. 030006052093280
Author(s):  
Meng Gao ◽  
Kuo Zeng ◽  
Ya Li ◽  
Yong-ping Liu ◽  
Xi Xia ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Neurodevelopmental Disorder ◽  
Haplotype Frequency ◽  
Northern China ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Gene Encoding ◽  
Frequency Distributions ◽  
And Control

Objective Schizophrenia is a severe neurodevelopmental disorder with a complex genetic and environmental etiology. The gene encoding EF-hand domain-containing protein D2 ( EFHD2) may be a genetic risk locus for schizophrenia. Methods We genotyped four EFHD2 single-nucleotide polymorphisms (281 schizophrenia cases [SCZ], 321 controls) from northern Chinese Han individuals using Sanger sequencing and polymerase chain reaction-restriction fragment length polymorphism analysis. Differences existed in genotype, allele, and haplotype frequency distributions between SCZ and control groups. Results The rs2473357 genotype and allele frequency distributions differed between SCZ and controls; however, this difference disappeared after Bonferroni correction. Differences in rs2473357 genotype and allele frequency distributions between SCZ and controls were more pronounced in men than in women. The G allele increased schizophrenia risk (odds ratio = 1.807, 95% confidence interval = 1.164–2.803). Among six haplotypes (G–, A–, G-insC, A-C, G-C, and G-T), the G– haplotype frequency distribution differed between SCZ and controls in women; the A-C and G-C haplotype frequency distributions differed between SCZ and controls in men. Conclusions EFHD2 may be involved in schizophrenia. Sex differences in EFHD2 genotype and allele frequency distributions existed among schizophrenia patients. Further research is needed to determine the role of EFHD2 in schizophrenia.

Unusual Wetting Behavior of Liquid Metals on Porous Layer Formed at Surface of Iron Substrate Prepared by Oxidation-Reduction Process

2007 ◽  
Vol 561-565 ◽  
pp. 1699-1701
Author(s):  
Nobuyuki Takahira ◽  
Takeshi Yoshikawa ◽  
Toshihiro Tanaka
Keyword(s):  
Liquid Metal ◽  
Porous Layer ◽  
Liquid Metals ◽  
Reduction Process ◽  
Surface Oxidation ◽  
Porous Iron ◽  
Normal Contact ◽  
Wetting Behavior ◽  
Oxidation Reduction ◽  
Oxidized Iron

Unusual wetting behavior of liquid Cu was found on a surface-oxidized iron substrate in reducing atmosphere. Liquid Cu wetted and spread very widely on the iron substrate when a droplet was attached with the substrate in Ar-10%H2 after the surface oxidation of the substrate. The oxidationreduction process fabricates a porous layer at the surface of the iron substrate. The pores in the porous iron layer are 3-dimensionally interconnected. Thus, liquid metals, which are contacted with the reduced iron samples, penetrate into these pores by capillary force to cause the unusual wetting behavior. It has been already confirmed that liquid Ag, Sn, In and Bi show this phenomenon onto surface-porous iron samples as well as liquid Cu. This unusual wetting behavior of a liquid metal has been correlated to the normal contact angle of the liquid metal on a flat iron substrate.

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