scholarly journals Transcriptome-Based Identification of Genes Responding to the Organophosphate Pesticide Phosmet in Danio rerio

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1738
Author(s):  
Bala Murali Krishna Vasamsetti ◽  
Kyongmi Chon ◽  
Juyeong Kim ◽  
Jin-A Oh ◽  
Chang-Young Yoon ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Sequencing Data ◽  
Developmental Abnormalities ◽  
Significant Enrichment ◽  
Spine Curvature ◽  
Pathway Regulation ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome ◽  
Regulation Of Actin Cytoskeleton

Organophosphate pesticides (OPPs) are one of the most widely used insecticides. OPPs exert their neurotoxic effects by inhibiting acetylcholine esterase (AChE). Most of the gross developmental abnormalities observed in OPP-treated fish, on the other hand, may not be explained solely by AChE inhibition. To understand the overall molecular mechanisms involved in OPP toxicity, we used the zebrafish (ZF) model. We exposed ZF embryos to an OPP, phosmet, for 96 h, and then analyzed developmental abnormalities and performed whole transcriptome analysis. Phenotypic abnormalities, such as bradycardia, spine curvature, and growth retardation, were observed in phosmet-treated ZF (PTZF). Whole transcriptome analysis revealed 2190 differentially expressed genes (DEGs), with 822 and 1368 significantly up-and downregulated genes, respectively. System process and sensory and visual perception were among the top biological pathways affected by phosmet toxicity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed significant enrichment of metabolic pathways, calcium signaling pathway, regulation of actin cytoskeleton, cardiac muscle contraction, drug metabolism–other enzymes, and phototransduction. Quantitative real-time PCR results of six DEGs agreed with the sequencing data expression profile trend. Our findings provide insights into the consequences of phosmet exposure in ZF, as well as an estimate of the potential risk of OPPs to off-target species.

scholarly journals Whole transcriptome analysis of adrenal glands from prenatal glucocorticoid programmed hypertensive rodents

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sujeenthar Tharmalingam ◽  
Sandhya Khurana ◽  
Alyssa Murray ◽  
Jeremy Lamothe ◽  
T. C. Tai
Keyword(s):  
Gene Expression ◽  
Circadian Rhythm ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Adrenal Glands ◽  
Genetic Model ◽  
Pathway Enrichment Analysis ◽  
Wistar Kyoto ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Prenatal glucocorticoid exposure is associated with the development of hypertension in adults. We have previously demonstrated that antenatal dexamethosone (DEX) administration in Wistar-Kyoto dams results in offspring with increased blood pressure coupled with elevated plasma epinephrine levels. In order to elucidate the molecular mechanisms responsible for prenatal DEX-mediated programming of hypertension, a whole-transcriptome analysis was performed on DEX programmed WKY male adrenal glands using the Rat Gene 2.0 microarray. Differential gene expression (DEG) analysis of DEX-exposed offspring compared with saline-treated controls revealed 142 significant DEGs (109 upregulated and 33 downregulated genes). DEG pathway enrichment analysis demonstrated that genes involved in circadian rhythm signaling were most robustly dysregulated. RT-qPCR analysis confirmed the increased expression of circadian genes Bmal1 and Npas2, while Per2, Per3, Cry2 and Bhlhe41 were significantly downregulated. In contrast, gene expression profiling of Spontaneously Hypertensive (SHR) rats, a genetic model of hypertension, demonstrated decreased expression of Bmal1 and Npas2, while Per1, Per2, Per3, Cry1, Cry2, Bhlhe41 and Csnk1D were all upregulated compared to naïve WKY controls. Taken together, this study establishes that glucocorticoid programmed adrenals have impaired circadian signaling and that changes in adrenal circadian rhythm may be an underlying molecular mechanism responsible for the development of hypertension.

scholarly journals Whole Transcriptome Analysis Provides Insights into Molecular Mechanisms for Molting in Litopenaeus vannamei

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0144350 ◽  
Author(s):  
Yi Gao ◽  
Xiaojun Zhang ◽  
Jiankai Wei ◽  
Xiaoqing Sun ◽  
Jianbo Yuan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Litopenaeus Vannamei ◽  
Molecular Mechanisms ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

scholarly journals Whole-Transcriptome Analysis of Serum L1CAM-Captured Extracellular Vesicles Reveals Neural And Glycosylation Changes In Autism Spectrum Disorder

2021 ◽  
Author(s):  
Yannan Qin ◽  
Li Cao ◽  
Haiqing Zhang ◽  
Shuang Cai ◽  
Jinyuan Zhang ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Predictive Biomarkers ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Serum Samples ◽  
Bioactive Substances ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract The pathophysiology of autistic spectrum disorder (ASD) is not fully understood and there are no diagnostic or predictive biomarkers. Extracellular vesicles (EVs) are cell-derived nano-sized vesicles, carrying nucleic acids, proteins, lipids and other bioactive substances. As reported, serum neural cell adhesion molecule L1 (L1CAM)-captured EVs (LCEVs) can provide reliable biomarkers for neurological diseases; however, little is known about the LCEVs in children with ASD. In this study, serum samples were collected from 100 ASD children and 60 age-matched typically developed (TD) children. LCEVs were isolated and characterized meticulously. Whole-transcriptome of LCEVs was analyzed by lncRNA microarray and RNA-Sequencing. All raw data was submitted on GEO Profiles, and GEO accession numbers is GSE186493. RNAs expressed differently in LCEVs from ASD sera vs. TD sera were screened, analyzed, and further validated. A total of 1418 mRNAs, 1745 lncRNAs and 11 miRNAs were differentially expressed, and most of them were down-regulated in ASD. Most RNAs were involved in neuron- and glycan-related networks implicated in ASD. The levels of EDNRA, SLC17A6, HTR3A, OSTC, TMEM165, PC-5p-139289_26, and hsa-miR-193a-5p changed significantly in ASD. In conclusion, whole-transcriptome analysis of serum LCEVs reveals neural and glycosylation changes in ASD, which may help detect predictive biomarkers and molecular mechanisms of ASD, and provide reference for diagnoses and therapeutic management of the disease.

scholarly journals Pistils may be required for anthocyanin synthesis —— the whole-transcriptome analysis of mutant and normal capitula of Chrysanthemum morifolium

2020 ◽  
Author(s):  
Hua Liu ◽  
Chang Luo ◽  
Dongliang Chen ◽  
Yaqin Wang ◽  
Shuang Guo ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Floral Organ ◽  
Chrysanthemum Morifolium ◽  
Anthocyanin Synthesis ◽  
Second Generation Sequencing ◽  
Photoperiod Pathway ◽  
Ray Florets ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Background Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in Asteraceae. Chrysanthemums have many different flower colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes is still an enigma. We obtained a cut chrysanthemum variety with mutant capitula in which the ray florets became green and the inside pistils became vegetative buds, while normal capitula have many rounds of purple ray florets and few disc florets. Results We conducted whole-transcriptome analysis of differentially expressed genes (DEGs) between the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified DEGs between the mutant and normal capitula to reveal important regulators underlying their differential development. Regulatory genes involved in the photoperiod pathway and the control of floral organ identification as well as important functional genes in the anthocyanin synthesis pathway were also identified. Therefore, a list of candidate genes for studying flower development and anthocyanin synthesis in chrysanthemums was generated. Qualitative analysis of pigments in the florets of normal and mutant capitula revealed anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. It was indicated that pistils may be required for anthocyanin synthesis in chrysanthemums. Conclusions These results will help to elucidate the molecular mechanisms of floral organ development and will contribute to the development of techniques for studying flower shape and color regulation to promote breeding in chrysanthemum.

scholarly journals Whole‐Transcriptome Analysis ofPlasmodium falciparumField Isolates: Identification of New Pathogenicity Factors

2007 ◽  
Vol 196 (11) ◽  
pp. 1603-1612 ◽  
Author(s):  
Anthony Siau ◽  
Fousseyni S. Touré ◽  
Odile Ouwe‐Missi‐Oukem‐Boyer ◽  
Liliane Cicéron ◽  
Nassira Mahmoudi ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Pathogenicity Factors ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome
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