Transcriptome Analyses Reveal Lipid Metabolic Process in Liver Related to the Difference of Carcass Fat Content in Rainbow Trout (<i>Oncorhynchus mykiss</i>)

Guo, Hongwei; Sun, Peng; Bai, Qingli; Wang, Bingqian

doi:10.1155/2016/7281585

Cited by 15 publications

(11 citation statements)

References 33 publications

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“…A drawback of our study is that it is mainly based on data from transcriptomic studies, and hence it may not precisely reflect metabolic fluxes (Chubukov et al, ). Nevertheless transcriptomic studies have previously led to the identification of metabolic pathways (Corominas et al, ; Hu, Gu, Sun, Bai, & Wang, ) and they are a sound approach to address brain metabolism in humans (Barros et al, ). Moreover, genomic‐based models have been extensively used to study metabolic networks (Duarte et al, ) and to simulate metabolic‐based phenotypes of cancer cells (Gruetter, Seaquist, & Ugurbil, ; Lewis & Abdel‐Haleem, ; Lewis et al, ).…”

Section: Discussionmentioning

confidence: 99%

GSEA of mouse and human mitochondriomes reveals fatty acid oxidation in astrocytes

Eraso-Pichot

Brasó-Vives

Golbano

et al. 2018

Glia

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The prevalent view in neuroenergetics is that glucose is the main brain fuel, with neurons being mostly oxidative and astrocytes glycolytic. Evidence supporting that astrocyte mitochondria are functional has been overlooked. Here we sought to determine what is unique about astrocyte mitochondria by performing unbiased statistical comparisons of the mitochondriome in astrocytes and neurons. Using MitoCarta, a compendium of mitochondrial proteins, together with transcriptomes of mouse neurons and astrocytes, we generated cell-specific databases of nuclear genes encoding for mitochondrion proteins, ranked according to relative expression. Standard and in-house Gene Set Enrichment Analyses (GSEA) of five mouse transcriptomes revealed that genes encoding for enzymes involved in fatty acid oxidation (FAO) and amino acid catabolism are consistently more expressed in astrocytes than in neurons. FAO and oxidative-metabolism-related genes are also up-regulated in human cortical astrocytes versus the whole cortex, and in adult astrocytes versus fetal astrocytes. We thus present the first evidence of FAO in human astrocytes. Further, as shown in vitro, FAO coexists with glycolysis in astrocytes and is inhibited by glutamate. Altogether, these analyses provide arguments against the glucose-centered view of energy metabolism in astrocytes and reveal mitochondria as specialized organelles in these cells.

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Section: Discussionmentioning

confidence: 99%

GSEA of mouse and human mitochondriomes reveals fatty acid oxidation in astrocytes

Eraso-Pichot

Brasó-Vives

Golbano

et al. 2018

Glia

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“…For example, Zhang et al found that in a mouse model, pharmaceutical inhibition of the fatty acid binding pathway reduced the symptoms of OA induced by a high-fat diet [65]. Also, lipid metabolism is a chemical reaction involving lipids, which are compounds soluble in organic solvents [66]. Park et al showed that the functional integrity of ABCD2 in modulating lipid metabolism was through the dysregulation of miR-141, and through ACSL4 in OA [67].…”

Section: Discussionmentioning

confidence: 99%

Network Pharmacology Identifies the Mechanisms of Action of Shaoyao Gancao Decoction in the Treatment of Osteoarthritis

Zhu

Hou

et al. 2019

Med Sci Monit

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Background Osteoarthritis (OA) affects the health and wellbeing of the elderly. Shaoyao Gancao decoction (SGD) is used in traditional Chinese medicine (TCM) for the treatment of OA and has two active components, shaoyao (SY) and gancao (GC). This study aimed to undertake a network pharmacology analysis of the mechanism of the effects of SGD in OA. Material/Methods The active compounds and candidates of SGD were obtained from the Traditional Chinese Medicine (TCM) Databases@Taiwan, the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, the STITCH database, the ChEMBL database, and PubChem. The network pharmacology approach involved network construction, target prediction, and module analysis. Significant signaling pathways of the cluster networks for SGD and OA were identified using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Results Twenty-three bioactive compounds were identified, corresponding to 226 targets for SGD. Also, 187 genes were closely associated with OA, of which 161 overlapped with the targets of SGD and were considered to be therapeutically relevant. Functional enrichment analysis suggested that SGD exerted its pharmacological effects in OA by modulating multiple pathways, including cell cycle, cell apoptosis, drug metabolism, inflammation, and immune modulation. Conclusions A novel approach was developed to systematically identify the mechanisms of the TCM, SGD in OA using network pharmacology analysis.

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“…To study the underlying genetic mechanism and divergence in gene expression pattern between species, the gill transcriptome of both the Zebra fish and Tilapia in response to cold stress has analysed and identified the presence of divergently expressed genes in metabolic pathways, insulin signalling pathways, pyrimidine metabolism, apoptosis and FoxO signalling pathway among species (Hu et al . ). Transcriptome profiling of Tilapia was also carried out in response to alkalinity stress (Zhao et al .…”

Section: Current Status Of Transcriptomics In Aquaculturementioning

confidence: 97%

Transcriptomics in aquaculture: current status and applications

Chandhini

Kumar

2018

Reviews in Aquaculture

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Transcriptomics is the analysis of total RNA transcript in a cell, which gives a broad idea of cellular processes that are active and dormant. Recent advancement in next-generation sequencing technologies like high-throughput mRNA sequencing (RNA-seq) facilitates in deciphering the functional complexity of the whole transcriptome of an organism. In the recent past, transcriptome profiling has been widely used in aquaculture for effective identification and expression analysis of candidate genes involved in growth, reproduction, development, immunity, disease, stress and toxicology. On the paucity of a comprehensive genome sequence, transcriptomics enables the detection of molecular markers such as simple sequence repeats and single-nucleotide polymorphism associated with the trait of interest. This review summarizes the process of transcriptome analysis and the current state of transcriptomics in aquaculture related to diseases and immunity, reproduction and development, growth and nutrition, toxicology and stress. Further, this review highlights the application of transcriptomics, including generation of genetic resources, differential gene expression, analysis of molecular pathways and development of molecular markers.

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Transcriptome Analyses Reveal Lipid Metabolic Process in Liver Related to the Difference of Carcass Fat Content in Rainbow Trout (Oncorhynchus mykiss)

Cited by 15 publications

References 33 publications

GSEA of mouse and human mitochondriomes reveals fatty acid oxidation in astrocytes

GSEA of mouse and human mitochondriomes reveals fatty acid oxidation in astrocytes

Network Pharmacology Identifies the Mechanisms of Action of Shaoyao Gancao Decoction in the Treatment of Osteoarthritis

Transcriptomics in aquaculture: current status and applications

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