Comprehensive mRNA and microRNA analysis revealed the effect and response strategy of freshwater fish, grass carp (Ctenopharyngodon idella) under geosmin exposure.

Geosmin is an environmental pollutant that causes off-flavor in water and aquatic products. The high occurrence of geosmin contamination in aquatic systems and aquaculture raises public awareness, however, few studies have investigated the response pathways of geosmin stress on freshwater fish. In this research, grass carp were exposed to 50 µg/L geosmin for 96 h, liver tissue was sequenced and validated using real-time qPCR. In total of 528 up-regulated genes and 488 down-regulated genes were observed, includes cytochrome P450 and uridine diphosphate (UDP)-glucuronosyltransferase related genes. KEGG analysis showed that chemical carcinogenesis-DNA adducts, metabolism of xenobiotics by cytochrome P450, drug metabolism-cytochrome P450 pathway was enriched. Common genes from the target genes of microRNAs and differential expression genes are enriched in metabolism of xenobiotics cytochrome P450 pathway. Two miRNAs (dre-miR-146a and miR-212-3p) down regulated their target genes (LOC127510138 and adh5, respectively) which are enriched cytochrome P450 related pathway. The results present that geosmin is genetoxic to grass carp and indicate that cytochrome P450 system and UDP-glucuronosyltransferase play essential roles in biotransformation of geosmin. MicroRNAs regulate the biotransformation of geosmin by targeting specific genes, which contributes to the development of strategies to manage its negative impacts in both natural and artificial environments.

Making Sense of Genetic Information: The Promising Evolution of Clinical Stratification and Precision Oncology Using Machine Learning.

Precision medicine is a medical approach to administer patients with a tailored dose of treatment by taking into consideration a person's variability in genes, environment, and lifestyles. The accumulation of omics big sequence data led to the development of various genetic databases on which clinical stratification of high-risk populations may be conducted. In addition, because cancers are generally caused by tumor-specific mutations, large-scale systematic identification of single nucleotide polymorphisms (SNPs) in various tumors has propelled significant progress of tailored treatments of tumors (i.e., precision oncology). Machine learning (ML), a subfield of artificial intelligence in which computers learn through experience, has a great potential to be used in precision oncology chiefly to help physicians make diagnostic decisions based on tumor images. A promising venue of ML in precision oncology is the integration of all available data from images to multi-omics big data for the holistic care of patients and high-risk healthy subjects. In this review, we provide a focused overview of precision oncology and ML with attention to breast cancer and glioma as well as the Bayesian networks that have the flexibility and the ability to work with incomplete information. We also introduce some state-of-the-art attempts to use and incorporate ML and genetic information in precision oncology.

Forkhead transcription factor O1 (FoxO1) in torafugu pufferfish Takifugu rubripes: Molecular cloning, in vitro DNA binding, and target gene screening in fish metagenome.

The fish insulin/insulin-like growth factor (IGF) pathway has weak control over carbohydrate metabolism. To understand the molecular basis for the metabolic diversity, we characterized the forkhead box transcription factor O1A (FoxO1A), a downstream target of the insulin/IGF pathway, in torafugu Takifugu rubripes. The cloned torafugu FoxO1A cDNA contained all conserved features critical for its transcriptional activity and a unique unspliced intron encoding a poly-glutamine stretch. Torafugu FoxO1A showed the IGF-dependent nuclear exclusion and in vitro binding to the well-conserved FoxO1 binding site, DAF-16 binding element (DBE), but failed to bind to the insulin-responsive element by which mammalian FoxO1 mediates insulin effects. The subsequent in silico genomic screening provided a list of 587 potential torafugu FoxO1A target genes containing the DBE. Some carbohydrate metabolic genes regulated by FoxO1 in mammals were not included in the list. We further identified about 250 potential fish FoxO1 target genes by integrating results of the DBE screening against fish metagenome that contained 262 species. Neuronal processes appeared to be the common major function of fish FoxO1, although further annotation of the potential target genes is required. These results provide a part of the molecular basis underlying the weak association between the insulin/IGF pathway and carbohydrate metabolism in fish.

Molecular characterization and homology modeling of liver X receptor in Asian seabass, Lates calcarifer: predicted functions in reproduction and lipid metabolism.

Liver X receptor (LXR) is a ligand-activated transcription factor that plays vital roles in maintaining cholesterol and lipid homeostasis. Much work has been done on mammalian LXRs, but the role of LXR in fish remains unclear. In the present study, LXR gene was identified from adult Asian seabass, Lates calcarifer, and its predicted protein structure was docked with several cholesterol derivatives at the binding site. The LXR cDNA consisted of 1495 bp encoding a putative LXR protein of 494 amino acids. The Asian seabass LXR retained many important structural features found in LXRs of other fishes and mammals, such as putative signal peptide, activation function-1 (AF-1) domain, DNA-binding domain (DBD), ligand-binding domain (LBD), activation function-2 (AF-2) domain, and eight conserved cysteine residues. The deduced amino acid sequence of LXR shared significant identity with those of other species ranging from 65.7 to 95.8%. The homology modeling and in silico molecular docking demonstrated that Asian seabass LXR could interact with cholesterol derivatives at amino acid residues Phe274 and Ile312. Real-time PCR further revealed that LXR transcripts are ubiquitously expressed in all tissues examined, with the highest levels detected in the gonad followed by the liver. Given the well-known importance of cholesterol-mediated signaling in these tissues, Asian seabass LXR may reasonably be involved in reproduction and lipid metabolism.

Comparative analysis of effects of dietary arachidonic acid and EPA on growth, tissue fatty acid composition, antioxidant response and lipid metabolism in juvenile grass carp, Ctenopharyngodon idellus.

Four isonitrogenous and isoenergetic purified diets containing free arachidonic acid (ARA) or EPA (control group), 0·30 % ARA, 0·30 % EPA and 0·30 % ARA+EPA (equivalent) were designed to feed juvenile grass carp (10·21 (sd 0·10) g) for 10 weeks. Only the EPA group presented better growth performance compared with the control group (P<0·05). Dietary ARA and EPA were incorporated into polar lipids more than non-polar lipids in hepatopancreas but not intraperitoneal fat (IPF) tissue. Fish fed ARA and EPA showed an increase of serum superoxide dismutase and catalase activities, and decrease of glutathione peroxidase activity and malondialdehyde contents (P<0·05). The hepatopancreatic TAG levels decreased both in ARA and EPA groups (P<0·05), accompanied by the decrease of lipoprotein lipase (LPL) activity in the ARA group (P<0·05). Fatty acid synthase (FAS), diacylglycerol O-acyltransferase and apoE gene expression in the hepatopancreas decreased in fish fed ARA and EPA, but only the ARA group exhibited increased mRNA level of adipose TAG lipase (ATGL) (P<0·05). Decreased IPF index and adipocyte sizes were found in the ARA group (P<0·05). Meanwhile, the ARA group showed decreased expression levels of adipogenic genes CCAAT enhancer-binding protein α, LPL and FAS, and increased levels of the lipid catabolic genes PPAR α, ATGL, hormone-sensitive lipase and carnitine palmitoyltransferase 1 (CPT-1) in IPF, whereas the EPA group only increased PPAR α and CPT-1 mRNA expression and showed less levels than the ARA group. Overall, dietary EPA is beneficial to the growth performance, whereas ARA is more potent in inducing lipolysis and inhibiting adipogenesis, especially in IPF. Meanwhile, dietary ARA and EPA showed the similar preference in esterification and the improvement in antioxidant response.

Constitutive expression of insulin receptor substrate (IRS)-1 inhibits myogenic differentiation through nuclear exclusion of Foxo1 in L6 myoblasts.

Insulin-like growth factors (IGFs) are well known to play essential roles in enhancement of myogenic differentiation. In this report we showed that initial IGF-I signal activation but long-term IGF-1 signal termination are required for myogenic differentiation. L6 myoblast stably transfected with myc-epitope tagged insulin receptor substrate-1, myc-IRS-1 (L6-mIRS1) was unable to differentiate into myotubes, indicating that IRS-1 constitutive expression inhibited myogenesis. To elucidate the molecular mechanisms underlying myogenic inhibition, IGF-I signaling was examined. IGF-I treatment of control L6 cells for 18 h resulted in a marked suppression of IGF-I stimulated IRS-1 association with the p85 PI 3-kinase and suppression of activation of Akt that correlated with a down regulation of IRS-1 protein. L6-mIRS1 cells, in contrast, had sustained high levels of IRS-1 protein following 18 h of IGF-I treatment with persistent p85 PI 3-kinase association with IRS-1, Akt phosphorylation and phosphorylation of the downstream Akt substrate, Foxo1. Consistent with Foxo1 phosphorylation, Foxo1 protein was excluded from the nuclei in L6-mIRS1 cells, whereas Foxo1 was localized in the nuclei in control L6 cells during induction of differentiation. In addition, L6 cells stably expressing a dominant-interfering form of Foxo1, Δ256Foxo1 (L6-Δ256Foxo1) were unable to differentiate into myotubes. Together, these data demonstrate that IGF-I regulation of Foxo1 nuclear localization is essential for the myogenic program in L6 cells but that persistent activation of IGF-1 signaling pathways results in a negative feedback to prevent myogenesis.

Molecular characterization of Japanese sillago vitellogenin and changes in its expression levels on exposure to 17beta-estradiol and 4-tert-octylphenol.

We cloned a full-length cDNA encoding vitellogenin (VTG) from a marine teleost, the Japanese sillago Sillago japonica. The cloned sillago VTG contained signal peptide, lipovitellin heavy chain, phosvitin, lipovitellin light chain, and beta'-component in the order from the N-terminus. An exposure to 17beta-estradiol significantly increased the levels of plasma VTG, but not hepatic VTG mRNA in males. Neither plasma VTG nor hepatic VTG mRNA levels were affected by the exposure to 4-tert-octylphenol. Hepatic VTG mRNA levels in males increased at 1 day after intraperitoneal administration of 17beta-estradiol but decreased in the subsequent 5 days. However, plasma VTG levels remained high for 5 days after administration, suggesting that the accumulation period of plasma VTG is longer than that of hepatic VTG mRNA in males. Therefore, VTG mRNA may be a suitable indicator of temporal exposure to estrogenic chemicals in the environment, whereas plasma VTG is useful to detect consecutive exposure.