Transcriptome Analysis of Juvenile Tilapia (Oreochromis niloticus) Blood, Fed With Different Concentrations of Resveratrol

Effects of methomyl on the intestinal microbiome and hepatic transcriptome of tilapia, and the modifying effects of mint co-culture

Methomyl (MET) is an oxime carbamate insecticide that can contaminate aquatic systems resulting in toxicological effects. It can harm some fish species possibly through the anti-oxidative, phagosome pathway. Mint is one of the most widely herbal plants exhibiting antioxidant activities. In this study, we investigated the impact of MET on the antioxidant system of Oreochromis niloticus in presence of mint as a floating bed. Results revealed that the superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase, and glutathione S-transferase significantly decreased and the GSH content significantly increased in the intestine. The hepatic peroxisome proliferator-activated receptor (PPAR) signalling pathway, carbon metabolism, renal phosphoinositide 3-kinase (PI3K)-Akt, mitogen-activated protein kinase (MAPK) signalling pathway, and phagosomes were significantly affected. Upon long-term exposure, circadian rhythm and phagosomes were enriched in the liver and kidney. However, mint increased the enriched pathways of Toll-like receptor, PPAR, p53, NF-kappa B, MAPK, oestrogen, and B cell receptor signalling pathways. MET with different concentrations destroyed the balance of gut microbiota, mint decreased Verrucomicrobia and Akkermansia for the maintenance resulted from MET. Cetobacterium had a positive impact on total nitrogen (TN), chemical oxygen demand (CODMn), and glutathione reductase (GR), while Akkermansia had a positive impact on feed conversion ratio (FCR), SOD and CAT, and the abundance of both decreased due to MET exposure. High mint density removed more concentrations of nitrogen and phosphorus in the tilapia cultivation wastewater. Therefore, planting with mint can alleviate the toxicological effects produced by MET, shape the intestinal microbiota, and strengthen the connection between water quality and the metabolic parameters.

Resveratrol attenuated fatty acid synthesis through MAPK-PPAR pathway in red tilapia

High-fat (HF) diets have been shown to cause hepatic impairment in fish species, but the mode of action, especially the pathways involved, has not yet been determined. In this study, the effects of resveratrol (RES) supplementation on the hepatic structure and fat metabolism of red tilapia (Oreochromis niloticus) were determined. Based on transcriptome and proteomics results, RES was found to promote fatty acid β-oxidation in the blood, liver, and liver cells associated with apoptosis and the MAPK/PPAR signaling pathway. RES supplementation was found to alter the expression of genes related to apoptosis and fatty acid pathways like blood itga6a and armc5 which were upregulated and downregulated respectively by high-fat feeding while ggh and ensonig00000008711 increased and decreased, respectively, with RES addition. Relative to the PPAR signaling pathway, fabp10a and acbd7 showed a reverse U-shaped tendency, both in different treatments and at different times. Proteomics results demonstrated that MAPK/PPAR, carbon/glyoxylate, dicarboxylate/glycine serine, and threonine/drug-other enzymes/beta-alanine metabolism pathways in the RES group were significantly affected, and Fasn and Acox1 decreased and increased, respectively, with RES addition. Seven subgroups were obtained using scRNA-seq, and enrichment analysis showed that the PPAR signaling pathway was upregulated with RES supplementation. RES significantly increased the expression of the marked genes (pck1) ensonig00000037711, fbp10a, granulin, hbe1, and zgc:136461, which are liver cell-specific genes. In conclusion, RES resulted in significantly enriched DGEs associated with fat metabolism and synthesis via the MAPK-PPAR signaling pathway.

Transcriptome analysis of the response of four immune related organs of tilapia (Oreochromis niloticus) to the addition of resveratrol in feed

Resveratrol (RES) has been found to have immunological enhancement effects on Oreochromis niloticus. In O. nilocticus, the liver, spleen and kidney act as immune target tissues, while intestine works for nutrition sensing organ. In the present study, we determined RES administration on these immune tissues transcriptomic response in genetically improved farmed tilapia (GIFT), and further analyzed the relationship between transcriptomic response and intestinal microbiota. As results, hepatic hemosiderin and intestinal goblet cells significantly increased with RES addition. Kyoto encyclopedia of genes and genomes (KEGG) pathways associated with herpes simplex virus 1 infection, calcium signaling pathway, cell adhesion molecules, apoptosis, and mitogen-activated protein kinase (MAPK)/peroxisome proliferators-activated receptors (PPAR) signaling pathways were enriched. In particular, the differentially enriched genes (DEGs) associated pathways were present in different sampling tissues, times, and comparisons, interestingly, the PPAR signaling pathway was enriched with increasing time of RES addition. The assembled DEGs presented verified expression in the kidney, liver, spleen, and intestine tissues, and fabp6 was highly expressed in the intestine. Serial DEGs of fatty acid-binding proteins (fabp7, fabp7a, fabp10a) decreased in the liver and kidney, and fabp6 significantly increased in the spleen. With time, the pathways of energy metabolism, glycan biosynthesis, and metabolism decreased and increased in the intestinal metagenome. Some Candidatus branches significantly increased (C. cerribacteria and C. harrisonbacteria) and while others decreased (C. glodbacteria, etc.), whereas C. verstraetearchaeota fluctuated with RES addition. slc27a6 and dbi were negatively correlated with bacteria involved in the lipid, energy, and carbohydrate metabolism pathways. The present study suggests that RES supplementation affected lipid metabolism in immune-related organs may be related to the PPAR signaling pathway.

Differentially expressed genes in head kidney of Pelteobagrus fulvidraco following Vibrio cholerae challenge

The yellow catfish (Pelteobagrus fulvidraco) is a freshwater fish with high economic value in eastern China. Nevertheless, pathogens causing bacterial diseases in P. fulvidraco have brought about huge economic loss and high mortality in artificial aquaculture. For disease control, it is critical to further understand the immune system of yellow catfish and immune-related genes with which they respond to pathogenic infections. In this study, high-throughput sequencing methods were used to analyze the transcriptomic spectrum of the head kidney from P. fulvidraco challenged by Vibrio cholera. A total of 45,544 unique transcript fragments (unigenes) were acquired after assembly and annotation, with an average length of 1,373 bp. Additionally, 674 differentially expressed genes (DEGs) were identified after stimulation with V. cholerae, 353 and 321 genes were identified as remarkably up- or downregulated, respectively. To further study the immune-related DEGs, we performed KEGG enrichment and GO enrichment. The results showed gene regulation of response to stimulus, immune response, immune system progress, response to external stimuli and cellular response to stimuli. Analysis of KEGG enrichment is important to identify chief immune related pathways. Real-time quantitative reverse transcription-PCR (qRT-PCR) results indicated 10 immune response genes that were found to be upregulated compared to a control group after 6 h of V. cholerae challenging. In summary, the results of our study are helpful to determine the defense mechanisms and immune system responses of yellow catfish in reaction to bacterial challenges.

Effects of resveratrol on lipid metabolism in liver of red tilapia Oreochromis niloticus

Resveratrol (RES), as a polyphenol natural plant extract, mainly accumulates in the root of Polygonum cuspidatum, which can alleviate liver injury in mammals. Our study aims to explore the effects and potential mechanism of RES on lipid metabolism of red tilapia, and the effects of RES on liver structure, fat synthesis and metabolism of red tilapia were determined. The present study designed four groups named as 8 % fat (8%CK), 10 % fat (10 % HF), 10 % HF + RES and 10 % HF + RES + EX527 (selisistat). The liver tissues of red tilapia were collected at 3 (3 W), 6 (6 W) and 9 (9 W) weeks for parameter determination. Compared to the normal diet group, the hepatocyte of tilapia showed nuclear shift and vacuoles of different sizes when fed a high-fat diet. Meanwhile, the high-fat diet increased the contents of LDL, TC and TG significantly at 6 W, and significantly decreased the content of NAD⁺ at 9 W. Compared to the high-fat group, the nuclei of tilapia fed with RES were increased and visible, the degree of steatosis and the number of vacuoles were both reduced. At 3/6/9 W, RES significantly decreased the contents of LDL, TG and TMAO, and significantly increased the content of NAD⁺. A total of 1416 genes were up-regulated and 1928 genes were down-regulated in the group with added RES when compared to the 10 % HF group. The pathways related to lipid metabolism including PPAR signaling pathway have been enriched. Interestingly, the expressions of sirt1, pparα, fabp7 and cpt1b genes were up-regulated in RES diet group, while the expressions of pparγ, me1, scd and lpl genes were down-regulated. After the addition of an inhibitor (EX527), the above indexes showed an opposite trend when compared to the group with added RES. The overall results showed that the high-fat diet could cause fatty liver lesions in the liver of red tilapia, and RES could activate the sirt1 gene, regulate the PPARα/γ pathway and related genes, and thus regulate liver fat synthesis and metabolism leading to the alleviation of damage to liver tissue.

Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment

BACKGROUND

RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. For organisms that lack a well-annotated reference genome or transcriptome, a conventional RNA-seq data analysis workflow requires constructing a de-novo transcriptome assembly and annotating it against a high-confidence protein database. The assembly serves as a reference for read mapping, and the annotation is necessary for functional analysis of genes found to be differentially expressed. However, assembly is computationally expensive. It is also prone to errors that impact expression analysis, especially since sequencing depth is typically much lower for expression studies than for transcript discovery.

RESULTS

We propose a shortcut, in which we obtain counts for differential expression analysis by directly aligning RNA-seq reads to the high-confidence proteome that would have been otherwise used for annotation. By avoiding assembly, we drastically cut down computational costs - the running time on a typical dataset improves from the order of tens of hours to under half an hour, and the memory requirement is reduced from the order of tens of Gbytes to tens of Mbytes. We show through experiments on simulated and real data that our pipeline not only reduces computational costs, but has higher sensitivity and precision than a typical assembly-based pipeline. A Snakemake implementation of our workflow is available at: https://bitbucket.org/project_samar/samar .

CONCLUSIONS

The flip side of RNA-seq becoming accessible to even modestly resourced labs has been that the time, labor, and infrastructure cost of bioinformatics analysis has become a bottleneck. Assembly is one such resource-hungry process, and we show here that it can be avoided for quick and easy, yet more sensitive and precise, differential gene expression analysis in non-model organisms.

Immersion Vaccination by a Biomimetic-Mucoadhesive Nanovaccine Induces Humoral Immune Response of Red Tilapia (Oreochromis sp.) against Flavobacterium columnare Challenge

Immersion vaccination with a biomimetic mucoadhesive nanovaccine has been shown to induce a strong mucosal immune response against columnaris disease, a serious bacterial disease in farmed red tilapia caused by Flavobacterium columnare. However, the induction of a systemic immune response by the vaccine is yet to be investigated. Here, we examine if a specific humoral immune response is stimulated in tilapia by a biomimetic-mucoadhesive nanovaccine against Flavobacterium columnare using an indirect-enzyme-linked immunosorbent assay (ELISA), serum bactericidal activity (SBA) and the expression of immune-related genes within the head-kidney and spleen, together with assessing the relative percent survival of vaccinated fish after experimentally infecting them with F. columnare. The anti-IgM antibody titer of fish at 14 and 21 days post-vaccination was significantly higher in chitosan complex nanoemulsion (CS-NE) vaccinated fish compared to fish vaccinated with the formalin-killed vaccine or control fish, supporting the serum bactericidal activity results at these time points. The cumulative mortality of the unvaccinated control fish was 87% after challenging fish with the pathogen, while the cumulative mortality of the CS-NE vaccinated group was 24%, which was significantly lower than the formalin-killed vaccinated and control fish. There was a significant upregulation of IgM, IgT, TNF α, and IL1-β genes in the spleen and kidney of vaccinated fish. Significant upregulation of IgM and IgT genes was observed in the spleen of CS-NE vaccinated fish. The study confirmed the charged-chitosan-based mucoadhesive nanovaccine to be an effective platform for immersion vaccination of tilapia, with fish generating a humoral systemic immune response against columnaris disease in vaccinated fish.

Discovering the Protective Effects of Resveratrol on Aflatoxin B1-Induced Toxicity: A Whole Transcriptomic Study in a Bovine Hepatocyte Cell Line

Aflatoxin B1 (AFB1) is a natural feed and food contaminant classified as a group I carcinogen for humans. In the dairy industry, AFB1 and its derivative, AFM1, are of concern for the related economic losses and their possible presence in milk and dairy food products. Among its toxic effects, AFB1 can cause oxidative stress. Thus, dietary supplementation with natural antioxidants has been considered among the strategies to mitigate AFB1 presence and its toxicity. Here, the protective role of resveratrol (R) has been investigated in a foetal bovine hepatocyte cell line (BFH12) exposed to AFB1, by measuring cytotoxicity, transcriptional changes (RNA sequencing), and targeted post-transcriptional modifications (lipid peroxidation, NQO1 and CYP3A enzymatic activity). Resveratrol reversed the AFB1-dependent cytotoxicity. As for gene expression, when administered alone, R induced neglectable changes in BFH12 cells. Conversely, when comparing AFB1-exposed cells with those co-incubated with R+AFB1, greater transcriptional variations were observed (i.e., 840 DEGs). Functional analyses revealed that several significant genes were involved in lipid biosynthesis, response to external stimulus, drug metabolism, and inflammatory response. As for NQO1 and CYP3A activities and lipid peroxidation, R significantly reverted variations induced by AFB1, mostly corroborating and/or completing transcriptional data. Outcomes of the present study provide new knowledge about key molecular mechanisms involved in R antioxidant-mediated protection against AFB1 toxicity.