Dietary inclusion of plant ingredients induces epigenetic changes in the intestine of zebrafish

Epigenetic changes in pyloric caeca of Atlantic salmon fed diets containing increasing levels of lipids and choline

An earlier study of ours investigating the effect of dietary lipid levels on the choline requirement of Atlantic salmon showed increasing severity of intestinal steatosis with increasing lipid levels. As choline is involved in epigenetic regulation by being the key methyl donor, pyloric caeca samples from the study were analysed for epigenetic effects of dietary lipid and choline levels. The diets varied in lipid levels between 16% and 28%, and choline levels between 1.9 and 2.3 g/kg. The diets were fed for 8 weeks to Atlantic salmon of 25 g of initial weight. Using reduced representation bisulfite sequencing (RRBS), this study revealed that increasing dietary lipid levels induced methylation differences in genes involved in membrane transport and signalling pathways, and in microRNAs important for the regulation of lipid homoeostasis. Increasing choline levels also affected genes involved in fatty acid biosynthesis and transport, lipolysis, and lipogenesis, as well as important immune genes. Our observations confirmed that choline is involved in epigenetic regulation in Atlantic salmon, as has been reported for higher vertebrates. This study showed the need for the inclusion of biomarkers of epigenetic processes in studies that must be conducted to define optimal choline levels in diets for Atlantic salmon.

Remodeling of the epigenetic landscape in rainbow trout, Oncorhynchus mykiss, offspring in response to maternal choline intake

This project focused on evaluating the effects of maternal dietary choline intake on global DNA methylation profiles and related transcriptional changes in rainbow trout offspring. Three experimental diets were formulated to test different levels of choline intake: (a) 2065 ppm choline (Low Choline, 0 % supplementation), (b) 5657 ppm choline (Medium Choline, 0.6 % supplementation), and (c) 9248 ppm choline (High Choline, 1.2 % choline supplementation). Six rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Reduced representation bisulfite sequencing (RRBS) was utilized to measure genome-wide methylation in offspring immediately after hatching. When comparing to the Medium Choline offspring, differential DNA methylation occurred more in the Low Choline offspring than High Choline, especially in genic features like promoters. The differentially methylated CpGs (q ≤ 0.01) were identified evenly between CpG islands and shores in the genome, mostly found in the introns of genes. Genes such as fabp2 and leap2B associated with protein binding, fatty acid binding, DNA binding, and response to bacteria were differentially methylated and detected as differentially regulated genes by previous RNA-seq analysis. Although these findings indicate that levels of dietary choline available in broodstock diets alter offspring DNA methylation;, most differentially expressed genes were not associated with differential DNA methylation, suggesting additional mechanisms playing a role in regulating gene expression in response to maternal choline intake.

Environmental epigenetics: Exploring phenotypic plasticity and transgenerational adaptation in fish

Epigenetics plays a vital role in the interaction between living organisms and their environment by regulating biological functions and phenotypic plasticity. Considering that most aquaculture activities take place in open or natural habitats that are vulnerable to environmental changes. Promising findings from recent research conducted on various aquaculture species have provided preliminary evidence suggesting a link between epigenetic mechanisms and economically valuable characteristics. Environmental stressors, including climate changes (thermal stress, hypoxia, and water salinity), anthropogenic impacts such as (pesticides, crude oil pollution, nutritional impacts, and heavy metal) and abiotic factors (infectious diseases), can directly trigger epigenetic modifications in fish. While experiments have confirmed that many epigenetic alterations caused by environmental factors have plastic responses, some can be permanently integrated into the genome through genetic integration and promoting rapid transgenerational adaptation in fish. These environmental factors might cause irregular DNA methylation patterns in genes related to many biological events leading to organs dysfunction by inducing alterations in genes related to oxidative stress or apoptosis. Moreover, these environmental issues alter DNA/histone methylation leading to decreased reproductive competence. This review emphasizes the importance of understanding the effects of environmentally relevant issues on the epigenetic regulation of phenotypic variations in fish. The goal is to expand our knowledge of how epigenetics can either facilitate or hinder species' adaptation to these adverse conditions. Furthermore, this review outlines the areas that warrant further investigation in understanding epigenetic reactions to various environmental issues.

Integrated transcriptomics and lipidomics investigation of the mechanism underlying the gastrointestinal mucosa damage of Loropetalum chinense (R.Br.) and its representative component

BACKGROUND

Loropetalum chinensis (R.Br) Oliv (Bhjm), a Chinese folk herbal medicine, was traditionally used in the treatment of wound bleeding and skin ulcers. A new drug named JIMUSAN granules used for gastrosia was developed by our group, and clinical trials have been approved. However, as the principal herb, the material basis and underlying mechanisms of Bhjm in attenuating gastrointestinal mucosa damage (GMD) remain to be systemically illuminated.

PURPOSE

An integrated strategy was used to explore the therapeutic effects and mechanisms of Bhjm and ellagic acid (EA) on GMD zebrafish, using network pharmacology, transcriptomics, lipidomics, and real-time quantitative PCR (RT-qPCR) verification.

METHODS

First, network pharmacological analysis was used to infer the major effective constituents and targets of Bhjm. Ultra high performance liquid chromatography-linear ion trap/orbitrap high resolution mass spectrometry (UHPLC-LTQ-Orbitrap HRMS) and ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) were employed to identify the chemical constituents and quantify the different types of constituents. Second, zebrafish model of GMD was established by using 2,4,6-trinitrobenzenesulfonic acid (TNBS) to evaluate the efficacy of Bhjm and EA. The potential mechanism was examined by integrated transcriptomics and lipidomics analysis. Finally, validation tests were implemented using RT-qPCR.

RESULTS

In this study, targets indentified by network pharmacology were related to inflammation and mucosal damage. Ten representative components that interacted with these targets were simultaneously determined by UHPLC-MS/MS. Sixty four compounds were identified or tentatively characterized, most of which were flavonoids and polyphenols. Bhjm and EA alleviated mucosal damage and reduced inflammation in a TNBS-induced zebrafish GMD model, indicating that EA was the main active compounds. Eight common differentially expressed genes were downregulated by Bhjm and EA, as determined by transcriptomics analysis. Lipidomics analysis confirmed 12 differential lipids, including phosphatidylcholine (PC) and triglyceride (TG). Further network enrichment analysis demonstrated that differential lipid metabolism was regulated by klf4 and hist1h2ba, and were validated by RT-qPCR.

CONCLUSION

In our study, the chemical profile of Bhjm was clarified. Moreover, the GMD repair effect and the mechanism of Bhjm and EA was comprehensively analyzed for the first time, involving inflammation and lipid metabolism. Collectively, these findings will be significantly helpful for deeply exploring the clinical application value of Bhjm.

An innovative insecticidal approach based on plant protease inhibitor and Bt protoxins inhibits trypsin-like activity in zebrafish

The Leucaena leucocephala trypsin inhibitor (LTI) + Bacillus thuringiensis (Bt) protoxins mix has been proposed as a novel larvicide agent in order to control the vector mosquito of dengue virus, Aedes aegypti, in their aquatic breeding sites. However, use of this insecticide formulation has raised concerns about its impacts on aquatic biota. In this context, this work aimed to assess the effects of LTI and Bt protoxins, separately or in combination, in zebrafish, in regard to the evaluation of toxicity at early life stages and to the presence of LTI inhibitory effects on intestinal proteases of this fish. Results showed that LTI and Bt concentrations (250 mg/L, and 0.13 mg/L, respectively), and LTI + Bt mix (250 mg/L + 0.13 mg/L) - 10 times superior to those with insecticidal action - did not cause death nor did it induce morphological changes during embryonic and larval development (3 to 144 h post-fertilization) of zebrafish. Molecular docking analyses highlighted a possible interaction between LTI and zebrafish trypsin, especially through hydrophobic interactions. In concentrations near to those with larvicidal action, LTI (0.1 mg/mL) was able to inhibit in vitro intestinal extracts of trypsin in female and male fish by 83 % and 85 %, respectively, while LTI + Bt mix promoted trypsin inhibition of 69 % in female and 65 % in male ones. These data show that the larvicidal mix can potentially promote deleterious effects to nutrition and survival in non-target aquatic organisms, especially those with trypsin-like dependent protein digestion.

Feeding Rate and Protein Quality Differentially Affect Growth and Feeding Efficiency Response Variables of Zebrafish (Danio rerio)

Manipulating feeding rate and protein quality may improve growth and feeding efficiency of cultured species. However, whether feeding rate, protein quality, or their interaction has a greater effect on growth and feeding efficiency response variables is unknown. To determine whether feeding rate and protein quality individually or interactively affect growth and feeding efficiency, juvenile Zebrafish (Danio rerio) were either offered nutritionally similar diet consisting of either menhaden fishmeal protein or a 100% replacement of fishmeal with soybean meal-based protein restrictively or to satiation. Total length, weight, feed intake, and feed conversion ratio (FCR) were measured throughout the duration of the study. Protein quality and feeding rate individually and interactively affected feed intake and FCR: Zebrafish offered feed to satiation had higher growth and FCR than those fed restrictively, and Zebrafish fed soybean meal-based diet showed lower growth and higher FCR and feed intake compared to those fed fishmeal-based diet, although magnitude of response depended on feeding rate. These findings likely indicate lower digestibility of soybean meal or the presence of antinutritional factors in soybean meal that led to impaired nutrient absorption of fish offered soybean meal-based diet. Differences in measured response variables between protein qualities and feeding rates highlight the importance of determining interactive effects in nutritional studies.

The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation

DNA methylation is one of the main epigenetic mechanisms that regulate gene expression in a manner that depends on the genomic context and varies considerably across taxa. This DNA modification was first found in nuclear genomes of eukaryote several decades ago and it has also been described in mitochondrial DNA. It has recently been shown that mitochondrial DNA is extensively methylated in mammals and other vertebrates. Our current knowledge of mitochondrial DNA methylation in fish is very limited, especially in non-model teleosts. In this study, using whole-genome bisulfite sequencing, we determined methylation patterns within non-CpG (CH) and CpG (CG) contexts in the mitochondrial genome of Nile tilapia, a non-model teleost of high economic importance. Our results demonstrate the presence of mitochondrial DNA methylation in this species predominantly within a non-CpG context, similarly to mammals. We found a strand-specific distribution of methylation, in which highly methylated cytosines were located on the minus strand. The D-loop region had the highest mean methylation level among all mitochondrial loci. Our data provide new insights into the potential role of epigenetic mechanisms in regulating metabolic flexibility of mitochondria in fish, with implications in various biological processes, such as growth and development.

Recent development in zebrafish model for bioactivity and safety evaluation of natural products

The zebrafish is a species of freshwater fish, popular in aquariums and laboratories. Several advantageous features have facilitated zebrafish to be extensively utilized as a valuable vertebrate model in the lab. It has been well-recognized that natural products possess multiple health benefits for humans. With the increasing demand for natural products in the development of functional foods, nutraceuticals, and natural cosmetics, the zebrafish has emerged as an unprecedented tool for rapidly and economically screening and identifying safe and effective substances from natural products. This review first summarized the key factors for the management of zebrafish in the laboratory, followed by highlighting the current progress on the establishment and applications of zebrafish models in the bioactivity evaluation of natural products. In addition, the zebrafish models used for assessing the potential toxicity or health risks of natural products were involved as well. Overall, this review indicates that zebrafish are promising animal models for the bioactivity and safety evaluation of natural products, and zebrafish models can accelerate the discovery of novel natural products with potential health functions.

Sensitivity to Dietary Wheat Gluten in Atlantic Salmon Indicated by Gene Expression Changes in Liver and Intestine

Feed safety is a necessity for animal health and welfare as well as prerequisite for food safety and human health. Wheat gluten (WG) is considered as a valuable protein source in fish feed due to its suitability as a feed binder, high digestibility, good amino acid profile, energy density and most importantly, due to its relatively low level of anti-nutritional factors (ANFs). The main aim of this study was to identify the impact of dietary WG on salmon health by analysing growth, feed efficiency and the hepatic and intestinal transcriptomes. The fish were fed either control diet with fishmeal (FM) as the only source of protein or diets, where 15% or 30% of the FM were replaced by WG. The fish had a mean initial weight of 223 g and approximately doubled their weight during the 9-week experiment. Salmon fed on 30% WG showed reduced feed intake compared to the 15% and FM fed groups. The liver was the less affected organ but fat content and activities of the liver health markers in plasma increased with the inclusion level of WG in the diet. Gene expression analysis showed significant changes in both, intestine and liver of fish fed with 30% WG. Especially noticeable were changes in the lipid metabolism, in particular in relation to the intestinal lipoprotein transport and sterol metabolism. Moreover, the intestinal transcriptome of WG-fed fish showed shifts in the expression of a large number of genes responsible for immunity and tissue structure and integrity. These observations implied that the fish receiving WG-containing diet were undergoing nutritional stress. Overall, the study provided evidence that a high dietary level of WG can have a negative impact on the intestinal and liver health of salmon with symptoms similar to gluten sensitivity in humans.

Plant-Based Diets Induce Transcriptomic Changes in Muscle of Zebrafish and Atlantic Salmon

With the expansion of the aquaculture industry in the last two decades, there has been a large increase in the use of plant ingredients in aquafeeds, which has created new challenges in fish growth, health and welfare. Fish muscle growth is an important trait that is strongly affected by diet, but our knowledge on the effect of plant protein-based diets on global gene expression in muscle is still scant. The present study evaluated nutrigenomic effects of the inclusion of proteins from pea, soy and wheat into aquafeeds, compared to a control diet with fishmeal as the main protein source using the zebrafish model by RNA-seq; these results were extended to an important aquaculture species by analyzing selected differentially expressed genes identified in the zebrafish model on on-growing Atlantic salmon fed with equivalent plant protein-based diets. Expression of selected Atlantic salmon paralogues of the zebrafish homologs was analyzed using paralogue-specific qPCR assays. Global gene expression changes in muscle of zebrafish fed with plant-based diets were moderate, with the highest changes observed in the soy diet-fed fish, and no change for the pea diet-fed fish compared to the control diet. Among the differentially expressed genes were mylpfb, hsp90aa1.1, col2a1a, and odc1, which are important in regulating muscle growth, maintaining muscle structure and function, and muscle tissue homeostasis. Furthermore, those genes and their paralogues were differentially expressed in Atlantic salmon fed with the equivalent percentage of soy or wheat protein containing diets. Some of these genes were similarly regulated in both species while others showed species-specific regulation. The present study expands our understanding on the molecular effects of plant ingredients in fish muscle. Ultimately, the knowledge gained would be of importance for the improved formulation of sustainable plant-based diets for the aquaculture industry.

Synergistic Effect of Dietary Betaines on SIRT1-Mediated Apoptosis in Human Oral Squamous Cell Carcinoma Cal 27

Simple Summary

Betaines are important human nutrients widely distributed in plants, animals, and dietary sources. δ-valerobetaine (δVB) is a naturally occurring betaine with antioxidant, anti-inflammatory and anticancer activities. The aim of our study was to investigate the possible synergism between δVB and the structurally related γ-butyrobetaine (γBB) by testing the in vitro anticancer activity in head and neck squamous cell carcinomas. Combined δVB and γBB caused a marked inhibition of cell proliferation and induction of apoptosis in Cal 27 cells. The increased reactive oxygen species accumulation influenced the nuclear expression of SIRT1. Gene silencing with small interfering RNA confirmed the role of SIRT1 in the apoptotic cell death. Synergism of δVB and γBB is useful for novel strategies to optimize their content in meat, milk and dairy products to sustain human health and wellbeing.

Abstract

Betaines are food components widely distributed in plants, animals, microorganisms, and dietary sources. Among betaines, δ-valerobetaine (N,N,N-trimethyl-5-aminovaleric acid, δVB) shares a metabolic pathway common to γ-butyrobetaine (γBB). The biological properties of δVB are particularly attractive, as it possesses antioxidant, anti-inflammatory and anticancer activities. Here, we investigated the possible synergism between δVB and the structurally related γBB, to date unexplored, by testing the in vitro anticancer activity in head and neck squamous cell carcinoma cell lines, FaDu, UM-SCC-17A and Cal 27. Among cell lines tested, results indicated that betaines showed the highest effect in reducing Cal 27 cell proliferation up to 72 h (p < 0.01). This effect was enhanced when betaines were administered in combination (δVB plus γBB) (p < 0.001). Inhibition of cell growth by δVB plus γBB involved reactive oxygen species (ROS) accumulation, upregulation of sirtuin 1 (SIRT1), and apoptosis (p < 0.001). SIRT1 gene silencing by small interfering RNA decreased the apoptotic effect of δVB plus γBB by modulating downstream procaspase-3 and cyclin B1 (p < 0.05). These findings might have important implications for novel prevention strategies for tongue squamous cell carcinoma by targeting SIRT1 with naturally occurring betaines.