Liver Metabolome and Proteome Response of Turbot (Scophthalmus maximus) to Lysine and Leucine in Free and Dipeptide Forms

Omics approaches provide more metabolic information to explain the relationship between dietary nutrition and fish growth. This study aimed to explore the metabolome and proteome response of turbot (Scophthalmus maximus) fed diets containing lysine and leucine in free and dipeptide forms by the approaches of integrated liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics and isobaric tags for relative and absolute quantification (iTRAQ)-based proteomics. Plant protein-based diets were formulated to contain the equivalent of lysine and leucine in free amino acid [crystalline amino acid (CAA)] and synthetic Lys-Leu (Lys-Leu) forms. The metabolome and proteome profiles of the liver were screened in fish fed either the CAA diet or the Lys-Leu diet after an 8-week feeding trial. Fish fed the Lys-Leu diet showed a significantly higher final body weight and a specific growth rate compared with fish fed the CAA diet. Protein- and amino acid-related metabolic processes in the liver were identified between the Lys-Leu and CAA groups based on differential metabolites and proteins. The proteolytic enzymes and amino acid transporters from differential proteins of the liver showed that the process of protein digestion and absorption may be affected by the different forms of lysine and leucine in the feed. A mechanistic target of rapamycin complex 1 and ubiquitin proteasome pathways were identified by differential proteins, which were involved in the processes of protein synthesis and degradation in the liver. Lysine degradation, tryptophan metabolism, alanine, aspartate, and glutamate metabolism, arginine biosynthesis, arginine and proline metabolism, and glycine, serine, and threonine metabolism were identified based on differential metabolites and proteins, which showed that the metabolism of various amino acids, including lysine, had been affected by both the CAA and Lys-Leu groups. In conclusion, the data of integrated metabonomics and proteomics suggested that different forms of lysine and leucine in the feed may affect liver metabolic processes including protein digestion and absorption, protein synthesis and degradation, and amino acid metabolism. In addition, a good correlation between differential metabolites and proteins was observed in amino acid metabolism by using the approaches of integrated LC-MS/MS-based metabolomics and iTRAQ-based proteomics

New insights into the characteristic skin microorganisms in different grades of acne and different acne sites

BackgroundThe increasing maturity of sequencing technology provides a convenient approach to studying the role of skin microorganisms in acne pathogenesis. However, there are still too few studies about the skin microbiota of Asian acne patients, especially a lack of detailed analysis of the characteristics of the skin microbiota in the different acne sites.MethodsIn this study, a total of 34 college students were recruited and divided into the health, mild acne, and severe acne groups. The bacterial and fungal flora of samples were separately detected by 16S and 18S rRNA gene sequencing. The biomarkers of different acne grades and different acne sites [forehead, cheek, chin, torso (including chest and back)] were excavated.Results and DiscussionOur results indicated that there was no significant difference in species diversity between groups. The genera like Propionibacterium, Staphylococcus, Corynebacterium, and Malassezia, which have a relatively high abundance in the skin microbiota and were reported as the most acne-associated microbes, were no obvious differences between groups. On the contrary, the abundance of less reported Gram-negative bacteria (Pseudomonas, Ralstonia, and Pseudidiomarina) and Candida has a significant alteration. Compared with the health group and the mild group, in the severe group, the abundance of Pseudomonas and Ralstonia sharply reduced while that of Pseudidiomarina and Candida remarkably raised. Moreover, different acne sites have different numbers and types of biomarkers. Among the four acne sites, the cheek has the greatest number of biomarkers including Pseudomonas, Ralstonia, Pseudidiomarina, Malassezia, Saccharomyces, and Candida, while no biomarker was observed for the forehead. The network analysis indicated that there might be a competitive relationship between Pseudomonas and Propionibacterium. This study would provide a new insight and theoretical basis for precise and personalized acne microbial therapy

Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios

Long non-coding RNAs (lncRNA) have emerged as important regulators of lipid metabolism and have been shown to play multifaceted roles in controlling transcriptional gene regulation, but very little relevant information has been available in fish, especially in non-model fish species. With a feeding trial on a typical marine teleost tongue sole C. semilaevis followed by transcriptomic analysis, the present study investigated the possible involvement of lncRNA in hepatic mRNA expression in response to different levels of dietary DHA and EPA, which are two most important fatty acids for marine fish. An 80-day feeding trial was conducted in a flow-through seawater system, and in this trial three experimental diets differing basically in DHA/EPA ratio, i.e., 0.61 (D/E-0.61), 1.46 (D/E-1.46), and 2.75 (D/E-2.75), were randomly assigned to 9 tanks of experimental fish. A total of 124.04 G high quality genome-wide clean data about coding and non-coding transcripts was obtained in the analysis of hepatic transcriptome. Compared to diet D/E-0.61, D/E-1.46 up-regulated expression of 178 lncRNAs and 2629 mRNAs, and down-regulated that of 47 lncRNAs and 3059 mRNAs, while D/E-2.75 resulted in much less change in gene expression. The co-expression and co-localization analysis of differentially expressed (DE) lncRNA and mRNA among dietary groups were then conducted. The co-expressed DE lncRNA and mRNA were primarily enriched in GO terms such as Metabolic process, Intracellular organelle, Catalytic activity, and Oxidoreductase activity, as well as in KEGG pathways such as Ribosome and Oxidative phosphorylation. Overlap of co-expression and co-localization analysis, i.e., lncRNA–mRNA matches “XR_523541.1–solute carrier family 16, member 5 (slc16a5)” and “LNC_000285–bromodomain adjacent to zinc finger domain 2A (baz2a),” were observed in all inter-group comparisons, indicating that they might crucially mediate the effects of dietary DHA and EPA on hepatic gene expression in tongue sole. In conclusion, this was the first time in marine teleost to investigate the possible lncRNA–mRNA interactions in response to dietary fatty acids. The results provided novel knowledge of lncRNAs in non-model marine teleost, and will serve as important resources for future studies that further investigate the roles of lncRNAs in lipid metabolism of marine teleost

ID Embedding as Subtle Features of Content and Structure for Multimodal Recommendation

Multimodal recommendation aims to model user and item representations comprehensively with the involvement of multimedia content for effective recommendations. Existing research has shown that it is beneficial for recommendation performance to combine (user- and item-) ID embeddings with multimodal salient features, indicating the value of IDs. However, there is a lack of a thorough analysis of the ID embeddings in terms of feature semantics in the literature. In this paper, we revisit the value of ID embeddings for multimodal recommendation and conduct a thorough study regarding its semantics, which we recognize as subtle features of content and structures. Then, we propose a novel recommendation model by incorporating ID embeddings to enhance the semantic features of both content and structures. Specifically, we put forward a hierarchical attention mechanism to incorporate ID embeddings in modality fusing, coupled with contrastive learning, to enhance content representations. Meanwhile, we propose a lightweight graph convolutional network for each modality to amalgamate neighborhood and ID embeddings for improving structural representations. Finally, the content and structure representations are combined to form the ultimate item embedding for recommendation. Extensive experiments on three real-world datasets (Baby, Sports, and Clothing) demonstrate the superiority of our method over state-of-the-art multimodal recommendation methods and the effectiveness of fine-grained ID embeddings

Comparative analysis of glucose and fructose tolerance in two marine fishes: effects on insulin secretion and acute hypoxia tolerance

Carbohydrates are a common and economical energy source in animal feeds. However, most fish show a persistent postprandial hyperglycemia after intake of a high-carbohydrate diet. Unfortunately, the mechanism of glucose metabolism in fish is still unclear. In the present study, tiger puffer (Takifugu rubripes) and turbot (Scophthalmus maximus) were intraperitoneally injected or orally administered with glucose or fructose (500 mg/kg body weight) to evaluate the ability of fish to utilize carbohydrates. Afterwards, serum glucose, fructose, pyruvate, insulin levels, and acute hypoxia tolerance were measured. Our results showed increased serum glucose level and then decreased post intraperitoneal injection with glucose, and reached a peak after 0.5 hours in turbot and 1 hour in tiger puffer. Tiger puffer had significantly lower liver glycogen, serum glucose, fructose, pyruvate, and insulin contents than turbot. Glucose and fructose only induced insulin secretion in turbot, but did not change serum insulin level in tiger puffer. Glucose was a stronger stimulator of insulin than fructose in the two marine species. Both intraperitoneal injection and oral fructose intake increased serum glucose level, while intraperitoneal or oral glucose also increased serum fructose level. Intraperitoneal injection of glucose promoted absorption and utilization of glucose in the blood more effectively than oral glucose intake. In addition, turbot and tiger puffer were intolerant to acute hypoxia, whereas supplementation with glucose or fructose improved hypoxia tolerance in the two marine fishes by activating anaerobic glycolysis. Taken together, our results provide important scientific information for understanding the mechanism for glucose and fructose utilization and improving hypoxia tolerance in fish