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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 April 2025 | Viewed by 2214

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Special Issue Editors

Dr. Fernando Naya-Català

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Guest Editor

Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Científicas (CSIC), 12595 Ribera de Cabanes, Spain
Interests: aquaculture; fish nutrition; fish physiology; metabolic regulation; intestinal microbiota; omics; bioinformatics

Dr. Paula Simó-Mirabet

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Guest Editor

Department of Biology, Faculty of Marine and Environmental Sciences, Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), University of Cádiz, 11519 Puerto Real, Cádiz, Spain
Interests: aquaculture; fish nutrition; functional additives; fish physiology; stress; animal welfare; metabolism; microbiota

Special Issue Information

Dear Colleagues,

The global commercial production of fish from capture fisheries and aquaculture is a vital future food source for human consumption, due to its high nutritional value and health benefits compared to those of other animals. However, to ensure production, these sectors have to tackle some future challenges, such as climate change and marine resource depletion. Fish nutrition is crucial to overcoming these challenges, as it can promote better growth and fish flesh quality, or can lead to stress in fish, affecting their physiology and metabolism. Research on fish nutrition focuses on nutrient requirements and metabolism, but recent decades have seen increased attention on the use of omics technologies (transcriptomics, metataxonomics, and metagenomics) to understand how fish respond to nutrient, dietary, and environmental changes. Thus, this Special Issue invites researchers to submit studies that delve into fish nutrition, metabolism, and physiology. Additionally, we welcome submissions focusing on the application of omics approaches in these areas, all with the ultimate aim of advancing knowledge about the global productive chain involving fish species.

Dr. Fernando Naya-Català
Dr. Paula Simó-Mirabet
Guest Editors

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Keywords

fish
nutrition
metabolism
physiology
growth performance
fish stress
transcriptomics
metataxonomics
metagenomics
aquaculture

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Published Papers (4 papers)

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Research

27 pages, 19927 KiB

Open AccessArticle

Metabonomics and Transcriptomics Analyses Reveal the Underlying HPA-Axis-Related Mechanisms of Lethality in Larimichthys polyactis Exposed to Underwater Noise Pollution

by Qinghua Jiang, Yu Zhang, Ting Ye, Xiao Liang and Bao Lou

Int. J. Mol. Sci. 2024, 25(23), 12610; https://doi.org/10.3390/ijms252312610 - 24 Nov 2024

Viewed by 211

Abstract

The problem of marine noise pollution has a long history. Strong noise (>120 dB re 1 µPa) will affects the growth, development, physiological responses, and behaviors of fish, and also can induce the stress response, posing a mortal threat. Although many studies have reported that underwater noise may affect the survival of fish by disturbing their nervous system and endocrine system, the underlying causes of death due to noise stimulation remain unknown. Therefore, in this study, we used the underwater noise stress models to conduct underwater strong noise (50–125 dB re 1 µPa, 10–22,000 Hz) stress experiments on small yellow croaker for 10 min (short-term noise stress) and 6 days (long-term noise stress). A total of 150 fishes (body weight: 40–60 g; body length: 12–14 cm) were used in this study. Omics (metabolomics and transcriptomics) studies and quantitative analyses of important genes (HPA (hypothalamic–pituitary–adrenal)-axis functional genes) were performed to reveal genetic and metabolic changes in the important tissues associated with the HPA axis (brain, heart, and adrenal gland). Finally, we found that the strong noise pollution can significantly interfere with the expression of HPA-axis functional genes (including corticotropin releasing hormone (CRH), corticotropin releasing hormone receptor 2 (CRHR2), and arginine vasotocin (AVT)), and long-term stimulation can further induce metabolic disorders of the functional tissues (brain, heart, and adrenal gland), posing a lethal threat. Meanwhile, we also found that there were two kinds of death processes, direct death and chronic death, and both were closely related to the duration of stimulation and the regulation of the HPA axis. Full article

(This article belongs to the Special Issue Fish Nutrition, Metabolism and Physiology)

19 pages, 2697 KiB

Open AccessArticle

Synergistic Effects of Dietary Tryptophan and Dip Vaccination in the Immune Response of European Seabass Juveniles

by Diogo Peixoto, Inês Carvalho, André Cunha, Paulo Santos, Lourenço Ramos-Pinto, Marina Machado, Rita Azeredo and Benjamín Costas

Int. J. Mol. Sci. 2024, 25(22), 12200; https://doi.org/10.3390/ijms252212200 - 13 Nov 2024

Viewed by 368

Abstract

Vaccination is an effective, cost-efficient method to preventing disease outbreaks. However, vaccine procedures can induce adverse reactions due to stress, increasing plasma cortisol in the short term. In this context, tryptophan may prove to be fundamental as it has been demonstrated to have various desirable neuroendocrine attributes in different fish species. Therefore, this study aimed to evaluate both short-term (3 days) and long-term (21 days) effects of dietary tryptophan supplementation on European seabass juveniles’ (26.23 ± 7.22 g) response to vaccination and disease resistance to Tenacibaculum maritimum. The short-term tryptophan-fed fish exhibited increased hepatic superoxide dismutase and plasma cortisol levels, along with the downregulation of immune-related genes. Despite these changes, disease resistance was unaffected. When fish were later dip vaccinated, tryptophan prevented the stress-induced plasma cortisol increase and upregulated the gene expression of igm, suggesting tryptophan’s role in enhancing vaccination efficiency by counteracting stress-associated effects. In the long term, the lowest supplementation dose counteracted vaccine-mediated reduced gene expression, and fish fed this diet showed a more modest molecular response. Overall, the findings suggest a complex interplay between tryptophan supplementation, immune responses, and vaccine efficiency in fish. Further research is necessary to clarify how tryptophan could consistently improve vaccine efficiency in aquaculture. Full article

(This article belongs to the Special Issue Fish Nutrition, Metabolism and Physiology)

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Figure 1
Plasma cortisol levels (A), hepatic superoxide dismutase activity (B), and head-kidney relative expression of genes (C–G) related to the immune response of vaccinated European seabass fed experimental diets (CTRL, TRP1 and TRP2) for 3 days before the dip vaccine. SOD—superoxide dismutase activity; il1β—interleukin 1 beta; ido2—indoleamine-dioxygenase 2; il10—interleukin 10; tph1α—tryptophan 5-hydroxylase-like alpha and igm—immunoglobulin M. Values are presented as means ± SD (n = 9). Multivariate ANOVA followed by Tukey post-hoc test (p ≤ 0.05). If the interaction was significant, Tukey post-hoc test was used to identify differences among treatments. Capital letters stand for significant differences between sampling times. Different low-case letters stand for statistically significant differences between dietary treatments. Full article ">Figure 2
Heatmap of relative mRNA gene expression on the head-kidney of vaccinated and non-vaccinated European seabass fed experimental diets (CTRL, TRP1, and TRP2) for 3 days before (A) and 3 days after the dip vaccine, and then vaccinated or not fish were fed CTRL until day 21 (B). tph1α—tryptophan 5-hydroxylase-like alpha; ido2—indoleamine-dioxygenase 2; c3—complement factor 3; il1β—interleukin 1 beta; il10—interleukin 10; and igm—immunoglobulin M. Lines represent the different dietary treatments and columns represent genes assessed. Pearson’s method was used to calculate the distance metric and relative mRNA levels were hierarchically clustered with the centroid linkage algorithm. Colours represent the intensity of the analysed gene; green more intense; red less intense. Full article ">Figure 3
Survival rate of European seabass juveniles fed dietary treatments for 3 days and subsequently bath challenged with T. maritimum (ACC13.1). Full article ">Figure 4
Haematologic profile (A–C), plasma alternative complement pathway and cortisol levels (D,E), as well as head-kidney relative expression of genes (F–H) related to the immune response of vaccinated and non-vaccinated European seabass fed experimental diets (CTRL, TRP1 and TRP2) for 3 days before and 3 days after the dip vaccine, and then vaccinated or not fish were fed CTRL until day 21. WBC—white blood cell count; ACH50—alternative complement pathway; il10—interleukin 10; ido2—indoleamine-dioxygenase 2; and il1β—interleukin 1 beta. Values are presented as means ± SD (n = 9). Multivariate ANOVA followed by Tukey post-hoc test (p ≤ 0.05). If the interaction was significant, Tukey post-hoc test was used to identify differences among treatments. Capital letters stand for significant differences between vaccinated or not fish. Different low-case letters stand for statistically significant differences between dietary treatments. Full article ">Figure 5
Canonical discriminant analysis of European seabass fed experimental diets (CTRL, TRP1, and TRP2) for 3 days and sampled before (0 h) and after 1 and 6 h after dip vaccination. (A)—Canonical discriminant scores of each group. Small circle marks represent group centroids. (B)—Variable/factor correlation (factor loads) for two main discriminant functions (F1 and F2). ◆ Plasma: ACH50—alternative complement pathway activity. ■ Liver: GSH: GSSG—reduced: oxidised glutathione ratio; tGSH—total glutathione content; rGSH—reduced glutathione content. • Head kidney: il1β—interleukin 1 beta; il10—interleukin 10; igm—immunoglobulin M. Full article ">Figure 6
Canonical discriminant analysis of vaccinated (V) and non-vaccinated (NV) European seabass fed experimental diets (CTRL, TRP1 and TRP2) for 3 days before and 3 days after dip vaccination and sampled 21 days after vaccination. (A)—Canonical discriminant scores of each group. Small circle marks represent group centroids. (B)—Variables/factors correlation (factor loads) for two main discriminant functions (F1 and F2). ◆ Plasma: ACH50—alternative complement pathway activity; IgM—plasma immunoglobulin M levels. • Head-kidney: il1β—interleukin 1 beta; il10—interleukin 10; igm—immunoglobulin M; ido2—indoleamine-dioxygenase 2; c3—complement factor 3; tph1α—tryptophan 5-hydroxylase-like alpha. Full article ">Figure 7
Experimental setup of a short-term dietary tryptophan supplementation prior to vaccination or to a bacterial challenge. Full article ">

16 pages, 8629 KiB

Open AccessArticle

The Identification of Proteomic Signatures Associated with Alkaline Tolerance in the Skin Mucus of Crucian Carp (Carassius auratus)

by Zhipeng Sun, Jing Huang, Xiaofeng Zhang, Yumei Chang and Guo Hu

Int. J. Mol. Sci. 2024, 25(21), 11618; https://doi.org/10.3390/ijms252111618 - 29 Oct 2024

Viewed by 479

Abstract

The skin is covered by a protective mucus layer, which is essential to the innate defense mechanism of fish. Investigating the response of skin mucus to various toxic stresses is crucial for enhancing its ability to tackle environmental challenges and developing strategies to mitigate toxic effects. Alkalinity stress assays (50 mmol/L NaHCO₃) were conducted on crucian carp (Carassius auratus) from Lake Dali Nur (pH = 9.6) and Ping Xiang red crucian carp from freshwater (pH = 7) over 7 days. The expression of skin mucous proteins was analyzed using the liquid chromatography (LC)-spectrometry (MS)/MS Analysis-Data-independent acquisition (DIA) mode. A total of 12,537 proteins were identified across 20 samples from four groups, with 12,025 quantified. In the alkaline water population, high alkali stress resulted in the up-regulation of 139 proteins and the down-regulation of 500 proteins. In contrast, the freshwater population showed an increase in 112 proteins and a decrease in 120; both populations had a total of 23 genes up-regulated and 21 down-regulated. The protein regulatory network for the alkaline water group included 3146 pairwise interactions among 464 nodes, with only 20 being differentially expressed proteins. Conversely, the freshwater group’s network comprised just 1027 specific interactions across 337 nodes, with 6 corresponding to differentially expressed proteins. A common protein regulatory network responding to high alkali stress was extracted and visualized for both populations. Based on their regulatory relationships and expression levels, these proteins are hypothesized to play similar roles under high alkali stress. Notably, the alpha-globin fragment and keratin type I cytoskeletal 13-like proteins showed markedly up-regulated expression, with the alpha-globin fragment increasing nearly a thousandfold from an extremely low level. This suggests it could serve as a potential biomarker for alkali tolerance, warranting further investigation. Full article

(This article belongs to the Special Issue Fish Nutrition, Metabolism and Physiology)

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23 pages, 3098 KiB

Open AccessArticle

Exploring Multifunctional Markers of Biological Age in Farmed Gilthead Sea Bream (Sparus aurata): A Transcriptomic and Epigenetic Interplay for an Improved Fish Welfare Assessment Approach

by Álvaro Belenguer, Fernando Naya-Català, Josep Àlvar Calduch-Giner and Jaume Pérez-Sánchez

Int. J. Mol. Sci. 2024, 25(18), 9836; https://doi.org/10.3390/ijms25189836 - 11 Sep 2024

Viewed by 822

Abstract

DNA methylation clocks provide information not only about chronological but also biological age, offering a high-resolution and precise understanding of age-related pathology and physiology. Attempts based on transcriptomic and epigenetic approaches arise as integrative biomarkers linking the quantification of stress responses with specific fitness traits and may help identify biological age markers, which are also considered welfare indicators. In gilthead sea bream, targeted gene expression and DNA methylation analyses in white skeletal muscle proved sirt1 as a reliable marker of age-mediated changes in energy metabolism. To complete the list of welfare auditing biomarkers, wide analyses of gene expression and DNA methylation in one- and three-year-old fish were combined. After discriminant analysis, 668 differentially expressed transcripts were matched with those containing differentially methylated (DM) regions (14,366), and 172 were overlapping. Through enrichment analyses and selection, two sets of genes were retained: 33 showing an opposite trend for DNA methylation and expression, and 57 down-regulated and hypo-methylated. The first set displayed an apparently more reproducible and reliable pattern and 10 multifunctional genes with DM CpG in regulatory regions (sirt1, smad1, ramp1, psmd2—up-regulated; col5a1, calcrl, bmp1, thrb, spred2, atp1a2—down-regulated) were deemed candidate biological age markers for improved welfare auditing in gilthead sea bream. Full article

(This article belongs to the Special Issue Fish Nutrition, Metabolism and Physiology)

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