Comp. Biochem. Physiol. Part D Genomics Proteomics [JOURNAL]
Sun
200 papers
Effect of dietary Pulsatilla chinensis (Bunge) Regel on Mastacembelus armatus intestinal health and transcriptomic analysis.
Chen Q, Chen J, Zhang T … +7 more , Tang S, Wang J, Lin Y, Shi J, Shu H, Lin L, Chen M
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42044566 · Publisher ↗
The aim of this study was to investigate dietary Pulsatilla chinensis (Bunge) Regel (PC) on Mastacembelus armatus (MA) intestinal health, focusing on transcriptomics. A total of 480 fish were fed 0, 150, 300, and 600 mg/...
The aim of this study was to investigate dietary Pulsatilla chinensis (Bunge) Regel (PC) on Mastacembelus armatus (MA) intestinal health, focusing on transcriptomics. A total of 480 fish were fed 0, 150, 300, and 600 mg/kg PC for 8 weeks, and they were fed daily at 3%-5% of their body weight. The results showed that fish in the 300 mg/kg PC group exhibited significantly higher weight gain rate (WGR) and specific growth rate (SGR), as well as a lower feed conversion ratio (FCR). The 300 mg/kg group significantly improved intestinal morphology (enhanced villus structural integrity and increased muscularis thickness in MA), antioxidant capacity (SOD and MDA activities), as well as the gene expression of inflammation cytokines (IL-10, TNF-α) and intestinal tight junction-associated proteins (Occludin, Claudin-14, Claudin-15) when compared with the control group (P < 0.05). Furthermore, transcriptome sequencing of control and 300 mg/kg group intestines identified 363 differentially expressed genes (190 up-regulated, 173 down-regulated). The most significant KEGG-enriched signaling pathways of these DEGs were Intestinal mucosal immunity, Tight junction, Antigen processing and presentation and FoxO signaling pathways. For validation, 12 differentially expressed genes were subjected to qRT-PCR, and three key proteins content to ELISA (HSP-70, IRS-2 and RAB13), corroborating the results of transcriptome sequencing. In conclusion, 300 mg/kg PC promotes MA intestinal health, with transcriptomics revealing key molecular mechanisms.
Transcriptome of muscle reveals resveratrol modulates energy metabolism and immunity in Litopenaeus vannamei.
Cheng S, Zheng J, Dong B … +3 more , Zhang Y, Qian W, Liang Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42034044 · Publisher ↗
Energy metabolism is the core bridge connecting external challenges (stress, infection) with internal life support systems. Although Resveratrol has been extensively studied as a feed additive in aquatic animals, its cru...
Energy metabolism is the core bridge connecting external challenges (stress, infection) with internal life support systems. Although Resveratrol has been extensively studied as a feed additive in aquatic animals, its crucial role in energy metabolism has been relatively overlooked. In this study, we investigated transcriptome profile and enzyme activity after feeding different concentrations of resveratrol (0%, 0.01%, and 0.02%) on the of shrimp muscle. GO and KEGG enrichment analyses showed that differentially expressed genes were mainly enriched in signaling pathways such as the cell cycle, Hippo, and PI3K-Akt. Functional analysis indicated that low-concentration Resveratrol primarily regulated the synthesis of intermediates in carbohydrate metabolism, inflammatory immunity, and cellular energy metabolism, whereas high-concentration resveratrol significantly affected pathways including the spliceosome and cell junctions. Correlation analysis revealed the regulatory relationships between genes in immune and metabolic-related signaling pathways in shrimp muscle under resveratrol supplementation. In physiological validation experiments, feeding 0.01% resveratrol significantly increased the activities of ACP, ALP, SOD, and the content of GSH in shrimp muscle at 24 h post-infection with V. parahaemolyticus, whereas the enhancing effect of 0.02% resveratrol was markedly attenuated. These results indicate that low concentrations of resveratrol resist Vibrio infection by regulating energy metabolism allocation in shrimp.
Proteomic and functional characterization of seminal and epididymal plasma proteins associated with male fertility in cattle: A comprehensive review.
R P, K K, P MK … +4 more , R G, K T, T B S, R B
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42034043 · Publisher ↗
The animal industry is associated with substantial economic losses due to infertility and subfertility, with male infertility being a major contributing factor to breeding failure. Studies in cattle have shown that a sig...
The animal industry is associated with substantial economic losses due to infertility and subfertility, with male infertility being a major contributing factor to breeding failure. Studies in cattle have shown that a significant proportion of these failures is primarily attributed to semen quality rather than female-related factors. Seminal plasma is a complex, protein-rich biological fluid composed of secretions from accessory sex glands and the cauda epididymis, containing functionally distinct groups of proteins such as enzymes, structural proteins, antioxidant proteins, and immune-modulatory factors. These proteins are involved in key reproductive processes including sperm motility regulation, capacitation, sperm-oocyte interaction, and protection against oxidative and immunological stress. Rather than individual protein listing, key functional protein groups such as fertility-associated glycoproteins, antioxidant enzymes (e.g., glutathione peroxidase), and molecular chaperones (e.g., heat shock proteins) have been shown to influence sperm function, with several studies reporting that these proteins are differentially expressed, showing approximately 1.5-3.0-fold higher abundance in high-fertility bulls compared to low-fertility counterparts. This review systematically synthesizes proteomic studies on cattle across different geographical regions, providing insights into how variations in seminal plasma protein composition contribute to fertility phenotypes. Furthermore, it highlights the potential application of these proteins as quantitative biomarkers for fertility prediction and as molecular targets to improve semen preservation and assisted reproductive technologies in livestock systems.
Genome-wide identification and evolutionary analysis of the Hsp70 gene family in mandarin fish (Siniperca chuatsi): Insights into their differential expression under thermal and bacterial stress.
Liu Y, Yao X, Gao J … +3 more , Ismaeel H, Chen X, Zhao J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42025242 · Publisher ↗
The heat shock protein 70 (Hsp70) family is essential for maintaining protein homeostasis and mediating responses to environmental stresses; however, comprehensive characterizations of this family in the mandarin fish (S...
The heat shock protein 70 (Hsp70) family is essential for maintaining protein homeostasis and mediating responses to environmental stresses; however, comprehensive characterizations of this family in the mandarin fish (Siniperca chuatsi) are presently absent. Through comparative genomic analysis, a total of 178 Hsp70 genes were identified across nine vertebrate species (human, mouse, and seven teleost fishes), including 17 unique members within the mandarin fish genome. Phylogenetic and gene structure analyses demonstrated that the mandarin fish Hsp70 family has remained highly conserved throughout teleost evolution, marked by lineage-specific expansions (notably in hspa1, hspa4, hspa8, and hspa12) and selective gene loss (e.g., the absence of hspa2 and hspa6). Specifically, tandem duplication was observed for hspa8.1 and hspa8.2, at the same time, two pairs of syntenic genes (hspa4a/hspa4b and hyou1/hspa8b) were found. Ka/Ks analysis further indicated that this gene family has mainly evolved under purifying selection. Transcriptomic profiling showed that hspa8.1 was constantly expressed across all examined tissues. In addition, under thermal stress and Aeromonas hydrophila infection, Hsp70 genes in mandarin fish exhibited divergent expression patterns: certain members contribute to basal homeostasis (e.g., hspa8.1), whereas others demonstrate specialized responses to heat/cold adaptation (e.g., hspa5) or pathogen infection (e.g., hspa1l). Respectively, these findings together provide a thorough understanding of the composition, evolutionary trajectory, and stress-responsive dynamics of the Hsp70 family, establishing a foundational molecular basis for understanding the environmental adaptation of mandarin fish.
Sodium butyrate stimulates intestinal health and immunity by reshaping the intestinal microbiota and metabolite profile in big-belly seahorses (Hippocampus abdominalis).
Zhang Y, Bai Y, Zhu L … +8 more , Zhang Z, Zhang L, Zhang J, Liu Q, Tang L, Su X, Li M, Wang K
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42019311 · Publisher ↗
This study examined the effects of sodium butyrate (SB) on growth, intestinal health and immunity of big-belly seahorses (Hippocampus abdominalis) suffering frozen diet-induced enteritis and stress. Total 750 seahorses w...
This study examined the effects of sodium butyrate (SB) on growth, intestinal health and immunity of big-belly seahorses (Hippocampus abdominalis) suffering frozen diet-induced enteritis and stress. Total 750 seahorses were randomly assigned to five groups in triplicate, and were fed frozen mysids mixed with SB at 0, 1.25, 2.5, 5 and 10 mg/L (based on culture water volume) for 8 weeks, followed by an Edwardsiella tarda challenge. Results demonstrated that the SB1.25 group had a significantly higher specific growth rate, hepatic T-SOD and CAT activities, and lower MDA content than the SB0 group. Compared with the SB0 group, the SB1.25 and SB2.5 groups exhibited significantly higher activities of intestinal lipase, trypsin and alkaline phosphatase, as well as longer intestinal villus length. The SB1.25 group demonstrated upregulation of tight junction-related genes (occludin, claudin5, and zo1), increased abundance of beneficial gut bacteria (Lactobacillus and Lactococcus), and reduced abundance of potential pathogenic bacteria (Rickettsiales and Nocardia). Moreover, the levels of immune-related metabolites including Periplocin and short peptides in the SB1.25 group were significantly higher than the SB0 group. The Edwardsiella tarda challenge test revealed that the SB1.25 group exhibited the highest survival rate among all treatments, indicating that SB supplementation improves the infection resistance of big-belly seahorses. In conclusion, SB mixed into frozen mysids improves intestinal health and immunity of big-belly seahorses by regulating intestinal microbiota and metabolites, with 1.25 mg/L (culture water-based) as the optimal concentration.
Characterization of morphological development and olfactory receptor genes in the olfactory system of red-eared slider (Trachemys scripta elegans).
Li L, Lan T, Ren Y … +3 more , Lu T, Sun Y, Hong M
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42019310 · Publisher ↗
Previous behavioral studies have confirmed that the globally invasive red-eared slider (Trachemys scripta elegans) exhibits acute chemical sensitivity and a preference for heterosexual odor cues. However, the integrated...
Previous behavioral studies have confirmed that the globally invasive red-eared slider (Trachemys scripta elegans) exhibits acute chemical sensitivity and a preference for heterosexual odor cues. However, the integrated developmental characteristics of its olfactory system and the key genes responsible for this specific chemical perception remain limited. We systematically analyzed the morphological structures of the nasal cavity and olfactory bulb across three developmental stages (juvenile, subadult, and adult), characterized the olfactory receptor (OR) gene repertoire, and identified differential expression patterns of key OR-related signaling molecules. Morphometric analysis revealed that the olfactory region consistently occupied over 58% of the total nasal cavity volume across all groups, indicating a central ecological role for olfaction throughout the life cycle. Genomic data showed that this species possessed 727 functional OR genes and 55 pseudogenes. This conserved and sizable genomic architecture likely underlies its chemical perception and environmental adaptation. qRT-PCR analysis demonstrated a significant developmental upregulation of olfactory marker protein (OMP), indicating continuous refinement of the olfactory neural circuitry. Notably, we found that the olfactory system primarily relied on the OR pathway, and multiple olfactory-related genes, including the OR genes OR52E4, OR51G1, OR51G2, OR52R1, OR52P1 as well as V2R, were specifically upregulated in adult males, implying their potential involvement in recognizing male-specific chemical cues, such as those used in courtship. However, the precise functions of these genes require further validation. In summary, the findings lay a solid foundation for elucidating the functional differentiation and ligand recognition mechanisms of chemosensory receptor genes in T. s. elegans.
Differential transcriptomic response of Atlantic salmon to fermented sunflower meal under commercial seawater farming conditions.
Morales-Lange B, Eide LH, Kuiper RV … +2 more , Dale OB, Øverland M
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42008906 · Publisher ↗
Dietary inclusion of plant-based ingredients is hampered by gastrointestinal inflammation in salmonids, as well as feed/food competition. Fermented sunflower meal (FSFM), a by-product from oil production under biorefiner...
Dietary inclusion of plant-based ingredients is hampered by gastrointestinal inflammation in salmonids, as well as feed/food competition. Fermented sunflower meal (FSFM), a by-product from oil production under biorefinery processing, can support fish health without compromising growth or competing with food production. Thus, this study assessed the physiological modulation of dietary FSFM in immune organs of post-smolts Atlantic salmon (Salmo salar) farmed under commercial conditions. Results showed that while the antioxidant properties of the diets (control diet with 5% non-FSFM, 5% FSFM, and 10% FSFM) did not change significantly, fish fed 5% FSFM exhibited a distinct transcriptional modulation (compared to all other groups) in the head kidney (HK) and spleen (SP) that was linked to metabolic and immune pathways. For instance, upregulation of oxidative phosphorylation, phagosome activity, and amino acid metabolism was detected, whereas melanogenesis and signaling cascades associated with VEGF, GnRH, and Wnt were downregulated. Regarding fish fed 10% FSFM, phagosome and oxidative phosphorylation pathways were also upregulated in the HK compared to the control. This was complemented by the upregulation of antibody production pathway in both HK and SP, and regulation of the actin cytoskeleton in SP. Conversely, the spliceosome and efferocytosis pathways were downregulated in the HK. Interestingly, a network analysis showed metabolic and immune clusters connected by cell death (i.e., necroptosis and ferroptosis) and lipid metabolism, highlighting the relation between nutrition and immunity. Overall, these findings demonstrate that FSFM is a suitable feed ingredient that modulates a balanced immune response in Atlantic salmon during the seawater stage.
Gut microbial restructuring in white spot syndrome virus-infected Penaeus vannamei: Insights from long-read metagenomics.
Devika NT, Jayaraman K, Nadimuthu S … +4 more , Nathamuni SP, Sreya PS, Jangam AK, Katneni VK
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42000463 · Publisher ↗
Microbial community restructuring following White Spot Syndrome Virus (WSSV) infection is a critical determinant in modulating the disease progression in Penaeus vannamei. In this study, full-length 16S rRNA sequencing (...
Microbial community restructuring following White Spot Syndrome Virus (WSSV) infection is a critical determinant in modulating the disease progression in Penaeus vannamei. In this study, full-length 16S rRNA sequencing (V1-V9) was employed to delineate the microbial shifts in healthy and WSSV-infected shrimp. The analysis revealed a pronounced reduction in Firmicutes in the WSSV-infected shrimp, a dysbiosis signature reported in WSSV-associated amplicon studies. With the advantage of full-length sequencing, this study achieved species-level resolution, identifying Vibrio alginolyticus (a known pathogen) alongside putative beneficial taxa such as Ruegeria conchae, R. arenilitoris, Demequina litorisediminis, and D.globuliformis, which were not captured in earlier amplicon-based studies. Diversity analysis demonstrated that, rather than loss of species, substantial restructuring in the form of abundance was observed between healthy and WSSV-infected shrimp, while the overall evenness of the community remained stable. Concurrently, WSSV-infection has triggered an increased abundance of core opportunistic pathogens, namely, Photobacterium damselae and V. alginolyticus, which clustered distinctly from putative beneficial taxa such as Ruegeria and Demequina species, reflecting a clear microbial imbalance. Collectively, these findings demonstrated that mortality in WSSV-infected shrimp is associated with dysbiosis characterized by a depletion of beneficial taxa and concomitant abundance of opportunistic pathogens. These insights provide a basis for developing targeted probiotic or therapeutic strategies to mitigate pathogen overgrowth.
Physiological and transcriptomic responses of the gills in Gymnocypris eckloni under acute and chronic hypoxia stress.
Wu S, Xia M, Wang Z … +6 more , Liu D, Wang W, Zhang C, Jia J, Tian F, Qi D
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41996822 · Publisher ↗
With the intensification of global warming and environmental pollution, hypoxia is an unavoidable environmental factor in aquatic ecosystems and has multiple adverse effects on fish. Gymnocypris eckloni, a representative...
With the intensification of global warming and environmental pollution, hypoxia is an unavoidable environmental factor in aquatic ecosystems and has multiple adverse effects on fish. Gymnocypris eckloni, a representative species of the Qinghai-Tibetan Plateau, exhibits excellent adaptability to hypoxic environments, however, little is known about the hypoxic adaptation mechanisms of G. eckloni. Herein, effects of acute hypoxia for 12 h (H12S) and chronic hypoxia for different durations (H24S, H96S and H168S) on biochemical parameters and transcriptome of G. eckloni gills were investigated. We found that the gills suffered severe oxidative damage and increased anaerobic glycolysis was observed across all groups, and aerobic glycolysis was elevated in H12S. Inflammatory response, apoptosis and translation process were markedly suppressed, and signal transmission and protein synthesis process were strengthened under acute hypoxia stress. Through STEM and WGCNA, we identified several key hub genes (egln, akt, pdk1, foxo1, pfk, gapdh, gk, bax, casp8, il-8 and il-1β) related to hypoxia from 3608 DEGs, and expression of akt, gk, sdh, gapdh and ldh was significantly upregulated under hypoxia stress, and sod1, cat, bax, casp8 and ccl8 showed an opposite trend. Enrichment analysis revealed that most DEGs were significantly enriched in MAPK signaling pathway, cytokine-cytokine receptor interaction, FoxO signaling pathway, mTOR signaling pathway, glycolysis/gluconeogenesis and apoptosis. The study revealed the differences in the molecular mechanisms of G. eckloni in responding to acute and chronic hypoxia stress, and provided valuable genetic resources for breeding hypoxic-tolerant fish.
Genome-wide in silico identification and characterization of the F-box gene family in water buffalo (Bubalus bubalis).
Nasir T, Safdar M, Imran S … +4 more , Tariq M, Junejo Y, Ozaslan M, Younus M
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41990482 · Publisher ↗
F-box proteins serve as substrate adapters in SCF ubiquitin ligase complexes, regulating proteolysis to modulate eukaryotic signaling, such as cell cycle progression and stress responses. Here, we characterize the F-box...
F-box proteins serve as substrate adapters in SCF ubiquitin ligase complexes, regulating proteolysis to modulate eukaryotic signaling, such as cell cycle progression and stress responses. Here, we characterize the F-box gene family in water buffalo (Bubalus bubalis), identifying 70 genes across 24 autosomes and the X chromosome using HMMER and BLASTP searches against Pfam domains. Phylogenetic analysis with orthologs from human, sheep, goat, horse, and cattle grouped them into four subfamilies (FBX, FBXL, FBXW, FBXO), with 58 core buffalo genes aligning closely to mammalian clades (bootstrap >95%). MEME analysis identified nine conserved motifs, including the F-box domain (motifs 1-2, e.g., LPDELLLYIFSYLDA), LRRs for specificity (motif 3), and WD40 repeats for scaffolding (motifs 5-7,9), confirmed by Pfam. Gene structures ranged from 2 to 23 exons, indicating regulatory diversity. Synteny with cattle conserved ∼85% of orthologs, reflecting artiodactyl ancestry. Physicochemical properties spanned MW 18.10-93.71 kDa (mean 49.2 kDa, excluding outliers), pI 4.27-10.41, and GRAVY -0.75 to 0.143 (mean - 0.32), consistent with hydrophilic profiles. Five segmental duplications (e.g., FBXO25/FBXO32) showed Ka/Ks ratios of 0.144-1.194 (four <1), suggesting purifying selection and divergence 48-220 MYA (Ks Poisson correction, refined ruminant rate). nsSNP analysis in 70 genes via nine tools predicted >95% benign/synonymous effects, with deleterious exceptions like FBXO16 V160T (consensus score 0.82, disrupting binding) and FBXO48 R7G (0.91, affecting stability). WoLF PSORT localized 17 nuclear, 10 cytoplasmic, 12 plasma membrane, 7 mitochondrial, 5 extracellular, and 7 dual sites, implying roles in transcription, degradation, and trafficking. These genes may represent potential candidates for future functional studies and genome-editing approaches; however, experimental validation will be required before their application in breeding programs.
Differential activation and gene-coupled transcriptional dynamics of transposable elements during Piscirickettsiosis in Atlantic salmon.
Madrid F, Bravo S, Lopez I … +6 more , Jofre C, Moya J, Guttler V, Hinostroza F, Guzman O, Vidal R
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41985373 · Publisher ↗
Transposable elements (TE) are increasingly recognized as dynamic regulatory components of vertebrate genomes, particularly under stress and disease conditions. However, their transcriptional role during bacterial infect...
Transposable elements (TE) are increasingly recognized as dynamic regulatory components of vertebrate genomes, particularly under stress and disease conditions. However, their transcriptional role during bacterial infections in teleost fish remains largely unexplored. Here, we performed a genome-wide analysis of TE expression in Atlantic salmon using RNA-seq datasets derived from head kidney tissue of control and Piscirickettsia salmonis-infected individuals. A curated species-specific TE library comprising 1641 consensus sequences was constructed to ensure intergenic accurate annotation and quantification. We identified widespread TE transcriptional activity, with 4550 locus-specific differentially expressed TEs, of which 84.35% were upregulated in infected fish. DNA transposons (Class II), particularly TIR elements, represented the largest fraction of upregulated loci. Importantly, 84 TE-gene pairs exhibited significant expression coupling, predominantly showing positive correlations. Functional enrichment of associated genes revealed overrepresentation of metabolic and immune-related pathways. These findings reveal extensive TE transcriptional activation during bacterial infection in Atlantic salmon and suggest coordinated TE-gene expression dynamics as part of the host response. Although causal regulatory relationships cannot be inferred from correlation-based analyses alone, this study provides a quantitative framework for investigating mobilome dynamics during host-pathogen interactions in salmonids.
Microbiome and multi-omics insights into sustainable aquaculture: A triennial systematic review.
Okoye CO, Okoye KC, Ezenwanne BC … +7 more , Olalowo OO, Andong FA, Echude D, Chukwudozie KI, Emencheta SC, Ezeonyejiaku CD, Ikele CB
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41967167 · Publisher ↗
Aquaculture is the fastest-growing food production sector, yet intensive practices drive disease outbreaks, antibiotic resistance, and environmental degradation, threatening long-term sustainability. The aquaculture micr...
Aquaculture is the fastest-growing food production sector, yet intensive practices drive disease outbreaks, antibiotic resistance, and environmental degradation, threatening long-term sustainability. The aquaculture microbiome, encompassing host-associated and environmental microbial communities, regulates nutrient cycling, pathogen suppression, immunity, and overall system resilience. This triennial systematic review (2023-2025), conducted according to PRISMA guidelines, synthesized 19 highly relevant peer-reviewed studies that applied multi-omics approaches (metagenomics, transcriptomics, metabolomics, SNP genotyping, and their integration) to aquaculture microbiomes across shrimp, finfish, and hybrid species. The studies collectively revealed diverse host-microbe-metabolite interactions underpinning growth, immunity, and disease resistance, with representative examples including microbial-metabolite-host signaling axes and microbiome-mediated immune modulation, as seen in Salinivibrio-AMP-mTOR axis, EHP-resistant shrimp via metabolic reprogramming and stable microbiota, and Bacillus-mediated diglyceride production. Beneficial taxa such as Cetobacterium and Salinivibrio, heritable microbiome traits, and sustainable interventions including insect-meal feeds, phytogenic additives, and organic copper consistently improved growth, immunity, and microbial stability while reducing dysbiosis under stress. Environmental stressors and pathogens induced reproducible shifts in microbial diversity, functional pathways, and host metabolism. These findings demonstrate that multi-omics integration is transforming aquaculture into a precision discipline, enabling microbiome-informed selective breeding, targeted probiotics, and environmentally sound nutrition. To translate these insights into practice, future research must emphasize functional validation, machine learning-driven predictive models, and ecosystem-level assessments to achieve resilient, antibiotic-reduced, and sustainable aquaculture systems.
Transcriptomic insights into myogenic differentiation using muscle-derived cell lines with distinct myogenic potentials from black sea bream (Acanthopagrus schlegelii).
Han DH, Jeong ES, Kang CW … +1 more , Gong SP
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41967166 · Publisher ↗
Skeletal muscle growth is a primary determinant of aquaculture productivity, yet the molecular mechanisms governing myogenesis in black sea bream (Acanthopagrus schlegelii) remain poorly characterized due to the lack of...
Skeletal muscle growth is a primary determinant of aquaculture productivity, yet the molecular mechanisms governing myogenesis in black sea bream (Acanthopagrus schlegelii) remain poorly characterized due to the lack of precise in vitro models. In this study, we performed a comparative transcriptomic analysis using two validated muscle-derived cell lines with distinct myogenic potentials, including one capable of forming myotubes (myogenic) and the other incapable of differentiation (non-myogenic), to isolate the core transcriptional signature of differentiation. Using a subtractive screening strategy, we identified 391 upregulated and 275 downregulated genes specifically driving the myogenic program. Functional enrichment analysis revealed that differentiation is orchestrated by a synchronized dual program: the vigorous activation of 'ECM-receptor interaction', 'focal adhesion', and 'sarcomere organization', coupled with the strategic suppression of 'metabolic pathways' and 'growth factor binding'. Specifically, Col1a1, Comp, and Thbs2a were identified as Representative Overlap Genes (ROGs), highlighting the critical role of matrix remodeling and cell-matrix interactions in supporting myoblast fusion. In parallel, the downregulation of the IGF signaling axis and autophagy-related genes indicated a metabolic shift from proliferation-driven biomass accumulation to energy-efficient tissue remodeling. The reliability of these transcriptomic profiles was confirmed by the high concordance of qRT-PCR validation for key structural (Col4a1, Itga6a, Mylpfb, Thbs2a) and metabolic (Acss2l, Pfkfb3) regulators. This study provides the first comprehensive transcriptomic framework for black sea bream myogenesis, offering robust molecular markers and foundational data for advancing aquaculture biotechnology and cellular agriculture applications.
Comparative transcriptomic analysis of AMPK function in lung tissues of yaks and cattle at the same altitude.
Zhang X, Ding W, Wang H … +3 more , Li J, Chen J, Wei Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41967165 · Publisher ↗
AMP-activated protein kinase (AMPK) serves as a crucial energy sensor, maintaining organismal energy homeostasis through the regulation of diverse metabolic pathways. However, the association between the AMPK signaling p...
AMP-activated protein kinase (AMPK) serves as a crucial energy sensor, maintaining organismal energy homeostasis through the regulation of diverse metabolic pathways. However, the association between the AMPK signaling pathway and hypoxia adaptation in yak lung tissue has not yet been elucidated. Consequently, this study focused on the lung tissues of yaks and cattle residing at the same altitude (2600 m). Morphological analysis demonstrated that, compared to cattle, yak lung tissue possessed significantly thicker alveolar septa (P < 0.05), a greater abundance of elastic fibers (P < 0.05), and a reduced blood-air barrier thickness (P < 0.05), suggesting substantial structural adaptations in the yak lung under identical altitudinal conditions. RNA-seq analysis identified 3684 genes with significant differential expression between yaks and cattle. KEGG pathway enrichment analysis showed significant enrichment for the AMPK signaling pathway under the "Environmental Information Processing" category, and Gene Set Enrichment Analysis (GSEA) further confirmed the activation of the AMPK signaling pathway in yak lung tissue. Despite qRT-PCR indicating reduced mRNA levels of key AMPK pathway genes (PRKAA1, PRKAA2, PRKAB1, PRKAG2) in yak lung tissue, Western blot analysis demonstrated a marked upregulation in the relative abundance of phosphorylated AMPK (P-AMPK α1 + α2), implying potential activation of the AMPK signaling pathway via phosphorylation in yak lung tissue. Further analysis of downstream gene expression within the AMPK signaling pathway indicated significant downregulation of genes associated with glucose metabolism (PCK2, G6PC1), lipid metabolism (FASN, ACACA), protein metabolism (MAPKAPK5, MTOR), cell proliferation and apoptosis (RPTOR, MTOR), and autophagy (TXNIP, NLRP3) in yak lung tissue. These findings suggest that, relative to cattle, the yak lung may adapt to hypoxic conditions by minimizing energy expenditure, suppressing aberrant cell proliferation, mitigating oxidative stress, and reducing inflammatory responses. In summary, the activation of the AMPK signaling pathway in yak lung tissue may play a crucial role in hypoxic adaptation by enhancing oxygen utilization and energy supply capacity.
Mechanisms by which α-ketoglutarate alleviates intestinal injury caused by carbonate-alkaline stress in crucian carp (Carassius auratus): Insights from metabolomics and microbiomics.
Liu Q, Wang J, Jin X … +5 more , Cheng H, Zhong G, Wu S, Yang Y, Sun Y
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41955839 · Publisher ↗
Carbonate alkalinity is a prevalent environmental stressor in inland waters and poses toxicological risks to aquatic organisms. While α-ketoglutarate (AKG) is known to alleviate the resulting intestinal injury in fish, i...
Carbonate alkalinity is a prevalent environmental stressor in inland waters and poses toxicological risks to aquatic organisms. While α-ketoglutarate (AKG) is known to alleviate the resulting intestinal injury in fish, its protective mechanisms remain unclear. Here, crucian carp (Carassius auratus) were exposed to carbonate-alkaline stress (20 and 40 mmol/L NaHCO) with or without exogenous AKG supplementation for 56 days. Histopathological examination, biochemical assays, 16S rRNA, and metabolomics were employed to investigate the effects of carbonate-alkaline stress on intestinal redox status, energy metabolism, and microbial community, and to evaluate the mitigating mechanism of exogenous AKG supplementation. Results indicated that carbonate-alkaline stress induced intestinal histopathological damage, with increased ROS and lipopolysaccharide, and decreased ATP levels. 16S rRNA sequencing revealed that carbonate-alkaline stress altered the gut microbial community, increasing Proteobacteria and decreasing Firmicutes abundance. Metabolomics indicated that energy pathways like glycolysis and TCA cycle were inhibited. Meanwhile, the activation of purine metabolism and inhibition of glutathione metabolism suggested intestinal redox imbalance. Notably, exogenous AKG supplementation alleviated these injuries. Metabolomics showed upregulation of key metabolites in glycolysis and TCA cycle, while abnormalities in purine and glutathione metabolism were mitigated. Additionally, the community structure shifted, decreasing Proteobacteria and increasing Firmicutes abundance. These findings indicate that carbonate-alkaline stress induces microbial dysbiosis and intestinal injury by disrupting energy and redox balance, a process mitigated by exogenous AKG supplementation which restores metabolic homeostasis. This study provides mechanistic insights into metabolic interventions alleviating intestinal toxicity under carbonate-alkaline stress and a theoretical basis for improving fish tolerance in carbonate-alkaline environments.
Density stress is associated with metabolic reprogramming underlying growth-related physiological adaptation in large yellow croaker (Larimichthys crocea): an integrated multi-omics analysis.
Jia S, Wang X, Lan T … +6 more , Ding J, Yang W, Meng R, Wu X, Zheng Z, Shen W
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41936320 · Publisher ↗
Stocking density is a key environmental stressor that influences growth performance and metabolic regulation in fish; however, the molecular mechanisms underlying density-dependent growth variation in large yellow croake...
Stocking density is a key environmental stressor that influences growth performance and metabolic regulation in fish; however, the molecular mechanisms underlying density-dependent growth variation in large yellow croaker (Larimichthys crocea) under recirculating aquaculture system (RAS) conditions remain poorly understood. In this study, we investigated the associations between density stress and changes in metabolic regulation and growth-related pathways in L. crocea using an integrated multi-omics approach. Fish were reared for 60 days at low, medium, and high final stocking densities of 7.02, 14.71, and 19.21 kg m, respectively. Integrated transcriptomic and metabolomic analyses of dorsal muscle revealed pronounced density-dependent metabolic remodeling. The greatest transcriptional divergence occurred between the medium- and high-density groups, whereas the most substantial metabolic differences were observed between the low- and high-density groups. Cross-omics analysis identified arginine and proline metabolism, as well as alanine, aspartate, and glutamate metabolism, as key pathways associated with changes in energy supply, anabolic processes, and nitrogen metabolism. High stocking density was associated with a shift toward immediate energy mobilization at the expense of structural maintenance and nitrogen homeostasis, whereas low stocking density showed metabolic instability and compensatory energy dissipation. In contrast, medium stocking density maintained coordinated regulation across these pathways, indicating greater metabolic efficiency. The expression patterns of key genes within these pathways were validated by quantitative real-time PCR. Collectively, these findings suggest that density-dependent differences in growth performance are associated with coordinated metabolic reprogramming in large yellow croaker, and highlight metabolic homeostasis as a key physiological factor associated with density-dependent growth outcomes under controlled RAS conditions.
Genome-wide association study reveals genetic loci associated with body shape related traits in Takifugu bimaculatus.
Zhao H, Wang L, Chang Y … +7 more , Liang S, Liang J, Liu H, Song A, Li L, Guo Y, Zhou Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41934866 · Publisher ↗
The twospot puffer (Takifugu bimaculatus) is a species of significant aquacultural value in East Asia, yet its production is constrained by slow growth rates and suboptimal body morphology. To advance genetic enhancement...
The twospot puffer (Takifugu bimaculatus) is a species of significant aquacultural value in East Asia, yet its production is constrained by slow growth rates and suboptimal body morphology. To advance genetic enhancement via marker-assisted selection, we conducted a genome-wide association study (GWAS) focusing on traits related to body shape. Utilizing a full-sib family comprising 167 individuals to reduce genetic variability, we employed whole-genome resequencing to identify 122,553 high-quality (SNPs) for association analysis. Our study identified 17 significant and suggestive SNP loci correlated with torso length (TL), body depth (BD), body width (BWI), head length (HL) and tail length (TAL). Functional annotation of surrounding genomic regions revealed 26 candidate genes associated with these traits, including lrp8, kank4 for TL; tfrc, dab1 for BD; pgm1, cp, rala, and cdh7 for BWI; gli3, sox17a, and zip12 for HL; myl9, smurf2 for TAL. These genes were implicated in skeletal development, cell migration, metabolism, and BMP/TGF-β signaling pathways. Our findings offered the first genetic insights into body shape in T. bimaculatus and provided valuable SNP markers for future genetic mapping of body shape related traits in multi-line famlies and marker-assisted selection breeding programs.
Multi-omics analysis reveals polyethylene microplastics-induced gill damage, metabolic disruption and immune dysregulation in Lateolabrax maculatus.
Lin C, Gao M, Chen H … +4 more , Guo J, Zhang B, Lin J, Zhao C
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41926903 · Publisher ↗
Microplastics (MPs) are emerging environmental pollutants that can induce physiological toxicity in aquatic organisms. This study investigated the toxicological effects of dietary exposure to polyethylene microplastics (...
Microplastics (MPs) are emerging environmental pollutants that can induce physiological toxicity in aquatic organisms. This study investigated the toxicological effects of dietary exposure to polyethylene microplastics (PE-MPs) on gill tissues of Lateolabrax maculatus, using diets containing 0%, 4%, and 8% (w/w) PE-MPs. Histological, transcriptomic, and biochemical analyses were performed to assess structural damage, alterations in gene expression, and changes in antioxidant and immune parameters. Histological examination revealed structural abnormalities, including bending of gill lamellae and epithelial cell swelling, suggesting that gills may be sensitive to MP exposure. Transcriptomic analysis indicated that differentially expressed genes were enriched in pathways related to energy metabolism and immune response, including glycolysis/gluconeogenesis, oxidative phosphorylation, and phagosome. Key glycolytic enzymes (HK, PFK, PK) were upregulated, and the PPAR signaling pathway was activated, suggesting enhanced energy demands under stress conditions. Biochemical assays showed dynamic changes in antioxidant enzyme activities, with increased malondialdehyde (MDA) content in the high-concentration group, indicating oxidative stress. Immune-related genes associated with the NF-κB pathway (e.g., IL-1β, TNF-α) were upregulated, while TGF-β expression showed no significant changes. Following a 14-day depuration period without MP exposure, most antioxidant and immune parameters showed a trend toward recovery, indicating that the observed effects may be partially reversible. These findings suggest that MP exposure can contribute to gill structural impairment and perturbations in energy metabolism, redox homeostasis, and immune regulation in Lateolabrax maculatus, providing insights into the potential ecological risks of microplastic pollution in aquaculture environments.
The Tudor gene family in the Pacific oyster reveals conserved gonadal enrichment of germline-associated factors.
Zhou Y, Zhao X, Yu H … +1 more , Li Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41921263 · Publisher ↗
Tudor domain-containing proteins function as epigenetic readers by recognizing methylated arginine or lysine residues and are widely implicated in RNA metabolism and germ cell development across metazoans. However, the e...
Tudor domain-containing proteins function as epigenetic readers by recognizing methylated arginine or lysine residues and are widely implicated in RNA metabolism and germ cell development across metazoans. However, the evolutionary composition and expression characteristics of this protein group remain poorly understood in mollusks. In this study, we characterized Tudor domain-containing proteins in the Pacific oyster (Crassostrea gigas) and examined their evolutionary features and expression patterns. A total of 26 Tudor genes were identified, including 14 containing extended Tudor domains (eTudor) and 12 harboring traditional non-extended domains. These genes displayed uneven chromosomal distribution and lineage-specific patterns of gene duplication and loss when compared with homologs from vertebrates and insects. Transcriptomic analyses indicated nine Tudor genes exhibited pronounced gonad-biased expression, particularly in female gonads, with distinct temporal dynamics during gonad development. Notably, CgPhf1 showed marked stage-specific upregulation in female gonads. Expression trends of representative gonad-enriched genes were further supported by quantitative PCR analyses. Together, these results highlight the evolutionary diversification and gonadal association of Tudor domain-containing proteins in C. gigas, providing a comparative framework for understanding their potential roles in germline-related processes in non-model marine invertebrates.
Liver metabolomic analysis and expression under hypotonicity in American eel (Anguilla rostrata).
Huang L, Yüce PA, Liu Z … +4 more , Qi T, Wei S, Faggio C, Cao Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 41921262 · Publisher ↗
Proper freshwater acclimation is crucial in aquaculture settings to maximize survival. The present study examined the physiological and molecular responses of eels following transfer from seawater (SW, 35‰) to either SW...
Proper freshwater acclimation is crucial in aquaculture settings to maximize survival. The present study examined the physiological and molecular responses of eels following transfer from seawater (SW, 35‰) to either SW or freshwater (FW, 0‰). In SW, plasma ion concentrations and osmolality remained stable throughout the experimental period. In contrast, FW exposure induced a significant decline in plasma sodium, chloride, and osmolality between 12 and 72 h, after which levels stabilized by 96 h. Metabolic analysis revealed significant responses of FOXO and mTOR signaling pathways, as well as pathways related to membrane transporters, including aquaporins (AQPs), in FW-acclimated eels. Among AQP family members, AQP5 showed the highest hepatic expression. To explore upstream regulatory mechanisms, we quantified mRNA and protein expression of key components of the SRC-RAS-RAF-MEK-MAPK cascade. Transcript levels of all examined genes were significantly upregulated in FW compared to SW. Consistently, protein expression of SRC, MEK, and AQP5 was elevated in FW. These findings demonstrate that eels effectively acclimate to low-salinity environments by rapidly restoring ionic homeostasis within hours, accompanied by transcriptional and translational responses of MAPK signaling and AQP5 in the liver.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe