Transcriptomic and proteomic analyses of splenic immune mechanisms of rainbow trout (Oncorhynchus mykiss) infected by Aeromonas salmonicida subsp. salmonicida

Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations

Gene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In the present study, the pan-genome of rainbow trout was constructed based on 268 whole-genome re-sequencing accessions (4.38 Tb data). It recovered an additional 62 Mb sequences and 1288 protein-coding genes. Then, 9831 (22.77%) gene PAVs were genotyped across the 268 individuals. PAV-based PCA analysis, together with phylogenetic topology and STRUCTURE, revealed the clear separation among the different wild and selection populations. Additionally, a PAV-based genome-wide association study (GWAS) identified three candidate PAVs significantly associated with artificial selection. Meanwhile, fixation index analysis revealed 35 PAVs with significant frequency differences between wild and selection populations in Canada, while 15 candidate PAVs were detected between the populations in America. Their biological functions have been reported to participate in the regulation of growth performance and stress response. The present study deepens our understanding of widespread gene PAVs and facilitates the identification of key candidates that contribute to important traits.

Mucosal Exosome Proteomics of Hybrid Grouper Epinephelus fuscoguttatus♀ × E. lanceolatus♂ Infected by Pseudomonas plecoglossicida

Pseudomonas plecoglossicida infection, which causes visceral white spot disease, is a significant and economically devastating disease in aquaculture. In this study, we investigated the impact of bacterial infection on the protein composition of exosomes derived from the surface mucus of the hybrid grouper Epinephelus fuscoguttatus♀ × E. lanceolatus♂. Two hundred healthy fish were randomly separated into challenge and control groups. Fish from the challenge group received 103 CFU/g of the bacterial pathogen P. plecoglossicida via intraperitoneal injection, while sterile PBS was used as a negative control. After injection, the mucus was collected and the exosomes were extracted for proteomic analysis. The results of proteomic analysis revealed that P. plecoglossicida infection significantly increased the levels of innate immune proteins, including lysosomal and peroxisomal proteins, within the exosomes. Furthermore, the CAD protein was found to play a pivotal role in the protein interaction networks involved in the response to P. plecoglossicida infection. Intriguingly, we also observed a significant increase in the levels of metal-binding proteins within the exosomes, providing important evidence of nutritional immunity on the surfaces of the fish hosts. Notably, several proteins, such as plasma kallikrein, Annexin A5, eukaryotic translation initiation factor 3 subunit M, and S-methyl-5-thioadenosine phosphorylase, exhibited a remarkable increase in abundance in exosomes after infection. These proteins show promising potential as noninvasive biomarkers for the diagnosis of visceral white spot disease. The study contributes to the understanding of the host response to P. plecoglossicida infection and may aid policymakers in implementing appropriate intervention measures for effective risk management of this devastating disease.

Molecular and structural analyses of voltage-dependent anion channel 2 and its anti-apoptotic function in stress and pollutant resistance in Pacific abalone

This study aimed to identify voltage-dependent anion channel 2 (Hdh-VDAC2) and determine its functional role in response to acute thermal stress, H2O2-induced stress, heavy metal toxicity, bacterial and viral infections, and during metamorphosis. Structural analysis confirmed that Hdh-VDAC2 is a pore-forming β-barrel protein. Molecular docking further confirmed the protein-protein interactions of Hdh-VDAC2 with Hdh-BAX, Hdh-caspase 3, and Hdh-BCL2. In the Hdh-VDAC2-inhibited hemocytes (HCY), apoptotic genes (Hdh-caspase-3 and Hdh-BAX) exhibited elevated mRNA expression, while the anti-apoptotic gene (Hdh-BCL2) was downregulated. Further, fluorescent techniques confirmed excessive reactive oxygen species (ROS) production, lower cell viability, elevated caspase 3 activity, and increased DNA fragmentation in Hdh-VDAC2-inhibited HCY, indicating an anti-apoptotic role of Hdh-VDAC2 in Pacific abalone. Transcriptomic analysis revealed differential expression patterns, with upregulation in the digestive gland (DG) and downregulation in the gill (GIL) and HCY when comparing heat-tolerant (HT) versus heat-sensitive (HS) abalone groups. Additionally, both cold and heat stresses induced Hdh-VDAC2 expression. Other environmental factors including H2O2, cadmium, bacteria, and viruses, were also shown to induce Hdh-VDAC2 mRNA expression in the GIL and DG of Pacific abalone. During metamorphosis, the blastula (BLS) stage exhibited higher Hdh-VDAC2 mRNA expression. These findings suggest that Hdh-VDAC2 plays a crucial anti-apoptotic role and may be a biomarker for summer mortality in Pacific abalone.

Proteomic and Transcriptomic Profiling Revealed Vital Molecular Events in the Transition from Goat Colostrum to Mature Milk

As an important nutrient source in large areas of the world, goat milk is favored by more and more consumers; however, the composition, nutritional value, and regulation mechanism of goat milk are not fully characterized. Mammary gland development is as important as detailed annotation of protein composition to address the physiological and nutritional values of goat milk. In the present study, 4353 colostrum and mature goat milk proteins were identified. The abundance of 118 proteins was significantly different between colostrum and mature milk proteins. Our results indicate that the milk protein changes were associated with a network of mammary gene expression changes; importantly, the prime factors include enhanced mammary growth/development, decreased protein translation, attenuated protein folding, and lower lip/carbohydrate metabolism. The present study provides insights into the changes in mammary metabolisms during the transition from colostrum to mature milk, which can help deeply explore the difference and regulation mechanism of active milk protein in colostrum and mature milk and provide references for the identification and functional study of bioactive milk proteins in colostrum.

Proteomic map of the differentially expressed proteins in the skin of Ctenopharyngodon idella against Aeromonas hydrophila infection

The skin mucus of fish is an important part of the innate immune system, which is poorly understood at the proteomic level. The study established a complete map of the proteins in the skin mucus of Ctenopharangdon idella (C. idella) and discussed the Differentially Expressed Proteins (DEPs) after Aeromonas hydrophila (A. hydrophila) infection. Using Label Free Liquid Chromatography-Mass Spectrometry (LC-MS/MS) analysis, a total of 126 proteins were identified as differentially expressed, 89 proteins of which were upregulated, and 37 proteins were downregulated. Functional annotations of DEPs showed that the upregulated proteins in the skin mucus of the treated group were mostly associated with complement system and cytoskeleton proteins, whereas downregulated proteins were associated with metabolism. The key upregulated immune proteins were transferrin variant C, lysozyme g, annexin A11, 26S proteasome non-ATPase regulatory subunit 8, hypothetical protein ROHU_000884, 60S ribosomal L7a, calpain-2 catalytic subunit-like protein, calpain-9-like protein, complement component C9, complement C3, cathepsin S, cathepsin Z, 14 kDa apolipo, heat shock protein and intelectin, whereas, leukocyte elastase inhibitor, annexin A11, C-factor-like protein, biotinidase isoform X1 and epidermal growth factor receptor substrate 15-like were the downregulated proteins. Moreover, we for the first-time report proteins such as coactosin, lamin-B2 and kelch 12, which were never reported in fish. Our study directly pointing out the possible immunological biomarkers in the skin mucus of C. idella after A. hydrophila treatment. Each of the protein we report in this study could be used as base to establish their mechanism of action during bacterial infection that may contribute to the strategies against bacterial prevention and control in fishes.

Rapid adaptive and acute stimulatory responses to low salinity stress in Pacific white shrimp (Litopenaeus vannamei): Insights from integrative transcriptomic and proteomic analysis

The Pacific white shrimp (Litopenaeus vannamei) is a euryhaline crustacean capable of tolerating a wide range of ambient salinity, but the strategies of hepatopancreas to rapid adaptive or acute stimulatory responses to extremely low salinity fluctuations remains unclear. In this study, we integrated transcriptomic and proteomic analyses on the hepatopancreas derived from rapid adaptative (RA) and acute stimulatory (AS) responses to extremely low salinity stress (0.3 ppt) to unveil specific regulatory mechanisms. The RA group displayed normal epithelial cells and tubule structures, while the AS group showed histological changes and lesions. A total of 754 and 649 differentially expressed genes (DEGs) were identified in RA and AS treatments, respectively. For proteome, a total of 206 and 66 differentially expressed proteins (DEPs) were obtained in the RA/CT and AS/CT comparison groups, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted among the DEGs and DEPs, revealing that metabolic related pathways were significantly enriched pathways in both comparison groups. In addition, correlation analysis of transcriptomic and proteomic results showed that 20 and 3 pairs of DEGs/DEPs were identified in RA vs. CT and AS vs. CT comparison groups, respectively. This study is the first report on the rapid adaptive and acute stimulatory transcriptomic and proteomic responses of L. vannamei to extremely low salinity, shedding light on the mechanisms underlying osmoregulation in euryhaline crustaceans.

Plasma proteomic profiling of bacterial cold water disease-resistant and -susceptible rainbow trout lines and biomarker discovery

Genetic variation for disease resistance is present in salmonid fish; however, the molecular basis is poorly understood, and biomarkers of disease susceptibility/resistance are unavailable. Previously, we selected a line of rainbow trout for high survival following standardized challenge with Flavobacterium psychrophilum (Fp), the causative agent of bacterial cold water disease. The resistant line (ARS-Fp-R) exhibits over 60 percentage points higher survival compared to a reference susceptible line (ARS-Fp-S). To gain insight into the differential host response between genetic lines, we compared the plasma proteomes from day 6 after intramuscular challenge. Pooled plasma from unhandled, PBS-injected, and Fp-injected groups were simultaneously analyzed using a TMT 6-plex label, and the relative abundance of 513 proteins was determined. Data are available via ProteomeXchange, with identifier PXD041308, and the relative protein abundance values were compared to mRNA measured from a prior, whole-body RNA-seq dataset. Our results identified a subset of differentially abundant intracellular proteins was identified, including troponin and myosin, which were not transcriptionally regulated, suggesting that these proteins were released into plasma following pathogen-induced tissue damage. A separate subset of high-abundance, secreted proteins were transcriptionally regulated in infected fish. The highest differentially expressed protein was a C1q family member (designated complement C1q-like protein 3; C1q-LP3) that was upregulated over 20-fold in the infected susceptible line while only modestly upregulated, 1.8-fold, in the infected resistant line. Validation of biomarkers was performed using immunoassays and C1q-LP3, skeletal muscle troponin C, cathelcidin 2, haptoglobin, leptin, and growth and differentiation factor 15 exhibited elevated concentration in susceptible line plasma. Complement factor H-like 1 exhibited higher abundance in the resistant line compared to the susceptible line in both control and challenged fish and thus was a baseline differentiator between lines. C1q-LP3 and STNC were elevated in Atlantic salmon plasma following experimental challenge with Fp. In summary, these findings further the understanding of the differential host response to Fp and identifies salmonid biomarkers that may have use for genetic line evaluation and on-farm health monitoring.

An Outbreak of Aeromonas salmonicida in Juvenile Siberian Sturgeons (Acipenser baerii)

Aeromonas salmonicida is one of the major threats to world aquaculture, causing fish furunculosis and high mortality rates in cultured fish, particularly salmonids. Although Aeromonas spp. is a thoroughly studied pathogen, little is known regarding aeromoniasis in sturgeons. After a mortality outbreak, four juvenile sturgeons (Acipenser baerii) were submitted for autopsy and tissue samples were collected for histopathological and microbiological studies. The external examination revealed size heterogenicity, skin hyperpigmentation and reduced body condition of sturgeons. Within the abdominal cavity, mild hepatomegaly and splenomegaly were observed, as well as generalized organic congestion. Histology revealed severe multifocal haemorrhagic and ulcerative dermatitis, mainly localized in the dorsal and latero-ventral areas of fish. The histological study also showed moderate to severe inflammation of gills and organic lesions compatible with septicaemia. Bacterial isolates were identified as Aeromonas salmonicida subsp. salmonicida using MALDI-TOF MS and PCR. Overall, the lesions first described here are consistent with those previously reported in other cultured fish species and contribute to a better understanding of the pathogenesis of Aeromonas salmonicida subsp. salmonicida in the Siberian sturgeon, aside from providing new diagnostic tools for bacterial diseases impacting the fast-growing industry of caviar.

Proteomic analysis of liver tissue reveals Aeromonas hydrophila infection mediated modulation of host metabolic pathways in Labeo rohita

Aeromonas hydrophila (Ah) is a Gram-negative bacterium and a serious global pathogen causing Motile Aeromonas Septicaemia (MAS) in fish leading to global loss in aquaculture. Investigation of the molecular alterations of host tissues such as liver could be a powerful approach to identify mechanistic and diagnostic immune signatures of disease pathogenesis. We performed a proteomic analysis of Labeo rohita liver tissue to examine the protein dynamics in the host cells during Ah infection. The proteomic data was acquired using two strategies; discovery and targeted proteomics. Label-free quantification was performed between Control and challenged group (AH) to identify the differentially expressed proteins (DEPs). A total of 2525 proteins were identified and 157 were DEPs. DEPs include metabolic enzymes (CS, SUCLG2), antioxidative proteins, cytoskeletal proteins and immune related proteins (TLR3, CLEC4E). Pathways like lysosome pathway, apoptosis, metabolism of xenobiotics by cytochrome P450 were enriched by downregulated proteins. However, upregulated proteins majorly mapped to innate immune system, signaling of B cell receptor, proteosome pathway, ribosome, carbon metabolism and protein processing in ER. Our study would help in exploring the role of Toll-like receptors, C-type lectins and, metabolic intermediates like citrate and succinate in Ah pathogenesis to understand the Ah infection in fish. SIGNIFICANCE: Bacterial diseases such as motile aeromonas septicaemia (MAS) are among the most serious problems in aquaculture industry. Small molecules that target the metabolism of the host have recently emerged as potential treatment possibilities in infectious diseases. However, the ability to develop new therapies is hampered due to lack of knowledge about pathogenesis mechanisms and host-pathogen interactions. We examined alterations in the host proteome during MAS caused by Aeromonas hydrophila (Ah) infection, in Labeo rohita liver tissue to find cellular proteins and processes affected by Ah infection. Upregulated proteins belong to innate immune system, signaling of B cell receptor, proteosome pathway, ribosome, carbon metabolism and protein processing. Our work is an important step towards leveraging host metabolism in targeting the disease by providing a bigger picture on proteome pathology correlation during Ah infection.

Comparative study on antibacterial characteristics of the multiple liver expressed antimicrobial peptides (LEAPs) in teleost fish

Antimicrobial peptides are important components of the host innate immune system, forming the first line of defense against infectious microorganisms. Among them, liver-expressed antimicrobial peptides (LEAPs) are a family of antimicrobial peptides that widely exist in vertebrates. LEAPs include two types, named LEAP-1 and LEAP-2, and many teleost fish have two or more LEAP-2s. In this study, LEAP-2C from rainbow trout and grass carp were discovered, both of which are composed of 3 exons and 2 introns. The antibacterial functions of the multiple LEAPs were systematically compared in rainbow trout and grass carp. The gene expression pattern revealed that rainbow trout and grass carp LEAP-1, LEAP-2A, LEAP-2B and/or LEAP-2C were differentially expressed in various tissues/organs, mainly in liver. After bacterial infection, the expression levels of LEAP-1, LEAP-2A, LEAP-2B and/or LEAP-2C in the liver and gut of rainbow trout and grass carp increased to varying degrees. Moreover, the antibacterial assay and bacterial membrane permeability assay showed that rainbow trout and grass carp LEAP-1, LEAP-2A, LEAP-2B and LEAP-2C all have antibacterial activities against a variety of Gram-positive and Gram-negative bacteria with varying levels through membrane rupture. Furthermore, cell transfection assay showed that only rainbow trout LEAP-1, but not LEAP-2, can lead to the internalization of ferroportin, the only iron exporter on cell surface, indicating that only LEAP-1 possess iron metabolism regulation activity in teleost fish. Taken together, this study systematically compared the antibacterial function of LEAPs in teleost fish and the results suggest that multiple LEAPs can enhance the immunity of teleost fish through different expression patterns and different antibacterial activities to various bacteria.

Gilthead Seabream Liver Integrative Proteomics and Metabolomics Analysis Reveals Regulation by Different Prosurvival Pathways in the Metabolic Adaptation to Stress

The study of the molecular mechanisms of stress appraisal on farmed fish is paramount to ensuring a sustainable aquaculture. Stress exposure can either culminate in the organism's adaptation or aggravate into a metabolic shutdown, characterized by irreversible cellular damage and deleterious effects on fish performance, welfare, and survival. Multiomics can improve our understanding of the complex stressed phenotype in fish and the molecular mediators that regulate the underlying processes of the molecular stress response. We profiled the stress proteome and metabolome of Sparus aurata responding to different challenges common to aquaculture production, characterizing the disturbed pathways in the fish liver, i.e., the central organ in mounting the stress response. Label-free shotgun proteomics and untargeted metabolomics analyses identified 1738 proteins and 120 metabolites, separately. Mass spectrometry data have been made fully accessible via ProteomeXchange, with the identifier PXD036392, and via MetaboLights, with the identifier MTBLS5940. Integrative multivariate statistical analysis, performed with data integration analysis for biomarker discovery using latent components (DIABLO), depicted the 10 most-relevant features. Functional analysis of these selected features revealed an intricate network of regulatory components, modulating different signaling pathways related to cellular stress, e.g., the mTORC1 pathway, the unfolded protein response, endocytosis, and autophagy to different extents according to the stress nature. These results shed light on the dynamics and extent of this species' metabolic reprogramming under chronic stress, supporting future studies on stress markers' discovery and fish welfare research.

Differential gene expression of red-spotted grouper (Epinephelus akaara) in response to lipopolysaccharide, poly I:C, and nervous necrosis virus revealed by RNA-seq data

Red-spotted grouper (Epinephelus akaara) is a popular aquaculture species with high commercial value in the food industry. However, some infectious diseases may cause mass mortality in cultural practice. Therefore, it is important to understand the immune responses of red-spotted groupers upon pathogenic invasion to develop successful disease prevention mechanisms. Here, we analyzed the transcriptomic profiles of red-spotted grouper head kidney stimulated with lipopolysaccharide (LPS), polyinosinic:polycytidylic acid (poly I:C), and nervous necrosis virus (NNV) and identified differentially expressed genes (DEGs) using RNA-sequencing technology. Cluster analysis of the identified DEGs showed DEG distribution in nine separate clusters based on their expression patterns. However, significant upregulation of most DEGs was observed 6 h after poly I:C stimulation. The DEGs were functionally annotated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, which revealed significant expression of many immune-related signaling pathways, including antiviral, protein translation, cellular protein catabolic process, inflammatory responses, DNA repair, and cell division. Furthermore, selected DEGs were validated by quantitative real-time PCR, confirming the reliability of our findings. Collectively, this study provides insight into the immune responses of red-spotted groupers, thereby expanding the understanding of fish immunity.

Multi-Organ Transcriptome Response of Lumpfish (Cyclopterus lumpus) to Aeromonas salmonicida Subspecies salmonicida Systemic Infection

Lumpfish is utilized as a cleaner fish to biocontrol sealice infestations in Atlantic salmon farms. Aeromonas salmonicida, a Gram-negative facultative intracellular pathogen, is the causative agent of furunculosis in several fish species, including lumpfish. In this study, lumpfish were intraperitoneally injected with different doses of A. salmonicida to calculate the LD50. Samples of blood, head-kidney, spleen, and liver were collected at different time points to determine the infection kinetics. We determined that A. salmonicida LD50 is 102 CFU per dose. We found that the lumpfish head-kidney is the primary target organ of A. salmonicida. Triplicate biological samples were collected from head-kidney, spleen, and liver pre-infection and at 3- and 10-days post-infection for RNA-sequencing. The reference genome-guided transcriptome assembly resulted in 6246 differentially expressed genes. The de novo assembly resulted in 403,204 transcripts, which added 1307 novel genes not identified by the reference genome-guided transcriptome. Differential gene expression and gene ontology enrichment analyses suggested that A. salmonicida induces lethal infection in lumpfish by uncontrolled and detrimental blood coagulation, complement activation, inflammation, DNA damage, suppression of the adaptive immune system, and prevention of cytoskeleton formation.

Enhanced Hemolytic Activity of Mesophilic Aeromonas salmonicida SRW-OG1 Is Brought about by Elevated Temperatures

Aeromonas salmonicida is a well-known cold-water pathogenic bacterium. Previously, we reported the first isolation of pathogenic A. salmonicida from diseased Epinephelus coioides, a kind of warm-water fish, and it was proved to be a putative mesophilic strain with potent pathogenicity to humans. In order to investigate the mechanisms underlying mesophilic growth ability and virulence, the transcriptome of A. salmonicida SRW-OG1 at 18, 28, and 37 °C was analyzed. The transcriptome of A. salmonicida SRW-OG1 at different temperatures showed a clear separation boundary, which might provide valuable information for the temperature adaptation and virulence regulation of A. salmonicida SRW-OG1. Interestingly, aerA and hlyA, the hemolytic genes encoding aerolysin and hemolysin, were found to be significantly up-regulated at 28 and 37 °C. Since aerolysin and hemolysin are the most well-known and -characterized virulence factors of pathogenic Aeromonas strains, the induction of aerA and hlyA was associated with the mesophilic virulence. Further study proved that the extracellular products (ECPs) purchased from A. salmonicida SRW-OG1 cultured at 28 and 37 °C showed elevated hemolytic activity and virulence than those at 18 °C. Moreover, the silence of aerA and hlyA led to significantly decreased hemolysis and virulence. Taken together, our results revealed that the mesophilic virulence of A. salmonicida SRW-OG1 might be due to the enhanced expression of aerA and hlyA induced by elevated temperatures.

Proteomic Profiling Skin Mucus of European Eel Anguilla anguilla Infected with Anguillid Herpesvirus

Anguillid herpesvirus 1 (AngHV) is an important viral pathogen affecting eel. This study was designed to investigate the potential molecular mechanisms and immune response elicited at the protein levels in the skin mucus of AngHV-infected Anguilla anguilla. Tandem mass tag (TMT)-labelling proteomics with the liquid chromatography tandem mass spectrometry (LC-MS/MS) was used for performing quantitative identification of the proteins. In addition, the quantitative protein amount was detected by parallel reaction monitoring (PRM) analysis. A total of 3486 proteins were identified, of which 2935 were quantified. When a protein fold change was greater than 1.3 or less than 0.76, it indicated a differentially expressed protein (DEP). Overall, 187 up-regulated proteins and 126 down-regulated proteins were detected, and most of the DEPs were enriched in the CAMs pathway, intestinal immune pathway, herpes simplex virus 1 infection pathway, phagosome pathway and p53 signaling pathway. The results of the DEPs detected by PRM were highly consistent with the results of the TMT-labelled quantitative proteomic analysis. The findings of this study provide an important research basis for further understanding the pathogenesis of AngHV.

Time-course transcriptome analyses of spleen in rainbow trout (Oncorhynchus mykiss) post-Flavobacterium psychrophilum infection

Flavobacterium psychrophilum, the etiological agent of bacterial coldwater disease and rainbow trout fry syndrome, causes considerable losses in salmonid aquaculture globally. Systemic F. psychrophilum infections in rainbow trout (Oncorhynchus mykiss) lead to a range of clinical signs, including ulcerative lesions in the skin and muscle and splenitis. Previous studies offered an integrative analysis of the skeletal muscle response to F. psychrophilum infection in rainbow trout. However, little is known about the molecular mechanism of immune response in the spleen, which is an important immune organ of rainbow trout. Here, we investigated the time-course splenic transcriptome profiles in uninfected rainbow trout (CK) and F. psychrophilum–infected rainbow trout at day 3 and day 7 (D3, D7) by RNA-seq analyses. Among the 7,170 differentially expressed genes (DEGs) in the three comparisons (D3 vs. CK, D7 vs. CK, D3 vs. D7), 1,286 DEGs showed consistent upregulation or downregulation at D3 and D7 and were associated with pattern recognition, acute-phase response, complement cascade, chemokine and cytokine signaling, and apoptosis. The Real time quantitative PCR (RT-qPCR) analysis of eight DEGs confirmed the accuracy of the RNA-Sequencing (RNA-seq) data. Our results reflected a general process from pathogen recognition to inflammatory cytokine generation and delineated a putative Toll-like receptor signaling pathway in rainbow trout spleen, following F. psychrophilum infection. Taken together, these results provide new insights into the molecular mechanism of the immune response to F. psychrophilum infection and are a valuable resource for future research on the prevention and control of bacterial coldwater disease during salmon culture.

Proteomic analysis of carp seminal plasma provides insights into the immune response to bacterial infection of the male reproductive system

Aeromonas salmonicida is recognized as a significant bacterial pathogen in ulcerative disease of cyprinid fish. However, the mechanism of immunity to these bacteria in common carp is still not well understood, especially the immune regulation in the gonad to bacterial infection. The aims of our study were to analyze changes in the seminal plasma proteome following A. salmonicida infection in carp males. The observed pathological changes in the tissue (liver, spleen, kidney and testis) morphology and upregulation of immune-related genes (tnfa2, il6a) confirmed the successful infection challenge. Using mass spectrometry-based label-free quantitative proteomics, we identified 1402 seminal plasma proteins, and 44 proteins (20 up- and 24 downregulated) were found to be differentially abundant between infected and control males. Most differentially abundant proteins were involved in the immune response mechanisms, such as acute phase response, complement activation and coagulation, inflammation, lipid metabolism, cell-cell and cell-matrix adhesion, creatine-phosphate biosynthesis and germ cell-Sertoli cell junction signaling. Bacterial infection also caused profound changes in expression of selected genes in the testis and hematopoietic organs, which contributed to changes in seminal proteins. The altered seminal proteins and bacterial proteins in seminal plasma may serve as valuable markers of infection in the testis.

Identification, expression patterns, evolutionary characteristics and recombinant protein activities analysis of CD209 gene from Megalobrama amblycephala

CD209 is a type II transmembrane protein in the C-type lectin family, which is involved in the regulation of innate and adaptive immune system. Although it has been widely studied in mammals, but little has been reported about fish CD209 genes. In the present study, Megalobrama amblycephala CD209 (MaCD209) gene was cloned and characterized, its expression patterns, evolutionary characteristics, agglutinative and bacteriostatic activities were analyzed. These results showed that the open reading frame (ORF) of MaCD209 gene was 795 bp, encoding 264 aa, and the calculated molecular weight of the encoded protein was 29.7 kDa. MaCD209 was predicted to contain 2 N-glycosylation sites, 1 functional domain (C-LECT-DC-SIGN-like) and 1 transmembrane domain. Multiple sequence alignment showed that the amino acid sequence of MaCD209 was highly homologous with that of partial fishes, especially the highly conserved C-LECT-DC-SIGN-like domain and functional sites of CD209. Phylogenetic analysis showed that the CD209 genes from M. amblycephala and other cypriniformes fishes were clustered into one group, which was reliable and could be used for evolutionary analysis. Then, adaptive evolutionary analysis of teleost CD209 was conducted, and several positively selected sites were identified using site and branch-site models. Quantitative real-time PCR analysis showed that MaCD209 gene was highly expressed in the liver and heart. Moreover, the expression of MaCD209 was significantly induced upon Aeromonas hydrophila infection, with the peak levels at 4 h or 12 h post infection. The immunohistochemical analysis also revealed increased distribution of MaCD209 protein post bacterial infection. In addition, recombinant MaCD209 (rMaCD209) protein was prepared using a pET32a expression system, which showed excellent bacterial binding and agglutinative activities in a Ca²⁺-independent manner. However, rMaCD209 could only inhibit the proliferation of Escherichia coli rather than A. hydrophila. In conclusion, this study identified the MaCD209 gene, detected its expression and evolutionary characteristics, and evaluated the biological activities of rMaCD209 protein, which would provide a theoretical basis for understanding the evolution and functions of fish CD209 genes.

Comprehensive transcriptome profiling and functional analysis of the meagre (Argyrosomus regius) immune system

Meagre (Argyrosomus regius) belongs to the family Sciaenidae and is a promising candidate for Mediterranean aquaculture diversification. As a relatively recent species in aquaculture, the physiological consequences of the immune system activation in meagre are understudied. Spleen, as a primary lymphoid organ has an essential role in meagre immune and inflammatory responses. In this study, we have evaluated the in vivo effects of lipopolysaccharide (LPS) on the spleen transcriptome of meagre by RNA-seq analysis at 4 and 24 h after injection.

Transcriptional Signatures of Immune, Neural, and Endocrine Functions in the Brain and Kidney of Rainbow Trout (Oncorhynchus mykiss) in Response to Aeromonas salmonicida Infection

Rainbow trout (Oncorhynchus mykiss) serves as one of the most important commercial fish with an annual production of around 800,000 tonnes. However, infectious diseases, such as furunculosis caused by Aeromonas salmonicida infection, results in great economic loss in trout culture. The brain and kidney are two important organs associated with “sickness behaviors” and immunomodulation in response to disease. Therefore, we worked with 60 trout and investigated transcriptional responses and enrichment pathways between healthy and infected trout. We observed that furunculosis resulted in the activation of toll-like receptors with neuroinflammation and neural dysfunction in the brain, which might cause the “sickness behaviors” of infected trout including anorexia and lethargy. We also showed the salmonid-specific whole genome duplication contributed to duplicated colony stimulating factor 1 (csf-1) paralogs, which play an important role in modulating brain immunomodulation. Enrichment analyses of kidneys showed up-regulated immunomodulation and down-regulated neural functions, suggesting an immune-neural interaction between the brain and kidney. Moreover, the kidney endocrine network was activated in response to A. salmonicida infection, further convincing the communications between endocrine and immune systems in regulating internal homeostasis. Our study provided a foundation for pathophysiological responses of the brain and kidney in response to furunculosis and potentially offered a reference for generating disease-resistant trout strains.

Dual-Organ Transcriptomic Analysis of Rainbow Trout Infected With Ichthyophthirius multifiliis Through Co-Expression and Machine Learning

Ichthyophthirius multifiliis is a major pathogen that causes a high mortality rate in trout farms. However, systemic responses to the pathogen and its interactions with multiple organs during the course of infection have not been well described. In this study, dual-organ transcriptomic responses in the liver and head kidney and hemato-serological indexes were profiled under I. multifiliis infection and recovery to investigate systemic immuno-physiological characteristics. Several strategies for massive transcriptomic interpretation, such as differentially expressed genes (DEGs), Poisson linear discriminant (PLDA), and weighted gene co-expression network analysis (WGCNA) models were used to investigate the featured genes/pathways while minimizing the disadvantages of individual methods. During the course of infection, 6,097 and 2,931 DEGs were identified in the head kidney and liver, respectively. Markers of protein processing in the endoplasmic reticulum, oxidative phosphorylation, and the proteasome were highly expressed. Likewise, simultaneous ferroptosis and cellular reconstruction was observed, which is strongly linked to multiple organ dysfunction. In contrast, pathways relevant to cellular replication were up-regulated in only the head kidney, while endocytosis- and phagosome-related pathways were notably expressed in the liver. Moreover, interestingly, most immune-relevant pathways (e.g., leukocyte trans-endothelial migration, Fc gamma R-mediated phagocytosis) were highly activated in the liver, but the same pathways in the head kidney were down-regulated. These conflicting results from different organs suggest that interpretation of co-expression among organs is crucial for profiling of systemic responses during infection. The dual-organ transcriptomics approaches presented in this study will greatly contribute to our understanding of multi-organ interactions under I. multifiliis infection from a broader perspective.

Comprehensive analysis of transcriptomics and metabolomics to understand the flesh quality regulation of crucian carp (Carassius auratus) treated with short term micro-flowing water system

The short term micro-flowing purification system (STMFPS) has been shown to improve the flesh quality of freshwater fish. However, few studies have focused on the involved underlying mechanisms. This study explored the effect of STMFPS on the flesh quality of market-size freshwater fish based on the combination of metabolomics and transcriptomics methods. The UPLC-QTOF/MS based metabolomics method was utilized to screen metabolites and predict the possible major metabolic pathways during different STMFPS treatment periods (0 d, 1 d, 5 d and 9 d). Furthermore, the transcriptomic data demonstrated that the differentially expressed genes detected in crucian carp muscle were 2915, 7852 and 7183 after 1 d, 5 d and 9 d STMFPS treatment. Results showed that the TCA cycle, ornithine cycle, purine metabolism and amino acid catabolism play important roles in improving the flesh quality of crucian carp. This study may help to understand the mechanism of improving the flesh quality of aquatic products using STMFPS.

Proteomics of mucosal exosomes of Cynoglossus semilaevis altered when infected by Vibrio harveyi

The cargo of exosomes contains proteins with various functions, which might be promising biomarkers for disease diagnosis and prognosis. To explore the impact of the Vibrio harveyi pathogen on Cynoglossus semilaevis from a different perspective and develop promising biomarkers for infection, the exosomes from epidermal mucus of healthy controls（EC）and sick fish（ES）were extracted and identified, coupled with proteomic screening through iTRAQ followed with LC-MS/MS. 1531 credible proteins were obtained relating to structural, metabolic and immunological functions. 359 different expressed proteins (DEPs) (FC > 2 or FC < 0.5) were found, with 161 up-regulated and 198 down-regulated in ES. Based on the database of C. semilaevis on Uniprot, 71 proteins were characterized as concrete names, including 19 up-regulated proteins and 52 down-regulated proteins, and were selected as subjects for further studies. Ferritin, Toll-like receptor 5S protein and Calcium-transporting ATPase were upregulated, while Histone H2B and Eukaryotic translation initiation factor 5A were downregulated, consistent with the expression levels of related mRNAs in skin tissue verified by qRT-PCR. The integrated analysis between miRomics and proteomics also provided possible regulatory relationships mediated by mucous exosomes during infection. The signature proteins in mucosal exosomes could make sense in the explanation of the infection defending mechanism and the development of biomarkers which can differentiate diseased and healthy C. semilaevis individuals.

Identification and characterization of caspases genes in rainbow trout (Oncorhynchus mykiss) and their expression profiles after Aeromonas salmonicida and Vibrio anguillarum infection

Caspases are highly conserved cysteine-dependent aspartyl-specific proteases that play an important role in regulating cell death and inflammation. However, the caspase genes have not been systematically studied in rainbow trout (Oncorhynchus mykiss). Rainbow trout experienced 4 rounds (4R) of genome duplication in the evolutionary history. Thereby an increased numbers of paralogs are observed in trout, probably with more complicated gene functions. We identified 18 caspase genes in rainbow trout, including two inflammatory caspases (casp1a, casp1b), six apoptosis executioner caspases (casp3, casp3a1, casp3a2, casp3b, casp6, and casp7), nine apoptosis initiator caspases (casp2a, casp2b, casp8, casp9a, casp9b, casp10a, casp10b, casp20a, and casp20b) and one uncategorized caspase gene (casp17). To investigate the potentially physiological functions of caspase genes, we challenged the rainbow trout with Aeromonas salmonicida (A. salmonicida) and Vibrio anguillarum (V. anguillarum). Results showed that the CASP3-regulated intrinsic apoptosis was activated after A. salmonicida infection, while the CASP8 and CASP6-regulated extrinsic apoptosis exerted the greatest effect on trout challenged with V. anguillarum. In response to V. anguillarum infection, the data of RNA-Seq further showed the casp8 was tightly integrated with the significantly enriched Gene Ontology terms and functional pathways, including apoptosis regulation, pathogen detection and immunomodulation. Our study provides a foundation for the physiological functions and regulatory network of the caspase genes in teleosts.

Transcriptome profiling of immune response to Yersinia ruckeri in spleen of rainbow trout (Oncorhynchus mykiss)

BACKGROUND

Yersinia ruckeri is a pathogen that can cause enteric redmouth disease in salmonid species, damaging global production of economically important fish including rainbow trout (Oncorhynchus mykiss). Herein, we conducted the transcriptomic profiling of spleen samples from rainbow trout at 24 h post-Y. ruckeri infection via RNA-seq in an effort to more fully understand their immunological responses.

RESULTS

We identified 2498 differentially expressed genes (DEGs), of which 2083 and 415 were up- and down-regulated, respectively. We then conducted a more in-depth assessment of 78 DEGs associated with the immune system including CCR9, CXCL11, IL-1β, CARD9, IFN, TNF, CASP8, NF-κB, NOD1, TLR8α2, HSP90, and MAPK11, revealing these genes to be associated with 20 different immunological KEGG pathways including the Cytokine-cytokine receptor interaction, Toll-like receptor signaling, RIG-I-like receptor signaling, NOD-like receptor signaling, and MAPK signaling pathways. Additionally, the differential expression of 8 of these DEGs was validated by a qRT-PCR approach and their immunological importance was then discussed.

CONCLUSIONS

Our findings provide preliminary insight on molecular mechanism underlying the immune responses of rainbow trout following Y. ruckeri infection and the base for future studies of host-pathogen interactions in rainbow trout.

The Dynamic Immune Response of Yellow Catfish (Pelteobagrus fulvidraco) Infected With Edwardsiella ictaluri Presenting the Inflammation Process

Edwardsiella ictaluri is a highly destructive pathogen in cultured yellow catfish, thus it was very necessary to study the immune response of yellow catfish against bacterial infection. In this study, RNA-Seq technology was used to study the immune response in two distinct tissues of yellow catfish at eight different time points (h) after E. ictaluri infection. The number of differentially expressed genes (DEGs) in the spleen and liver was low at 3 h and 6 h post-infection, respectively. Afterwards, the most number of DEGs in the spleen was detected at 72 h, while the number of DEGs in the liver maintained a high level from 24 h to 120 h. The GO and KEGG enrichment analyses of DEGs at different time points uncovered that cytokines were continuously transcribed at 6 h to 120 h; whereas the liver is the main organ that secretes the components of the complement system, and metabolic regulation was activated from 12 h to 120 h. Moreover, an overview of the inflammation response of yellow catfish was exhibited including pattern-recognition receptors, inflammatory cytokines, chemokines, complements, and inflammation-related signal pathways. The similar expression tendency of nine genes by qRT-PCR validated the accuracy of transcriptome analyses. The different transcriptomic profiles obtained from the spleen and liver will help to better understand the dynamic immune response of fish against bacterial infection, and will provide basic information for establishing effective measures to prevent and control diseases in fish.

Environmental salinity influences the branchial expression of TCR pathway related genes based on transcriptome of a catadromous fish

Environmental salinity not only affects the physiological processes such as osmoregulation and hormonal control, but also changes the immune system in fishes. Studies are limited in fish on the roles of the T cell receptor (TCR)-related genes in relation to changes in environmental salinity. A large group of salinity-challenged transcripts was obtained in gills of marbled eel (Anguilla marmorata). Moreover, bioinformatic ways were used to identify the enriched TCR pathway related genes which were significantly different expressed in fresh water (FW), brackish water (BW) and seawater (SW). Meanwhile, the RT-qPCR results were validated and consistent with the RNA-seq results. TCR a, TCR b, CD45, CD28, PI3K, LCK and LAT were up-regulated when the salinity increases in BW and SW, which connected with the related signaling pathways (Ras-MAPK and PKC pathway). CD4 and Zap70 were down-regulated when the salinity increases in BW and SW, which connected with the PLC pathway. The research offers a novel viewpoint to explore the immune pathways including the TCR pathway in fish based on transcriptome.

Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective

One of the main constraints in aquaculture production is farmed fish vulnerability to diseases due to husbandry practices or external factors like pollution, climate changes, or even the alterations in the dynamic of product transactions in this industry. It is though important to better understand and characterize the intervenients in the process of a disease outbreak as these lead to huge economical losses in aquaculture industries. High-throughput technologies like proteomics can be an important characterization tool especially in pathogen identification and the virulence mechanisms related to host-pathogen interactions on disease research and diagnostics that will help to control, prevent, and treat diseases in farmed fish. Proteomics important role is also maximized by its holistic approach to understanding pathogenesis processes and fish responses to external factors like stress or temperature making it one of the most promising tools for fish pathology research.

The immune response of a warm water fish orange-spotted grouper (Epinephelus coioides) infected with a typical cold water bacterial pathogen Aeromonas salmonicida is AhR dependent

The present study reported the first pathogenic Aeromonas salmonicida (SRW-OG1) isolated from the warm water fish orange-spotted grouper (Epinephelus coioides), and investigated the function of Aryl hydrocarbon receptor (AhR), a ligand-dependent transcriptional factor which has been recently found to be closely associated with immune response in mammals and E. coioides. Our results showed that AhR was activated by an unknown ligand in the spleen, intestine and macrophages. Meanwhile, ahr1a and ahr1b were significantly increased in the spleen, intestine and macrophages, whereas ahr2 was only increased in the intestine, which indicated that the contribution of AhR2 to the immune response may be less than that of AhR1a and AhR1b. Some key genes involved in the macrophage inflammatory response, bacterial recognition, and intestinal immunity were significantly up-regulated in the SRW-OG1 infected E. coioides. Nevertheless, declining macrophage ROS production and down-regulation of related genes were also observed, suggesting that SRW-OG1 utilized its virulence mechanisms to prevent macrophage ROS production. Furthermore, AhR inhibitor 3', 4'-DMF and the silence of ahr1a or ahr1b significantly rescued the increased IL-1β and IL-8 induced by SRW-OG1 infection, which proved that the induction of IL-1β and IL-8 in E. coioides macrophages was mediated by AhR. However, BPI/LBP, ROS production and related genes were not affected by AhR. The survival rate and immune escape rate of SRW-OG1 in the ahr1a/ahr1b knocked-down and 3', 4'-DMF treated macrophages were significantly increased compared with those in wild type macrophages. Taken together, it was preliminarily confirmed that ahr1a and ahr1b played an important role in the immune response against A. salmonicida SRW-OG1.

Complement proteins detected through iTRAQ-based proteomics analysis of serum from black carp Mylopharyngodon piceus in response to experimentally induced Aeromonas hydrophila infection

The black carp Mylopharyngodon piceus is one of the culturally important '4 famous domestic fishes' in China. Recently, infectious diseases caused by Aeromonas hydrophila have drastically altered the operation of the black carp farming industry. In the present study, isobaric tags for relative and absolute quantitation (iTRAQ) were combined with mass spectrometry analysis to screen for differentially abundant black carp serum proteins in response to experimentally induced A. hydrophila infection. A total of 86 differentially abundant proteins were quantified at 24 h post-infection, including 78 down-regulated proteins and 8 up-regulated proteins. The down-regulated proteins included complement C1q subcomponent subunit C, complement factor B/C2A, complement factor B/C2B, complement C3-Q1, complement C3, and complement C4-2. Bioinformatic analysis indicated that the differentially abundant proteins were mainly associated with complement and coagulation cascades (27.9%). Moreover, real-time PCR (qPCR) analysis revealed changes in the gene expression of both C3 and B/C2A in blood cells, liver, kidney, gills, and intestines of the black carp infected with A. hydrophila. However, mRNA expression levels did not consistently correlate with the corresponding protein levels. A polyclonal antibody was prepared using a synthetic C3 peptide. Immunofluorescence analysis showed that the expression of C3 in the kidney was increased with A. hydrophila infection. This work provides a useful characterization of the impact of A. hydrophila infection on the complement system of the black carp.

OMICs Approaches in Diarrhetic Shellfish Toxins Research

Diarrhetic shellfish toxins (DSTs) are among the most prevalent marine toxins in Europe's and in other temperate coastal regions. These toxins are produced by several dinoflagellate species; however, the contamination of the marine trophic chain is often attributed to species of the genus Dinophysis. This group of toxins, constituted by okadaic acid (OA) and analogous molecules (dinophysistoxins, DTXs), are highly harmful to humans, causing severe poisoning symptoms caused by the ingestion of contaminated seafood. Knowledge on the mode of action and toxicology of OA and the chemical characterization and accumulation of DSTs in seafood species (bivalves, gastropods and crustaceans) has significantly contributed to understand the impacts of these toxins in humans. Considerable information is however missing, particularly at the molecular and metabolic levels involving toxin uptake, distribution, compartmentalization and biotransformation and the interaction of DSTs with aquatic organisms. Recent contributions to the knowledge of DSTs arise from transcriptomics and proteomics research. Indeed, OMICs constitute a research field dedicated to the systematic analysis on the organisms' metabolisms. The methodologies used in OMICs are also highly effective to identify critical metabolic pathways affecting the physiology of the organisms. In this review, we analyze the main contributions provided so far by OMICs to DSTs research and discuss the prospects of OMICs with regard to the DSTs toxicology and the significance of these toxins to public health, food safety and aquaculture.

Comparative Transcriptome Analysis of Gill Tissue in Response to Hypoxia in Silver Sillago (Sillago sihama)

Silver sillago (Sillago sihama) is a commercially important marine fish species in East Asia. In this study, we compared the transcriptome response to hypoxia stress in the gill tissue of S. sihama. The fish were divided into four groups, such as 1 h of hypoxia (hypoxia1h, DO = 1.5 ± 0.1 mg/L), 4 h of hypoxia (hypoxia4h, DO = 1.5 ± 0.1 mg/L), 4 h of reoxygen (reoxygen4h, DO = 8.0 ± 0.2 mg/L) after 4 h of hypoxia (DO = 1.5 mg/L), and normoxia or control (DO = 8.0 ± 0.2 mg/L) groups. Compared to the normoxia group, a total of 3550 genes were identified as differentially expressed genes (DEGs) (log₂foldchange > 1 and padj < 0.05), including 1103, 1451 and 996 genes in hypoxia1h, hypoxia4h and reoxygen4h groups, respectively. Only 247 DEGs were differentially co-expressed in all treatment groups. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, DEGs were significantly enriched in steroid biosynthesis, biosynthesis of amino acids, glutathione metabolism and metabolism of xenobiotics by cytochrome P450, ferroptosis and drug metabolism-cytochrome P450 pathways. Of these, the cytochrome P450 (CYP) and glutathione S-transferase (GST) gene families were widely expressed. Our study represents the insights into the underlying molecular mechanisms of hypoxia stress.

An iTRAQ-Based Comparative Proteomics Analysis of the Biofilm and Planktonic States of Aeromonas veronii TH0426

Aeromonas veronii is a virulent fish pathogen that causes extensive economic losses in the aquaculture industry worldwide. In this study, a virulent strain of A. veronii TH0426 was used to establish an in vitro biofilm model. The results show that the biofilm-forming abilities of A. veronii TH0426 were similar in different media, peaking under conditions of 20 °C and pH 6. Further, isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics methods were used to compare the differential expression of A. veronii between the biofilm and planktonic cells. The results show alterations in 277 proteins, with 130 being upregulated and 147 downregulated. Pathway analysis and GO (Gene Ontology) annotations indicated that these proteins are mainly involved in metabolic pathways and the biosynthesis of secondary metabolites and antibiotics. These proteins are the main factors affecting the adaptability of A. veronii to its external environment. MRM (multiple reaction 27 monitoring) and qPCR (qPCR) were used to verify the differential proteins of the selected A. veronii. This is the first report on the biofilm and planktonic cells of A. veronii, thus contributing to studying the infection and pathogenesis of A. veronii.

Transcriptome analysis and the effects of polyunsaturated fatty acids on the immune responses of the critically endangered angtze sturgeon (Acipenser dabryanus)

The poor understanding of nutrition needed has become a significant obstruction to artificial conservation of Yangtze sturgeon (Acipenser dabryanus) and the relationship between ployunsaturated fatty acid nutrition and the immune response of Yangtze sturgeon is remains unclear. To explore this relationship, the immune response was determined by the activities of serum immune-related enzymes and the transcriptome pattern in the spleen after feeding different fat source diets for 7 weeks. In addition, the gene expression pattern after a lipopolysaccharide (LPS) challenge was investigated in the presence of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Long-term feeding of the fish oil diets increased the serum immune-related enzyme activities, including lysozyme, acid phosphatase, and alkaline phosphatase of Yangtze sturgeon. More than 653,999 transcripts with an N50 length of 1047 bp were obtained and a final set of 280,408 unigenes was generated. After annotating the unigenes, 3549 genes were assigned to the immune system and 2839 were identified to participate in the response to the different fat sources. A transcriptome assay showed the fish oil diets moderately upregulated immune-related signaling pathways in the spleen of Yangtze sturgeon, including NLR signaling, platelet activation, Fc gamma R-mediated phagocytosis, Th17 cell differentiation, and Th1 and Th2 cell differentiation. The quantitative polymerase chain reaction (qPCR) results of candidate genes for these pathways showed similar results. The LPS challenge study revealed that DHA and EPA moderately upregulated the candidate immune-related genes and modulated excessive activation of the immune pathway by the pathogen. This study confirmed the immunomodulatory function of unsaturated fatty acids in Yangtze sturgeon. This research will provide a reference for the preparation of artificial diets for Yangtze sturgeon.

Integrating multi-omics and regular analyses identifies the molecular responses of zebrafish brains to graphene oxide: Perspectives in environmental criteria

With the broad application of nanoparticles, nanotoxicology has attracted substantial attention in environmental science. However, the methods for detecting few and targeted genes or proteins, even single omics approaches, may miss other responses, including the major responses induced by nanoparticles. To determine the actual toxicological mechanisms of zebrafish brains induced by graphene oxide (GO, a popular carbon-based nanomaterial applied in various fields) at nonlethal concentrations, multi-omics and regular analyses were combined. The biomolecule responses were remarkable, although GO was not obviously observed in brain tissues. The trends for gene and protein changes were the same and accounted for 3.53% and 5.36% of all changes in the genome and proteome, respectively, suggesting a limitation of single omics analysis. Transcriptomics and proteomics analyses indicated that GO affected the functions or pathways of the troponin complex, actin cytoskeleton, monosaccharide transmembrane transporter activity, oxidoreductase activity and focal adhesion. Both metabolomics and proteomics revealed mitochondrial dysfunction and disruption of the citric acid cycle. The integrated analysis of omics, transmission electron microscopy and immunostaining confirmed that GO induced energy disruptions and mitochondrial damage by downregulating tubulin. The combination of multi-omics and regular analyses provides insights into the actual and highly influential mechanisms underlying nanotoxicity.

Development of Teleost Intermuscular Bones Undergoing Intramembranous Ossification Based on Histological-Transcriptomic-Proteomic Data

Intermuscular bones (IBs) specially exist in lower teleost fish and the molecular mechanism for its development remains to be clarified. In this study, different staining methods and comparative proteomics were conducted to investigate the histological structure and proteome of IB development in Megalobrama amblycephala, including four key IB developmental stages (S1-IBs have not emerged in the tail part; S2-several small IBs started to ossify in the tail part; S3-IBs appeared rapidly; S4-all the IBs appeared with mature morphology). Alcian blue and alizarin red S stained results indicated that IBs were gradually formed from S2 to S4, undergoing intramembranous ossification without a cartilaginous phase. A total of 3368 proteins were identified by using the isobaric tags for relative and absolute quantitation (iTRAQ) approach. Functional annotation showed that proteins which were differentially expressed among stages were involved in calcium, MAPK, Wnt, TGF-β, and osteoclast pathways which played a critical role in bone formation and differentiation. Three proteins (collagen9α1, stat1, tnc) associated with chondrocytes did not exhibit significant changes through S2 to S4; however, proteins (entpd5, casq1a, pvalb, anxa2a, anxa5) which associated with osteoblasts and bone formation and differentiation showed significantly a higher expression level from S1 to S2, as well as to S3 and S4. These further demonstrated that development of IBs did not go through a cartilaginous phase. The inhibitors of TGF-β and Wnt pathways were tested on zebrafish (sp7/eGFP) and the results indicated that both inhibitors significantly delayed IB development. This study provides a comprehensive understanding of the IB ossification pattern, which will help further elucidate the molecular mechanisms for IB development in teleosts.

Proteomics for understanding pathogenesis, immune modulation and host pathogen interactions in aquaculture

Proteomic analyses techniques are considered strong tools for identifying and quantifying the protein contents in different organisms, organs and secretions. In fish biotechnology, the proteomic analyses have been used for wide range of applications such as identification of immune related proteins during infections and stresses. The proteomic approach has a significant role in understanding pathogen surviving strategies, host defence responses and subsequently, the fish pathogen interactions. Proteomic analyses were employed to highlight the virulence related proteins secreted by the pathogens to invade the fish host's defence barriers and to monitor the kinetics of protein contents of different fish organs in response to infections. The immune related proteins of fish and the virulence related proteins of pathogens are up or down regulated according to their functions in defence or pathogenesis. Therefore, the proteomic analyses are useful in understanding the virulence mechanisms of microorganisms and the fish pathogen interactions thereby supporting the development of new effective therapies. In this review, we focus and summarise the recent proteomic profiling studies exploring pathogen virulence activities and fish immune responses to stressors and infections.

Integrated analysis of proteomics and metabolomics reveals the potential sex determination mechanism in Odontobutis potamophila

Odontobutis potamophila is a valuable species for aquaculture in China, which shows asexually dimorphic growth pattern. In this study, the integrated proteomics and metabolomics were used to analyze the sex determination mechanism. A total of 2781 significantly different regulated proteins were identified by proteomics and 2693 significantly different expressed metabolites were identified by metabolomics. Among them, 2560 proteins and 1701 metabolites were significantly up-regulated in testes, whereas 221 proteins and 992 metabolites were significantly up-regulated in ovaries. Venn diagram analysis showed 513 proteins were differentially regulated at both protein and metabolite levels. Correlation analysis of differentially-regulated proteins and metabolites were identified by Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The results showed lipid metabolism plays an important role in sex determination. The metabolites decanoyl-CoA, leukotriene, 3-dehydrosphinganine, and arachidonate were the biomarkers in testes, whereas estrone and taurocholate were the biomarkers in ovaries. Interaction networks of the significant differentially co-regulated proteins and metabolites in the process of lipid metabolism showed arachidonic acid metabolism and steroid hormone biosynthesis were the most important pathways in sex determination. The findings of this study provide valuable information for selective breeding of O. potamophila. SIGNIFICANCE OF THE STUDY: The male O. potamophila grows substantially larger and at a quicker rate than the female. Thus, males have greater economic value than females. However, limited research was done to analyze the sex determination mechanism of O. potamophila, which seriously hindered the development of whole-male O. potamophila breeding. In this study, four key proteins (Ctnnb1, Piwil1, Hsd17b1, and Dnali1), six most important biomarkers (decanoyl-CoA, leukotriene, 3-dehydrosphinganine, arachidonate, estrone, and taurocholate) and two key pathways (arachidonic acid metabolism and steroid hormone biosynthesis) in sex determination of O. potamophila were found by integrated application of iTRAQ and LC-MS techniques. The results give valuable information for molecular breeding of O. potamophila in aquaculture.

A transcriptome analysis focusing on splenic immune-related mciroRNAs of rainbow trout upon Aeromonas salmonicida subsp. salmonicida infection

MicroRNAs (miRNAs) are a class of small non-coding RNAs that can regulate the immune responses during pathogen infection. Aeromonas salmonicida (A. salmonicida) subsp. salmonicida is the causative agent of furunculosis in salmon and trout. To identify the miRNAs and investigate the specific miRNAs in rainbow trout upon A. salmonicida subsp. salmonicida infection, we performed high throughput sequencing using the spleens of rainbow trout infected with and without an A. salmonicida subsp. salmonicida clinical isolate. A total of 381 known miRNAs and 926 novel miRNAs were identified. Eleven known and 16 novel miRNAs were found to be differentially expressed upon infection. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that the target genes of the differentially expressed miRNAs were closely associated with immune responses and biological regulations. Additionally, over- and suppressed expression of miR-155-5p significantly enhanced and reduced the IL-2 and IL-1β expressions in RTG-2 cells induced by A. salmonicida, respectively. To our knowledge, this is the first experimental study on the miRNAs of rainbow trout upon A. salmonicida infection. The results here might lay a foundation for the further understanding of the roles of miRNAs in the immune responses during A. salmonicida infection in rainbow trout.

Lipidomic alteration and stress-defense mechanism of soil nematode Caenorhabditis elegans in response to extremely low-frequency electromagnetic field exposure

To assess the impacts of man-made extremely low-frequency electromagnetic field (ELF-EMF) on soil ecosystems, the soil nematode was applied as a biological indicator to characterize ecotoxicity of ELF-EMF. In this paper, a soil-living model organism, Caenorhabditis elegans (C. elegans) was exposed to 50 Hz, 3 mT ELF-EMF. The integrated lipidome, proteome and transcriptome analysis were applied to elucidate physiological acclimations. Lipidomic analysis showed that ELF-EMF exposure induced significant alterations of 64 lipids, including significant elevation of triacylglycerols (TGs). Proteome results implied 157 changed protein expressions under ELF-EMF exposure. By transcriptomic analysis, 456 differently expressed genes were identified. Gene Ontology (GO) function and pathway analyses showed lipidomic alteration, mitochondrial dysfunction and the stress defense responses following ELF-EMF exposure in C. elegans. Conjoint analysis of proteome and transcriptome data showed that a higher expression of genes (sip-1, mtl-1 and rpl-11.1, etc.) were involved in stress defense responses to ELF-EMF exposure. These results indicated that ELF-EMF can induce effects on soil nematodes, mainly through disturbing lipid metabolism such as increasing TGs content, and eliciting stress defense responses. This study provided a new understanding in ELF-EMF exposure effects on soil nematodes and suggested a potential way of interpreting ELF-EMF influences on soil ecosystems.

iTRAQ analysis of liver immune-related proteins from darkbarbel catfish (Pelteobagrus vachelli) infected with Edwardsiella ictaluri

Edwardsiella ictaluri causes enteric septicemia of catfish (ESC), a major disease occurring in these siluriform fish. As the liver is an important organ for defending against bacterial pathogens in fish, this study aimed to determine the liver immune response at the protein level. The differential proteomes of the darkbarbel catfish liver in response to E. ictaluri infection were identified with isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using a 1.2-fold change in expression as a physiologically significant benchmark, a total of 819 differentially expressed proteins were reliably quantified using iTRAQ analysis, including 6 up-regulated proteins and 813 down-regulated proteins. GO enrichment analysis indicated that the "complement activation, alternative pathway" and "complement activation, classical pathway" were significantly enriched. KEGG enrichment analysis indicated the "antigen processing and presentation" and "bacterial secretion system" were significantly enriched. We selected the 6 up-regulated proteins and 10 immune-related down-regulated proteins for validation using real-time PCR. The 10 immune-related proteins included complement component C1r, C3, C5, C7, and C9 and plasma protease C1 inhibitor (C1-INH), signal recognition particle 54 kDa protein (SRP54), SRP receptor, proteasome activator complex subunit 1 (PSME1) and major histocompatibility complex class I (MHC class I) were selected from the GO clusters and KEGG pathways. The variations in mRNA expression for these genes were similar to the results of iTRAQ. This is the first report detailing the proteome response in the darkbarbel catfish liver during E. ictaluri infection and markedly contributes to our understanding of the defense mechanisms in the livers of darkbarbel catfish.

Comparative Study of Immune Reaction Against Bacterial Infection From Transcriptome Analysis

Transcriptome analysis is a powerful tool that enables a deep understanding of complicated physiological pathways, including immune responses. RNA sequencing (RNA-Seq)-based transcriptome analysis and various bioinformatics tools have also been used to study non-model animals, including aquaculture species for which reference genomes are not available. Rapid developments in these techniques have not only accelerated investigations into the process of pathogenic infection and defense strategies in fish, but also used to identify immunity-related genes in fish. These findings will contribute to fish immunotherapy for the prevention and treatment of bacterial infections through the design of more specific and effective immune stimulants, adjuvants, and vaccines. Until now, there has been little information regarding the universality and diversity of immune reactions against pathogenic infection in fish. Therefore, one of the aims of this paper is to introduce the RNA-Seq technique for examination of immune responses in pathogen-infected fish. This review also aims to highlight comparative studies of immune responses against bacteria, based on our previous findings in largemouth bass (Micropterus salmoides) against Nocardia seriolae, gray mullet (Mugil cephalus) against Lactococcus garvieae, orange-spotted grouper (Epinephelus coioides) against Vibrio harveyi, and koi carp (Cyprinus carpio) against Aeromonas sobria, using RNA-seq techniques. We demonstrated that only 39 differentially expressed genes (DEGs) were present in all species. However, the number of specific DEGs in each species was relatively higher than that of common DEGs; 493 DEGs in largemouth bass against N. seriolae, 819 DEGs in mullets against L. garvieae, 909 in groupers against V. harveyi, and 1471 in carps against A. sobria. The DEGs in different fish species were also representative of specific immune-related pathways. The results of this study will enhance our understanding of the immune responses of fish, and will aid in the development of effective vaccines, therapies, and disease-resistant strains.

Vaccine-Induced Protection Against Furunculosis Involves Pre-emptive Priming of Humoral Immunity in Arctic Charr

With respect to salmonid aquaculture, one of the most important bacterial pathogens due to high mortality and antibiotic usage is the causative agent of typical furunculosis, Aeromonas salmonicida spp. salmonicida (Asal). In Atlantic salmon, Salmo salar, the host response during infections with Asal is well-documented, with furunculosis outbreaks resulting in significant mortality in commercial settings. However, less is known about the host-pathogen interactions in the emerging aquaculture species, Arctic charr Salvelinus alpinus. Furthermore, there is no data on the efficacy or response of this species after vaccination with commonly administered vaccines against furunculosis. To this end, we examined the immunological response of S. alpinus during infection with Asal, with or without administration of vaccines (Forte Micro®, Forte Micro® + Renogen®, Elanco Animal Health). Artic charr (vaccinated or unvaccinated) were i.p.-injected with a virulent strain of Asal (10⁶ CFUs/mL) and tissues were collected pre-infection/post-vaccination, 8, and 29 days post-infection. Unvaccinated Arctic charr were susceptible to Asal with 72% mortalities observed after 31 days. However, there was 72–82% protection in fish vaccinated with either the single or dual-vaccine, respectively. Protection in vaccinated fish was concordant with significantly higher serum IgM concentrations, and following RNA sequencing and transcriptome assembly, differential expression analysis revealed several patterns and pathways associated with the improved survival of vaccinated fish. Most striking was the dramatically higher basal expression of complement/coagulation factors, acute phase-proteins, and iron hemostasis proteins in pre-challenged, vaccinated fish. Remarkably, following Asal infection, this response was abrogated and instead the transcriptome was characterized by a lack of immune-stimulation compared to that of unvaccinated fish. Furthermore, where pathways of actin assembly and FcγR-mediated phagocytosis were significantly differentially regulated in unvaccinated fish, vaccinated fish showed either the opposite regulation (ForteMicro®), or no impact at all (ForteMicro®Renogen®). The present data indicates that vaccine-induced protection against Asal relies on the pre-activation and immediate control of humoral immune parameters that is coincident with reduced activation of apoptotic (e.g., NF-κB) and actin-associated pathways.

Transcriptome analysis of the critically endangered Dabry's sturgeon (Acipenser dabryanus) head kidney response to Aeromonas hydrophila

Dabry's sturgeon (Acipenser dabryanus), as a living fossil, is considered a critically endangered aquatic animal in China. To date, the immune system of this species remains largely unknown, with limited available sequence information. In addition, increasing incidence of bacterial pathogenic diseases has been reported. Hence, the present study aimed to characterize comprehensively transcriptome profile of the head kidney from Dabry's sturgeon infected with Aeromonas hydrophila using Illumina platform. Over 42 million high-quality reads were obtained and de novo assembled into a final set of 195240 unique transcript fragments (unigenes), with an average length of 564 bp. Approximately 41702 unigenes were annotated in the NR NCBI database. Dabry's sturgeon unigenes had the highest number of hits with 14365 (34.45%) to Lepisosteus oculatus. The 195240 unigenes were assigned to three Gene Ontology (GO) categories: biological process, cellular component, and molecular function. Among them, 27770 unigenes were clustered into 26 Eukaryotic Orthologous Group (KOG) functional categories, and 36031 unigenes were mapped to 335 known Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. After A. hydrophila administration, 1728 differentially expressed unigenes were identified, including 980 upregulated and 748 downregulated unigenes. Further KEGG enrichment analysis of these unigenes identified 16 immune-related pathways, including the Toll-like receptor signaling pathway, chemokine signaling pathway, complement and coagulation pathway, RIG-I-like receptor signaling pathway, and NOD-like receptor signaling pathway. 20 DEGs were selected and their expression patterns are largely consistent with the transcriptome profile analysis, which clearly validated the reliability of the DEGs in transcriptome analysis. This work revealed novel gene expression patterns of Dabry's sturgeon host defense and contributes to a better understanding of the immune system and defense mechanisms of Dabry's sturgeon in response to bacterial infection. The results provide valuable references for studies in sturgeons that lack complete genomic sequences, and could also be helpful for the analyzing evolution among cartilaginous and teleost fish.

High-throughput proteomic profiling of the fish liver following bacterial infection

Background

High-throughput proteomics was used to determine the role of the fish liver in defense responses to bacterial infection. This was done using a rainbow trout (Oncorhynchus mykiss) model following infection with Aeromonas salmonicida, the causative agent of furunculosis. The vertebrate liver has multifaceted functions in innate immunity, metabolism, and growth; we hypothesize this tissue serves a dual role in supporting host defense in parallel to metabolic adjustments that promote effective immune function. While past studies have reported mRNA responses to A. salmonicida in salmonids, the impact of bacterial infection on the liver proteome remains uncharacterized in fish.

Results

Rainbow trout were injected with A. salmonicida or PBS (control) and liver extracted 48 h later for analysis on a hybrid quadrupole-Orbitrap mass spectrometer. A label-free method was used for protein abundance profiling, which revealed a strong innate immune response along with evidence to support parallel rewiring of metabolic and growth systems. 3076 proteins were initially identified against all proteins (n = 71,293 RefSeq proteins) annotated in a single high-quality rainbow trout reference genome, of which 2433 were maintained for analysis post-quality filtering. Among the 2433 proteins, 109 showed significant differential abundance following A. salmonicida challenge, including many upregulated complement system and acute phase response proteins, in addition to molecules with putative functions that may support metabolic re-adjustments. We also identified novel expansions in the complement system due to gene and whole genome duplication events in salmonid evolutionary history, including eight C3 proteins showing differential changes in abundance.

Conclusions

This study provides the first high-throughput proteomic examination of the fish liver in response to bacterial challenge, revealing novel markers for the host defense response, and evidence of metabolic remodeling in conjunction with activation of innate immunity.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5092-0) contains supplementary material, which is available to authorized users.

Proteome Profiles of Head Kidney and Spleen of Rainbow Trout (Oncorhynchus Mykiss)

The head kidney and spleen are major lymphoid organs of the teleost fish. The authors identify proteome profiles of head kidney and spleen of rainbow trout (Oncorhynchus mykiss) using a shotgun proteomic approach. Gene ontology annotation of proteins is predicted using bioinformatic tools. This study represents detailed proteome profiles of head kidney and spleen of rainbow trout, with a total of 3241 and 2542 proteins identified, respectively. It is found that lymphoid organs are equipped with a variety of functional proteins related to defense, receptor, signal transduction, antioxidant, cytoskeleton, transport, binding, and metabolic processes. The identified proteome profiles will serve as a template for understanding lymphoid organ functions in salmonids and will increase the amount of spectra information of rainbow trout proteins in the public data repository PRIDE. This data can be accessed via ProteomeXchange with identifiers PXD008473 and PXD008478.

Applications of transcriptomics and proteomics in understanding fish immunity

With the development of intensive aquaculture, economic losses increasingly result from fish mortality due to pathogen infection. In recent years, a growing number of researchers have used transcriptomic and proteomic analyses to study fish immune responses to exogenous pathogen infection. Integrating transcriptomic and proteomic analyses provides a better understanding of the fish immune system including gene expression, regulation, and the intricate biological processes underlying immune responses against infection. This review focuses on the recent advances in the fields of transcriptomics and proteomics, which have contributed to our understanding of fish immunity to exogenous pathogens.

Understanding the regulatory mechanisms of milk production using integrative transcriptomic and proteomic analyses: improving inefficient utilization of crop by-products as forage in dairy industry

BACKGROUND

Bovine milk is an important nutrient source for humans. Forage plays a vital role in dairy husbandry via affecting milk quality and quantity. However, the differences in mammary metabolism of dairy cows fed different forages remain elucidated. In this study, we utilized transcriptomic RNA-seq and iTRAQ proteomic techniques to investigate and integrate the differences of molecular pathways and biological processes in the mammary tissues collected from 12 lactating cows fed corn stover (CS, low-quality, n = 6) and alfalfa hay (AH, high-quality, n = 6).

RESULTS

A total of 1631 differentially expressed genes (DEGs; 1046 up-regulated and 585 down-regulated) and 346 differentially expressed proteins (DEPs; 138 increased and 208 decreased) were detected in the mammary glands between the CS- and AH-fed animals. Expression patterns of 33 DEPs (18 increased and 15 decreased) were consistent with the expression of their mRNAs. Compared with the mammary gland of AH-fed cows, the marked expression changes found in the mammary gland of CS group were for genes involved in reduced mammary growth/development (COL4A2, MAPK3, IKBKB, LGALS3), less oxidative phosphorylation (ATPsynGL, ATP6VOA1, ATP5H, ATP6VOD1, NDUFC1), enhanced lipid uptake/metabolism (SLC27A6, FABP4, SOD2, ACADM, ACAT1, IDH1, SCP2, ECHDC1), more active fatty acid beta-oxidation (HMGCS1), less amino acid/protein transport (SLC38A2, SLC7A8, RAB5a, VPS18), reduced protein translation (RPS6, RPS12, RPS16, RPS19, RPS20, RPS27), more proteasome- (PSMC2, PSMC6, PSMD14, PSMA2, PSMA3) and ubiquitin-mediated protein degradation (UBE2B, UBE2H, KLHL9, HSPH1, DNAJA1 and CACYBP), and more protein disassembly-related enzymes (SEC63, DNAJC3, DNAJB1, DNAJB11 and DNAJC12).

CONCLUSION

Our results indicate that the lower milk production in the CS-fed dairy cows compared with the AH-fed cows was associated with a network of mammary gene expression changes, importantly, the prime factors include decreased energy metabolism, attenuated protein synthesis, enhanced protein degradation, and the lower mammary cell growth. The present study provides insights into the effects of the varying quality of forages on mammary metabolisms, which can help the improvement of strategies in feeding dairy cows with CS-based diet.

Acute Heat Stress Changes Protein Expression in the Testes of a Broiler-Type Strain of Taiwan Country Chickens

Heat stress leads to decreased fertility in roosters. This study investigated the global protein expression in response to acute heat stress in the testes of a broiler-type strain of Taiwan country chickens (TCCs). Twelve 45-week-old roosters were randomly allocated to the control group maintained at 25°C, and three groups subjected to acute heat stress at 38°C for 4 h, with 0, 2, and 6 h of recovery, respectively. Testis samples were collected for hematoxylin and eosin staining, apoptosis assay, and protein analysis. The results revealed 101 protein spots that differed significantly from the control following exposure to acute heat stress. The proteins that were differentially expressed participated mainly in protein metabolism and other metabolic processes, responses to stimuli, apoptosis, cellular organization, and spermatogenesis. Proteins that negatively regulate apoptosis were downregulated and proteins involved in autophagy and major heat shock proteins (HSP90α, HSPA5, and HSPA8) were upregulated in the testes of heat-stressed chickens. In conclusion, acute heat stress causes a change in protein expression in the testes of broiler-type B strain TCCs and may thus impair cell morphology, spermatogenesis, and apoptosis. The expression of heat shock proteins increased to attenuate the testicular injury induced by acute heat stress.