Characteristics of cathepsin members and expression responses to poly I:C challenge in Pacific cod (Gadus macrocephalus)

Cathepsins are major lysosomal enzymes that participate in necessary physiological processes, including protein degradation, tissue differentiation, and innate or adaptive immune responses. According to their proteolytic activity, vertebrate cathepsins are classified as cysteine proteases (cathepsins B, C, F, H, K, L, O, S, V, W, and X or Z), aspartic proteases (cathepsin D and E), and serine proteases (cathepsin A and G). Several cathepsins were reported in teleosts, however, no cathepsin gene has been identified from Pacific cod so far. In the present study, a total of 13 cathepsin genes were identified for Pacific cod. The evolutionary path of each cathepsin gene was demonstrated via analysis of phylogenetic trees, multiple alignments, conserved domains, motif compositions, and tertiary structures. Tissue distribution analysis showed that all cathepsin genes were ubiquitously expressed in eight healthy tissues but they exhibited diverse levels of expression. Several cathepsin genes were found to be highly expressed in the kidney, spleen, head kidney and liver, whereas low or modest levels were detected in the gills, skin, intestines, and heart. Temporal-specific expression of cathepsins in early developmental stages of Pacific cod were also conducted. CTSK, S, F, and Z were highly expressed at 1 dph and 5 dph and decreased later, while CTSL, L1, and L.1 transcript levels gradually increased in a time-dependent manner. Additionally, the expression profiles of cathepsin genes in Pacific cod were evaluated in the spleen and liver after poly I:C challenge. The results indicated that all cathepsin genes were significantly upregulated upon poly I:C stimulation, suggesting that they play key roles in antiviral immune responses in Pacific cod. Our findings establish a foundation for future exploration of the molecular mechanisms of cathepsins in modulating antiviral immunity in Pacific cod.

Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change

Small and isolated peripheral populations, which are often remnants of glacial refugia, offer an opportunity to determine the magnitude and direction of fine-scale connectivity in high gene flow marine species. When located at the equatorial edge of a species' range, these populations may also harbor genetic diversity related to survival and reproduction at higher temperatures, a critical resource for marine species facing warming ocean temperatures. Pacific cod (Gadus macrocephalus), a marine fish in the North Pacific, has already experienced major shifts in biomass and distribution linked to climate change. We estimated the magnitude and direction of connectivity between peripheral populations of Pacific cod at the southern edge of the species' range, by conducting restriction site-associated DNA (RAD) sequencing and individual assignment on fish collected around the Korean Peninsula during the spawning season. Three populations on the western, eastern, and southern Korean coasts were highly differentiated (FST  = 0.025-0.042) and relatively small (Ne  = 433-1,777). Ten putative dispersers and estimates of contemporary migration rates revealed asymmetrical, west-to-east movement around the Korean Peninsula, at a higher rate than predicted by indirect estimates of connectivity (FST ). Allele frequencies at 87 RAD loci were decisively correlated with strong marine temperature gradients between the warmer southern coast and the cooler waters of the eastern and western coasts. Despite relatively small sample sizes, our data suggest asymmetrical dispersal and gene flow, potentially involving adaptive alleles, between peripheral populations inhabiting markedly different thermal regimes. Our study emphasizes the conservation value of peripheral populations in high gene flow marine fish species.

Evidence for selection and spatially distinct patterns found in a putative zona pellucida gene in Pacific cod, and implications for management

Genetic differentiation has been observed in marine species even when no obvious barriers to gene flow exist, and understanding such differentiation is essential for effective fisheries management. Highly differentiated outlier loci can provide information on how genetic variation might not only contribute to local adaptation but may also be affected by historical demographic events. A locus which aligned to a predicted zona pellucida sperm-binding protein 3 gene (ZP3) in Atlantic cod (Gadus morhua) was previously identified as the highest outlier based on F ST in a RADseq study of Pacific cod (Gadus macrocephalus) across the West Coast of North America. However, because of the limited length of the RAD sequence and restricted geographic area of sampling, no conclusion on the functional significance of the observed variation was possible. In other marine species, ZP3 is involved in reproductive isolation, local adaptation, and has neofunctionalized as an antifreeze gene, and so it may provide important insights in functional population structure of Pacific cod. Here, we sequenced a 544-bp region of ZP3 in 230 Pacific cod collected from throughout their geographic range. We observed striking patterns of spatial structuring of ZP3 haplotypes, with a sharp break near Kodiak, Alaska, USA where populations within ~200 km of each other are nearly fixed for different haplotypes, contrasting a pattern of isolation by distance at other genetic markers in this region (F ST = 0.003). Phylogenetic analysis of ZP3 haplotypes revealed that the more southern haplotypes appear to be ancestral, with the northern haplotype evolving more recently, potentially in response to a novel selective pressure as Pacific cod recolonized northern latitudes after glaciation. The sharp break in haplotype frequencies suggests strong selective pressures are operating on small spatial scales and illustrates that selection can create high divergence even in marine species with ample opportunities for gene flow.

Application of the Gadidae Fish Processing Waste for Food Grade Gelatin Production

Waste from fish cutting (heads, swim bladders, fins, skin, and bones) is a high-value technological raw material for obtaining substances and products with a wide range of properties. The possibility of using waste from cutting fish of the Gadidae family: the Alaska pollock (Gadus chalcogrammus) and the Pacific cod (Gadus macrocephalus), processed in the coastal zone, is scientifically substantiated. In this work, a technology has been developed for processing accumulated waste from fish cutting in order to obtain fish gelatin, which is characterized by high protein content (more than 80.0%) and a full set of essential and nonessential amino acids. We studied the quality of fish gelatin obtained from wastes from cutting the fish of the Gadidae family. The possibility of using fish gelatin as a component of fish products is shown; the dose of its introduction into the fish products is substantiated. The data obtained made it possible to recommend the use of fish processing waste products as a gelling component and a source of amino acids in multicomponent food systems.

Anisakis spp. in fishery products from Japanese waters: Updated insights on host prevalence and human infection risk factors

The nematodes of the genus Anisakis are among the most relevant parasitic hazards in fishery products since they are responsible for human infection and allergy cases. In a food safety and epidemiological perspective, several marine hosts from different locations around Japan were examined to characterize the parasitism of Anisakis larvae. Chum salmon (Oncorhynchus keta) and Alaska pollock (Gadus chalcogrammus) showed the highest overall prevalence (100%), followed by blue mackerel (Scomber australasicus) (97.5%), Pacific cod (Gadus macrocephalus) (80%), chub mackerel (Scomber japonicus) (60.1%), Japanese flying squid (Todarodes pacificus) (17%) and Japanese pilchard (Sardinops sagax melanostictus) (2%). In Pacific krill (Euphausia pacifica), apart from one Hysterothylacium aduncum larva, no Anisakis specimens were detected. Anisakis simplex sensu stricto was molecularly identified (PCR-RFLP) for the first time in Japanese flying squid and Japanese pilchard distributed in the Northwestern Pacific ocean. That was the most frequent parasitic species detected followed by A. pegreffii, mostly in the western areas of Japan, hybrid genotypes between the two sibling species as well as A. typica and A. berlandi. Surprisingly, A. simplex s.s. was the most abundant species in one batch of chub mackerel from the East China Sea and A. pegreffii was the main species found in one batch from the Pacific coast of Aomori, which seems to indicate that the ranges of these two sibling species might be more variable than previously thought.

Conserved function of Pacific cod Caspase-3 in apoptosis

Apoptosis plays a significant role in the cellular immune responses against infections, especially those related to viruses. Across various species, Caspase 3 is a prominent mediator of apoptosis and participates in the cell death signaling cascade. However, its role remains relatively unknown in cod fish. In this study, we aimed to reveal the role of Pacific cod Caspase-3 (GmCasp3) in apoptosis and its evolutionary position. Our results showed that the GmCasp3 cDNA contains an open reading frame of 864 nucleotides; that codes for 287 amino acids long protein with a molecular weight of 32.03 kDa. The sequence alignments and 3-D model indicated that GmCasp3 contained highly conserved domains, such as "QACRG", "GSWFI" and "HG" active sites, however, the phylogenetic tree analysis revealed that both GmCasp3 and Atlantic cod caspase-3 clustered together are far from the high vertebrate branch, indicating they are at a lower position in vertebrate evolution. Red fluorescent labeling vector pDsRed2-C1-GmCasp3 was constructed and it was transfected into EPC cell lines. The result showed that GmCasp3 protein was distribute in the protoplasm and expressed in apoptotic cell debris. Moreover, the GmCasp3 enzyme activity increased with the increased post-transfection analysis time, while the genome DNA was visibly fragmented at 36 h post transfection. Flow cytometry analysis showed that the proportion of apoptosis cells increased from 12 h to 24 h post transfection. In conclusion, the conserved functions of GmCasp3 in apoptosis indicated that Pacific cod has the similar apoptotic characteristics as other animals.

Molecular characterization and expression analysis of the interleukin 1b gene in Pacific cod (Gadus macrocephalus)

Interleukin 1b (IL-1b) is a member of the cytokine family that serves as major mediators for early pro-inflammatory responses. During artificial breeding of Pacific cod (Gadus macrocephalus), outbreaks of NNV in the early development stages could lead to high mortality. Recent research reported that IL-1b participated in the host-virus interaction against NNV infection, however, no IL-1b gene has been identified from Pacific cod so far. In this study, we described the identification and characterization of a IL-1b from Pacific cod transcriptome at both transcript and protein level. Sequence alignment and phylogenetic analysis were conducted to determine and confirm their evolutionary relationship. Expression analysis revealed that IL-1b was expressed in all tested tissues and the western blot analysis confirmed the same expression profiles using purified recombinant IL-1b protein. In addition, significant up-regulation was detected in IL-1b transcripts during early development stages at 30dph and 50dph. After challenged with poly I:C, IL-1b was significantly induced after 24 h. Taken together, these results strongly suggested that IL-1b might play an essential role in innate defense mechanism of Pacific cod.

Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod (Gadus macrocephalus)

The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation by distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction-site-associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation-by-distance signal along coastlines that mirrored previous microsatellite results and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea, with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coastal samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs. offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation by distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low FST marine species.

Ichthyophonus in sport-caught groundfishes from southcentral Alaska

This report of Ichthyophonus in common sport-caught fishes throughout the marine waters of southcentral Alaska represents the first documentation of natural Ichthyophonus infections in lingcod Ophiodon elongates and yelloweye rockfish Sebastes ruberrimus. In addition, the known geographic range of Ichthyophonus in black rockfish S. melanops has been expanded northward to include southcentral Alaska. Among all species surveyed, the infection prevalence was highest (35%, n = 334) in Pacific halibut Hippoglossus stenolepis. There were no gross indications of high-level infections or clinically diseased individuals. These results support the hypothesis that under typical conditions Ichthyophonus can occur at high infection prevalence accompanied with low-level infection among a variety of fishes throughout the eastern North Pacific Ocean, including southcentral Alaska.

Molecular characterization of caspase members and expression response to Nervous Necrosis Virus outbreak in Pacific cod

Multiple functions of caspases include normal cell turnover, proper development and function of the immune system, hormone-dependent atrophy, embryonic development and chemical-induced cell injury. During artificial propagation of Pacific cod, Gadus macrocephalus, high mortality occurred during early development stages. Here, we performed various analyses on the cDNA and protein sequences of six different G. macrocephalus caspases namely GmCasp3, 6, 7, 8, 9 and 10, and tried to investigate the contributions of caspase family to the development and Nervous Necrosis Virus (NNV) resistance. Sequence analysis of GmCaspase proteins showed that each caspase shared conserved domains like "HG", "QACXG (X for R, G or Q)" and "GSWF" except GmCasp10. Sequence alignment and phylogenetic tree showed that GmCasp8 and GmCasp10 were quite different from those of other fishes. 3-D models indicated that structure of GmCasp3 is very conservative, but GmCasp6, 7, 8, 9 and 10 are less conservative. Tissue distribution analysis showed that six Gmcaspases mRNA transcripts were detected in tissues of intestine, gill, thymus, head-kidney and spleen with different abundance, but Gmcasp7 were not detected in the brain. GmCasp3 transcript was kept at very low level in the early development stages, while the expression levels of GmCasp6, 7, 8, 10 were different at various development stages. GmCasp8 level seemed to be much higher than other caspases in the heads of 65dph and 75dph juveniles. To understand the role of caspases during NNV outbreak, modulation in expression of each Gmcaspases were investigated. The results showed that GmCasp3 transcript level increased significantly when NNV broke out, while GmCasp7, 8, 9 and 10 in cod heads decreased obviously at 69dph and 77dph. The results suggest that caspases in Pacific cod should be diverse in their structure and function, and their unique features and response to NNV outbreak add more evidences for the specificity of immune system in Pacific cod.

Protective effect of gelatin peptides from pacific cod skin against photoaging by inhibiting the expression of MMPs via MAPK signaling pathway

Chronic exposure to ultraviolet (UV) irradiation causes skin photoaging. This study was undertaken to identify the anti-photoaging mechanisms of gelatin hydrolysate (CH) derived from pacific cod skin. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) and ELISA assays were used to investigate the effects of CH on matrix metalloproteinases (MMPs) and the signaling pathways after UV irradiation by using a mice skin photoaging model. The average molecular weight of CH was 1200Da, and 273/1000 residues were hydrophobic, Gly-Pro and Gly-Leu sequences and Arg at C-terminus appeared frequently in CH. CH improved pathological changes of collagen fibers and significantly inhibited collagen content reduction in photoaging skin. Moreover, CH blocked the up-regulated expression of interstitial collagenase (MMP-1), stromelysin 1 (MMP-3), and gelatinase (MMP-9) in photoaging skin. Besides, CH suppressed the activities of MMPs by increasing the contents of tissue inhibitors of matrix metalloproteinases (TIMPs). CH significantly reduced the UV irradiation-dependent up-regulated phosphorylation of ERK and p38 in the mitogen-activated protein kinase (MAPK) signaling pathway. Furthermore, it inhibited the activation of activator protein 1 (AP-1) by down-regulating the mRNA level of c-Jun and c-Fos, which are the two transcription factors responsible for the regulation of MMPs expression. CH can effectively protect against UV irradiation-induced skin photoaging by inhibiting the expression and the activity of MMPs.

Restricted Gene Flow for Gadus macrocephalus from Yellow Sea Based on Microsatellite Markers: Geographic Block of Tsushima Current

The Pacific cod Gadus macrocephalus is a demersal, economically important fish in the family Gadidae. Population genetic differentiation of Pacific cod was examined across its northwestern Pacific range by screening variation of eight microsatellite loci in the present study. All four populations exhibited high genetic diversity. Pairwise fixation index (Fst) suggested a moderate to high level of genetic differentiation among populations. Population of the Yellow Sea (YS) showed higher genetic difference compared to the other three populations based on the results of pairwise Fst, three-dimensional factorial correspondence analysis (3D-FCA) and STRUCTURE, which implied restricted gene flow among them. Wilcoxon signed rank tests suggested no significant heterozygosity excess and no recent genetic bottleneck events were detected. Microsatellite DNA is an effective molecular marker for detecting the phylogeographic pattern of Pacific cod, and these Pacific cod populations should be three management units.