The transcriptomic response to copper exposure by the gill tissue of Japanese scallops (Mizuhopecten yessoensis) using deep-sequencing technology

Hexavalent chromium damages intestinal cells and coelomocytes and impairs immune function in the echiuran worm Urechis unicinctus by causing oxidative stress and apoptosis

Hexavalent chromium (Cr(VI)) is a common pollutant in the marine environment, which impairs immunity and causes reproductive and heredity disorders in organisms. To clarify the immunotoxic effects of Cr (VI) on the marine worm Urechis unicinctus, we analyzed tissue damage and immune dysfunction caused by Cr (VI) in this organism at histopathologic, zymologic, apoptotic and molecular levels. The results indicated that the bioaccumulation of Cr (VI) bioaccumulation levels in coelomocytes was significantly higher than in the intestines and muscles. Pathological observation showed that Cr (VI) caused damage to the respiratory intestine, stomach and midgut. Cr (VI) also increased the replication of goblet cells and a reduction in the replication of epithelial cells. Meanwhile, Cr (VI) induced apoptosis of intestinal cells and coelomocytes, accompanied by an increase in the expression of Caspase-3, COX-2, and MyD88 in the intestine and coelomocytes. At the same time, Cr (VI) significantly affected the activities of antioxidant enzymes such as SOD, ACP, CAT, CAT, and GST, and increased H2O2 and MDA contents in U. unicinctus. Moreover, Cr (VI) exposure also up-regulated the transcription of hsc70, mt and jnk genes but decreased that of sod in the intestines. In contrast, Cr (VI) down-regulated the expression of sod, hsc70, mt, and jnk genes in coelomocytes. Collectively, Cr (VI) bioaccumulated in U. unicinctus cells and tissues, causing several histopathological changes, oxidative stress, and apoptosis of several cells in the organism, resulting in intestinal and coelomocyte damage and immune dysfunctioning.

Combined transcriptomics and metabolomics to reveal the effects of copper exposure on the liver of rainbow trout(Oncorhynchus mykiss)

Copper (Cu) is recognized as an essential trace elements for the body; However, excessive levels of Cu can lead to toxic effects. We investigated the effects of Cu2+(75 μg/L, 150 μg/L, and 300 μg/L) on the rainbow trout liver. Combination of transcriptome and metabolome analyses, the regulatory mechanisms of the liver under Cu stress were elucidated. The results showed that Cu affected the antioxidant levels, leading to disruptions in the normal tissue structure of the liver. Combined transcriptome and metabolome analyses revealed significant enrichment of the insulin signaling pathway and the adipocytokine signaling pathway. Additionally, Cu2+ stress altered the amino acid metabolism in rainbow trout by reducing serine and arginine levels while increasing proline content. Apoptosis is inhibited and autophagy and lipid metabolism are suppressed; In summary, Cu2+ stress affects energy and lipid metabolism, and the reduction of serine and arginine represents a decrease in the antioxidant capacity, whereas the increase in proline and the promotion of apoptosis potentially serving as crucial strategies for Cu2+ resistance in rainbow trout. These findings provided insights into the regulatory mechanisms of rainbow trout under Cu2+ stress and informed the prevention of heavy metal pollution and the selection of biomarkers under Cu pollution.

First evidence of meso- and microplastics on the mangrove leaves ingested by herbivorous snails and induced transcriptional responses

Although evidence suggests the ubiquity of meso- and microplastics (MMPs) in mangrove forests, our knowledge of their bioavailability and risk on mangrove leaves is scarce. Here, we investigated MMP contamination concerning submerged mangrove leaves and herbivorous snails that mainly feed on them from the four mangrove forests located in Beibu Gulf, Guangxi Province, China. Results showed that the MMP abundance on the mangrove leaves ranged from 0.01 ± 0.00 to 0.42 ± 0.15 items cm^-2, while it ranged from 0.33 ± 0.21 to 6.20 ± 2.91 items individual^-1 in the snails. There were significant positive correlations between snails and leaves regarding the abundance of total MMPs and the proportions of MMPs with the same characteristics. Expanded polystyrene (EPS) that mainly derived from aquaculture rafts, accounted for a major component both on the leaves and in the snails in Shi Jiao (SJ). Both the detection frequency and percentage of larger EPS (2.00-17.50 mm) on the leaves in SJ were higher than other sites. Meanwhile, the detection frequency, abundance and percentage of larger EPS on the leaves had significant positive correlations with those of micro-EPS in the snails. These findings suggested that mangrove leaves may represent a viable pathway for MMPs to enter the herbivorous snails. Larger EPS with higher frequency of occurrence on mangrove leaves were more likely to be encountered and ingested by snail considering its opportunistic feeding behavior. In addition, 11 sensitive genes involved in the processes of metabolism, intestinal mucosal immune systems, and cellular transduction in the snails were significantly suppressed by MMP exposure, which may be potentially used as early biomarkers to indicate the biological effects of MMPs under realistic environmental conditions. Overall, this study provides novel insights into the fate, sources, and biological effects of MMPs on mangrove leaves.

Comparative transcriptome analyses of the liver between Xenocypris microlepis and Xenocypris davidi under low copper exposure

Copper is one of the most ubiquitous environmental pollutants worldwide. Previous studies have focused on the toxicology of high copper exposure, while there has been comparatively less research on the biological effects of low copper exposure. Low concentrations of copper often exist in freshwater ecosystems, and its impact on the fish is unclear. Both Xenocypris microlepis and Xenocypris davidi are bottom-feeding fishes widely distributed in freshwater ecosystems of China, and they are more likely to be contaminated by low concentrations of copper. Low copper exposure may have effects on molecular regulation at the level of gene expression in the two Xenocypris species. To investigate gene expression differences involved in the response to low copper concentrations between X. microlepis and X. davidi, we established the responses to low copper exposure of 0.01 mg/L for 14 days at the transcriptional level, and RNA-Seq was used to perform a comparative transcriptomic analysis of the liver. A total of 74,135 and 60,894 unigenes from X. microlepis and X. davidi were assembled by transcriptome profiling, respectively. Among these, 84 genes of X. microlepis and 165 genes of X. davidi were identified as differentially expressed genes (DEGs). There were 60 and 135 up-regulated, 24 and 30 down-regulated genes in the two species, respectively. Comparative transcriptome analyses identified five differentially co-expressed genes (DCGs) related to low copper exposure from the DEGs of the two Xenocypris species. The five DCGs were related to the fishes' growth, antioxidant system, immune system and heavy metal tolerance. The results could help us to understand the molecular mechanisms of the response to low copper exposure, and the data should provide a valuable transcriptomic resource for the genus Xenocypris.

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.

New insight into the molecular basis of chromium exposure of Litopenaeus vannamei by transcriptome analysis

Heavy metal pollution arising from agricultural and industrial activities poses a significant threat to the aquatic environment, especially the increasing levels of chromium (Cr) that is exacerbating marine pollution. Given the economic importance of the Pacific white shrimp Litopenaeus vannamei (L. vannamei), understanding the impact of marine Cr pollution is deemed to be significant. In this study, we used the transcriptome sequencing (RNA-seq) technique to characterize the molecular mechanism of Cr exposure in L. vannamei. Gene ontology enrichment analysis showed substrate-specific and ion transport-related functions were mainly influenced by Cr exposure. We further identified genes involved in protein digestion and absorption (PEPT1, BAT1, MDU1), chemical carcinogenesis (GST and UGTs), ABC transporters (ABCC2), apoptosis (CAPN1, CASP10, PARP), implying the potentially Cr disintoxication mechanisms in L. vannamei. Genes within pancreatic secretion (ALT, LDH), lysosome (CTSL and HEXB), and peroxisome (ACOX1, ECI2, NUDT12) pathways implied the potentially Cr toxicity mechanisms in L. vannamei.

Transcriptome analysis and histopathological observations of Geloina erosa gills upon Cr(VI) exposure

The heavy metal contamination like Cr(VI) has been increased by human activities and that threats the ecosystem health of mangrove areas. Bioindicator is an emerging tool in the environmental contamination assessment. The objective of this study was to investigate the Geloina erosa response mechanisms and sensitivities of several biomarkers in the Cr(VI) exposure and identify the G. erosa capability of being used as heavy metals bioindicator. In this study, G. erosa was exposed to 100 μmol·L^-1 Cr(VI) for 48 h. After transcriptome sequencing, a total of 134,817 unigenes were obtained, including 12,555 up-regulated and 18,829 down-regulated differentially expressed genes and were validated through quantitative real-time PCR. In addition, a total of 12,185 SSRs and 1,428,214 candidate SNPs were identified from all the G. erosa transcriptome libraries. Histopathology of the gill indicated the Cr(VI) exposure induced damage of the organ leading to its immunization, detoxification or apoptosis reactions. Among eight genes of the selected biomarkers, Calm, HSP70, CYP450, ATG5, TLR2, MYD88 and CASP8 were up-regulated, while TLR4 was down-regulated in response to the Cr(VI) exposure.

Comparative study of β-thymosin in two scallop species Argopecten irradians and Chlamys farreri

The β-thymosin (Tβ) proteins participate in numerous biological processes, such as cell proliferation and differentiation, anti-inflammatory and antimicrobial mechanism. To date, Tβ proteins have been well studied in vertebrates, especially mammals. While limited Tβ or Tβ-like proteins have been reported in invertebrates. Moreover, rare information of Tβ or Tβ-like proteins is available in scallop species yet. In the present study, two Tβ homologues, AiTβ and CfTβ, were identified and characterized from two scallop species bay scallop Argopecten irradians and Zhikong scallop Chlamys farreri. They were both 41 amino acid peptide and contained one THY domain, a highly conserved actin-binding motif and two conserved helix forming regions. Tissue distribution and expression profiles of their mRNA transcripts were roughly similar yet different in detail, while their recombinant proteins exhibited different immunomodulation activity on the downstream immune parameters. These results collectively indicated that the function of Tβ family in scallop were functionally differentiated.

Intestinal microbiota and lipid metabolism responses in the common carp (Cyprinus carpio L.) following copper exposure

The present study was conducted to determine the effects of waterborne copper exposure on the lipid metabolism and intestinal microbiota of juvenile common carp (Cyprinus carpio L.). Common carp were exposed to four waterborne copper (Cu) concentrations (0 (control), 0.07 (low), 0.14 (medium), and 0.28 (high) mg Cu/L) for 8 weeks. Exposure to a high concentration of Cu had a negative effect on growth indices (weight gain rate (WGR) and specific growth rate (SGR)). The biochemical indices measured in serum (low-density lipoprotein (LDL) and triglycerides (TGs)) were significantly affected by exposure to medium concentration levels of Cu. The mRNA levels of lipogenic enzymes (acetyl-CoA carboxylase 1 (ACC-1) and fatty acid synthase (FAS)) and sterol-regulator element-binding protein-1 (SREBP-1) in liver tissue and tight binding protein genes (ZO-1 and occludin) in intestinal epithelial tissue were significantly downregulated in the 0.14 and 0.28 mg/L Cu treatment groups, accompanied by upregulated mRNA levels of lipolysis enzymes (lipoprotein lipase (LPL) and carnitine palmitoyl transferase 1 (CPT-1)) in the liver. The data also showed that the composition of intestinal microbiota was changed following Cu exposure and could alter the α-diversity and β-diversity. The abundances of few putative short-chain fatty acid (SCFA)-producing bacteria, including Allobaculum, Blautia, Coprococcus, Faecalibacterium, Roseburia, and Ruminococcus, decreased significantly. More specifically, Roseburia sequences were positively associated with lipogenic enzymes, total protein (TP), and TGs and negatively associated with lipolysis enzymes. Other sequences related to probiotics (Lactobacillus, Bacillus and Akkermansia) were also found to decrease, accompanied by an increase in sequences related to pathogens (Pseudomonas and Acinetobacter). To the best of our knowledge, the present study provides the first evidence that waterborne, chronic Cu exposure can disturb the composition of intestinal microbiota related to lipid metabolism and immunity in freshwater fish, thereby increasing the risk of pathogen invasion.

A novel toll-like receptor from Mytilus coruscus is induced in response to stress

Toll-like receptor (TLR) is considered to be an evolutionarily conserved transmembrane protein which promotes the Toll signal pathway to active the expression of transcription factors in the innate immunity of the organism. In this study, a full length of TLR homologue of 2525bp in Mytilus coruscus (named as McTLR-a, GenBank accession no: KY940571) was characterized. Its ORF was 1815 bp with a 5'untranslated region (UTR) of 128 bp and a 3'UTR of 582 bp, encoding 602 amino acid residues with a calculated molecular weight of 70.870 kDa (pI = 6.10). BLASTn analysis and phylogenetic relationship strongly suggested that this cDNA sequence was a member of TLR family. Quantitative real time RT-PCR showed that constitutive expression of McTLR-a was occurred, with increasing order in hemocyte, gonad, mantle, adducter, gill and hepatopancreas. Bacterial infection and heavy metals stimulation up-regulated the expression of McTLR-a mRNA in hepatopancreas with time-dependent manners. The maximum expression appeared at 12 h after pathogenic bacteria injection, with approximately 22-fold in Aeromonas hydrophila and 17-fold in Vibrio parahemolyticus higher than that of the blank group. In heavy metals stress group, they all reached peaks at 3d, while the diverse concentration caused the maximum expression were different. The highest expression reached approximately 7-fold higher than the blank in low concentration of Pb²⁺ exposure. In Cu²⁺ treated group, it reached the peak (approximately 12-fold higher than the blank)in middle concentration. These results indicated that McTLR-a might be involved in the defense response and had a significant role in mediating the environmental stress.

Evaluating Macrophages in Immunotoxicity Testing

Macrophages are a heterogeneous group of cells that have a multitude of functions depending on their differentiation state. While classically known for their phagocytic and antigen presentation abilities, it is now evident that these cells fulfill homeostatic functions beyond the elimination of invading pathogens. In addition, macrophages have also been implicated in the downregulation of inflammatory responses following pathogen removal, tissue remodeling, repair, and angiogenesis. Alterations in macrophage differentiation and/or activity due to xenobiotic exposure can have grave consequences on organismal homeostasis, potentially contributing to disease due to immunosuppression or chronic inflammatory responses, depending upon the pathways affected. In this chapter, we provide an overview of the macrophages subtypes, their origin and a general discussion of several different assays used to assess their functional status.

Cloning, characterization and functional analysis of dctn5 in immune response of Chinese tongue sole (Cynoglossus semilaevis)

In mammals, microtubule-dependent trafficking could participate the immune response, where the motor proteins are suggested to play an important role in this process, while the related study in fish was rare. In this study, dctn5, a subunit of dyactin complex for docking motor protein, was obtained by previous immune QTL screening. The full-length cDNAs of two dctn5 transcript variants were cloned and identified (named dctn5_tv1 and dctn5_tv2, respectively). Tissue distribution showed that dctn5_tv1 was widely distributed and high transcription was observed in immune tissue (skin), while dctn5_tv2 was predominantly detected in gonad and very low in other tissues. Time-course expression analysis revealed that dctn5_tv1 could be up-regulated in gill, intestine, skin, spleen, and kidney after Vibrio harveyi challenge. Moreover, recombinant Dctn5_tv1 exhibited high antimicrobial activity against Escherichia coli and Streptococcus agalactiae due to binding to bacteria cells. Taken together, these data suggest Dctn5_tv1 is involved in immune response of bacterial invasion in Chinese tongue sole.

Transcriptome Analysis of Hepatopancreas from the Cr (VI)-Stimulated Mantis Shrimp ( Oratosquilla oratoria) by Illumina Paired-End Sequencing: Assembly, Annotation, and Expression Analysis

Cr (VI), the pathogenicity factor, is widely known to cause toxic effects in living organisms. Given the economic importance of the mantis shrimp ( Oratosquilla oratoria), the understanding of impacts by Cr (VI) is considered important. In this study, transcriptome of mantis shrimp was characterized by a comparison between control and Cr (VI)-treated samples using RNA-seq approach. Totally, 88 234 826 bp and 13.24G clean reads were obtained. The total length and number of unigenes were 68 411 206 bp and 100 918, respectively. The maximal and average length of unigenes was 24 906 bp and 678 bp, respectively (N50, 798 bp). 7115 of these unigenes accounted for 7.05% of the total that were annotated in all databases. After annotation of assembled unigenes, 35 619 of them were assigned into 3 functional categories and 56 subcategories using Gene Ontology; 18 580 of them were assigned into 26 functional categories using Clusters of Orthologous Groups of proteins; 16 864 of them were assigned into 5 major categories and 32 subclasses using KEGG. Finally, 1730 genes were differentially expressed (DGEs), 9 up-regulated pathways (protein digestion and absorption, neuroactive ligand-receptor interaction, pancreatic secretion, tyrosine metabolism, amoebiasis, ECM-receptor interaction, riboflavin metabolism, amino sugar and nucleotide sugar metabolism and AGE-RAGE signaling pathway in diabetic complications) were significantly enriched ( q < 0.05), and one down-regulated pathway ( Staphylococcus aureus infection) was significantly enriched ( q < 0.05). Up-regulation of genes in pathways of protein digestion/absorption ( PepT1/SLC15A and ATP1B) and environment information processing ( COL1AS, COL4A; LAMA3_5, LAMB3; FN1 and TN) may imply the potentially positive toxicity resistance mechanisms.

Identification of immune-related genes in gill cells of Japanese eels (Anguilla japonica) in adaptation to water salinity changes

The changes in ambient salinity influence ion and water homeostasis, hormones secretion, and immune response in fish gills. The physiological functions of hormones and ion transporters in the regulation of gill-osmoregulation have been widely studied, however the modulation of immune response under salinity changes is not determined. Using transcriptome sequencing, we obtained a comprehensive profile of osmo-responsive genes in gill cells of Japanese eel (Anguilla japonica). Herein, we applied bioinformatics analysis to identify the immune-related genes that were significantly higher expressed in gill pavement cells (PVCs) and mitochondrial-rich cells (MRCs) in freshwater (FW) than seawater (SW) adapted fish. We validated the data using the real-time qPCR, which showed a high correlation between the RNA-seq and real-time qPCR data. In addition, the immunohistochemistry results confirmed the changes of the expression of selected immune-related genes, including C-reactive protein (CRP) in PVCs, toll-like receptor 2 (TLR2) in MRCs and interleukin-1 receptor type 2 (IL-1R2) in both PVCs and MRCs. Collectively our results demonstrated that those immune-related genes respond to salinity changes, and might trigger related special signaling pathways and network. This study provides new insights into the impacts of ambient salinity changes on adaptive immune response in fish gill cells.

Molecular characterization and expression analysis of a novel r-spondin member (rspo2l) in Chinese tongue sole (Cynoglossus semilaevis)

Numerous studies suggest R-spondins (Rspos) plays a role in mammalian sex development and differentiation by activating WNT signaling pathways. However, Rspos are frequently less reported in teleosts. In this study, a molecular characterization and expression analysis was conducted with a new rspondin member in the Chinese tongue sole, rspondin2-like (rspo2l). The length of rspo2l cDNA is 1251 bp with 732 bp of coding sequence. A qRT-PCR analysis revealed that the transcription of rspo2l was distributed in various tissues, with high transcription levels in the liver, skin, and gills which might indicate a possible role in immunity. We next examined a time-course of transcription levels in four immune tissues (gill, liver, spleen, and kidney) after Vibrio harveyi challenge. It was found that rspo2l was up-regulated in the gills, spleen, and kidney and down-regulated in the liver, and the greatest responses occurred at 24 and 48 h after bacterial challenge. An assessment of β-catenin, the key regulator of the canonical WNT signaling pathway, at different time points in four immune organs revealed that its transcription profile was similar to that of rspo2l after bacterial challenge. The results suggest that tongue sole rspo2l might play a role in immune responses after bacterial challenge, while the potential link with the WNT signaling pathway still requires further investigation. This is the first report about the involvement of rspondins in fish immune responses.

Functional and molecular responses of the blue mussel Mytilus edulis' hemocytes exposed to cadmium - An in vitro model and transcriptomic approach

The bivalve mollusk, Mytilus edulis, is used as a sentinel species in several monitoring programs due to its ability to bio-accumulate contaminants. Its immune system consists of hemocytes and humoral components, which constitute the main part of the hemolymph. The present study is aimed at understanding the effects of Cd on the differentially expressed genes involved in the phagocytosis of M. edulis' hemocytes. Our approach focuses on an in vitro model by exposing hemocytes to different concentrations of Cd ranging from 10^-9 M to 10^-3 M. Phagocytosis and cell viability as functional markers were measured using flow cytometry. The molecular mechanisms regulated by Cd were investigated using RNA-seq and DGE analysis. Results showed that viability and phagocytosis of hemocytes exposed to 10^-3 M of Cd were significantly decreased after 21 h of exposure. RNA sequencing data showed that 1112 transcripts (out of 352,976 contigs) were differentially regulated by the highest concentration of Cd. Among these identified transcripts, 1028 and 84 were up and down-regulated respectively. The induction of super oxide dismutase (SOD), glutathion-s-transferase (GST), cytochrome P450 2C8 (CYP2C8), multidrug resistance protein (MRP1) and heat shock protein 70 (HSP70) suggests that Cd can regulate key molecular mechanisms. In addition, several toll-like receptors (TLR) as well as genes involved in phagocytosis (actin and CDC42) and apoptosis (caspase 8 and XIAP/IAP) were induced by Cd. Thus, our model highlights the effect of Cd on the phagocytic function of M. edulis' hemocytes along with the regulation of gene expression involved in innate immunity, detoxification and apoptosis. Further investigations need to be pursued to unravel the effects of Cd on the molecular mechanisms identified in this study.

Transcriptome Analysis of the Sydney Rock Oyster, Saccostrea glomerata: Insights into Molluscan Immunity

BACKGROUND

Oysters have important ecological functions in their natural environment, acting as global carbon sinks and improving water quality by removing excess nutrients from the water column. During their life-time oysters are exposed to a variety of pathogens that can cause severe mortality in a range of oyster species. Environmental stressors encountered in their habitat can increase the susceptibility of oysters to these pathogens and in general have been shown to impact on oyster immunity, making immune parameters expressed in these marine animals an important research topic.

RESULTS

Paired-end Illumina high throughput sequencing of six S. glomerata tissues exposed to different environmental stressors resulted in a total of 484,121,702 paired-end reads. When reads and assembled transcripts were compared to the C. gigas genome, an overall low level of similarity at the nucleotide level, but a relatively high similarity at the protein level was observed. Examination of the tissue expression pattern showed that some transcripts coding for cathepsins, heat shock proteins and antioxidant proteins were exclusively expressed in the haemolymph of S. glomerata, suggesting a role in innate immunity. Furthermore, analysis of the S. glomerata ORFs showed a wide range of genes potentially involved in innate immunity, from pattern recognition receptors, components of the Toll-like signalling and apoptosis pathways to a complex antioxidant defence mechanism.

CONCLUSIONS

This is the first large scale RNA-Seq study carried out in S. glomerata, showing the complex network of innate immune components that exist in this species. The results confirmed that many of the innate immune system components observed in mammals are also conserved in oysters; however, some, such as the TLR adaptors MAL, TRIF and TRAM are either missing or have been modified significantly. The components identified in this study could help explain the oysters' natural resilience against pathogenic microorganisms encountered in their natural environment.

The transcriptomic response to copper exposure in the digestive gland of Japanese scallops (Mizuhopecten yessoensis)

The present study was conducted to elucidate the effects of copper exposure on the immune system and lipid metabolism of the Japanese scallop, Mizuhopecten yessoensis. Transcriptional levels of differentially expressed genes (DEGs)in M. yessoensis digestive gland tissue were analyzed using the deep-sequencing platform Illumina HiSeq™ 2000. In total, 841 and 877 genes were identified as significantly up- or down-regulated, respectively. In addition, significant enrichment analysis identified 3 gene ontology terms and 15 pathways involved in the response to copper exposure. Analysis of transcripts related to the immune response revealed a complex pattern of innate recognition receptors, including toll-like receptors, NOD-like receptors and downstream pathway effectors, including those involved in apoptosis. Furthermore, genomic analysis revealed that genes involved in extracellular matrix (ECM)-receptor interactions were enriched in Cu-exposed scallop glands. These results will provide a resource for subsequent gene expression studies regarding heavy metal exposure and the identification of copper-sensitive biomarkers for the aquaculture of M. yessoensis.

The immune system and its modulation mechanism in scallop

Scallops are a cosmopolitan family of bivalves, and some of them are highly prized as dominant aquaculture species. In the past decades, there have been increasing studies on the basic biology and immunology of scallops, and this review summarizes the research progresses of immune system and its modulation mechanism in scallop. As invertebrate, scallops lack adaptive immunity and they have evolved an array of sophisticated strategies to recognize and eliminate various invaders by employing a set of molecules and cells. It is evident that basic immune reactions such as immune recognition, signal transduction, and effector synthesis involved in immune response are accomplished in a variety of ways. They rely upon an extensive repertoire of phagocytosis, apoptosis and encapsulation of the circulating hemocytes for eliminating invasive pathogens, as well as the production of immune effectors that are active against a large range of pathogens or sensitive for the environmental stress. Furthermore, the molecular constitutions, metabolic pathways and immunomodulation mechanisms of the primitive catecholaminergic, cholinergic, enkephalinergic system and NO system in scallop are also discussed, which can be taken as an entrance to better understand the origin and evolution of the neuroendocrine-immune regulatory network in lower invertebrates.

Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning

It is commonly known that the nature of the diet has diverse consequences on larval performance and longevity, however it is still unclear which genes have critical impacts on bivalve development and which pathways are of particular importance in their vulnerability or resistance. First we show that a diet deficient in essential fatty acid (EFA) produces higher larval mortality rates, a reduced shell growth, and lower postlarval performance, all of which are positively correlated with a decline in arachidonic and eicosapentaenoic acids levels, two EFAs known as eicosanoid precursors. Eicosanoids affect the cell inflammatory reactions and are synthesized from long-chain EFAs. Second, we show for the first time that a deficiency in eicosanoid precursors is associated with a network of 29 genes. Their differential regulation can lead to slower growth and higher mortality of Mytilus edulis larvae. Some of these genes are specific to bivalves and others are implicated at the same time in lipid metabolism and defense. Several genes are expressed only during pre-metamorphosis where they are essential for muscle or neurone development and biomineralization, but only in stress-induced larvae. Finally, we discuss how our networks of differentially expressed genes might dynamically alter the development of marine bivalves, especially under dietary influence.

Deep sequencing of the scallop Chlamys farreri transcriptome response to tetrabromobisphenol A (TBBPA) stress

Tetrabromobisphenol-A (TBBPA) is currently the most widely used brominated flame retardant (BFR) and has been proven to have a very high toxicity to aquatic organisms including bivalves. However, molecular responses to TBBPA in bivalve remain largely unknown. Novel high-throughput deep sequencing technology has been a powerful tool for looking at molecular responses to toxicological stressors in organisms. Using Illumina's digital gene expression (DGE) system, we investigated TBBPA-induced transcriptome response in the digestive gland tissue of scallop Chlamys farreri. In total, 173 and 266 genes were identified as significantly up- or down-regulated, respectively. Functional analysis based on gene ontology (GO) classification system and Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that TBBPA significantly altered the expression of genes involved in stress response, detoxification, antioxidation, and innate immunity which were extensively discussed. In particular, evidence for the endocrine disrupting effect of TBBPA on bivalve was first obtained in this study. Quantitative real-time PCR was performed to ascertain the mRNA expression of several genes identified by the DGE analysis. The results of this study may serve as a basis for future research on molecular mechanism of toxic effects of TBBPA on marine bivalves.