Digital gene expression analysis in hemocytes of the white shrimp Litopenaeus vannamei in response to low salinity stress

Physiological and transcriptomic analysis provides new insights into osmoregulation mechanism of Ruditapes philippinarum under low and high salinity stress

The Manila clam (Ruditapes philippinarum) is a commercially important marine bivalve, which inhabits the estuarine and mudflat areas. The osmoregulation is of great significance for molluscs adaptation to salinity fluctuations. In this study, we investigated the effects of low salinity (10 psu) and high salinity (40 psu) stress on survival and osmoregulation of the R. philippinarum. The results of physiological parameters showed that the ion (Na+, K+, Cl-) concentrations and Na+/K+-ATPase (NKA) activity of R. philippinarum decreased significantly under low salinity stress, but increased significantly under high salinity stress, indicating that there are differences in physiological adaptation of osmoregulation of R. philippinarum. In addition, we conducted the transcriptome analysis in the gills of R. philippinarum exposed to low (10 psu) and high (40 psu) salinity challenge for 48 h using RNA-seq technology. A total of 153 and 640 differentially expressed genes (DEGs) were identified in the low salinity (LS) group and high salinity (HS) group, respectively. The immune (IAP, TLR6, C1QL4, Ank3), ion transport (Slc34a2, SLC39A14), energy metabolism (PCK1, LDLRA, ACOX1) and DNA damage repair-related genes (Gadd45g, HSP70B2, GATA4) as well as FoxO, protein processing in endoplasmic reticulum and endocytosis pathways were involved in osmoregulation under low salinity stress of R. philippinarum. Conversely, the ion transport (SLC6A7, SLC6A9, SLC6A14, TRPM2), amino acid metabolism (GS, TauD, ABAT, ALDH4A1) and immune-related genes (MAP2K6, BIRC7A, CTSK, GVIN1), and amino acid metabolism pathways (beta-Alanine, Alanine, aspartate and glutamate, Glutathione) were involved in the process of osmoregulation under high salinity stress. The results obtained here revealed the difference of osmoregulation mechanism of R. philippinarum under low and high salinity stress through physiological and molecular levels. This study contributes to the assessment of salinity adaptation of bivalves in the context of climate change and provides useful information for marine resource conservation and aquaculture.

Meta-analysis to Unravel Core Transcriptomic Responses in Penaeus vannamei Exposed to Biotic and Abiotic Stresses

Shrimp farming, a dominant economic activity in coastal areas, is affected by different abiotic and biotic stress factors. These stressors, under poor management conditions, could affect growth and health of farmed animals. Understanding the common gene expressions in response to stress, regardless of the specific stress factor, holds significant importance in the field of functional genomics. Scope of this study is to identify the core transcriptomic responses in the shrimp species Penaeus vannamei exposed to various abiotic and biotic stress conditions and to decipher their functional importance. To achieve our objective, we gathered and analyzed multiple RNA-seq datasets related to twelve abiotic and nine biotic stress conditions. Through the in silico meta-analysis, we predicted 961 differentially expressed genes (meta-DEGs) for abiotic stress conditions and 517 meta-DEGs for biotic stress conditions, respectively. These meta-DEGs represent genes that are commonly expressed across different stress factors and are indicative of the organism's general response to stress. The annotation of nineteen core up-regulated meta-DEGs revealed their diverse functions in detoxification, cell adhesion, metal ion binding, and oxidative phosphorylation. These genes play a crucial role in stress response and immune defense. For abiotic stress, significant pathways associated with the stress response include tryptophan metabolism, starch and sucrose metabolism, fatty acid degradation, carbohydrate digestion and absorption, phenylalanine metabolism, drug metabolism-other enzymes, arachidonic acid metabolism, and fatty acid elongation. Similarly, for biotic stress, metabolism of xenobiotics by cytochrome P450, pentose and glucuronate interconversions, steroid hormone biosynthesis, and drug metabolism-cytochrome P450 were found to be significant pathway associations. In addition, the study also predicted 17 stress regulatory motifs present in the identified meta-DEGs. These motifs have significance in identifying the stress responses of the organism. The metabolic pathways and regulatory motifs associated with abiotic and biotic stress factors identified through this study could be a valuable resource for developing stress management approaches in shrimp aquaculture.

First identification and histopathological analysis of Lactococcus garvieae infection in whiteleg shrimp, Penaeus vannamei cultured in low salinity water

The isolation and characterization of bacterial species Lactococcus garvieae, previously unreported in whiteleg shrimp, Penaeus vannamei, has now been identified in the species. The pathogen was recovered from an affected shrimp farm in southern Taiwan. Bacterial characterization first identified the isolate as Gram-positive cocci, and biochemical profiles demonstrated that the causative agent of mortality was 97% L. garvieae. The bacterial cell DNA resulted in amplification of 1522 bp with 99.6% confirmation by PCR analysis. The phylogenetic tree revealed 100% evolutionary similarity among previously isolated strains. Experimental infection further confirmed higher susceptibility of whiteleg shrimp to L. garvieae in waters of lower salinity, particularly 5 ppt, than in higher salinity. Histopathological analysis showed severely damaged hepatopancreas with necrotized, elongated, collapsed tubules, dislodged membranes and granuloma formation in infected shrimp. Transmission electron microscopy observation indicated a hyaluronic acid capsular layer surrounding bacterial cell which is a virulence factor of L. garvieae and likely responsible for immunosuppression and higher mortality of shrimp cultured in lower salinity. Collectively, these findings report the first isolation of L. garvieae from whiteleg shrimp and shed new light on the disease that threatens the highly valuable species and accentuates the need for finding a solution.

Transcriptional and metabolomic investigation of the stress response in snow crab during simulated transport condition (Chionoecetes opilio)

The molecular mechanisms underlying the stress response are poorly described in crustaceans. This includes the snow crab (Chionoecetes opilio), a commercially important stenotherm species distributed throughout the northern hemisphere. A better understanding of the stress response in C. opilio is desperately needed for commercial and conservation purposes. The purpose of this study was to investigate the transcriptional and metabolomic response of C. opilio exposed to stressors. Crabs were randomly assigned to 24 or 72 h treatment groups where they were exposed to conditions simulating live transport (handling and air exposure). A control group was kept in cold (2 °C) and well‑oxygenated saltwater. The hepatopancreas of the crabs was sampled to perform RNA-sequencing and high-performance chemical isotope labeling metabolomics. Differential gene expression analyses showed that classic crustaceans' stress markers, such as crustacean hyperglycemic hormones and heat shock proteins, were overexpressed in response to stressors. Tyrosine decarboxylase was also up-regulated in stressed crabs, suggesting an implication of the catecholamines tyramine and octopamine in the stress response. Deregulated metabolites revealed that low oxygen was an important trigger in the stress response as intermediate metabolites of the tricarboxylic acid cycle (TCA) accumulated. Lactate, which accumulated unevenly between crabs could potentially be used to predict mortality. This study provides new information on how stressors affect crustaceans and provides a basis for the development of stress markers in C. opilio.

Thermotolerance improvement of engineered Saccharomyces cerevisiae ERG5 Delta ERG4 Delta ERG3 Delta, molecular mechanism, and its application in corn ethanol production

BACKGROUND

The thermotolerant yeast is beneficial in terms of efficiency improvement of processes and reduction of costs, while Saccharomyces cerevisiae does not efficiently grow and ferment at high-temperature conditions. The sterol composition alteration from ergosterol to fecosterol in the cell membrane of S. cerevisiae affects the thermotolerant capability.

RESULTS

In this study, S. cerevisiae ERG5, ERG4, and ERG3 were knocked out using the CRISPR-Cas9 approach to impact the gene expression involved in ergosterol synthesis. The highest thermotolerant strain was S. cerevisiae ERG5ΔERG4ΔERG3Δ, which produced 22.1 g/L ethanol at 37 °C using the initial glucose concentration of 50 g/L with an increase by 9.4% compared with the wild type (20.2 g/L). The ethanol concentration of 9.4 g/L was produced at 42 ℃, which was 2.85-fold of the wild-type strain (3.3 g/L). The molecular mechanism of engineered S. cerevisiae at the RNA level was analyzed using the transcriptomics method. The simultaneous deletion of S. cerevisiae ERG5, ERG4, and ERG3 caused 278 up-regulated genes and 1892 down-regulated genes in comparison with the wild-type strain. KEGG pathway analysis indicated that the up-regulated genes relevant to ergosterol metabolism were ERG1, ERG11, and ERG5, while the down-regulated genes were ERG9 and ERG26. S. cerevisiae ERG5ΔERG4ΔERG3Δ produced 41.6 g/L of ethanol at 37 °C with 107.7 g/L of corn liquefied glucose as carbon source.

CONCLUSION

Simultaneous deletion of ERG5, ERG4, and ERG3 resulted in the thermotolerance improvement of S. cerevisiae ERG5ΔERG4ΔERG3Δ with cell viability improvement by 1.19-fold at 42 °C via modification of steroid metabolic pathway. S. cerevisiae ERG5ΔERG4ΔERG3Δ could effectively produce ethanol at 37 °C using corn liquefied glucose as carbon source. Therefore, S. cerevisiae ERG5ΔERG4ΔERG3Δ had potential in ethanol production at a large scale under supra-optimal temperature.

Interaction between nanomaterials and the innate immune system across evolution

Interaction of engineered nanomaterials (ENMs) with the immune system mainly occurs with cells and molecules of innate immunity, which are present in interface tissues of living organisms. Immuno-nanotoxicological studies aim at understanding if and when such interaction is inconsequential or may cause irreparable damage. Since innate immunity is the first line of immune reactivity towards exogenous agents and is highly conserved throughout evolution, this review focuses on the major effector cells of innate immunity, the phagocytes, and their major sensing receptors, Toll-like receptors (TLRs), for assessing the modes of successful versus pathological interaction between ENMs and host defences. By comparing the phagocyte- and TLR-dependent responses to ENMs in plants, molluscs, annelids, crustaceans, echinoderms and mammals, we aim to highlight common recognition and elimination mechanisms and the general sufficiency of innate immunity for maintaining tissue integrity and homeostasis.

Transcriptome and molecular regulatory mechanisms analysis of gills in the black tiger shrimp Penaeus monodon under chronic low-salinity stress

Background: Salinity is one of the main influencing factors in the culture environment and is extremely important for the survival, growth, development and reproduction of aquatic animals. Methods: In this study, a comparative transcriptome analysis (maintained for 45 days in three different salinities, 30 psu (HC group), 18 psu (MC group) and 3 psu (LC group)) was performed by high-throughput sequencing of economically cultured Penaeus monodon. P. monodon gill tissues from each treatment were collected for RNA-seq analysis to identify potential genes and pathways in response to low salinity stress. Results: A total of 64,475 unigenes were annotated in this study. There were 1,140 upregulated genes and 1,531 downregulated genes observed in the LC vs. HC group and 1,000 upregulated genes and 1,062 downregulated genes observed in the MC vs. HC group. In the LC vs. HC group, 583 DEGs significantly mapped to 37 signaling pathways, such as the NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, and PI3K-Akt signaling pathway; in the MC vs. HC group, 444 DEGs significantly mapped to 28 signaling pathways, such as the MAPK signaling pathway, Hippo signaling pathway and calcium signaling pathway. These pathways were significantly associated mainly with signal transduction, immunity and metabolism. Conclusions: These results suggest that low salinity stress may affect regulatory mechanisms such as metabolism, immunity, and signal transduction in addition to osmolarity in P. monodon. The greater the difference in salinity, the more significant the difference in genes. This study provides some guidance for understanding the low-salt domestication culture of P. monodon.

Immune regulation mediated by JAK/STAT signaling pathway in hemocytes of Pacific white shrimps, Litopenaeus vannamei stimulated by lipopolysaccharide

To understand the regulatory mechanism of Janus kinase/Signal Transducers and Activators of Transcription (JAK/STAT) signaling pathway on the immune system of the Pacific white shrimp, Litopenaeus vannamei, RNA interference technique was used to investigate the effects of JAK/STAT signaling pathway on the immune response of hemocyte in Litopenaeus vannamei stimulated by lipopolysaccharide (LPS). The results showed that 1) after 6 h of LPS stimulation, the expression levels of immune genes in hemocyte were significantly up-regulated (P < 0.05), the immune defense ability (hemocyte number, phagocytosis rate, hemagglutination activity, bacteriolytic activity, antibacterial activity, prophenoloxidase system activity) and the hemocyte antioxidant ability were significantly higher than the control group, especially at 12 h. 2) After 48 h of STAT gene interference, the expression levels of immune genes in hemocytes were significantly down-regulated, and the immune defense ability (hemocyte count, phagocytosis rate, plasma agglutination activity, lysozyme activity, antibacterial activity, proPO system activity) and the antioxidant ability were reduced and significantly lower than control. Concurrently, after LPS stimulation, the immune indexes were significantly up-regulated at 12 h to the maximum but was still lower the undisturbed LPS group. These results indicate that JAK/STAT signaling pathway is involved in the immune regulation mechanism of L. vannamei against LPS stimulation through positive regulation of cellular immune and humoral immune. These results provide a basis for further research on the role and status of JAK/STAT signaling pathway in the immune defense of crustaceans.

Ethanol yield improvement in Saccharomyces cerevisiae GPD2 Delta FPS1 Delta ADH2 Delta DLD3 Delta mutant and molecular mechanism exploration based on the metabolic flux and transcriptomics approaches

Background

Saccharomyces cerevisiae generally consumes glucose to produce ethanol accompanied by the main by-products of glycerol, acetic acid, and lactic acid. The minimization of the formation of by-products in S. cerevisiae was an effective way to improve the economic viability of the bioethanol industry. In this study, S. cerevisiae GPD2, FPS1, ADH2, and DLD3 genes were knocked out by the Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR-Cas9) approach. The mechanism of gene deletion affecting ethanol metabolism was further elucidated based on metabolic flux and transcriptomics approaches.

Results

The engineered S. cerevisiae with gene deletion of GPD2, FPS1, ADH2, and DLD3 was constructed by the CRISPR-Cas9 approach. The ethanol content of engineered S. cerevisiae GPD2 Delta FPS1 Delta ADH2 Delta DLD3 Delta increased by 18.58% with the decrease of glycerol, acetic acid, and lactic acid contents by 22.32, 8.87, and 16.82%, respectively. The metabolic flux analysis indicated that the carbon flux r_ethanol in engineered strain increased from 60.969 to 63.379. The sequencing-based RNA-Seq transcriptomics represented 472 differential expression genes (DEGs) were identified in engineered S. cerevisiae, in which 195 and 277 genes were significantly up-regulated and down-regulated, respectively. The enriched pathways of up-regulated genes were mainly involved in the energy metabolism of carbohydrates, while the down-regulated genes were mainly enriched in acid metabolic pathways.

Conclusions

The yield of ethanol in engineered S. cerevisiae increased with the decrease of the by-products including glycerol, acetic acid, and lactic acid. The deletion of genes GPD2, FPS1, ADH2, and DLD3 resulted in the redirection of carbon flux.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01885-3.

Effects and Molecular Regulation Mechanisms of Salinity Stress on the Health and Disease Resistance of Grass Carp

Though some freshwater fish have been successfully cultivated in saline-alkali water, the survival rates of freshwater fish are greatly affected by different saline-alkali conditions. The mechanisms of immune adaptation or immunosuppression of freshwater fish under different saline-alkali stress remain unclear. Here, grass carp were exposed to 3‰ and 6‰ salinity for 30 days. It was observed that salinity treatments had no obvious effects on survival rates, but significantly increased the percent of unhealthy fish. Salinity treatments also increased the susceptibility of grass carp against Flavobacterium columnare infection. The fatality rate (16.67%) of grass carp treated with 6‰ salinity was much lower than that treated with 3‰ salinity (40%). In the absence of infection, higher numbers of immune-related DEGs and signaling pathways were enriched in 6‰ salinity-treated asymptomatic fish than in 3‰ salinity-treated asymptomatic fish. Furthermore different from salinity-treated symptomatic fish, more DEGs involved in the upstream sensors of NOD-like receptor signaling pathway, such as NLRs, were induced in the gills of 6‰ salinity-treated asymptomatic fish. However in the case of F. columnare infection, more immune-related signaling pathways were impaired by salinity treatments. Among them, only NOD-like receptor signaling pathway was significantly enriched at early (1 and/or 2 dpi) and late (7 dpi) time points of infection both for 3‰ salinity-treated and 6‰ salinity-treated fish. Besides the innate immune responses, the adaptive immune responses such as the production of Ig levels were impaired by salinity treatments in the grass carp infected with F. columnare. The present study also characterized two novel NLRs regulated by salinity stress could inhibit bacterial proliferation and improve the survival rate of infected cells. Collectively, the present study provides the insights into the possible mechanisms why the percent of unhealthy fish in the absence of infection and mortality of grass carp in the case of F. columnare infection were much lower in the 6‰ salinity-treated grass carp than in 3‰ salinity-treated grass carp, and also offers a number of potential markers for sensing both environmental salinity stress and pathogen.

Transcriptome analysis of the mantle tissue of Pinctada fucata with red and black shells under salinity stress

To understand the molecular responses of Pinctada fucata with different shell colors to salinity stress, we used transcriptome sequencing on the mantle of P. fucata with a black shell and red shell color under the salinity of 20, 35, and 50. The 414 and 2371 differentially expressed genes (DEGs) in P. fucata with a black shell under low- or high-salt stress, while there were 588 and 3009 DEGs in P. fucata with a red shell. KEGG pathway enrichment analysis showed that, under low salt stress, the DEGs of P. fucata with the black shell were significantly enriched in pathways MAPK signaling pathway, protein processing in endoplasmic reticulum, vitamin B6 metabolism, longevity regulating pathway-multiple species, estrogen signaling pathway and antigen processing and presentation, the DEGs of P. fucata with a red shell were significantly enriched in pathways vitamin B6 metabolism. Under high salt stress, the DEGs of P. fucata with a red shell were significantly enriched in pathways arginine biosynthesis. 11 DEGs were randomly selected for quantitative real-time PCR, and the results were consistent with the RNA-seq. In addition, under high salt stress, DEGs were enriched into some pathways related to osmotic regulation and immune defense of P. fucata with black shell and red shell, such as Glycolysis / Gluconeogenesis, AMPK signaling pathway, Beta-Alanine metabolism, Glycine, serine and threonine metabolism, MAPK signaling pathway and Phagosome. The study showed that high salt stress had a greater influence on P. fucata with two shell colors, and P. fucata with a black shell made a positive immune defense response. Our results will improve to further understand the salt tolerance mechanism of P. fucata with different shell colors.

Proteomic analysis of hemocyte reveals the immune regulatory mechanisms after the injection of corticosteroid-releasing hormone in mud crab Scylla Paramamosain

Corticosteroid-releasing hormone (CRH) is a crucial neuroendocrine-immune factor regulating the immune response of Scylla paramamosain. To understand the regulatory mechanisms of CRH in S. paramamosain, the hemolymph of S. paramamosain with injection of CRH (1.5 ng/crab) at 24 h were chosen to perform proteomic analysis in this study. Furthermore, quantitative real-time PCR (RT-PCR) method was used to validate the accuracy of proteomic data at 24 h after CRH injection. The proteomic data showed that 255 DEPs were identified, in which 231 and 24 were up- or down-regulated, respectively. Besides, the results of enriched pathways showed that the DEPs were involved in signaling pathways, cellular immunity, humoral immunity and the response of immune related processes. These results revealed that CRH promoted the activation of signal transduction, regulated immune systems and antioxidation, and enhanced the immune related processes (such as protein synthesis, protein transport, carbohydrate mobilization and energy redistribution). These findings will benefit to foster the understanding on the effects of glucocorticoids on neuroendocrine-immune (NEI) networks of crustacean, and supply a substantial material and foundation for further researching of the NEI response. SIGNIFICANCE: Corticotrophin-releasing hormone (CRH) is a 41-amino acid neuropeptide and has been preliminarily studied in aquatic animals. CRH can regulate many important physiological activities comprising protein synthesis, energy metabolism, growth, breeding and behavior in fish, which play an important roles in neuroendocrine-immune (NEI) regulatory network of fish. The neuroendocrine system of crustacean has a primary research, that inspired by fish NEI network. Despite the research on the neuroendocrine system in crustacean has rapidly increased in recent years, our understanding of the regulation between neuroendocrine system and immune system in crustacean is still limited. The research on the strategy of NEI network in crustaceans becomes a significant issue. In the present study, the isobaric tags for relative and absolute quantification (iTRAQ) technology approach were applied to examine the NEI network of Scylla Paramamosain. control group and treatment group (CRH: 1.5 ng/crab) were settled for the iTRAQ experiment, and sampled at 24 h after CRH injection. The study aimed to gain knowledge on the immune response in Scylla Paramamosain after CRH injection and identify related differentially expressed proteins (DEPs) of the crab. The results of this study provide a preliminary resource for analysis the immune mechanism for crustaceans. In general, our work represents the first report of the utilization of the iTRAQ proteomics method for the study of NEI regulatory network in Scylla Paramamosain after CRH injection. We identified a number of DEPs involved in diverse pathways including immune signaling pathways, cellular immunity, humoral immunity, immune related process. These results demonstrated a very complex network involving immune and multiple related metabolic pathways in hemocytes of Scylla Paramamosain and will be of great value in understanding the crab neuroendocrine-immune immune mechanism.

Expression analysis of immune-associated genes in hemocytes of mud crab Scylla paramamosain under low salinity challenge

To gain knowledge on the immune response in Scylla paramamosain under low salinity challenge, S. paramamosain we investigated digital gene expression (DEG) in S. paramamosain hemocytes using the deep-sequencing platform Illumina Hiseq XTen. A total of 97,257 high quality unigenes with mean length 786.59 bp were found to be regulated by low salinity challenge, among which 93 unigenes were significantly up regulated, and 71 were significantly down regulated. Functional categorization and pathways analysis of differentially expressed genes revealed that immune signaling pathway including cAMP and cGMP signaling pathway were affected in low salinity stress. Cellular immunity-related genes including low-density lipoprotein receptor-related protein 6 (LRP6) and xanthine dehydrogenase (XDH) were down-regulated, indicating phagocytosis and oxygen dependent mechanism of phagocyte were suppressed in low salinity stress; Humoral immunity-related genes serine proteases and serpins 3 were up- and down-regulated, respectively, suggest that the proPO system was influenced by low salinity significantly; Moreover, processes related to immune response including carbohydrate metabolism, protein synthesis and lipid transport were found differentially regulated, implying the integrity of the immune response in low salinity stress. This study gained comprehensive insights on the immune mechanism of S. paramamosain at low salinity stress at the molecular level. The findings provide a theoretical basis for understanding immune mechanisms of S. paramamosain under low salinity stress, and technical reference for evaluating physiological adaptation in fresh water environment.

Transcriptomic analysis of Litopenaeus vannamei hepatopancreas under cold stress in cold-tolerant and cold-sensitive cultivars

Litopenaeus vannamei (L. vannamei) is one of the most widely cultured shrimp species in the world. The species often suffers from cold stress. To understand the molecular mechanism of cold tolerance, we performed transcriptomic analysis on two contrasting cultivars of L. vannamei, namely, cold-tolerant Guihai 2 (GH2) and cold-sensitive Guihai1 (GH1), under a control temperature (28 °C), cold stress (16 °C), and recovery to 28 °C. A total of 84.5 Gb of sequences were generated from 12 L. vannamei hepatopancreas libraries. The de-novo assembly generated a total of 143,029 unigenes with a mean size of 1,052 bp and an N50 of 2,604 bp, of which 34.08% were annotated in the Nr database. We analyzed the differentially expressed genes (DEGs) between nine comparison groups and detected a total of 21,026 DEGs. KEGG pathways, including lysosome, sphingolipid metabolism and nitrogen metabolism, were significantly enriched by DEGs between different temperatures in GH2. Furthermore, eight of the most significantly DEGs under cold stress from the transcriptomic analysis were selected for quantitative real-time PCR (qPCR) validation. Overall, we compared gene expression changes under cold stress in cold-tolerant and cold-sensitive L. vannamei for the first time. The results may further extend our understanding of the cold stress-response mechanism in L. vannamei.

Effects of dopamine on immune signaling pathway factors, phagocytosis and exocytosis in hemocytes of Litopenaeus vannamei

Dopamine (DA) is an important neuroendocrine factor, which can act as neurotransmitter and neurohormone. In this study, we explored the immune defense mechanism in Litopenaeus vannamei with injection of dopamine at 10^-7 and 10^-6 mol shrimp^-1, respectively. The genes expressions of dopamine receptor (DAR), G proteins (Gs, Gi, Gq), phagocytosis and exocytosis-related proteins, as well as intracellular signaling pathway factors, and immune defense parameters were measured. Results showed that mRNA expression levels of dopamine receptor D4 (D4), Gi, nuclear transcription factors and exocytosis-related proteins decreased significantly and reached the minimum at 3 h, while the genes expressions of Gs, Gq and phagocytosis-related proteins reached the highest and lowest levels at 3 h and 6 h, respectively. The second messenger synthetases increased significantly in treatment groups within 3 h. Simultaneously, the second messengers and protein kinases shared a similar trend, which were significantly elevated and reached the peak value at 3 h. Ultimately lead to the total hemocyte count (THC), proPO activity and phagocytic activity decreased significantly, reaching minimum values at 3 h, 3 h and 6 h, respectively. While PO activity showed obvious peak changes, which maximum value reached at 3 h. These results suggested that DA receptor could couple with G protein after DA injection and might regulate immunity through cAMP-PKA, DAG-PKC or CaM pathway.

Transcriptome analysis of hemocytes from the white shrimp Litopenaeus vannamei with the injection of dopamine

As a crucial neuroendocrine-immune factor, dopamine (DA) could regulate the immune system of Litopenaeus vannamei. To understand the immune mechanisms and regulatory pathways of DA in L. vannamei, the transcriptome analysis of hemocytes of L. vannamei with injection of DA (10^-6 mol/shrimp) at 3 and 12 h were performed in this study. Moreover, quantitative real-time PCR (qPCR) method was applied to validate the accuracy of transcriptome sequencing and analyze the expression pattern of candidate differentially expressed genes (DEGs) at different time points (0, 3, 6, 12, and 24 h) after DA injection. The results showed that a total of 51382 unigenes with a N50 length of 2341 bp were generated. And 1397 and 457 DEGs were obtained by comparative transcriptome at 3 and 12h respectively. Moreover, the results of functional annotation and enriched pathway showed that the DEGs were involved in phagosome (ko04145), lysosome (ko04142), Endocytosis (ko04144), and NOD-like receptor signaling pathway (ko04621). Besides, the Pearson's correlation coefficient (R) between transcriptome sequencing and qPCR was 0.845, which confirmed the reliability of the transcriptome sequencing results and the accuracy of assembly. Furthermore, the expression pattern of 15 candidate DEGs, containing 9 up-regulated and 6 down-regulated DEGs at 3 h, indicated the regulation of DA in physiological functions especially in the immune system. Therefore, these results revealed that DA induced the expressions of membrane receptors or proteins, activated intracellular signaling pathways, regulated cellular and humoral immune systems, controlled antioxidation and apoptosis, and was involved in the regulation of neuroendocrine system. These findings are helpful to promote the understanding on the effects of biogenic amines on physiological functions and regulatory networks of crustacean, and offer a substantial material and foundation for researching the immune response of crustacean.

Transcriptome signatures of the Pacific white shrimp Litopenaeus vannamei hepatopancreas in response to stress in biofloc culture systems

Comparative transcriptome analysis via high throughput sequencing was applied to gain knowledge on the immune response in Litopenaeus vannamei reared in biofloc technology systems (BFT). Two types of carbon sources, namely, traditional carbon sources (molasses) and biodegradable polymers [hydroxybutyric acid-co-3-hydroxyvaleric acid (PHBV)] were used in BFT systems. Clear water systems without the addition of carbon sources were treated as the control. Water quality assays showed that the average concentrations of several stress factors, including nitrite, nitrate and TSS, were the highest in molasses-based BFT systems. After sequencing and comparing the transcriptome profiles of the L. vannamei hepatopancreas, 743 and 201 genes were significantly differentially expressed in molasses- and PHBV-based BFT systems, respectively. GO enrichment analysis, which was performed using the differentially expressed genes, revealed seven significantly over-represented GO terms in molasses-based BFT systems, including catabolic process, hydrolase activity, cellular localization, organic substance metabolic process, cellular metabolic process, establishment of localization and response to stress. The captured key genes were mainly involved in the pathways including cellular stress response, immune response and pathogen recognition. However, no GO terms were significantly over-represented in PHBV-based BFT systems compared with control. This study indicates that shrimp are subject to stress in BFT systems when molasses serves as the carbon source. Thus, PHBV may be a better alternative.

Transcriptome profiling of the low-salinity stress responses in the gills of the juvenile Pseudopleuronectes yokohamae

Salinity is an important environmental factor that affects the life cycle of fish, including their growth, development and reproduction. The marbled flounder, Pseudopleuronectes yokohamae, is an important economic resource and serves as a good model to investigate osmoregulation, as it can adapt to a wide range of salinity levels. However, the lack of genomic resources for this species has hampered the understanding of the mechanisms underlying its salinity tolerance. In this study, RNA-Seq analysis was conducted to identify genes related to salinity adaptation and osmotic regulation in the gill tissue of marbled flounder exposed to different concentrations of environmental salinity (6 and 30 ppt). After de novo assembly, 19,265 genes were annotated by the Nr database. A comparison of expression between the two salinity groups revealed 673 differentially expressed genes, of which 180 were upregulated and 493 were downregulated in the low salinity group relative to the high salinity group. The related molecular biological processes were explored from several important perspectives, and potential functions were determined by enrichment analyses, including those of metabolites in ion transportation, energy metabolism and protein synthesis, and immune responses. This study is the first transcriptomic study conducted on marbled flounder, and it revealed many novel sequences for further biological analyses. In addition, the candidate genes identified in the gene expression analysis provided insights into responses to salinity change and molecular mechanisms underlying osmoregulation in the gills of marbled flounder.

Crustacean hyperglycemic hormone (CHH) affects hemocyte intracellular signaling pathways to regulate exocytosis and immune response in white shrimp Litopenaeus vannamei

Recombinant Litopenaeus vannamei CHH (rLvCHH) was obtained from a bacterial expression system and the intracellular signaling pathways involved in exocytosis and immune response after rLvCHH injection (0.2 and 2 μg/shrimp) was investigated in this study. The results showed that CHH contents increased 51.4%-110.2% (0.2 μg/shrimp) and 65.0%-211.3% (2 μg/shrimp) of the control level. And the contents of three biogenic amines in hemolymph presented a similar variation pattern after rLvCHH injection, but reached the highest level at different time points. Furthermore, the mRNA expression levels of membrane-bound guanylyl cyclase (mGC) (1.20-1.93 fold) and biogenic amine receptors, including type 2 dopamine receptor (DA2R) (0.72-0.89 fold), α2 adrenergic receptor (α2-AR) (0.72-0.91 fold) and 5-HT7 receptor (5-HT7R) (1.37-3.49 fold) in hemocytes were changed consistently with their ligands. In addition, the second messenger and protein kinases shared a similar trend and reached the maximum at the same time respectively. The expression levels of nuclear transcription factor (cAMP response element-binding protein, CREB) and exocytosis-related proteins transcripts were basically overexpressed after rLvCHH stimulation, which reached the peaks at 1 h or 3 h. Eventually, the phenoloxidase (PO) activity (37.4%-158.5%) and antibacterial activity (31.8%-122.3%) in hemolymph were dramatically enhanced within 6 h, while the proPO activity in hemocytes significantly decreased (11.2%-62.6%). Collectively, these results indicate that shrimps L. vannamei could carry out a simple but 'smart' NEI regulation by releasing different neuroendocrine factors at different stages after rLvCHH stimulation, which could couple with their receptors and trigger the downstream signaling pathways during the immune responses in hemocytes.

Effects of environmental stress on shrimp innate immunity and white spot syndrome virus infection

The shrimp aquaculture industry is plagued by disease. Due to the lack of deep understanding of the relationship between innate immune mechanism and environmental adaptation mechanism, it is difficult to prevent and control the diseases of shrimp. The shrimp innate immune system has received much recent attention, and the functions of the humoral immune response and the cellular immune response have been preliminarily characterized. The role of environmental stress in shrimp disease has also been investigated recently, attempting to clarify the interactions among the innate immune response, the environmental stress response, and disease. Both the innate immune response and the environmental stress response have a complex relationship with shrimp diseases. Although these systems are important safeguards, allowing shrimp to adapt to adverse environments and resist infection, some pathogens, such as white spot syndrome virus, hijack these host systems. As shrimp lack an adaptive immune system, immunization therapy cannot be used to prevent and control shrimp disease. However, shrimp diseases can be controlled using ecological techniques. These techniques, which are based on the innate immune response and the environmental stress response, significantly reduce the impact of shrimp diseases. The object of this review is to summarize the recent research on shrimp environmental adaptation mechanisms, innate immune response mechanisms, and the relationship between these systems. We also suggest some directions for future research.

Analysis of the transcriptome data in Litopenaeus vannamei reveals the immune basis and predicts the hub regulation-genes in response to high-pH stress

Soil salinization erodes the farmlands and poses a serious threat to human life, reuse of the saline-alkali lands as cultivated resources becomes increasingly prominent. Pacific white shrimp (Litopenaeus vannamei) is an important farmed aquatic species for the development and utilization of the saline-alkali areas. However, little is known about the adaptation mechanism of this species in terms of high-pH stress. In the present study, a transcriptome analysis on the gill tissues of L. vannamei in response to high-pH stress (pH 9.3 ± 0.1) was conducted. After analyzing, the cyclic nucleotide gated channel-Ca2+ (CNGC-Ca2+) and patched 1 (Ptc1) were detected as the majority annotated components in the cAMP signaling pathway (KO04024), indicating that the CNGC-Ca2+ and Ptc1 might be the candidate components for transducing and maintaining the high-pH stress signals, respectively. The immunoglobulin superfamily (IgSF), heat shock protein (HSP), glutathione s-transferase (GST), prophenoloxidase/phenoloxidase (proPO/PO), superoxide dismutase (SOD), anti-lipopolysaccharide factor (ALF) and lipoprotein were discovered as the major transcribed immune factors in response to high-pH stress. To further detect hub regulation-genes, protein-protein interaction (PPI) networks were constructed; the genes/proteins "Polymerase (RNA) II (DNA directed) polypeptide A" (POLR2A), "Histone acetyltransferase p300" (EP300) and "Heat shock 70kDa protein 8" (HSPA8) were suggested as the top three hub regulation-genes in response to acute high-pH stress; the genes/proteins "Heat shock 70kDa protein 4" (HSPA4), "FBJ murine osteosarcoma viral oncogene homolog" (FOS) and "Nucleoporin 54kDa" (NUP54) were proposed as the top three hub regulation-genes involved in adapting endurance high-pH stress; the protein-interactions of "EP300-HSPA8" and "HSPA4-NUP54" were detected as the most important biological interactions in response to the high-pH stress; and the HSP70 family genes might play essential roles in the adaptation of the high-pH stress environment in L. vannamei. These findings provide the first insight into the molecular and immune basis of L. vannamei in terms of high-pH environments, and the construction of a PPI network might improve our understanding in revealing the hub regulation-genes in response to abiotic stress in shrimp species and might be beneficial for further studies.

Independent and simultaneous effect of crustacean hyperglycemic hormone and dopamine on the hemocyte intracellular signaling pathways and immune responses in white shrimp Litopenaeus vannamei

Immune responses and intracellular signaling pathways were examined after hemolymph of Litopenaeus vannamei being incubated in Crustacean hyperglycemic hormone (CHH), dopamine (DA) and DA antagonist (Y). The results showed that the effect CHH and CHH + DA + Y on viability of hemocytes were no significant changes compared to the control group. However, in DA, DA + Y and CHH + DA groups, the viability of hemocytes decreased significantly. The phagocytic activity and the antibacterial activity of CHH group were increased significantly within 12h. Whereas the CHH + DA, DA were significantly lower than the control. PO in haemolymph was up-regulated after CHH and DA incubation. The proPO has the opposite change in all groups. In addition, DA + Y, CHH + DA + Y has a similar trend with the DA and CHH respectively. Furthermore, a significant increase of cAMP, CaM and cGMP were found in treatment groups except for the CaM concentration of the CHH group and the cGMP concentration of DA group. There is no significant change observed in the CHH group about CaM concentration. Whereas the cGMP of DA group decreased within 12h. The results suggest that DA could depress the immune responses by cAMP-, CaM-pathways. However, the CHH is on the contrary, which transduced the signals from cAMP, cGMP to PKA, PKC and PKG to enhance the immune response parameters.

Fipronil-induced toxic effects in zebrafish (Danio rerio) larvae by using digital gene expression profiling

Fipronil residue has caused widespread concern around the world, especially after the recent "toxic eggs" event in seven European countries. To evaluate the effects of fipronil on vertebrates, zebrafish larvae were used as an animal model to examine the lethal effect, developmental phenotypes at high doses, and possible mechanisms of toxicity by employing digital gene expression (DGE) profiling at environmentally relevant doses. The results of acute toxicity test indicated that treatment with fipronil from 75 h post-fertilization (hpf) led to the death of larvae with a 96-h LC50 value of 459 μg/L, as well as abnormal development including bent spine and shortened body length. Besides, we obtained high-quality-sequencing DGE profilings at fipronil concentrations of 0.5, 5, and 50 μg/L, respectively. The results revealed that 44 differentially expressed genes, 10 GO terms, and 3 KEGG pathways were overlapped among the three concentrations. MIDN, one of the 44 differentially expressed genes, showed dose-dependent responses at the transcriptional level, indicating that it was possibly a potential biomarker to reflect fipronil toxicity in zebrafish. Furthermore, we presumed that the changing transcriptional level of AP-1 family was possibly a reason for bent spine and shortened body length in larvae exposed to fipronil. Concurrently, altered abundance of transcripts of the ELOVL family in a key step of fatty acid elongation could possibly lead to the accumulation of long-chain fatty acids. Collectively, our results suggested that exposure to fipronil caused lethal and developmental toxicity in zebrafish larvae, and demonstrated the need for a comprehensive understanding of the potential mechanisms of fipronil toxicity due to fipronil's frequent presence in the environment and its potential threat to human health.

Effects of ammonia-N exposure on the concentrations of neurotransmitters, hemocyte intracellular signaling pathways and immune responses in white shrimp Litopenaeus vannamei

The effects of ammonia-N exposure (transferred from 0.07 to 2, 10 and 20 mg L^-1) on the mechanism of neuroendocrine-immunoregulatory network were investigated in Litopenaeus vannamei. The results showed that biogenic amines (dopamine, noradrenaline, 5-hydroxytryptamine) concentrations in treatment groups increased significantly within 12 h. The gene expression of guanylyl cyclase increased significantly from 3 h to 24 h. And dopamine receptor D₄ and α₂ adrenergic receptor gene expression in treatment groups decreased significantly within 12 h, whereas the mRNA expression of 5-HT₇ receptor increased significantly within 3 h and reached the peak levels at 6 h. The second messengers (cAMP, cGMP) and Calmodulin (CaM) increased significantly in treatment groups after 3 h. The concentrations of protein kinases (PKA, PKG) shared a similar trend in cAMP and cGMP which were up-regulated and reached the peak value at 6 h, while the PKC decreased within 3 h and arrived at its bottom at 6 h. The nuclear factor kappa-b and cAMP-response element binding protein mRNA expression levels of treatment shrimps increased sharply and reached maximum values at 6 h. The total hemocyte count, phagocytic activity, antibacterial activity in treatment groups decreased dramatically within 48 h. Whereas the phenoloxidase activities slightly up-regulated. Then it was decreased significantly up to 48 h. α₂-macroglobulin activity decreased at the first 3 h-stress. Then they up-regulated significantly in 6 h. The results suggest that there are two crucial neuroendocrine substances (biogenic amine and CHH), which play a principal role in adapting to ammonia-N exposure and cause immune response through cAMP-, CaM- and cGMP-dependent pathways.

Microbiome Dynamics in a Shrimp Grow-out Pond with Possible Outbreak of Acute Hepatopancreatic Necrosis Disease

Acute hepatopancreatic necrosis disease (AHPND) (formerly, early mortality syndrome) is a high-mortality-rate shrimp disease prevalent in shrimp farming areas. Although AHPND is known to be caused by pathogenic Vibrio parahaemolyticus hosting the plasmid-related PirAB^vp toxin gene, the effects of disturbances in microbiome have not yet been studied. We took 62 samples from a grow-out pond during an AHPND developing period from Days 23 to 37 after stocking white postlarvae shrimp and sequenced the 16S rRNA genes with Illumina sequencing technology. The microbiomes of pond seawater and shrimp stomachs underwent varied dynamic succession during the period. Despite copies of PirAB^vp, principal co-ordinates analysis revealed two distinctive stages of change in stomach microbiomes associated with AHPND. AHPND markedly changed the bacterial diversity in the stomachs; it decreased the Shannon index by 53.6% within approximately 7 days, shifted the microbiome with Vibrio and Candidatus Bacilloplasma as predominant populations, and altered the species-to-species connectivity and complexity of the interaction network. The AHPND-causing Vibrio species were predicted to develop a co-occurrence pattern with several resident and transit members within Candidatus Bacilloplasma and Cyanobacteria. This study’s insights into microbiome dynamics during AHPND infection can be valuable for minimising this disease in shrimp farming ponds.

Transcriptomic analyses on muscle tissues of Litopenaeus vannamei provide the first profile insight into the response to low temperature stress

The Pacific white shrimp (Litopenaeus vannamei) is an important cultured crustacean species worldwide. However, little is known about the molecular mechanism of this species involved in the response to cold stress. In this study, four separate RNA-Seq libraries of L. vannamei were generated from 13°C stress and control temperature. Total 29,662 of Unigenes and overall of 19,619 annotated genes were obtained. Three comparisons were carried out among the four libraries, in which 72 of the top 20% of differentially-expressed genes were obtained, 15 GO and 5 KEGG temperature-sensitive pathways were fished out. Catalytic activity (GO: 0003824) and Metabolic pathways (ko01100) were the most annotated GO and KEGG pathways in response to cold stress, respectively. In addition, Calcium, MAPK cascade, Transcription factor and Serine/threonine-protein kinase signal pathway were picked out and clustered. Serine/threonine-protein kinase signal pathway might play more important roles in cold adaptation, while other three signal pathway were not widely transcribed. Our results had summarized the differentially-expressed genes and suggested the major important signaling pathways and related genes. These findings provide the first profile insight into the molecular basis of L. vannamei response to cold stress.

Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress

Hybrid oysters often show heterosis in growth rate, weight, survival and adaptability to extremes of salinity. Oysters have also been used as model organisms to study the evolution of host-defense system. To gain comprehensive knowledge about various physiological processes in hybrid oysters under low salinity stress, we performed transcriptomic analysis of gill tissue of Crassostrea sikamea ♀ × Crassostrea angulata♂ hybrid using the deep-sequencing platform Illumina HiSeq. We exploited the high-throughput technique to delineate differentially expressed genes (DEGs) in oysters maintained in hypotonic conditions. A total of 199,391 high quality unigenes, with average length of 644 bp, were generated. Of these 35 and 31 genes showed up- and down-regulation, respectively. Functional categorization and pathway analysis of these DEGs revealed enrichment for immune mechanism, apoptosis, energy metabolism and osmoregulation under low salinity stress. The expression patterns of 41 DEGs in hybrids and their parental species were further analyzed by quantitative real-time PCR (qRT-PCR). This study will serve as a platform for subsequent gene expression analysis regarding environmental stress. Our findings will also provide valuable information about gene expression to better understand the immune mechanism, apoptosis, energy metabolism and osmoregulation in hybrid oysters under low salinity stress.

Transcriptional changes in oysters Crassostrea brasiliana exposed to phenanthrene at different salinities

Euryhaline animals from estuaries, such as the oyster Crassostrea brasiliana, show physiological mechanisms of adaptation to tolerate salinity changes. These ecosystems receive constant input of xenobiotics from urban areas, including polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene (PHE). In order to understand the influence of salinity on the molecular responses of C. brasiliana exposed to PHE, oysters were acclimatized to different salinities (35, 25 and 10) for 15days and then exposed to 100μgL^-1 PHE for 24h and 96h. Control groups were kept at the same salinities without PHE. Oysters were sampled for chemical analysis and the gills were excised for mRNA quantification by qPCR. Transcript levels of different genes were measured, including some involved in oxidative stress pathways, phases I and II of the xenobiotic biotransformation systems, amino acid metabolism, fatty acid metabolism and aryl hydrocarbon receptor nuclear translocator putative gene. Higher transcript levels of Sulfotransferase-like gene (SULT-like) were observed in oysters exposed to PHE at salinity 10 compared to control (24h and 96h); cytochrome P450 isoforms (CYP2AU1, CYP2-like1) were more elevated in oysters exposed for 24h and CYP2-like2 after 96h of oysters exposed to PHE at salinity 10 compared to control. These results are probably associated to an enhanced Phase I biotransformation activity required for PHE detoxification under hyposmotic stress. Higher transcript levels of CAT-like, SOD-like, GSTm-like (96h) and GSTΩ-like (24h) in oysters kept at salinity 10 compared to organisms at salinities 25 and/or 35 are possibly related to enhaced ROS production. The transcription of these genes were not affected by PHE exposure. Amino acid metabolism-related genes (GAD-like (24h), GLYT-like, ARG-like (96h) and TAUT-like at 24h and 96h) also showed different transcription levels among organisms exposed to different salinities, suggesting their important role for oyster salinity adaptation, which is not affected by exposure to these levels of PHE.

A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)

Background

Understanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salinity levels, and efficient osmoregulatory (ionic balance) ability is the main mechanism to overcome the problems related to environmental salinity gradients.

Methods

To better understand how osmoregulatory performance in freshwater (FW) crustaceans allow individuals to acclimate and adapt to raised salinity conditions, here we (i), reviewed the literature on genes that have been identified to be associated with osmoregulation in FW crustaceans, and (ii), performed a transcriptomic analysis using cDNA libraries developed from mRNA isolated from three important osmoregulatory tissues (gill, antennal gland, hepatopancreas) and total mRNA from post larvae taken from the freshwater prawn, Macrobrachium australiense using Illumina deep sequencing technology. This species was targeted because it can complete its life cycle totally in freshwater but, like many Macrobrachium sp., can also tolerate brackish water conditions and hence should have genes associated with tolerance of both FW and saline conditions.

Results

We obtained between 55.4 and 65.2 million Illumina read pairs from four cDNA libraries. Overall, paired end sequences assembled into a total of 125,196 non-redundant contigs (≥200 bp) with an N50 length of 2,282 bp and an average contig length of 968 bp. Transcriptomic analysis of M. australiense identified 32 different gene families that were potentially involved with osmoregulatory capacity. A total of 32,597 transcripts were specified with gene ontology (GO) terms identified on the basis of GO categories. Abundance estimation of expressed genes based on TPM (transcript per million) ≥20 showed 1625 transcripts commonly expressed in all four libraries. Among the top 10 genes expressed in four tissue libraries associated with osmoregulation, arginine kinase and Na+/K+- ATPase showed the highest transcript copy number with 7098 and 660, respectively in gill which is considered to be the most important organ involved in osmoregulation.

Discussion

The current study provides the first broad transcriptome from M. australiense using next generation sequencing and identifies potential candidate genes involved in salinity tolerance and osmoregulation that can provide a foundation for investigating osmoregulatory capacity in a wide variety of freshwater crustaceans.

Analysis of digital gene expression profiling in hemocytes of white shrimp Litopenaeus vannamei under nitrite stress

Accumulation of nitrite in water is highly toxic to aquatic animals. To understand immune responses in shrimp under such environmental stress, a digital gene expression (DGE) technology was applied to detect the gene expression profile of the Litopenaeus vannamei hemocytes in response to nitrite for 48 h. A total of 1922 differently expressed unigenes were generated. Of these transcripts, 1269 and 653 genes were up- or down-regulated respectively. Functional categorization and pathways of the differentially expressed genes revealed that immune defense, xenobiotics biodegradation and metabolism, amino acid and nucleobase metabolic process, apoptosis were the differentially regulated processes occurring during nitrite stress. We selected 19 differential expression transcripts (DETs) to validate the sequencing results by real time quantitative PCR (qPCR). The Pearson's correlation coefficient (R) of the 19 DETs was 0.843, which confirmed the consistency and accuracy between these two approaches. Subsequently, we screened 10 genes to examine the changes in the time course of gene expression in more detail. The results indicated that expressions of ATP-binding cassette transporter (ABC transporter), caspase10, QM protein, C type lectin 4 (CTL4), protein disulfide isomerase (PDI), serine protease inhibitor 8 (SPI8), transglutaminase (TGase), chitinase1, inhibitors of apoptosis proteins (IAP) and cytochrome P450 enzyme (CYP450) were induced to participate in the anti-stress defense against nitrite. These results will provide a reference for follow-up study of molecular toxicology and valuable gene information for better understanding of immune response in L. vannamei under environmental stress.

Effect of salinity on regulation mechanism of neuroendocrine-immunoregulatory network in Litopenaeus vannamei

The effects of low salinity (transferred from 31‰ to 26‰, 21‰, and 16‰) on the regulation pathways of neuroendocrine-immunoregulatory network were investigated in Litopenaeus vannamei. The results showed that the hormones (corticotrophin-releasing hormone, adrenocorticotropic hormone) and biogenic amines (dopamine, noradrenaline, 5-hydroxytryptamine) concentrations in lower salinity groups increased significantly within 12 h. The gene expression of biogenic amine receptors showed that dopamine receptor D4 and α2 adrenergic receptor in lower salinity groups decreased significantly within 12 h, whereas the 5-HT7 receptor significantly increased within 1d. The second messenger synthetases (adenylyl cyclase, phospholipase C) and the second messengers (cyclic adenosine monophosphate, cyclic guanosine monophosphate) of lower salinity groups shared a similar trend in which adenylyl cyclase and cyclic adenosine monophosphate reached the maximum at 12 h, whereas phospholipase C and cyclic guanosine monophosphate reached the minimum. The immune parameters (total hemocyte count, phenoloxidase activity, phagocytic activity, crustin expression, antibacterial activity, C-type lectin expression, hemagglutinating activity) in lower salinity groups decreased significantly within 12 h. Except for the total hemocyte count, all the parameters recovered to the control levels afterwards. Therefore, it may be concluded that the neuroendocrine-immunoregulatory network plays a principal role in adapting to salinity changes as the main center for sensing the stress and causes immune response in L. vannamei.

Gene Expression Analysis of Pak Choi in Response to Vernalization

Pak choi is a seed vernalization-type plant whose vernalization mechanism is currently unclear. Therefore, it is critical to discover genes related to vernalization and research its functions during vernalization in pak choi. Here, the gene expression profiles in the shoot apex were analyzed after low temperature treatment using high-throughput RNA sequencing technology. The results showed that there are 1,664 and 1,192 differentially expressed genes (DEGs) in pak choi in cold treatment ending and before flower bud differentiation, respectively, including 42 genes that exhibited similar expression trend at both stages. Detailed annotation revealed that the proteins encoded by the DEGs are located in the extracellular region, cell junction and extracellular matrix. These proteins exhibit activity such as antioxidant activity and binding protein/transcription factor activity, and they are involved in signal transduction and the immune system/biological processes. Among the DEGs, Bra014527 was up-regulated in low temperature treatment ending, Bra024097 was up-regulated before flower bud differentiation and Bra035940 was down-regulated at both stages in low temperature-treated shoot apices. Homologues of these genes in A. thaliana, AT3G59790, AT4G30200 and AT5G61150, are involved in flowering and vernalization, suggesting that they take part in the vernalization process in pak choi. Further pathway enrichment analysis revealed that most genes were enriched in the tryptophan metabolism and glucosinolate biosynthesis pathways. However, the functions of tryptophan and glucosinolate in vernalization are not yet clear and require further analysis.

Transcriptome Profiling and Molecular Pathway Analysis of Genes in Association with Salinity Adaptation in Nile Tilapia Oreochromis niloticus

Nile tilapia Oreochromis niloticus is a freshwater fish but can tolerate a wide range of salinities. The mechanism of salinity adaptation at the molecular level was studied using RNA-Seq to explore the molecular pathways in fish exposed to 0, 8, or 16 (practical salinity unit, psu). Based on the change of gene expressions, the differential genes unions from freshwater to saline water were classified into three categories. In the constant change category (1), steroid biosynthesis, steroid hormone biosynthesis, fat digestion and absorption, complement and coagulation cascades were significantly affected by salinity indicating the pivotal roles of sterol-related pathways in response to salinity stress. In the change-then-stable category (2), ribosomes, oxidative phosphorylation, signaling pathways for peroxisome proliferator activated receptors, and fat digestion and absorption changed significantly with increasing salinity, showing sensitivity to salinity variation in the environment and a responding threshold to salinity change. In the stable-then-change category (3), protein export, protein processing in endoplasmic reticulum, tight junction, thyroid hormone synthesis, antigen processing and presentation, glycolysis/gluconeogenesis and glycosaminoglycan biosynthesis—keratan sulfate were the significantly changed pathways, suggesting that these pathways were less sensitive to salinity variation. This study reveals fundamental mechanism of the molecular response to salinity adaptation in O. niloticus, and provides a general guidance to understand saline acclimation in O. niloticus.

Transcriptome and Molecular Pathway Analysis of the Hepatopancreas in the Pacific White Shrimp Litopenaeus vannamei under Chronic Low-Salinity Stress

The Pacific white shrimp Litopenaeus vannamei is a euryhaline penaeid species that shows ontogenetic adaptations to salinity, with its larvae inhabiting oceanic environments and postlarvae and juveniles inhabiting estuaries and lagoons. Ontogenetic adaptations to salinity manifest in L. vannamei through strong hyper-osmoregulatory and hypo-osmoregulatory patterns and an ability to tolerate extremely low salinity levels. To understand this adaptive mechanism to salinity stress, RNA-seq was used to compare the transcriptomic response of L. vannamei to changes in salinity from 30 (control) to 3 practical salinity units (psu) for 8 weeks. In total, 26,034 genes were obtained from the hepatopancreas tissue of L. vannamei using the Illumina HiSeq 2000 system, and 855 genes showed significant changes in expression under salinity stress. Eighteen top Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly involved in physiological responses, particularly in lipid metabolism, including fatty-acid biosynthesis, arachidonic acid metabolism and glycosphingolipid and glycosaminoglycan metabolism. Lipids or fatty acids can reduce osmotic stress in L. vannamei by providing additional energy or changing the membrane structure to allow osmoregulation in relevant organs, such as the gills. Steroid hormone biosynthesis and the phosphonate and phosphinate metabolism pathways were also involved in the adaptation of L. vannamei to low salinity, and the differential expression patterns of 20 randomly selected genes were validated by quantitative real-time PCR (qPCR). This study is the first report on the long-term adaptive transcriptomic response of L. vannamei to low salinity, and the results will further our understanding of the mechanisms underlying osmoregulation in euryhaline crustaceans.