Integrative transcriptome and metabolome analysis reveals the discrepancy in the accumulation of active ingredients between Lycium barbarum cultivars.

MAIN CONCLUSION: The combined analysis of transcriptome and metabolome provided molecular insight into the dynamics of multiple active ingredients biosynthesis and accumulation across different cultivars of Lycium barbarum. Lycium barbarum L. has a high concentration of active ingredients and is well known in traditional Chinese herbal medicine for its therapeutic properties. However, there are many Lycium barbarum cultivars, and the content of active components varies, resulting in inconsistent quality between Lycium barbarum cultivars. At present, few research has been conducted to reveal the difference in active ingredient content among different cultivars of Lycium barbarum at the molecular level. Therefore, the transcriptome of 'Ningqi No.1' and 'Qixin No.1' during the three development stages (G, T, and M) was constructed in this study. A total of 797,570,278 clean reads were obtained. Between the two types of wolfberries, a total of 469, 2394, and 1531 differentially expressed genes (DEGs) were obtained in the 'G1 vs. G10,' 'T1 vs. T10,' and 'M1 vs. M10,' respectively, and were annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology identifiers. Using these transcriptome data, most DEGs related to the metabolism of the active ingredients in 'Ningqi No.1' and 'Qixin No.1' were identified. Moreover, a widely targeted metabolome analysis of the metabolites of 'Ningqi 1' and 'Qixin 1' fruits at the maturity stage revealed 1,135 differentially expressed metabolites (DEMs) in 'M1 vs. M10,' and many DEMs were associated with active ingredients such as flavonoids, alkaloids, terpenoids, and so on. We further quantified the flavonoid, lignin, and carotenoid contents of the two Lycium barbarum cultivars during the three developmental stages. The present outcome provided molecular insight into the dynamics of multiple active ingredients biosynthesis and accumulation across different cultivars of Lycium barbarum, which would provide the basic data for the formation of Lycium barbarum fruit quality and the breeding of outstanding strains.

Identification, diversity, and evolution analysis of thioester-containing protein family in Pacific oyster (Crassostrea gigas) and immune response to biotic and abiotic stresses.

Thioester-containing proteins (TEPs) play a vital role in the innate immune response to biotic and abiotic stresses. In this study, the TEPs in C. gigas were identified, and their gene structure, phylogenetic relationships, collinearity relationships, expression profiles, sequence diversity, and alternative splicing were analyzed. Eight Tep genes were identified in C. gigas genome. Functional analysis and evolutionary relationships indicated a high level of homology to other mollusks TEPs. The transcriptome quantitative analysis results showed that the Tep genes in C. gigas respond to heat stress and Vibrio stress. Alternative splicing analysis revealed four Tep genes (designated A2M_1, CD109_3, CD109_5, complement C3) encode multiple alternative splice variants. Analysis of gene structure and multiple alignments revealed that seven CD109_5 variants are produced through the alternative splicing of the 19th exon, which encodes the highly variable central region. Sequence diversity analysis revealed thirteen missense variants within the 19th exon region of these seven CD109_5 alternative splice variants. Furthermore, the differential alternative splicing analysis showed significant induction of CD109_5, A2M_1 and A2M_2 variants after infection with V. parahaemolyticus. This study explores the Tep genes of C. gigas, providing insights into the molecular mechanisms underlying the involvement of C. gigas TEPs in innate immunity.

Identification of toll-like receptor family and the immune function of new Sptlr-6 gene of Scylla paramamosain.

As a crucial member of pattern-recognition receptors (PRRs), the Tolls/Toll-like receptors (TLRs) gene family has been proven to be involved in innate immunity in crustaceans. In this study, nine members of TLR gene family were identified from the mud crab (Scylla paramamosain) transcriptome, and the structure and phylogeny of different SpTLRs were analyzed. It was found that different SpTLRs possessed three conserved structures in the TIR domain. Meanwhile, the expression patterns of different Sptlr genes in examined tissues detected by qRT-PCR had wide differences. Compared with other Sptlr genes, Sptlr-6 gene was significantly highly expressed in the hepatopancreas and less expressed in other tissues. Therefore, the function of Sptlr-6 was further investigated. The expression of the Sptlr-6 gene was up-regulated by Poly I: C, PGN stimulation and Vibrio parahaemolyticus infection. In addition, the silencing of Sptlr-6 in hepatopancreas mediated by RNAi technology resulted in the significant decrease of several conserved genes involved in innate immunity in mud crab after V. parahaemolyticus infection, including relish, myd88, dorsal, anti-lipopolysaccharide factor (ALF), anti-lipopolysaccharide factor 2 (ALF-2) and glycine-rich antimicrobial peptide (glyamp). This study provided new knowledge for the role of the Sptlr-6 gene in defense against V. parahaemolyticus infection in S. paramamosain.

Identification, diversity, and evolution analysis of Commd gene family in Haliotis discus hannai and immune response to biotic and abiotic stresses.

The Commd (Copper Metabolism gene MURR1 Domain) family genes play crucial roles in various biological processes, including copper and sodium transport regulation, NF-κB activity, and cell cycle progression. Their function in Haliotis discus hannai, however, remains unclear. This study focused on identifying and analyzing the Commd genes in H. discus hannai, including their gene structure, phylogenetic relationships, expression profiles, sequence diversity, and alternative splicing. The results revealed significant homology between H. discus hannai's Commd genes and those of other mollusks. Both transcriptome quantitative analysis and qRT-PCR demonstrated the responsiveness of these genes to heat stress and Vibrio parahaemolyticus infection. Notably, alternative splicing analysis revealed that COMMD2, COMMD4, COMMD5, and COMMD7 produce multiple alternative splice variants. Furthermore, sequence diversity analysis uncovered numerous missense mutations, specifically 9 in COMMD5 and 14 in COMMD10. These findings contribute to expanding knowledge on the function and evolution of the Commd gene family and underscore the potential role of COMMD in the innate immune response of H. discus hannai. This research, therefore, offers a novel perspective on the molecular mechanisms underpinning the involvement of Commd genes in innate immunity, paving the way for further explorations in this field.

Genome-wide identification of toll-like receptors in Octopus sinensis and expression analysis in response to different PAMPs stimulation.

Toll-like receptors (TLRs) are one of the extensively studied pattern recognition receptors (PRRs) and play crucial roles in the immune responses of vertebrates and invertebrates. In this study, 14 TLR genes were identified from the genome-wide data of Octopus sinensis. Protein structural domain analysis showed that most TLR proteins had three main structural domains: extracellular leucine-rich repeats (LRR), transmembrane structural domains, and intracellular Toll/IL-1 receptor domain (TIR). The results of subcellular localization prediction showed that the TLRs of O. sinensis were mainly located on the plasma membrane. The results of quantitative real-time PCR (qPCR) showed that the detected TLR genes were differentially expressed in the hemolymph, white bodies, hepatopancreas, gills, gill heart, intestine, kidney, and salivary gland of O. sinensis. Furthermore, the present study investigated the expression changes of O. sinensis TLR genes in hemolymph, white bodies, gills, and hepatopancreas in different phases (6 h, 12 h, 24 h, 48 h) after stimulation with PGN, poly(I: C) and Vibrio parahaemolyticus. The expression of most of the TLR genes was upregulated at different time points after infection with pathogens or stimulation with PAMPs, a few genes were unchanged or even down-regulated, and many of the TLR genes were much higher after V. parahaemolyticus infection than after PGN and poly(I:C) stimulation. The results of this study contribute to a better understanding of the molecular immune mechanisms of O. sinensis TLRs genes in resistance to pathogen stimulation.

Transcriptional regulation of IAG by dsx and foxl-2 in mud crab (Scylla paramamosain).

Scylla paramamosain is an important cultured crab species on the southeast coast of China. However, the molecular regulation mechanism of its gonadal development still has not been thoroughly studied. Dsx (doublesex) and foxl-2 (forkhead transcription factor gene 2) are important transcription factors involved in gonadal development. So far, studies on the functions of dsx and foxl-2 in crustaceans are very limited. Insulin-like androgenic gland hormone (IAG) is an effector molecule that regulates the differentiation, development and sex maintenance of testes in crustaceans. In this study, the promoter region of Sp-IAG was predicted, and several potential binding sites of dsx and foxl-2 were found. Site-directed mutagenesis was performed on the predicted potential binding sites, and their promoter activity was analyzed. The results showed that there was a dsx and a foxl-2 binding site, respectively, that could regulate the expression of Sp-IAG. In order to verify the regulatory effect of these two transcription factors on Sp-IAG, we constructed the expression plasmids of dsx and foxl-2 and co-transfected them into HEK293T cell lines with the promoter of Sp-IAG, respectively. The results showed that dsx could significantly promote the expression of Sp-IAG, while foxl-2 could inhibit its expression substantially. Then we carried out in vivo RNA interference experiment on mud crabs. The expression of dsx and foxl-2 in crabs was interfered respectively. The results of qRT-PCR showed that the expression of Sp-IAG was significantly inhibited after interfering with dsx, while significantly increased after interfering with foxl-2, which was consistent with the cell experiment. In conclusion, dsx and foxl-2 transcription factors play opposite roles in regulating the expression of Sp-IAG.

ERß activation improves nonylphenol-induced depression and neurotransmitter secretion disruption via the TPH2/5-HT pathway.

The aim of this study is to investigate the role of estrogen receptor ß (ERß) in nonylphenol (NP) - induced depression - like behavior in rats and its impact on the regulation of the TPH2/5-HT pathway. In the in vitro experiment, rat basophilic leukaemia cells (RBL-2H3) cells were divided into the four groups: blank group, NP group (20 µM), ERß agonist group (0.01 µM), and NP＋ERß agonist group (20 µM＋0.01 µM). For the in vivo experiment, 72 adult male Sprague-Dawley rats were randomly divided into following six groups: the Control, NP (40 mg/kg) group, ERß agonist (2 mg/kg, Diarylpropionitrile (DPN)) group, ERß inhibitor (0.1 mg/kg, 4-(2-phenyl-5,7-bis(trifluoromethyl)pyrazolo[1,5-a]pyrimidin-3-yl) phenol (PHTPP)) group, NP+ERß agonist (40 mg/kg NP ＋ 2 mg/kg DPN) group, and NP+ERß inhibitor (40 mg/kg NP + 0.1 mg/kg PHTPP) group, with 12 rats in each group. Each rat in drug group were given NP by gavage and/or received a single intraperitoneal injection of DPN 2 mg/kg or PHTPP 0.1 mg/kg. Both in vivo and in vitro, NP group showed a decrease in the expression levels of ERß, tryptophan hydroxylase (TPH1), and tryptophan hydroxylase-2 (TPH2) genes and proteins, and reduced levels of DA, NE, and 5-hydroxytryptophan (5-HT) neurotransmitters. RBL-2H3 cells showed signs of cell shrinkage, with rounded cells, increased suspension and more loosely arranged cells. The effectiveness of the ERß agonist stimulation exhibited an increase exceeding 60% in RBL-2H3 cells. The application of ERß agonist resulted in an alleviation the aforementioned alterations. ERß agonist activated the TPH2/5-HT signaling pathways. Compared to the control group, the NP content in the brain tissue of the NP group was significantly increased. The latency to eat for the rats was longer and the amount of food consumed was lower, and the rats had prolonged immobility time in the behavioral experiment of rats. The expression levels of ERß, TPH1, TPH2, 5-HT and 5-HITT proteins were decreased in the NP group, suggesting NP-induced depression-like behaviours as well as disturbances in the secretion of serum hormones and monoamine neurotransmitters. In the NP group, the midline raphe nucleus showed an elongated nucleus with a dark purplish-blue colour, nuclear atrophy, displacement and pale cytoplasm. ERß might ameliorate NP-induced depression-like behaviors, and secretion disorders of serum hormones and monoamine neurotransmitters via activating TPH2/5-HT signaling pathways.

dmrtb1 is involved in the testicular development in Larimichthys crocea.

In brief: dmrtb1 performs critical functions in sex determination/differentiation and gonadal development in many organisms, but its role in teleost is rarely studied. Through gene cloning, in situ hybridization, and RNA interference technology, the function of dmrtb1 in testicular development of large yellow croaker (Larimichthys crocea) was studied; our study will be helpful in understanding further the molecular regulation mechanism of Lcdmrtb1/Lcdmrt6 in testicular development in L. crocea, and our results enrich the theory of fish dmrts involved in reproductive regulation and provide a new idea for sex control breeding of L. crocea by manipulating reproductive pathway. Abstract: Doublesex- and mab-3-related transcription factor B1 (dmrtb1/dmrt6) belongs to one of the members of DMRT family, which performs critical functions in sex determination and differentiation, gonadal development, and functional maintenance. However, knowledge of its exact mechanism remains unclear in teleost. Very little is known about the role of dmrtb1 in the gonad development of Larimichthys crocea. In this study, a dmrtb1 homolog in L. crocea named as Lcdmrtb1 with the full-length cDNA was isolated and characterized. Except for the conserved DM domain, the other regions had low homology. Of the tissues sampled, Lcdmrtb1 was only found to be highly expressed in the testis. In situ hybridization of testis revealed Lcdmrtb1 in both spermatogonia and spermatocytes. After Lcdmrtb1 interference in the testis cells (LYCT) of L. crocea, the expression levels of Lcdmrtb1 and Lcdmrt1 were significantly decreased; subsequently, testicular cell morphology changed from fibrous to round and their growth rate slowed. Similarly, the expression levels of Lcdmrtb1, Lcdmrt1, sox9a/b, and amh were significantly decreased after RNAi in the testis. Furthermore, it was discovered that the spermatogonia had disappeared, and the Sertoli cells had been reduced. The results of immunohistochemistry showed that the expression of Sox9 protein in the testis was not detected after dmrtb1 was knocked down. These results indicated that the absence of Lcdmrtb1 not only greatly inhibited cell growth and destroyed the morphology of testis cells but also down-regulated Lcdmrt1 expression in the testis. This study will be helpful in understanding further the molecular regulation mechanism of Lcdmrtb1/Lcdmrt6 in testicular development in L. crocea.

Genome-wide identification and characterization of Toll-like receptors (TLR) genes in Haliotis discus hannai, H. rufescens, and H. laevigata.

Toll-like receptors (TLRs) play essential roles in the innate immune system and have been extensively studied in mollusks. In this study, through a genome-wide search, TLR genes were identified as 29 in Haliotis discus hannai, 33 in H. rufescens, and 16 in H. laevigata. Domain analysis indicated that these TLR genes contain leucine-rich repeat (LRR) and Toll/IL-1 receptor (TIR) domains and exons ranging from 1 to 5. Polymorphism analysis showed that the TLRs in abalones did not have high diversities with 143 SNPs and no Indel in H. discus hannai, 92 SNPs and 3 Indels together with 6 missense mutations in H. rufescens, and no SNP or Indel in H. laevigata. The expression of 8 TLR genes in H. discus hannai was confirmed in the hepatopancreas, gill, hemolymph, gonads, intestine, muscle, and mantle. The expression of five TLR genes (out of 8) in gills (p < 0.05), three in hepatopancreas (p < 0.05), and three in hemolymph (p < 0.05) was upregulated separately in response to the infection caused by Vibrio parahaemolyticus. The findings in this study would contribute to a better understanding of the molecular immune mechanism of H. discus hannai against stimulation by V. parahaemolyticus and provide a basis for the study of TLRs in abalones.

Thionine-mediated electrocatalytic reduction for electrochemical detection of EDTA-Fe(III) in soy sauce.

Electrocatalytic reactions based on electron transfer mediators provide a simple and effective route for the development of convenient and sensitive electrochemical assays. Here, we report a novel electrocatalytic assay for detection of EDTA-Fe(III), which is widely used as a supplement in iron-fortified foods to reduce prevalence of iron deficiency. Unlike conventional electrochemical methods to detect Fe(III) ion, signaling mechanism of our electrocatalytic assay relies on the previously unexplored thionine-mediated electrochemical reduction of EDTA-Fe(III). This electrocatalytic detection method is sensitive for EDTA-Fe(III) detection in the linear concentration range from 10 to 750 µM with a detection limit of 2.5 µM. It is also specific enough and applicable to detection of EDTA-Fe(III) in real soy sauce samples with satisfactory recovery. The one-step electrocatalytic reduction for signal generation enables the direct and sensitive electrochemical detection of EDTA-Fe(III). We believe that this electrocatalytic assay can serve as a general platform for quantification of EDTA-Fe(III) in many EDTA-Fe(III)-fortified foods. And because thionine is increasingly used as a signal reporter in electrochemical DNA/aptamer sensors, the engineered electrocatalytic reaction of thionine-mediated electrochemical reduction of EDTA-Fe(III) will also provide a simple signal amplification means for the development of highly sensitive electrochemical biosensors.

A new insight into potential roles of Spfoxl-2 in the testicular development of Scylla paramamosain by RNAi and transcriptome analysis.

In our previous study, we found that the Spfoxl-2 transcript was highly expressed in gonads and explored its potential target genes in the ovary of Scylla paramamosain. In the current study, we primally analyzed its potential target genes in the testis through RNAi and RNA-Seq technology and compared with that in the ovary. The results showed that a total of 7892 unigenes were differentially expressed after Spfoxl-2 silencing in the testis, including plenty of conserved genes involved in testicular development, such as Dmrt family genes, Sox family genes, Caspase family genes, Cdk family genes, Kinesin family genes, Fox family genes and other genes. Further analysis revealed that these differentially expressed genes (DEGs) were enriched in crucial pathways involved in spermatogenesis, such as DNA replication, Cell cycle, Spliceosome, Homologous recombination, Meiosis and Apoptosis. The comparison results of potential target genes in the ovary and testis reveal 135 common potential target genes, including some genes involved in the immune response. According to our knowledge, the present work was the first to disclose the functions of foxl-2 in the testis of crustacean species using transcriptome analysis. It not only identifies key genes and pathways involved in the testicular development of S. paramamosain, but also reveals a new molecular-level understanding of the function of foxl-2 in testicular development.

Dietary supplementations modulate the physiological parameters, fatty acids profile and the growth of red claw crayfish (Cherax quadricarinatus).

An optimal diet is an important factor for the proper growth and health of crustaceans. However, the regulation of antioxidant activity and non-specific immunity related to the consumption of feed additives has not been studied in RC-crayfish. Triplicate groups of 20 crayfish/tank (36.72 ± 0.70 g) fed with a basal diet and sixteen experimental diets that contained five feed additives with four grade levels (40, 160, 240 and 320 mg/kg vitamin E, 2, 4, 6 and 8 g/kg nucleotides, 2, 4, 6 and 8 g/kg Haematococcus pluvialis, 5, 10, 15 and 20 g/kg arachidonic acid and 2.5, 5, 10 and 15 g/kg yeast extract) on physiological parameters, fatty acids profile and growth of Cherax quadricarinatus for a period of 70 days by using orthogonal array method (L16 45 ). The results showed that the antioxidants activity in the haemolymph and hepatopancreas were both higher in crayfish fed with diets NO. 9 to 12 than others. Also, all the diets except diets NO. 13 to 16 showed lower free radicals contents than the control group. Similarly, significantly higher non-specific immune parameters were observed in the hepatopancreas of crayfish supplementations than those fed a control diet. Biochemical parameters related to protein profile in haemolymph increased in diets NO. 9 to 12 and then decreased in control and diets NO. 13 to 16, while the highest biochemical parameters related to lipid profile except HDL-c contents in haemolymph were observed in crayfish fed the control diet. Fatty acid composition in the hepatopancreas, muscle and ovary of RC-crayfish was significantly influenced by using the combination of Vit E, NT, H. pluvialis and YP compared to the control group. Compared to all treatments, RC-crayfish fed with diets NO. 2 and 12 had significantly stimulated higher growth performance and feed utilisation. Overall, our results suggest that diets supplemented with Vit E level of 240 mg/kg, in combination with 8 g/kg NT, 4 g/kg, H. pluvialis, 5 g/kg ARA and 10 g/kg YP are the promising treatments to increase antioxidants activity, non-specific immune response, fatty acids composition and growth of RC-crayfish. However, high dietary supplementations level can reduce antioxidants activity, immunity and inhibit growth.

Long-read RNA sequencing of Pacific abalone Haliotis discus hannai reveals innate immune system responses to environmental stress.

Haliotis discus hannai is a commercially important mollusk species, and the abalone aquaculture sector has been jeopardized by deteriorating environmental circumstances such as bacterial infection and thermal stress during the hot summers. However, due to a paucity of genetic information, such as transcriptome resources, our understanding of their stress adaptation is restricted. In this research, using single-molecule long-read (SMRT) sequencing technology, a library composed of ten tissues (i.e., haemocytes, gills, muscle, hepatopancreas, digestive tract, mantle, mucous gland, ovary, testis and head) was constructed and sequenced. In all, 41,855 high-quality unique transcripts, among which 24,778 were successfully annotated. Additionally, 13,463 SSRs, 1,169 transcription factors, and 18,124 lncRNAs were identified in H. discus hannai transcriptome. Furthermore, multiple immune-related transcripts were identified according to KEGG annotation, and a portion of these transcripts were mapped into several classical immune-related pathways, including the PI3K-AKT signaling pathway and Toll-like receptor signaling pathway. Additionally, 24 typical sequences related to the immunity pathway were detected by RT-PCR; the results showed that most of the immune-related genes showed significantly high expression at 72 h after bacterial challenges and thermal stress, especially the expression level of genes in gills was significantly higher than that in haemocytes under V. parahaemolyticus stress at 24 h. At the same time. The analysis of alternative splicing identified several innate immunity-related functions genes, including CD109 and caspase 2. These results suggest that the complex immune system, particularly the powerful innate immunity system, was crucial for H. discus hannai response to numerous environmental challenges.

Transcriptomic analysis and discovery of genes involving in enhanced immune protection of Pacific abalone (Haliotis discus hannai) in response to the re-infection of Vibrio parahaemolyticus.

Traditionally, invertebrates were thought to lack immune memory owing to a lack of acquired immune-related factors such as immunoglobulin. Nonetheless, with the in-depth consideration of invertebrate immune priming, scholars have gradually realized that the immune defenses of invertebrates are more complex than previously imagined. In the current investigation, the survival rate of Vibrio parahaemolyticus re-infected Haliotis discus hannai (VV group) was significantly different from the other groups (p < 0.05), indicating that an enhanced immune response may commence after first exposure to the same strain of V. parahaemolyticus. The transcriptome profiles of hemocytes obtained 102,052 unigenes, and 27,449 of them were annotated successfully. Venn diagram analysis showed that 2832 DEGs commonly responded to the first and second immune responses. 1734 "immune response genes" and 1460 "potential immune-enhancing genes" were also identified. A comparison of both "immune response genes" and "potential immune-enhancing genes" revealed 1019 immune-enhancing regulatory genes and 281 essential immune-enhancing genes. According to the KEGG enrichment analysis results of ERGs and EEGs, classical immune-related signaling pathways, such as NF-kappa B signaling pathway, NOD-like receptor signaling pathway, IL-17 signaling pathway, and TLR signaling pathway were significantly enriched, indicating that they were all involved in the response to V. parahaemolyticus re-infection and were likely dominant in the immune enhancement process of H. discus hannai hemocytes. The intermolecular interactions generated by Cytoscape after re-infection of V. parahaemolyticus appear more intuitively to demonstrate that hemocytes regulation was not an independent process, but rather an intricate regulatory network. H. discus hannai demonstrated enhanced immunological activity after re-infection with V. parahaemolyticus, showing immune memory in hemocytes. The current study's findings have broadened the study of immune enhancement in invertebrates and laid the framework for future research into the molecular mechanism of immune enhancement in abalones.

The potential role of eyestalk in the immunity of Litopenaeus vannamei to Vibrio parahaemolyticus infection II. From the perspective of long non-coding RNA.

Long non-coding RNAs (lncRNAs) have been linked to immunological modulation. Unfortunately, little is known about the processes of immune control in shrimp. In crustaceans such as Litopenaeus vannamei, a prominent aquaculture species, the X-organ-sinus gland complex (XO-SG) in the eyestalk is an essential neuroendocrine regulatory organ. Eyestalk ablation is commonly employed in aquaculture to accelerate ovarian maturation in shrimp. It does, however, have a negative impact on the shrimps' immunocompetence and causes death. As a result, we used RNA-seq to profile the transcriptomes of L. vannamei hemocytes infected with Vibrio parahaemolyticus after the eyestalk ablation. Following strict transcript screening procedures, 2307 lncRNAs were identified from L. vannamei hemocytes in this study. Pearson correlation analysis was finally used to uncover 535 DElncRNAs and 1566 DEmRNA targets. According to the Venn diagram analysis, 326 non-eyestalk regulatory lncRNAs (NElncRNAs) with a target of 1014 non-eyestalk regulatory genes (NEmRNAs), 47 eyestalk negative regulatory lncRNAs (ENRlncRNAs) with a target of 95 eyestalk negative regulatory genes (ENRmRNAs), and 162 eyestalk positive regulatory lncRNAs (EPRlncRNAs) with a target of 457 eyestalk positive regulatory genes (EPRmRNAs) were screened. The bioinformatics analysis revealed that lncRNAs were associated with Axon regeneration, Rap1 signaling pathway, Thyroid hormone signaling pathway, TGF-beta signaling pathway, and PI3K-Akt signaling pathway, implying that lncRNAs may play a role in the regulation of the neuroendocrine-immune (NEI) system. Furthermore, several lncRNAs targeting HSP70, YWHAZ, FER2, HIF1α, and Notch were discovered and verified by qRT-PCR. These findings showed that regulation of lncRNAs in hemocytes which were controlled by the eyestalk might be one of the impact variables in controlling the differential expression of mRNAs associated with immune response in L. vannamei infected with V. parahaemolyticus.

The potential role of eyestalk in the immunity of Litopenaeus vannamei to Vibrio infection.

The X-organ-sinus gland complex (XO-SG) in the eyestalk is an important neuroendocrine regulatory organ of crustaceans such as Litopenaeus vannamei, a prominent aquaculture species. The current study found significant changes in the enzyme activities of ALP, ACP, and T-SOD of hepatopancreatic in response to Vibrio parahaemolyticus exposure following eyestalk ablation, indicating that they were all involved in the immunological regulation of shrimps against V. parahaemolyticus infection. A total of 52,656 unigenes were obtained after RNA-Seq, with an average length of 1036 bp and an N50 of 1847 bp. Subsequently, 1899 eyestalk positive regulation genes (EPRGs), 745 eyestalk negative regulation genes (ENRGs), and 2077 non-eyestalk regulatory genes (NEGs) were identified. KEGG analysis of EPRGs revealed that eyestalk ablation might activate the neuroendocrine-immune (NEI) system. The RNA-Seq data were validated using quantitative real-time PCR (qRT-PCR). The findings suggested that eyestalk ablation might affect the expression of genes involved in the prophenoloxidase-activating system, the TLR signaling pathway, and numerous other immune-related genes in L. vannamei. All of these findings revealed that the eyestalk might have a role in the immune response of L. vannamei. The genes and pathways discovered in this study will help to elucidate the molecular mechanisms of hemocytes' immune response to V. parahaemolyticus following eyestalk ablation in shrimp, as well as provide the framework for building crustacean immunity theory.

Nutrigenomics in crustaceans: Current status and future prospects.

In aquaculture, nutrigenomics or "nutritional genomics" is concerned with studying the impacts of nutrients and food ingredients on gene expressions and understanding the interactions that may occur between nutrients and dietary bioactive ingredients with the genome and cellular molecules of the treated aquatic animals at the molecular levels that will, in turn, mediate gene expression. This concept will throw light on or provide important information to recognize better how specific nutrients may influence the overall health status of aquatic organisms. In crustaceans, it is well known that the nutritional requirements vary among different species. Thus, studying the nutrigenomics in different crustacean species is of significant importance. Of interest, recognition of the actual mechanisms that may be associated with the effects of the nutrients on the immune responses of crustaceans will provide clear outstanding protection, build a solid immune system, and also decrease the possibilities of the emergence of infectious diseases in the culture systems. Similarly, the growth, molting, lipid metabolism, antioxidant capacity, and reproduction could be effectively enhanced by using specific nutrients. In the area of crustacean research, nutrigenomics has been rapidly grown for addressing several aspects related to the influences of nutrients on crustacean development. Several researchers have studied the relationships between several functional genes and their expression profile with several physiological functions of crustaceans. They found a close association between the effects of optimal feeding with efficient production, growth, reproduction development, and health status of several crustacean species. Moreover, they illustrated that regulation of the gene expression in individual cells by different nutrients and formulated feeds could improve the growth development and immunity-boosting of several crustacean species. The present review will spotlight on such relationships between the dietary nutrients and expression of genes linked with growth, metabolism, molting, antioxidant, reproduction, and immunity of several crustacean species. The literature included in this review article will provide references and future outlooks for the upcoming research plans. This will contribute positively for maintaining the sustainability of the sector of the crustacean industry.

Cloning, expression, and function of the Spdmrt-like gene in Scylla paramamosain.

BACKGROUND: The mud crab Scylla paramamosain is an economically important species for aquaculture in China and has sexually dimorphic between females and males. Understanding sex differentiation in this species is essential for the development of monosex aquaculture. The Dmrt genes play a vital role in sex differentiation in animals. METHODS AND RESULTS: In this study, two dmrt-like transcript variants, Spdmrt-like-tv1 and Spdmrt-like-v2, were cloned. SpDmrt-like-tv1 contained a DM domain, while SpDmrt-like-tv2 contained a DM and a DMA domain. Spdmrt-like-tv1 and Spdmrt-like-tv2 were both specifically expressed in testis. During testicular development, the expression level of Spdmrt-like-tv1 increased from stage I to stage II (P > 0.05) and then decreased from stage II to stage III (P < 0.05). The expression level of Spdmrt-like-tv2 in stages I and II was significantly higher than that in stage III (P < 0.05). During embryonic development, the expression level of Spdmrt-like-tv1 was higher in the mid-embryonic stage compared with the early and late stages, but the differences were not significant. Moreover, the expression level of Spdmrt-like-tv2 was stable and remained high throughout embryonic development. Furthermore, the expression level of Spdmrt-like-tv2 was significantly higher than that of Spdmrt-like-tv1. Knockdown of Spdmrt-like variants indicated that the regulative target gene of Spdmrt-like-tv1 was Spsox21, and the regulative target genes of Spdmrt-like-tv2 were Spfoxl2 and Spsox21. Combined with the results in our previously published peer-reviewed articles that the expression of Spfoxl2 in the testis was significantly higher than that in the ovary, and Spfoxl2 negatively regulated Spvtg expression. Spsox21 played a role in the development and maintenance of testis as well as in the process of neural development and regulation of body segmentation. CONCLUSION: Therefore, we suggest that Spdmrt-like-tv1 and Spdmrt-like-tv2 might be involved in testicular development and embryonic development, and Spdmrt-like-tv2 might play more important roles in these two developmental processes by regulating the expression of Spfoxl2 and Spsox21 due to its high expression.

Regulation of vtg and VtgR in mud crab Scylla paramamosain by miR-34.

BACKGROUND: Vitellogenin (Vtg) is the precursor of major yolk protein and plays a crucial role in the maturation of oocytes and the production of eggs in oviparous animals. Vitellogenin receptor (VtgR) mediates the transport of Vtg explicitly to oocytes in the membrane. In a previous study, we found that miR-34 can regulate the expression of some eyestalk genes and affect reproduction in mud crab Scylla paramamosain, one of the most important economic crabs on the coasts of southern China. METHODS AND RESULTS: In this study, firstly, we found that miR-34 can target at 3'-UTR of Vtg and VtgR genes by using bioinformatic tools and predicted miR-34 might depress the expression of Vtg and VtgR. Secondly, the relative luciferase activity of HEK293T cells co-transfected with miRNA mimic and pmir-RB-REPORTTM-Vtg/VtgR-3'UTR was significantly lower than those of cells co-transfected with mimic NC and pmir-RB-REPORTTM-Vtg/VtgR-3'UTR. Finally, in vivo experiments showed that agomiR-34 could repress the expression of Vtg and VtgR genes, while Antigomir-34 could promote the expression of these two genes. CONCLUSIONS: These results confirm our hypothesis and previous published results that miR-34 may indirectly regulate ovarian development by binding to the 3'-UTR of Vtg and VtgR genes and inhibiting their expression.

Preparation of flower-like molybdenum disulfide for solid-phase extraction of N-nitrosoamines in environmental water samples.

In this paper, a flower-like molybdenum disulfide material was prepared by hydrothermal method and was first used as adsorbents in the solid-phase extraction process for enriching N-nitrosoamines. Molybdenum disulfide exhibited three-dimensional petal-like microspheres with about 500 nm in diameter. The relevant analyte extraction and elution parameters (sample volumes, solution pH, washing solvents, elution solvents, and elution volumes) were optimized to improve the solid-phase extraction efficiency. The solid-phase extraction process coupled with high-performance liquid chromatography-tandem mass spectrometry for determining N-nitrosoamines in environmental water samples was established. The limits of detection were in the range of 0.01-0.05 ng/mL. The satisfactory recoveries (68.9-106.1%) were obtained at three different spiked concentrations (2, 5, and 8 ng/mL) in water samples, and the relative standard deviations were between 1.96 and 8.38%. This proposed method not only showed high sensitivity and good reusability but also provided a new adsorbent for enriching trace N-nitrosoamines in environmental water samples.