Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

The differences in intestinal microbiota composition are synergistically shaped by internal and external factors of the host. The core microbiota plays a vital role in maintaining intestinal homeostasis. In this study, we conducted 16S rRNA sequencing analysis to investigate the stability of intestinal microbiota and sex-bias of six stocks of Chinese mitten crabs (105 females; and 110 males). The dominant phyla in all six stocks were Proteobacteria, Tenericutes, Bacteroidetes and Firmicutes; however, their relative abundance differed significantly. Twenty-seven core operational taxonomic units (OTUs), corresponding to 18 genera, were screened. Correlation analysis revealed that OTUs of four stocks in the Yangtze River system play important roles in maintaining the stability of intestinal microbiota. Additionally, the core intestinal microbiota was significantly sex-biased, and the top three genera in terms of relative abundance (Acinetobacter, Vibrio, and Candidatus_Hepatoplasma) were significantly dominant in female crabs. Network structure analysis also confirmed gender differences in the association pattern of intestinal microbiota. The intestinal microbiota of male crabs has a higher degree of functional enrichment. This study provided a theoretical basis for further investigating exploring the shaping effect of gender and geographical factors on the intestinal microbiota of Chinese mitten crabs.

Salinity acclimatization refers to the physiological and behavioral adjustments made by crustaceans to adapt to varying salinity environments. The eyestalk, a neuroendocrine organ in crustaceans, plays a crucial role in salinity acclimatization. To elucidate the molecular mechanisms underlying eyestalk involvement in mud crab (Scylla paramamosain) acclimatization, we employed RNA-seq technology to analyze transcriptomic changes in the eyestalk under low (5 ppt) and standard (23 ppt) salinity conditions. This analysis revealed 5431 differentially expressed genes (DEGs), with 2372 upregulated and 3059 downregulated. Notably, these DEGs were enriched in crucial biological pathways like metabolism, osmoregulation, and signal transduction. To validate the RNA-seq data, we further analyzed 15 DEGs of interest using qRT-PCR. Our results suggest a multifaceted role for the eyestalk: maintaining energy homeostasis, regulating hormone synthesis and release, PKA activity, and downstream signaling, and ensuring proper ion and osmotic balance. Furthermore, our findings indicate that the crustacean hyperglycemic hormone (CHH) may function as a key regulator, modulating carbonic anhydrase expression through the activation of the PKA signaling pathway, thereby influencing cellular osmoregulation, and associated metabolic processes. Overall, our study provides valuable insights into unraveling the molecular mechanisms of mud crab acclimatization to low salinity environments.

Rainbow trout (Oncorhynchus mykiss) is an economically significant freshwater-farmed fish worldwide, and the frequent outbreaks of infectious hematopoietic necrosis (IHN) in recent years have gravely compromised the healthy growth of the rainbow trout aquaculture industry. Fish skin is an essential immune barrier against the invasion of external pathogens, but it is poorly known about the role of circRNAs in rainbow trout skin. Therefore, we examined the expression profiles of circRNAs in rainbow trout skin following IHNV infection using RNA-seq. A total of 6607 circRNAs were identified, of which 34 circRNAs were differentially expressed (DE) and these DE circRNA source genes were related to immune-related pathways such as Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, Cytokine-cytokine receptor interaction, ubiquitin mediated proteolysis, and ferroptosis. We used qRT-PCR, Sanger sequencing, and subcellular localization to validate the chosen DE circRNAs, confirming their localization and expression patterns in rainbow trout skin. Further, 12 DE circRNAs were selected to construct the circRNA-miRNA-mRNA regulatory network, finding one miRNA could connect one or more circRNAs and mRNAs, and some miRNAs were reported to be associated with antiviral immunity. The functional prediction findings revealed that novel_circ_002779 and novel_circ_004118 may act as sponges for miR-205-z and miR-155-y to regulate the expression of target genes TLR8 and PIK3R1, respectively, and participated in the antiviral immune responses in rainbow trout. These results shed light on the immunological mechanism of circRNAs in rainbow trout skin and offer fundamental information for further research on the innate immune system and breeding rainbow trout resistant to disease.

Sea cucumber is a valuable seafood product and autolysis is the main concern for the aquaculture industry. This study employed proteomics and transcriptomics to investigate the autolysis mechanism of sea cucumbers. The fresh sea cucumber was exposed to UV light to induce autolysis. The body wall samples were cut off to analyze by proteomics and transcriptomics. The angiotensin-converting enzyme (ACE) inhibitor of teprotide and the activator of imatinib were gastric gavage to live sea cucumbers, respectively, to identify the regulation target. Autolysis occurrence was evaluated by appearance, soluble peptide, and hydroxyproline content. Four gene-protein pairs were ACE, AJAP10923, Heme-binding protein 2-like, and Ficolin-2-like. Only the ACE protein and gene changed synchronously and a significant down-regulation of ACE occurred in the autolysis sea cucumbers. Teprotide led to a 1.58-fold increase in the TCA-soluble protein content and a 1.57-fold increase in hydroxyproline content. No significant differences were observed between imatinib-treated sea cucumbers and fresh ones regarding TCA-soluble protein content or hydroxyproline levels (P > 0.05). ACE inhibitor accelerated the autolysis of sea cucumber, but ACE activator inhibited the autolysis. Therefore, ACE can serve as a regulatory target for autolysis in sea cucumbers.

Bombyx mori is an oligophagous economic insect. Cis-Jasmone is one of the main substances in mulberry leaf that attract silkworm for feeding and BmOR56 is its receptor. Potential interaction ways between BmOR56 and cis-Jasmone were explored, which included some crucial amino acids such as Gln172, Val173, Ser176, Lys182, His322, and Arg345. BmOR56 was edited using CRISPR/cas9 for Qiufeng, and a homozygous knockout strain QiufengM was obtained. Compared with Qiufeng, the feeding ability of QiufengM on mulberry leaf did not change significantly, but on artificial diet decreased significantly. QiufengM also showed a dependence on the concentration of mulberry leaf powder. The result indicated that other olfactory genes had a compensatory effect on the attractance of mulberry leaf after the loss of BmOR56. Transcriptome analysis of antennae showed that many genes differentially expressed between Qiufeng and QiufengM, which involved in olfactory system, glucose metabolism, protein metabolism, amino acid metabolism, and insect hormone biosynthesis. Particularly, BmIR21, BmOR53 and BmOR27 were significantly up-regulated, which may have a compensatory effect on BmOR56 loss. In addition, detoxification mechanism was activated and may cause the passivation of feeling external signals in silkworm.

The intestine is an important organ for food digestion and absorption and body immunity in fish. In this study, we investigated the abundance of transcripts from different segments of the intestinal tract using transcriptome sequencing technology in Hemibarbus labeo, to provide functional insights into digestion, absorption, and immunity in the anterior intestine (AI), middle intestine (MI), and posterior intestine (PI). We found 5646 differentially expressed genes (DEGs), which were significantly enriched to GO terms of carbohydrate metabolic process, transmembrane transport, iron ion binding, lipid metabolic process, and KEGG pathway of fat digestion and absorption, mineral absorption, protein digestion and absorption, vitamin digestion and absorption, indicating that the digestion and absorption function of food is different in AI, MI, and PI. In practice, most genes, enriched in the KEGG pathway for digestion and absorption of nutrients, are upregulated in AI and MI, indicating stronger roles for food digestion and absorption in these segments. Furthermore, we found that genes involved in the KEGG pathway of lysosome and endocytosis pathway are upregulated in PI, suggesting stronger antigen-presenting capabilities in PI. However, some cytokine receptor genes, including ccr4, cxcr2, tnfrsf9, il6r, csf3r, and cxcr4, are highly expressed in AI, reflecting the regional immune specialization in different segments. This study provides functional insights into digestion, absorption, and immunity in different segments of the intestine and supports the regional functional specialization within different segments of the intestine in H. labeo.

The objective was to assess the impact of melatonin supplementation on the growth performance and intestinal health of rice field eel, Monopterus albus. Three hundred and sixty fish (28.46 ± 0.24 g) were fed five diets supplemented with melatonin of 0, 30, 60, 120, and 240 mg/kg for 70 days. The study found that the variables FBW, WGR, SGR, and FCR exhibited a statistically significant quadratic relationship (P < 0.05) with the dietary melatonin concentrations, and the highest FBW, WGR and SGR as well as lowest FCR were observed in the 120 mg/kg melatonin group, digestive enzymes activities (such as amylase, trypsin, and lipase) also had significant quadratic relationship (P < 0.05), and the highest intestinal villus height and goblet cells were found in the 120 mg/kg diet (P < 0.01), melatonin in diets significantly increased SOD and CAT activities in serum, up-regulated the expression of anti-inflammatory factors (IL-10) and tight junction protein (ZO-1), and down-regulated the expression of pro-inflammatory factors (IL-1β, IL-8, IL-15, and TNF-α) in the gut, dietary melatonin improved the intestinal microflora compositions, in the group that supplementation a dosage of 120 mg/kg, there was a noticeable rise in the abundance of Firmicutes and the ratio of Firmicutes/Bacteroidota, compared with control group (P < 0.1). Conclusively, dietary supplementation of melatonin promoted growth performance, enhanced intestinal immune capacity and serum antioxidant level, and improved intestinal morphology properties and intestinal flora composition in M. albus. In conclusion, based on quadratic broken-line regression analysis of WGR and FCR, the optimal concentration of melatonin to be supplied is predicted to be 146–148 mg/kg.

Environmental factors play a key role in individual adaptation to different local conditions. Because of this, studies about the physiological and genetic responses of individuals exposed to different natural environments offer clues about mechanisms involved in population differentiation, and as a subsequent result, speciation. Marine environments are especially suited to survey this kind of phenomena because they commonly harbor species adapted to different local conditions along a geographic continuum. Silversides belonging to Odontesthes are commonly distributed in tropical and temperate regions of South America and exhibit noticeable phenotypic plasticity, which allows them to adapt to contrasting environments. In this study, the genetic expression of O. argentinensis sampled along the Uruguayan Atlantic coast and estuarine adjacent areas was investigated. In addition, the correlation between individual genotypes and environmental variables was also analysed in O. argentinensis and O. bonariensis. Results obtained suggest a differential expression pattern of low magnitude among individuals from the different areas sampled and a correlation between several SNP loci and environmental variables. The analyses carried out did not show a clear differentiation among individuals sampled along different salinity regimens, but enriched GOTerms seem to be driven by water oxygen content. On the other hand, a total of 46 SNPs analysed in O. argentinensis and O. bonariensis showed a correlation with salinity and temperature. Although none of the correlated SNPs and corresponding genes from our both analyses were directly associated with hypoxia, genes related to the cardiovascular system and muscle cell differentiation were found. All these genes are interesting candidates for future studies since they are closely related to the differentially expressed genes. Although salinity was also mentioned as an important parameter limiting introgression between O. argentinensis and O. bonariensis, it was found that salinity does not drive differential expression in O. argentinensis, but rather oxygen levels. Moreover, salinity does not directly affect the structure and genetic divergence of the populations, they appear to be structured based on their degree of isolation and geographical distance between them. Further studies, like genome-wide analyses, could help to elucidate additional genes adapted to the different environments in these silverside species.

Elite performing exercise requires an intricate modulation of the blood pressure to support the working muscles with oxygen. We have previously identified a genomic regulatory module that associates with differences in blood pressures of importance for elite performance in racehorses. This study aimed to determine the effect of the regulatory module on the protein repertoire. We sampled plasma from 12 Coldblooded trotters divided into two endothelial regulatory module haplotype groups, a sub-elite performing haplotype (SPH) and an elite performing haplotype (EPH), each at rest and exercise. The haplotype groups and their interaction were interrogated in two analyses, i) individual paired ratio analysis for identifying differentially abundant proteins of exercise (DAPE) and interaction (DAPI) between haplotype and exercise, and ii) unpaired ratio analysis for identifying differentially abundant protein of haplotype (DAPH). The proteomics analyses revealed a widespread change in plasma protein content during exercise, with a decreased tendency in protein abundance that is mainly related to lung function, tissue fluids, metabolism, calcium ion pathway and cellular energy metabolism. Furthermore, we provide the first investigation of the proteome variation due to the interaction between exercise and related blood pressure haplotypes, which this difference was related to a faster switch to the lipoprotein and lipid metabolism during exercise for EPH. The molecular signatures identified in the present study contribute to an improved understanding of exercise-related blood pressure regulation.

The echinoderm nervous system has been studied as a model for understanding the evolution of the chordate nervous system. Neuronal cells are essential groups that release a ‘cocktail’ of messenger molecules providing a spectrum of biological actions in the nervous system. Among echinoderms, most evidence on neuronal cell types has been obtained from starfish and sea urchin. In sea cucumbers, most research has focused on the location of neuronal cells, whereas their transcriptional features have rarely been investigated. Here, we observed the ultrastructure of neuronal cells in the sea cucumber, Apostichopus japonicus. The transcriptional profile of neuronal cells from the circumoral nerve ring (CNR) was investigated using single-cell RNA sequencing (scRNA-seq), and a total of six neuronal cell types were identified. 26 neuropeptide precursor genes (NPPs) and 28 G-protein-coupled receptors (GPCR) were expressed in the six neuronal cell types, comprising five NPP/NP-GPCR pairs. Unsupervised pseudotime analysis of neuronal cells showed their different differentiation status. We also located the neuronal cells in the CNR by immunofluorescence (IF) and identified the potential hub genes of key cell populations. This broad resource serves as a valuable support in the development of cell-specific markers for accurate cell-type identification in sea cucumbers. It also contributes to facilitating comparison across species, providing a deeper understanding of the evolutionary processes of neuronal cells.