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

Anisakidae parasitism is a prevalent disease in wild populations of Coilia nasus, and can result in a significant loss of germplasm resources. To elucidate the immune response mechanism of C. nasus livers to Anisakidae infection, we collected and analysed 18 parasitic and 18 non-parasitic livers at gonadal developmental stages II, III, and V using histopathology, molecular biology and transcriptome methods. The hepatic portal area of the parasitic group exhibited an increase in the fibrous stroma and thickened hepatic arteries with positive Ly-6G staining, indicating inflammation and immune responses in the liver. Hepatocyte cytokine levels and the expression of liver function-related genes indicated that fish livers responded similarly to Anisakidae parasitism across different gonadal developmental stages. Oxidative stress indices showed more intense changes in stage II samples, whereas gene expression levels of Nrf2 and C3 were significantly increased in parasitised livers during stage III and V. Liver transcriptome sequencing identified 2575 differentially expressed genes between the parasitic and non-parasitic groups at the three gonadal developmental stages. KEGG pathway analysis showed that natural killer cell-mediated cytotoxicity, the NOD-like receptor signaling pathway, neutrophil extracellular trap formation, and other immune pathways were significantly enriched. Expression patterns varied across developmental stages, suggesting that innate immunity was primarily responsible for the liver immune response to Anisakidae infection during C. nasus migration, possibly related to water temperature changes or shifts in the gonadal developmental stage. In summary, this study investigated the immune response of C. nasus to Anisakidae parasitism under natural conditions, focusing on reproductive aspects and environmental changes, thereby establishing a foundation for elucidating the molecular mechanisms underlying the immune response of Anisakidae in C. nasus.

The northern house mosquito, Culex pipiens, employs diapause as an essential survival strategy during winter, inducing important phenotypic changes such as enhanced stress tolerance, lipid accumulation, and extended longevity. During diapause, the cessation of reproductive development represents another distinctive phenotypic change, underlining the need for adjusted modulation of gene expressions within the ovary. Although considerable advancements in screening gene expression profiles in diapausing and non-diapausing mosquitoes, there remains a gap in tissue-specific transcriptomic profiling that could elucidate the complicated formation of diverse diapause features in Cx. pipiens. Here, we filled this gap by utilizing RNA sequencing, providing a detailed examination of gene expression patterns in the fat body and ovary during diapause compared to non-diapause conditions. Functional annotation of upregulated genes identified associations with carbohydrate metabolism, stress tolerance, immunity, and epigenetic regulation. The validation of candidate genes using quantitative real-time PCR verified the differentially expressed genes identified in diapausing mosquitoes. Our findings contribute novel insights into potential regulators during diapause in Cx. pipiens, thereby opening possible avenues for developing innovative vector control strategies.

Low temperature in winter poses a threat to the Manila clam Ruditapes philippinarum in North China. However, a number of low-temperature-tolerant clams could survive such condition. It is therefore of interest to explore the survival mechanisms underlying the cold tolerance of R. philippinarum. The Zebra II population of R. philippinarum (Zebra II) from North China and the native Putian population from South China were used as experimental materials. Both populations were stressed with low-temperature and the differences in their survival rates, energy metabolism and transcriptional responses were compared. The results shown that after cold treatment at −1.9 °C, survival rate of Zebra II was higher than that of the Putian group. For both groups, the respiration, ammonia excretion, and ingestion rates continuously decreased till 0 with reductions temperature. In addition, RNA-seq revealed that as compared with the Putian group, there were 3682 up-regulated differentially expressed genes (DEGs) and 3361 down-regulated DEGs in Zebra II group. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGs were mostly enriched in the purine, pyrimidine, and pyruvate metabolism pathways in Zebra II under low-temperature stress. Furthermore, qRT–PCR analysis further confirmed that Zebra II responded to low-temperature stress through upregulating genes involved in purine, pyrimidine, and pyruvate metabolism pathways. Taken together, all these results indicated that Zebra II has higher cold tolerance than the Putian group. Therefore, Zebra II is capable for overwintering in the intertidal zone of North China.

Circular RNA (circRNA) represents a type of newly discovered non-coding RNA, distinguished by its closed loop structure formed through covalent bonds. Recent studies have revealed that circRNAs have crucial influences on host anti-pathogen responses. Yellow catfish (Pelteobagrus fulvidraco), an important aquaculture fish with great economic value, is susceptible to Aeromonas veronii, a common aquatic pathogen that can cause acute death. Here, we reported the first systematic investigation of circRNAs in yellow catfish, especially those associated with A. veronii infection at different time points. A total of 1205 circRNAs were identified, which were generated from 875 parental genes. After infection, 47 circRNAs exhibited differential expression patterns (named DEcirs). The parental genes of these DEcirs were functionally engaged in immune-related processes. Accordingly, seven DEcirs (novel_circ_000226, 278, 401, 522, 736, 843, and 975) and six corresponding parental genes (ADAMTS13, HAMP1, ANG3, APOA1, FGB, and RALGPS1) associated with immunity were obtained, and their expression was confirmed by RT-qPCR. Moreover, we found that these DEcir-gene pairs likely acted through pathways, such as platelet activation, antimicrobial humoral response, and regulation of Ral protein signal transduction, to influence host immune defenses. Additionally, integrated analysis showed that, of the 7 immune-related DEcirs, three targeted 16 miRNAs, which intertwined into circRNA-miRNA networks. These findings revealed that circRNAs, by targeting genes or miRNAs are highly involved in anti-bacterial responses in yellow catfish. Our study comprehensively illustrates the roles of circRNAs in yellow catfish immune defenses. The identified DEcirs and the circRNA-miRNA network will contribute to the further investigations on the molecular mechanisms underlying yellow catfish immune responses.

Chironomidae, non-biting midges, a diverse and abundant insect group in global aquatic ecosystems, represent an exceptional model for investigating genetic adaptability mechanisms in aquatic insects due to their extensive species diversity and resilience to various environmental conditions. The cuticle in insects acts as the primary defense against ecological pressures. Cuticular Proteins (CPs) determine cuticle characteristics, facilitating adaptation to diverse challenges. However, systematic annotation of CP genes has only been conducted for one Chironomidae species, Propsilocerus akamusi, by our team. In this study, we expanded this annotation by identifying CP genes in eight additional Chironomidae species, covering all Chironomidae species with available genome data. We identified a total of 889 CP genes, neatly categorized into nine CP families: 215 CPR RR1 genes, 272 CPR RR2 genes, 23 CPR RR3 genes, 21 CPF genes, 16 CPLCA genes, 19 CPLCG genes, 28 CPLCP genes, 77 CPAP genes, and 37 Tweedle genes. Subsequently, we conducted a comprehensive phylogenetic analysis of CPs within the Chironomidae family. This expanded annotation of CP genes across diverse Chironomidae species significantly contributes to our understanding of their remarkable adaptability.

Previous research has shown that leucine (Leu) can stimulate and enhance the proliferation of equine skeletal muscle satellite cells (SCs). The gene expression profile associated with Leu-induced proliferation of equine SCs has also been documented. However, the specific role of Leu in regulating the expression of slow-twitch muscle fibers (slow-MyHC) and mitochondrial function in equine SCs, as well as the underlying mechanism, remains unclear. During this investigation, equine SCs underwent culturing in differentiation medium and were subjected to varying concentrations of Leu (0 mM, 0.5 mM, 1 mM, 2 mM, 5 mM, and 10 mM) over a span of 3 days. AMP-activated protein kinase (AMPK) inhibitor Compound C and mammalian target of rapamycin complex (mTOR) inhibitor Rapamycin were utilized to explore its underlying mechanism. Here we showed that the expression of slow-MyHC at 2 mM Leu level was significantly higher than the concentration levels of 0 mM,0.5 mM and 10 mM (P <0.01), and there was no significant difference compared to other groups (P > 0.05); the basal respiration, maximum respiration, standby respiration and the expression of slow-MyHC, PGC-1α, Cytc, ND1, TFAM, and COX1 were significantly increased with Leu supplementation (P < 0.01). We also found that Leu up-regulated the expression of key proteins on AMPK and mTOR signaling pathways, including LKB1, p-LKB1, AMPK, p-AMPK, S6, p-S6, 4EBP1, p-4EBP1, mTOR and p-mTOR (P < 0.05 or P < 0.01). Notably, when we treated the equine SCs with the AMPK inhibitor Compound C and the mTOR inhibitor Rapamycin, we observed a reduction in the beneficial effects of Leu on the expression of genes related to slow-MyHC and signaling pathway-related gene expressions. This study provides novel evidence that Leu promotes slow-MyHC expression and enhances mitochondrial function in equine SCs through the AMPK/mTOR signaling pathways, shedding light on the underlying mechanisms involved in these processes for the first time.

Ovarian development in animals is a complicated biological process, requiring the simultaneous coordination among various genes and pathways. To understand the dynamic changes and molecular regulatory mechanisms of ovarian development in mud crab (Scylla paramamosain), both histological observation and whole transcriptome sequencing of ovarian tissues at different mating stages were implemented in this study. The histological results revealed that ovarian development was delayed in unmated females (60 days after courtship behavior but not mating), who exhibited an oocyte diameter of 56.38 ± 15.17 μm. Conversely, mated females exhibited accelerated the ovarian maturation process, with females reaching ovarian stage III (proliferative stage) 23 days after mating and attained an average oocyte diameter of 132.19 ± 15.07 μm. Thus, mating process is essential in promoting the rapid ovarian development in mud crab. Based on the whole transcriptome sequencing analysis, a total of 518 mRNAs, 1502 lncRNAs, 18 circRNAs and 151 miRNAs were identified to be differentially expressed between ovarian tissues at different mating stages. Notably, six differentially expressed genes (DEGs) associated with ovarian development were identified, including ovary development-related protein, red pigment concentrating hormone receptor, G2/mitotic-specific cyclin-B3-like, lutropin-chorio gonadotropic hormone receptor, renin receptor, and SoxB2. More importantly, both DEGs and targets of differentially expressed non-coding RNAs (DEncRNAs) were enriched in renin-angiotensin system, TGF-β signaling, cell adhesion molecules, MAPK signaling pathway, and ECM-receptor interaction, suggesting that these pathways may play significant roles in the ovarian development of mud crabs. Moreover, competition endogenous RNA (ceRNA) networks were constructed while mRNAs were differentially expressed between mating stages were involved in Gene Ontology (GO) biological processes such as developmental process, reproduction, and growth. These findings could provide solid foundations for the future development of female mud crab maturation enhancement strategy, and improve the understanding of the ovarian maturation process in crustaceans.

Owing to population growth and environmental pollution, freshwater aquaculture has been rapidly shrinking in recent years. Aquaculture in saline-alkaline waters is a crucial strategy to meet the increasing demand for aquatic products. The Chinese mitten crab is an important economic food in China, but the molecular mechanism by which it tolerates carbonate alkalinity (CA) in water remains unclear. Here, we found that enzyme activities of the tricarboxylic acid (TCA) cycle in the gills, such as citrate synthase, isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, and malate dehydrogenase, were markedly reduced under CA stress induced by 40 mM NaHCO₃. Secondly, the TCA cycle in the gills is inhibited under acute CA stress, according to proteomic and metabolomic analyses. The expressions of six enzymes, namely aconitate hydratase, isocitrate dehydrogenase, 2-oxoglutarate dehydrogenase, dihydrolipoyl dehydrogenase, succinate-CoA ligase, and malate dehydrogenase, were downregulated, resulting in the accumulation of phosphoenolpyruvic acid, citric acid, cis-aconitate, and α-ketoglutaric acid. Finally, we testified that if the TCA cycle is disturbed by malonate, the survival rate increases in CA water. To our knowledge, this is the first study to show that the TCA cycle in the gills is inhibited under CA stress. Overall, the results provide new insights into the molecular mechanism of tolerance to saline-alkaline water in crabs, which helped us expand the area for freshwater aquaculture and comprehensively understand the physiological characteristics of crab migration.

The bay scallop is a eurythermal species with high economic value and now represents the most cultured bivalve species in China. Two subspecies of the bay scallop, the northern subspecies Argopecten irradians irradians Korean population (KK) and the southern subspecies Argopecten irradians concentricus (MM), exhibited distinct adaptations to heat stress. However, the molecular mechanism of heat resistance of the two subspecies remains unclear. In this study, we compared the transcriptomic responses of the two subspecies to heat stress and identified the involved differentially expressed genes (DEGs) and pathways. More DEGs were found in the KK than in the MM when exposed to high temperatures, indicating elevated sensitivity to thermal stress in the KK. Enrichment analysis suggests that KK scallops may respond to heat stress more swiftly by regulating GTPase activity. Meanwhile, MM scallops exhibited higher resistance to heat stress mainly by effective activation of their antioxidant system. Chaperone proteins may play different roles in responses to heat stress in the two subspecies. In both subspecies, the expression levels of antioxidants such as GST were significantly increased; the glycolysis process regulated by PC and PCK1 was greatly intensified; and both apoptotic and anti-apoptotic systems were significantly activated. The pathways related to protein translation and hydrolysis, oxidoreductase activity, organic acid metabolism, and cell apoptosis may also play pivotal roles in the responses to heat stress. The results of this study may provide a theoretical basis for marker-assisted breeding of heat-resistant strains.

Pigmentation genes expressed in skin, body muscle and tail of Thai-flag compared with Blue, White and Red varieties of Siamese fighting fish Betta splendens were identified. In total, 22,919 new unigenes were found. Pearson correlation and PCA analysis revealed that expression profiles of genes in muscle, skin and tail across solid color variety were similar. In contrast, those in skin and red tail part of Thai-flag were closely related but they showed different expression profiles with the white tail part. Moreover, 21,347–64,965 SNPs were identified in exonic regions of identified genes. In total, 28,899 genes were differentially expressed between paired comparisons of libraries where 13,907 genes (48.12 %) were upregulated and 14,992 genes (51.88 %) were downregulated. DEGs between paired libraries were 106–5775 genes relative to the compared libraries (56–2982 and 50–2782 for upregulated and downregulated DEGs). Interestingly, 432 pigmentation genes of B. splendens were found. Of these, 297 DEGs showed differential expression between varieties. Many DEGs in melanogenesis (Bsmcr1r, Bsmcr5r, and Bsslc2a15b), tyrosine metabolism (Bstyr, Bstyrp1b and Bsdct), stripe repressor (BsAsip1 and BsAsip2b), pteridine (Bsgch2) and carotenoid (BsBco2) biosynthesis were downregulated in the Thai-flag compared with solid color varieties. Expression of Bsbco1l, Bsfrem2b, Bskcnj13, Bszic2a and Bspah in skin, muscle and tail of Thai-flag, Blue, Red and White varieties was analyzed by qRT-PCR and revealed differential expression between fish varieties and showed anatomical tissue-preferred expression patterns in the same fish variety. The information could be applied to assist genetic-based development of new B. splendens varieties in the future.