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

Among terrestrial ectotherms, hibernation is a common response to extreme cold temperatures and is associated with reduced physiological rates, including immunity. When winter wanes and temperatures increase, so too do vital rates of both ectothermic hosts and their parasites. Due to metabolic scaling, if parasite activity springs back faster than host immune functions then cold seasons and transitions between cold and warm seasons may represent periods of vulnerability for ectothermic hosts. Understanding host regulation of physiological rates at seasonal junctions is a first step toward identifying thermal mismatches between hosts and parasites. Here we show that immune gene expression is responsive to transitions into and out of the cold season in a winter-adapted amphibian, the wood frog (Lithobates sylvaticus), and that frogs experienced parasitism by at least two nematode species throughout the entirety of the cold season. In both splenic and skin tissues, we observed a decrease in immune gene expression going from fall to winter, observed no changes between winter and emergence from hibernation, and observed increases in immune gene expression after hibernation ended. At all timepoints, differentially expressed genes from spleens were more highly enriched for immune system processes than those from ventral skin, especially with respect to terms related to adaptive immune processes. Infection with nematode lungworms was also associated with upregulation of immune processes in the spleen. We suggest that rather than being a period of stagnation, during which physiological processes and infection potential cease, the cold season is immunologically dynamic, requiring coordinated regulation of many biological processes, and that the reemergence period may be an important time during which hosts invest in preparatory immunity.

Macrobrachium rosenbergii is an economically important crustacean in many parts of the world, but in recent years, growth retardation has become an increasingly serious issue. While the underlying causes remain unclear, this has inevitably impacted on aquaculture and production outputs. In this study, gill, hepatopancreas, and muscle tissue samples from M. rosenbergii, with distinct growth differences, underwent transcriptome sequencing and bioinformatics analyses using high-throughput sequencing. In total, 59,796 unigenes were annotated. Differential expression analyses showed that the most differentially expressed genes (DEGs) were screened in gill tissue (1790 DEGs). In muscle and hepatopancreas tissues, 696 and 598 DEGs were screened, respectively. These DEGs were annotated to Kyoto Encyclopedia of Genes and Genomes pathways, which identified several significantly enriched pathways related to growth metabolism, such as PI3K-AKT, glycolysis/gluconeogenesis, and starch and sucrose metabolism. These results suggest that low growth metabolism levels may be one cause of M. rosenbergii growth retardation. Our data provide support for further investigations into the causes and molecular mechanisms underpinning growth retardation in M. rosenbergii.

The molecular mechanism of sex determination has long been considered conserved in insects. However, recent studies of hemimetabolous insects have challenged this notion. One notable example is termites. In Reticulitermes speratus, a homolog of sex determination gene, Doublesex (RsDsx), exhibits characteristics that are distinct from those of other insects, including sister-group cockroaches. It comprises a single exon, contains only doublesex/mab-3 DNA-binding domain (DM) but lacks a conserved oligomerization domain (OD), and exhibits transcriptional activity only in males. To investigate whether these characteristics are widespread within the termite lineage, we identified Dsx homologs in three different families. The absence of the conserved OD sequences was observed in all termite species examined, whereas the number of exons and expression patterns between sexes varied among families. Particularly, distinctive differences in Dsx were found in species from the Archotermopsidae and Kalotermitidae, both of which have a linear caste developmental pathway. Our findings indicate that diversification of Dsx structure and expression patterns may have contributed to ecological diversification, such as caste developmental pathways, within the termite lineage.

Rising ocean temperatures due to global warming pose a significant threat to the bay scallop aquaculture industry. Understanding the mechanisms of thermotolerance in bay scallops is crucial for developing thermotolerant breeds. Our prior research identified Arg0230340.1, part of the positive cofactor 4 (PC4) family, as a key gene associated with the thermotolerance index Arrhenius break temperature (ABT) in bay scallops. Further validation through RNA interference (RNAi) reinforced PC4's role in thermotolerance, offering a solid basis for investigating thermal response mechanisms in these scallops. In this study, we performed a comparative transcriptomic analysis on the temperature-sensitive hearts of bay scallops after siRNA-mediated RNAi targeting Arg0230340.1, to delve into the detailed molecular mechanism of PC4's participation in thermotolerance regulation. The analysis revealed that silencing Arg0230340.1 significantly reduced the expression of mitochondrial tRNA and rRNA, potentially affecting mitochondrial function and the heart's blood supply capacity. Conversely, the up-regulation of genes involved in energy metabolism, RNA polymerase II (RNAPII)-mediated basal transcription, and aminoacyl-tRNA synthesis pathways points to an intrinsic protective response, providing energy and substrates for damage repair and maintenance of essential functions under stress. GO and KEGG enrichment analyses indicated that the up-regulated genes were primarily associated with energy metabolism and spliceosome pathways, likely contributing to myocardial remodeling post-Arg0230340.1 knockdown. Down-regulated genes were enriched in ion channel pathways, particularly those for Na⁺, K⁺, and Ca²⁺ channels, whose dysfunction could disrupt normal myocardial bioelectric activity. The impaired cardiac performance resulting from RNAi targeting Arg0230340.1 reduced the cardiac workload in scallop hearts, thus affecting myocardial oxygen consumption and thermotolerance. We propose a hypothetical mechanism where PC4 down-regulation impairs cardiac bioelectric activity, leading to decreased thermotolerance in bay scallops, providing theoretical guidance for breeding thermotolerant scallop varieties and developing strategies for sustainable aquaculture in the face of long-term environmental changes.

In this study, our objective was to investigate the impact of dietary butyric acid (BA) on the homeostasis mechanism of Pacific shrimp under cold stress. Specifically, we analyzed its effects on immunity, antioxidant capacity, gene expression, and metabolomics response. To carry out this research, Litopenaeus vannamei were fed a diet supplemented with BA for 8 weeks. Following this feeding period, a total of 180 shrimp, with an average weight of 12.76 ± 0.38 g, were exposed to cold conditions, with the temperature decreasing from 28 °C to 14 °C within an hour. The results of our study revealed survival rates ranging from 90 % to 100 %. Shrimp that were fed a diet containing 1.5 % BA exhibited a significant increase in acid phosphatase (ACP) and alkaline phosphatase (AKP) activity. Conversely, the control groups showed an increase in aspartate aminotransferase (AST) and alanine transaminase (ALT) activity. Shrimp that consumed diets containing 1.5 % BA displayed the lowest malondialdehyde (MDA) levels with the highest superoxide dismutase (SOD) content. The shrimp fed the BA diet exhibited tightly organized hepatic tubules with a star-shaped lumen filled with numerous B and R cells. Furthermore, shrimp fed the BA diet demonstrated a significant increase in caspase 3 (CASP) expression. There were no significant variations in the expression levels of prophenoloxidase (ProPO), manganese superoxide dismutase (MnSOD), and glutathione S-transferase (GST) The metabolites of Dl-carnitine, acetyl-l-carnitine, propionylcarnitine, hexanoylcarnitine, palmitoylcarnitine, decanoylcarnitine, and Dl-carnitine exhibited significantly increased expression in shrimp that were fed BA, suggesting their role in the lipolysis process. Based on the findings, adding 2 % BA to the diet of Pacific shrimp helps reduce inflammation and oxidative stress when they are under cold stress.

The growth and development of myofibers, as the fundamental units comprising muscle tissue, and their composition type are indeed among the most crucial factors influencing skeletal muscle types. Muscle fiber adaptation is closely associated with alterations in physiological conditions. Muscle fiber types undergo dynamic changes in fetus and adult horses. Our aim is to investigate the mechanisms influencing the differences in muscle fiber types between fetal and adult stages of Mongolian horses. The study investigated the distribution of muscle fiber types within longissimus dorsi muscle of fetus and adult Mongolian horses. A total of 652 differentially expressed genes (DEGs), 476 Differentially expressed lncRNAs (DELs), and 174 Differentially expressed miRNAs (DEMIRs) were identified using deep RNA-seq analysis. The results of functional analysis reveal the transformations in muscle fiber type from the fetal to adult stage in Mongolian horses. The up-regulated DEGs were implicated in the development and differentiation of muscle fibers, while down-regulated DEGs were associated with muscle fiber contraction, transformation, and metabolism. Additionally, connections between non-coding RNA and mRNA landscapes were identified based on their functional alterations, some non-coding RNA target genes may be associated with immunity. These data have broadened our understanding of the specific roles and interrelationships among regulatory molecules involved in Mongolian horse development, this provides new perspectives for selecting and breeding superior individuals and for disease prevention.

Inhabiting some of the world's most inhospitable climatic regions, the Sunite Mongolian sheep generates average temperatures as low as 4.3 °C and a minimum temperature of −38.8 °C; in these environments, they make essential cold adaptations. In this regard, scapular fat tissues from Mongolian sheep were collected both in winter and summer for transcriptomic and proteomic analyses to identify genes related to adaptive thermogenesis. In the transcriptome analysis, 588 differentially expressed genes were identified to participate in smooth muscle activity and fat metabolism, as well as in nutrient regulation. There were 343 upregulated and 245 downregulated genes. GO and KEGG pathway analyses on these genes revealed their participation in regulating smooth muscle activity, metabolism of fats, and nutrients. Proteomic analysis showed the differential expression of 925 proteins: among them, there are 432 up- and 493 down-expressed proteins. These proteins are mainly involved in oxidative phosphorylation, respiratory chain complex assembly, and ATP production by electron transport. Furthermore, using both sets at a more detailed level of analysis revealed over-representation in gene ontology categories related to hormone signaling, metabolism of lipids, the pentose phosphate pathway, the TCA cycle, and especially the process of oxidative phosphorylation. The identified essential genes and proteins were further validated by quantitative real-time polymerase chain reaction and Western blotting, respectively; key metabolic network constriction was constructed. The present study emphasized the critical role of lipid turnover in scapular fat for thermogenic adaptation in Sunite sheep.

The cytochrome P450 (CYP) gene superfamily plays a significant role in various physiological processes, producing different compounds such as hormones, fatty acids, and biomolecules. However, little information is known their roles during gonad development in Pacific oyster (Crassostrea gigas). In this study, total of 116 CgCYP (Crassostrea gigas cytochrome P450) genes were identified and their expression pattern was analyzed for the first time. The relative molecular weights of these CgCYP genes ranged from 63.52 to 113.41 kDa, and the length of encoded amino acids ranged from 103 to 993. And total 26 cis-acting elements of these CgCYP genes were identified. GO and KEGG enrichment analysis showed some CgCYP genes are essential for the metabolism of male and female sex hormones. Additionally, expression anslysis showed 69 CgCYP genes were over-expressed in early gonad development and triploid infertile individuals. More importantly, expression levels of CgCYP1, CgCYP15, CgCYP34, CgCYP46, CgCYP69, CgCYP87, CgCYP88, and CgCYP103, were found to be significantly higher in female gonad, suggesting their important roles in female gonad development. The results of this study will provide a better understanding of the CgCYP genes in the gonad development of Pacific oyster.

High temperature and hypoxia in water due to global warming threaten the growth and development of aquatic animals. In natural or cultured environments, stress usually does not occur independently, whereas the synergistic effect of high temperature and hypoxia on Chinese mitten crab (Eriocheir sinensis) are rarely reported. In this study, 450 juvenile crabs were equally divided into control group (24 °C ± 0.5 °C, DO 6.8 ± 0.1 mg/L), hypoxia stress group (24 °C ± 0.5 °C, DO 1 ± 0.1 mg/L) and combined stress group (30 °C ± 0.5 °C, DO 1 ± 0.1 mg/L), and the intestinal health status, microbial diversity and metabolite profiles were evaluated for 24 h treatment. The results showed that hypoxia stress induced the expression level of pro-inflammatory related genes were significantly up-regulated in intestine of juvenile E. sinensis, and intestinal peritrophic membrane factor related genes were significantly down-regulated. High temperature further amplified the effects of hypoxia on pro-inflammatory and peritrophic membrane factor-related genes. Interesting, hypoxia stress induced a significant up-regulated of intestinal antioxidant-related genes, whereas high temperature reversed this trend. In addition, single stress or/and combined stress led to changes in intestinal microbiota diversity and abundance, and intestinal metabolite profiles. Compared with hypoxia stress, the synergistic effect of high temperature and hypoxia led to an increase in the abundance of pathogenic bacteria and a decrease in the abundance of probiotic bacteria. Moreover, intestinal metabolic pathways were significantly changed, especially amino acid metabolism and glycerophospholipid metabolism. Therefore, the results indicated that hypoxia stress could induce intestinal inflammatory response and oxidative stress, and lead to abnormal changes in intestinal microbiota and metabolic profiles, whereas high temperature further aggravate the toxic effects of hypoxia on the intestine. This study preliminarily revealed the synergistic toxic effects of high temperature and hypoxia on the intestine of juvenile E. sinensis.

Preliminary experiments in our laboratory have demonstrated that common carp (Cyprinus carpio) cultivated for two months in land-based container recirculating aquaculture systems (C-RAS) exhibit superior muscle quality compared to those raised in traditional pond systems (TP). To elucidate the molecular mechanisms underlying muscle quality variations in common carp cultured under two aquaculture systems, transcriptomic and metabolomic analyses were performed on muscle tissues of specimens aged 11 to 23 months. Comparison of muscle histological sections between the two groups indicated a significantly lower long diameter of muscle fibers in the C-RAS group compared to the TP group (P < 0.01). Conversely, the muscle fiber density was significantly higher in the C-RAS group than in the TP group (P < 0.05). Transcriptomic and metabolomic analyses identified 3390 differentially expressed genes (DEGs)—1558 upregulated and 1832 downregulated—and 181 differentially expressed metabolites (DEMs)—124 upregulated and 57 downregulated—between the groups. Based on integrated transcriptomic and metabolomic analyses, the significant differences focus on metabolic pathways involving glycolysis/gluconeogenesis, arginine and proline metabolism, arginine biosynthesis, and purine metabolism. The study revealed that the muscle quality of common carp in two aquaculture systems is primarily regulated through improvements in energy metabolism, amino acid metabolism, fatty acid metabolism, and purine metabolism. These metabolic processes play significant roles in promoting muscle fiber hyperplasia and hypertrophy, enhancing muscle flavor, and increasing muscle antioxidant capacity. This study provides new insights into the molecular and metabolic pathways that control muscle quality in common carp under different environmental factors.