Pub Date : 2024-10-31DOI: 10.1016/j.cbd.2024.101350
Zhi Luo , Yuxing Huang , Jinquan Fan, Erchao Li, Liqiao Chen, Xiaodan Wang
This study investigated the genetic response of tilapia (Oreochromis mossambicus) brain cells to hypertonic stress, focusing on miRNAs regulation. Three hundred and thirty-one known miRNAs and 163 novel miRNAs which responded to hypertonic stress were identified by high-throughput sequencing in tilapia brain cells. Differential expression analysis revealed that 16 miRNAs were significantly upregulated, while 11 miRNAs were significantly downregulated. These differentially expressed miRNAs are closely related to metabolism, immune response, and neural regulation. The target genes of these miRNAs are implicated in neurotrophic and synaptic signaling pathways, potentially affecting metabolic and apoptotic processes. GO and KEGG enrichment analyses provided insights into the biological processes and pathways affected by hypertonic stress. Furthermore, correlation analysis between mRNA and miRNA highlighted miRNA-mRNA interactions related to cell cycle and apoptosis regulation. These results indicated significant changes of miRNA expression under hypertonic stress and their crucial role in osmotic pressure regulation. This study offers a basis for further exploration of miRNA functions and molecular mechanisms in tilapia, potentially informing practices for aquaculture in challenging environments such as saline-alkaline waters.
{"title":"Construction and integrative analysis of miRNA-mRNA response to salinity stress in Oreochromis mossambicus cells","authors":"Zhi Luo , Yuxing Huang , Jinquan Fan, Erchao Li, Liqiao Chen, Xiaodan Wang","doi":"10.1016/j.cbd.2024.101350","DOIUrl":"10.1016/j.cbd.2024.101350","url":null,"abstract":"<div><div>This study investigated the genetic response of tilapia (<em>Oreochromis mossambicus</em>) brain cells to hypertonic stress, focusing on miRNAs regulation. Three hundred and thirty-one known miRNAs and 163 novel miRNAs which responded to hypertonic stress were identified by high-throughput sequencing in tilapia brain cells. Differential expression analysis revealed that 16 miRNAs were significantly upregulated, while 11 miRNAs were significantly downregulated. These differentially expressed miRNAs are closely related to metabolism, immune response, and neural regulation. The target genes of these miRNAs are implicated in neurotrophic and synaptic signaling pathways, potentially affecting metabolic and apoptotic processes. GO and KEGG enrichment analyses provided insights into the biological processes and pathways affected by hypertonic stress. Furthermore, correlation analysis between mRNA and miRNA highlighted miRNA-mRNA interactions related to cell cycle and apoptosis regulation. These results indicated significant changes of miRNA expression under hypertonic stress and their crucial role in osmotic pressure regulation. This study offers a basis for further exploration of miRNA functions and molecular mechanisms in tilapia, potentially informing practices for aquaculture in challenging environments such as saline-alkaline waters.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142586509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-29DOI: 10.1016/j.cbd.2024.101346
Bohong Liu , Shilin Liu , Lina Sun , Lili Xing
Global warming has multi-dimensional and complex impacts on the Earth's system, among which changes in light intensities cannot be overlooked. Sea cucumbers are a marine biological resource with significant economic and ecological value. Their presence and activity help maintain the balance and stability of marine ecosystems. The variation in light intensities have important ecological effects on sea cucumbers. Light intensities can alter the synthesis and degradation of metabolic substances within the bodies of Apostichopus japonicus by changing their body color. Their changes affect the production of microorganisms in the environment, thereby achieving the goal of bioremediation. This study investigated metabolic variations in green, purple, and white sea cucumber Apostichopus japonicus under different light conditions (0 lx and 910 lx) with a 12-h light and 12-h dark photoperiod. The findings indicated that the sea cucumbers displayed more diverse metabolic alterations under 910 lx illumination compared to 0 lx. Specifically, these color morphs primarily responded to changes in light intensities through “tryptophan metabolism” and “biosynthesis of steroid hormones”. Additionally, high light intensities environment exacerbated the consumption of fatty acids by sea cucumbers. Different color morphs of sea cucumbers have differences in key metabolites in response to changes in light intensities. Green and white sea cucumbers primarily adapt to environment through phospholipids, while purple sea cucumbers mainly utilize fatty acids. These results enhance our comprehension of how sea cucumbers adapt ecologically to varying light intensities, and they offer valuable insights for systematically uncovering the regulatory processes that marine animals employ in response to environmental changes.
{"title":"Revealing the adaptation mechanism of different color morphs of sea cucumber Apostichopus japonicus to light intensities from the perspective of metabolomics","authors":"Bohong Liu , Shilin Liu , Lina Sun , Lili Xing","doi":"10.1016/j.cbd.2024.101346","DOIUrl":"10.1016/j.cbd.2024.101346","url":null,"abstract":"<div><div>Global warming has multi-dimensional and complex impacts on the Earth's system, among which changes in light intensities cannot be overlooked. Sea cucumbers are a marine biological resource with significant economic and ecological value. Their presence and activity help maintain the balance and stability of marine ecosystems. The variation in light intensities have important ecological effects on sea cucumbers. Light intensities can alter the synthesis and degradation of metabolic substances within the bodies of <em>Apostichopus japonicus</em> by changing their body color. Their changes affect the production of microorganisms in the environment, thereby achieving the goal of bioremediation. This study investigated metabolic variations in green, purple, and white sea cucumber <em>Apostichopus japonicus</em> under different light conditions (0 lx and 910 lx) with a 12-h light and 12-h dark photoperiod. The findings indicated that the sea cucumbers displayed more diverse metabolic alterations under 910 lx illumination compared to 0 lx. Specifically, these color morphs primarily responded to changes in light intensities through “tryptophan metabolism” and “biosynthesis of steroid hormones”. Additionally, high light intensities environment exacerbated the consumption of fatty acids by sea cucumbers. Different color morphs of sea cucumbers have differences in key metabolites in response to changes in light intensities. Green and white sea cucumbers primarily adapt to environment through phospholipids, while purple sea cucumbers mainly utilize fatty acids. These results enhance our comprehension of how sea cucumbers adapt ecologically to varying light intensities, and they offer valuable insights for systematically uncovering the regulatory processes that marine animals employ in response to environmental changes.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142570704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-28DOI: 10.1016/j.cbd.2024.101347
Wenhao Wang , Junrou Huang , Wenyu Fang , Hongyun Zhang , Zhiqiang Chen , Jianguo Lu
Litopenaeus vannamei is a crucial species in aquaculture. The gene expression patterns associated with distinct growth rates are not well understood. To investigate this, we used RNA-seq to study the underlying growth mechanism of L. vannamei with varying growth rates. Individuals of higher growth performance (HG), middle growth performance (MG), and lower growth performance (LG) were examined. A total of 8422 and 4560 differentially expressed genes (DEGs) were identified in gill and muscle samples, respectively. Genes related to growth were significantly up-regulated in HG gills, such as cuticle protein, chitin synthase, pupal cuticle protein, titin myosin G heavy chain, and myosin heavy chain 10. The GO enrichment analysis revealed that the DEGs of HG gills were significantly enriched in “structural constituent of cuticle”, “primary metabolic process” and “chitin binding”. The growth-related genes were highly expressed in HG muscle, such as myosin heavy chain, myosin heavy chain type A and myosin 3. The GO enrichment analysis revealed that the DEGs of HG muscle were significantly enriched in “myosin filament”, “myosin complex” and “myofibril”. These findings provide insights into mechanisms underlying the growth performance of superior L. vannamei, and identify candidate genes for genetic improvement programs aimed at enhancing this trait.
{"title":"Transcriptome analysis uncovers the expression of genes associated with growth in the gills and muscles of white shrimp (Litopenaeus vannamei) with different growth rates","authors":"Wenhao Wang , Junrou Huang , Wenyu Fang , Hongyun Zhang , Zhiqiang Chen , Jianguo Lu","doi":"10.1016/j.cbd.2024.101347","DOIUrl":"10.1016/j.cbd.2024.101347","url":null,"abstract":"<div><div><em>Litopenaeus vannamei</em> is a crucial species in aquaculture. The gene expression patterns associated with distinct growth rates are not well understood. To investigate this, we used RNA-seq to study the underlying growth mechanism of <em>L. vannamei</em> with varying growth rates. Individuals of higher growth performance (HG), middle growth performance (MG), and lower growth performance (LG) were examined. A total of 8422 and 4560 differentially expressed genes (DEGs) were identified in gill and muscle samples, respectively. Genes related to growth were significantly up-regulated in HG gills, such as cuticle protein, chitin synthase, pupal cuticle protein, titin myosin G heavy chain, and myosin heavy chain 10. The GO enrichment analysis revealed that the DEGs of HG gills were significantly enriched in “structural constituent of cuticle”, “primary metabolic process” and “chitin binding”. The growth-related genes were highly expressed in HG muscle, such as myosin heavy chain, myosin heavy chain type A and myosin 3. The GO enrichment analysis revealed that the DEGs of HG muscle were significantly enriched in “myosin filament”, “myosin complex” and “myofibril”. These findings provide insights into mechanisms underlying the growth performance of superior <em>L. vannamei,</em> and identify candidate genes for genetic improvement programs aimed at enhancing this trait.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-18DOI: 10.1016/j.cbd.2024.101345
Ruijie Guo , Kai Huang , Kai Yu , Fei Xue , Yixin Liang , Xuhong Yang , Jiao Huang , Yaoting Wu , Dandan Wang
The effect of dietary protein on fish is widely studied. However, the high-protein diet effects and mechanisms on growth and amino acid metabolism in Procypris merus remain unclear. In this study, we investigated the effect of dietary protein levels (38 %, 44 %, 50 %) on the growth performance and amino acid contents in larvae and juveniles of P. merus. Transcriptome sequencing was used to study the adaptation mechanism of P. merus to a high-protein diet. The final length, specific growth rate, and protein efficiency ratio were remarkably decreased with increasing dietary protein levels, while the amino acid content of the body was significantly increased. In addition, 370,513,858 reads were obtained and assembled into 278,939 unigenes, with an average length of 559 bp. KEGG analysis revealed that differentially expressed genes were mainly involved in protein digestion and absorption, carbohydrate digestion and absorption, starch and sucrose metabolism, and pancreatic secretion. Moreover, high-protein increased the expression of genes involved in trypsin (prss, ctrl, cpa, cpb), peptide transporter (pept), amino acid transporter (b0at1), and gluconeogenesis (g6pase), which could digest and absorb the dietary protein, and converse amino acids into energy, resulting in adaption to a high-protein diet.
膳食蛋白质对鱼类的影响已被广泛研究。然而，高蛋白日粮对梅氏原鲤生长和氨基酸代谢的影响及其机制仍不清楚。本研究探讨了日粮蛋白质水平（38%、44%、50%）对梅花鱼幼体和幼鱼生长性能和氨基酸含量的影响。转录组测序被用来研究梅花鱼对高蛋白食物的适应机制。结果表明，随着日粮蛋白质水平的增加，美罗鱼的最终体长、特定生长率和蛋白质效率比明显下降，而体内氨基酸含量则显著增加。此外，研究人员还获得了 370,513,858 个读数，并将其组装成 278,939 个平均长度为 559 bp 的单基因。KEGG 分析显示，差异表达基因主要涉及蛋白质消化吸收、碳水化合物消化吸收、淀粉和蔗糖代谢以及胰腺分泌。此外，高蛋白增加了参与胰蛋白酶（prss、ctrl、cca、ccb）、肽转运体（pept）、氨基酸转运体（b0at1）和糖元生成（g6pase）的基因的表达，这些基因可以消化吸收食物中的蛋白质，并将氨基酸转化为能量，从而适应高蛋白饮食。
{"title":"Effects of high-protein feeds on growth, free amino acid metabolism and protein metabolism-related genes in larvae and juveniles of rice flower carp (Procypris merus)","authors":"Ruijie Guo , Kai Huang , Kai Yu , Fei Xue , Yixin Liang , Xuhong Yang , Jiao Huang , Yaoting Wu , Dandan Wang","doi":"10.1016/j.cbd.2024.101345","DOIUrl":"10.1016/j.cbd.2024.101345","url":null,"abstract":"<div><div>The effect of dietary protein on fish is widely studied. However, the high-protein diet effects and mechanisms on growth and amino acid metabolism in <em>Procypris merus</em> remain unclear. In this study, we investigated the effect of dietary protein levels (38 %, 44 %, 50 %) on the growth performance and amino acid contents in larvae and juveniles of <em>P. merus</em>. Transcriptome sequencing was used to study the adaptation mechanism of <em>P. merus</em> to a high-protein diet. The final length, specific growth rate, and protein efficiency ratio were remarkably decreased with increasing dietary protein levels, while the amino acid content of the body was significantly increased. In addition, 370,513,858 reads were obtained and assembled into 278,939 unigenes, with an average length of 559 bp. KEGG analysis revealed that differentially expressed genes were mainly involved in protein digestion and absorption, carbohydrate digestion and absorption, starch and sucrose metabolism, and pancreatic secretion. Moreover, high-protein increased the expression of genes involved in trypsin (<em>prss</em>, <em>ctrl</em>, <em>cpa</em>, <em>cpb</em>), peptide transporter (<em>pept</em>), amino acid transporter (<em>b0at1</em>), and gluconeogenesis (<em>g6pase</em>), which could digest and absorb the dietary protein, and converse amino acids into energy, resulting in adaption to a high-protein diet.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-16DOI: 10.1016/j.cbd.2024.101341
Shengli Fu , Kun Qian , Xiao Tu , Jie Lu , Tuo Yao , Lingtong Ye , Jianmin Ye
The structure of fish intestines does not have a clear regional division, while the function of the intestines may be related to their structure. Therefore, in this study, the delimitation of intestinal segments in pufferfish (Takifugu obscurus) was achieved by morphological analysis. Subsequently, enzyme activity, intestinal microbiota, and gene expression were examined to compare the differences among the pufferfish various segments. According to four morphological parameters: height of mucosa folds (HF), width of mucosa folds (WF), thickness of muscularis (TM), and cross-sectional area (CSA), the pufferfish's intestine was divided into anterior intestine (AI), middle intestine (MI), and posterior intestine (PI). The activity levels of amylase, lipase, and trypsin in the AI and MI were significantly higher than these in the PI. According to the analysis of 16S rDNA, the dominant microbiota at the phylum level in the different segments were Epsilonbacteraeota, Spirochaetes, and Proteobacteria. At the genus level, there were variations observed in the relative abundance of Brevinema, Mycobacterium, Bradyrhizobium, and Microvirga. α diversity analysis revealed that the richness indexes (Ace and Chao1) were the lowest in the MI, while β diversity analysis revealed significant difference in intestinal microbial community composition among the three intestinal segments. Furthermore, RNA-Seq was used to identify differential expression genes (DEGs) and biological pathways among the different intestinal segments. The DEGs between the AI and MI were enriched in pancreatic secretion and protein digestion and absorption, those between AI and PI were involved in ascorbate and aldarate metabolism and glutathione metabolism, and those between MI and PI were involved in steroid biosynthesis, fat digestion and absorption, vitamin digestion and absorption, and glycine, serine and threonine metabolism. In conclusion, the presented results compare and analyze the differences in various intestinal segments of pufferfish, which will be conductive to future exploration of the functions of these different segments.
{"title":"Comparative analysis of intestinal structure, enzyme activity, intestinal microbiota and gene expression in different segments of pufferfish (Takifugu Obscurus)","authors":"Shengli Fu , Kun Qian , Xiao Tu , Jie Lu , Tuo Yao , Lingtong Ye , Jianmin Ye","doi":"10.1016/j.cbd.2024.101341","DOIUrl":"10.1016/j.cbd.2024.101341","url":null,"abstract":"<div><div>The structure of fish intestines does not have a clear regional division, while the function of the intestines may be related to their structure. Therefore, in this study, the delimitation of intestinal segments in pufferfish (<em>Takifugu obscurus</em>) was achieved by morphological analysis. Subsequently, enzyme activity, intestinal microbiota, and gene expression were examined to compare the differences among the pufferfish various segments. According to four morphological parameters: height of mucosa folds (HF), width of mucosa folds (WF), thickness of muscularis (TM), and cross-sectional area (CSA), the pufferfish's intestine was divided into anterior intestine (AI), middle intestine (MI), and posterior intestine (PI). The activity levels of amylase, lipase, and trypsin in the AI and MI were significantly higher than these in the PI. According to the analysis of 16S rDNA, the dominant microbiota at the phylum level in the different segments were Epsilonbacteraeota, Spirochaetes, and Proteobacteria. At the genus level, there were variations observed in the relative abundance of Brevinema, Mycobacterium, Bradyrhizobium, and Microvirga. <em>α</em> diversity analysis revealed that the richness indexes (Ace and Chao1) were the lowest in the MI, while <em>β</em> diversity analysis revealed significant difference in intestinal microbial community composition among the three intestinal segments. Furthermore, RNA-Seq was used to identify differential expression genes (DEGs) and biological pathways among the different intestinal segments. The DEGs between the AI and MI were enriched in pancreatic secretion and protein digestion and absorption, those between AI and PI were involved in ascorbate and aldarate metabolism and glutathione metabolism, and those between MI and PI were involved in steroid biosynthesis, fat digestion and absorption, vitamin digestion and absorption, and glycine, serine and threonine metabolism. In conclusion, the presented results compare and analyze the differences in various intestinal segments of pufferfish, which will be conductive to future exploration of the functions of these different segments.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142483143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Peltogasterella gracilis (Cirripedia: Rhizocephala), a crustacean parasite of hermit crabs, displays genotypic sex determination. Its larvae are planktonic, and female larvae settle on the host. Subsequently, the females control the host's behavior by spreading a root-like structure called “the interna” within the host's body, and form sacs containing eggs called “the externae” outside the host's body. On the other hand, male larvae settle on immature externae and become dwarf males. The cypris larvae of P. gracilis show sexual dimorphism in size and morphology. However, there is no understanding of the molecular mechanisms underlying the sexual dimorphism observed at the larval stage. Here, we conducted a transcriptome analysis and compared the expression of genes in male and female cyprids to better understand their sexual differentiation and settlement processes. A total of 2870 differentially expressed transcripts, comprising 456 female- and 2414 male-biased transcripts were identified. Among the male-biased ones, ionotropic glutamate receptor-, heat shock protein-, acetylcholine-, and homeobox-, cuticle-related transcripts were included. Additionally, 29 gene ontology terms were associated with the sex-specific traits. The present study improves our understanding of sex determination, sexual differentiation, and settlement processes of rhizocephalans.
{"title":"Transcriptomic analysis of sexually dimorphic cypris larvae of the rhizocephalan barnacle Peltogasterella gracilis","authors":"Asami Kajimoto , Kenji Toyota , Tsuyoshi Ohira , Yoichi Yusa","doi":"10.1016/j.cbd.2024.101342","DOIUrl":"10.1016/j.cbd.2024.101342","url":null,"abstract":"<div><div><em>Peltogasterella gracilis</em> (Cirripedia: Rhizocephala), a crustacean parasite of hermit crabs, displays genotypic sex determination. Its larvae are planktonic, and female larvae settle on the host. Subsequently, the females control the host's behavior by spreading a root-like structure called “the interna” within the host's body, and form sacs containing eggs called “the externae” outside the host's body. On the other hand, male larvae settle on immature externae and become dwarf males. The cypris larvae of <em>P. gracilis</em> show sexual dimorphism in size and morphology. However, there is no understanding of the molecular mechanisms underlying the sexual dimorphism observed at the larval stage. Here, we conducted a transcriptome analysis and compared the expression of genes in male and female cyprids to better understand their sexual differentiation and settlement processes. A total of 2870 differentially expressed transcripts, comprising 456 female- and 2414 male-biased transcripts were identified. Among the male-biased ones, ionotropic glutamate receptor-, heat shock protein-, acetylcholine-, and homeobox-, cuticle-related transcripts were included. Additionally, 29 gene ontology terms were associated with the sex-specific traits. The present study improves our understanding of sex determination, sexual differentiation, and settlement processes of rhizocephalans.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-15DOI: 10.1016/j.cbd.2024.101344
Liang Chen , Jiaxin Zhang , Lei Ding , Tongyu Gu , Vivian Andoh , Aiqin Ma , Chun Yao
The growing elderly population presents a significant concern, with the prolongation of life expectancy, aging diseases are becoming increasingly common. Resveratrol (RSV) has emerged as a promising compound for disease prevention. However, the effect of RSV on lifespan extension in different organisms, particularly the model organism silkworm, remains inconsistent. We conducted aging experiments using silkworm (B. mori) and employed transcriptomics to investigate the therapeutic effects of RSV on lifespan extension and healthy lifespan in silkworms. RSV increased the survival rate by 8.57 %–12.12 % and enhanced the antioxidant capacity of silkworms. Transcriptomic analysis demonstrated that genes in signaling pathways such as AMPK and FoxO were significantly upregulated. 16SrRNA sequencing of gut contents showed an increase in beneficial bacterial strains under the action of RSV. This study aims to enhance our understanding of lifespan regulation mechanisms using the silkworm model and provide new targets for anti-aging antioxidants research to delay the onset of age-related diseases.
{"title":"Transcriptomics analyses combined with intestinal microorganism survey suggest Resveratrol (RSV) anti-aging and anti-oxidant effects in silkworm (Bombyx mori)","authors":"Liang Chen , Jiaxin Zhang , Lei Ding , Tongyu Gu , Vivian Andoh , Aiqin Ma , Chun Yao","doi":"10.1016/j.cbd.2024.101344","DOIUrl":"10.1016/j.cbd.2024.101344","url":null,"abstract":"<div><div>The growing elderly population presents a significant concern, with the prolongation of life expectancy, aging diseases are becoming increasingly common. Resveratrol (RSV) has emerged as a promising compound for disease prevention. However, the effect of RSV on lifespan extension in different organisms, particularly the model organism silkworm, remains inconsistent. We conducted aging experiments using silkworm (<em>B. mori</em>) and employed transcriptomics to investigate the therapeutic effects of RSV on lifespan extension and healthy lifespan in silkworms. RSV increased the survival rate by 8.57 %–12.12 % and enhanced the antioxidant capacity of silkworms. Transcriptomic analysis demonstrated that genes in signaling pathways such as <em>AMPK</em> and <em>FoxO</em> were significantly upregulated. 16SrRNA sequencing of gut contents showed an increase in beneficial bacterial strains under the action of RSV. This study aims to enhance our understanding of lifespan regulation mechanisms using the silkworm model and provide new targets for anti-aging antioxidants research to delay the onset of age-related diseases.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142483220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-14DOI: 10.1016/j.cbd.2024.101343
Fengfang Zhou , Mengyang Chang , Yan Lan , Weiqing Huang , Zhenxia Sha , Jiafu Liu , Zipeng Zhang , Shaojiang Ruan , Zheng Liu
China has several saline-alkaline bodies. Studies on the adaptation of fish in saline-alkaline conditions are important for the efficient utilization of such areas. In this study, we employed a comprehensive approach combining histopathological analysis, biochemical markers, and metabolomic profiling to examine the impact of saline-alkaline stress on the liver of the large yellow croaker (Larimichthys crocea). It was found that the survival rate of L. crocea in the saline-alkaline treated group (EX) was significantly higher than that of the control group (CK). Saline-alkaline stress could not influence the structure of the liver of L. crocea, and not change the levels of superoxide dismutase (SOD), catalase (CAT), alkaline phosphatase (ALP), acid phosphatase (ACP). In addition, we identified 5953 metabolites, and 312 differentially expressed metabolites (DEMs) showed significant differential expression between the CK and EX groups. In the positive ion mode, 216 DEMs were identified, including 120 up-regulated and 96 down-regulated DEMs, and in the negative ion mode, 178 DEMs were identified, including 131 up-regulated and 47 down-regulated DEMs. Pathway enrichment analysis revealed significant involvement in 58 metabolic pathways, primarily linked to energy metabolism. These included the metabolism of amino acid, carbohydrate, and lipid pathways, including cysteine and methionine metabolism, biosynthesis of valine, leucine, isoleucine, and ascorbate; aldarate metabolism; galactose metabolism; glycerophospholipid metabolism; and the biosynthesis of unsaturated fatty acids. Metabolomics revealed that increased synthesis of compounds, such as succinic acid, arachidonic acid, and L-gulonic acid in the liver of L.crocea, is associated with adaptation to saline-alkaline aquaculture conditions. The findings of this study indicated that the fish mitigate reactive oxygen species induced by hyperosmotic environments and improve cellular membrane fluidity and intercellular signal transduction through the metabolism of unsaturated fatty acids and carbohydrates, facilitating adaptation to saline-alkaline conditions.
中国有多个盐碱地。研究鱼类在盐碱地条件下的适应性对于有效利用盐碱地非常重要。本研究采用组织病理学分析、生化标记和代谢组学分析相结合的综合方法，研究盐碱胁迫对大黄鱼肝脏的影响。结果发现，盐碱处理组（EX）的大黄鱼存活率明显高于对照组（CK）。盐碱胁迫不会影响黄花鱼肝脏的结构，也不会改变超氧化物歧化酶（SOD）、过氧化氢酶（CAT）、碱性磷酸酶（ALP）和酸性磷酸酶（ACP）的水平。此外，我们还鉴定了 5953 种代谢物，其中 312 种差异表达代谢物（DEMs）在 CK 组和 EX 组之间有显著的差异表达。在正离子模式下，共鉴定出216个差异表达代谢物，其中包括120个上调的差异表达代谢物和96个下调的差异表达代谢物；在负离子模式下，共鉴定出178个差异表达代谢物，其中包括131个上调的差异表达代谢物和47个下调的差异表达代谢物。通路富集分析表明，有 58 个代谢通路显著参与了研究，这些通路主要与能量代谢有关。其中包括氨基酸、碳水化合物和脂质的代谢途径，包括半胱氨酸和蛋氨酸代谢，缬氨酸、亮氨酸、异亮氨酸和抗坏血酸的生物合成；醛酸代谢；半乳糖代谢；甘油磷脂代谢；以及不饱和脂肪酸的生物合成。代谢组学研究发现，黄花鱼肝脏中琥珀酸、花生四烯酸和L-谷甾醇酸等化合物的合成增加与适应盐碱水产养殖条件有关。研究结果表明，鱼类通过不饱和脂肪酸和碳水化合物的新陈代谢，缓解高渗环境诱导的活性氧，改善细胞膜流动性和细胞间信号转导，从而促进对盐碱条件的适应。
{"title":"Effects of saline-alkaline stress on metabolomics profiles, biochemical parameters, and liver histopathology in large yellow croaker (Larimichthys crocea)","authors":"Fengfang Zhou , Mengyang Chang , Yan Lan , Weiqing Huang , Zhenxia Sha , Jiafu Liu , Zipeng Zhang , Shaojiang Ruan , Zheng Liu","doi":"10.1016/j.cbd.2024.101343","DOIUrl":"10.1016/j.cbd.2024.101343","url":null,"abstract":"<div><div>China has several saline-alkaline bodies. Studies on the adaptation of fish in saline-alkaline conditions are important for the efficient utilization of such areas. In this study, we employed a comprehensive approach combining histopathological analysis, biochemical markers, and metabolomic profiling to examine the impact of saline-alkaline stress on the liver of the large yellow croaker (<em>Larimichthys crocea</em>). It was found that the survival rate of <em>L. crocea</em> in the saline-alkaline treated group (EX) was significantly higher than that of the control group (CK). Saline-alkaline stress could not influence the structure of the liver of L. <em>crocea</em>, and not change the levels of superoxide dismutase (SOD), catalase (CAT), alkaline phosphatase (ALP), acid phosphatase (ACP). In addition, we identified 5953 metabolites, and 312 differentially expressed metabolites (DEMs) showed significant differential expression between the CK and EX groups. In the positive ion mode, 216 DEMs were identified, including 120 up-regulated and 96 down-regulated DEMs, and in the negative ion mode, 178 DEMs were identified, including 131 up-regulated and 47 down-regulated DEMs. Pathway enrichment analysis revealed significant involvement in 58 metabolic pathways, primarily linked to energy metabolism. These included the metabolism of amino acid, carbohydrate, and lipid pathways, including cysteine and methionine metabolism, biosynthesis of valine, leucine, isoleucine, and ascorbate; aldarate metabolism; galactose metabolism; glycerophospholipid metabolism; and the biosynthesis of unsaturated fatty acids. Metabolomics revealed that increased synthesis of compounds, such as succinic acid, arachidonic acid, and L-gulonic acid in the liver of <em>L.crocea</em>, is associated with adaptation to saline-alkaline aquaculture conditions. The findings of this study indicated that the fish mitigate reactive oxygen species induced by hyperosmotic environments and improve cellular membrane fluidity and intercellular signal transduction through the metabolism of unsaturated fatty acids and carbohydrates, facilitating adaptation to saline-alkaline conditions.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142483219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-11DOI: 10.1016/j.cbd.2024.101340
Rongxiao Wang , Yuke Bu , Kefan Xing , Longbin Yuan , Zixuan Wu , Yuying Sun , Jiquan Zhang
Low salinity environment is one of the key factors threatening the survival of aquatic organisms. Due to the strong adaptability of low salinity, Exopalaemon carinicauda is an ideal model to study the low salinity adaptation mechanism of crustaceans. In this study, E. carinicauda from the same family were divided into two groups, which were reared at salinity of 4 ‰ and 30 ‰, respectively. Integrated analysis of transcriptome and metabolome was used to uncover the mechanisms of E. carinicauda adaptation to chronic low salinity environment. Under the chronic low salinity stress, a total of 651 differentially expressed genes (DEGs) and 386 differential metabolites (DMs) were obtained, with the majority showing downregulation. These DEGs mainly involved MAPK signal transduction pathway and structural constituent of cuticle. Besides, chitin binding and chitin metabolism process were inhibited significantly. Among the DMs, lipids and lipid-like molecules, flavor amino acids and nucleotides were detected, which may be related to the adjustment of energy metabolism and flavor of muscle. In addition, ubiquinone and other terpenoid-quinone biosynthesis pathway and alanine, aspartate, and glutamate metabolic pathway were induced. These results will enrich our understanding of the molecular mechanism underlying the chronic low salinity tolerance in E. carinicauda, providing an important theoretical basis and practical guidance for the research and breeding, thereby promoting the sustainable development of aquaculture.
{"title":"Integrated analysis of transcriptome and metabolome reveals chronic low salinity stress responses in the muscle of Exopalaemon carinicauda","authors":"Rongxiao Wang , Yuke Bu , Kefan Xing , Longbin Yuan , Zixuan Wu , Yuying Sun , Jiquan Zhang","doi":"10.1016/j.cbd.2024.101340","DOIUrl":"10.1016/j.cbd.2024.101340","url":null,"abstract":"<div><div>Low salinity environment is one of the key factors threatening the survival of aquatic organisms. Due to the strong adaptability of low salinity, <em>Exopalaemon carinicauda</em> is an ideal model to study the low salinity adaptation mechanism of crustaceans. In this study, <em>E. carinicauda</em> from the same family were divided into two groups, which were reared at salinity of 4 ‰ and 30 ‰, respectively. Integrated analysis of transcriptome and metabolome was used to uncover the mechanisms of <em>E. carinicauda</em> adaptation to chronic low salinity environment. Under the chronic low salinity stress, a total of 651 differentially expressed genes (DEGs) and 386 differential metabolites (DMs) were obtained, with the majority showing downregulation. These DEGs mainly involved MAPK signal transduction pathway and structural constituent of cuticle. Besides, chitin binding and chitin metabolism process were inhibited significantly. Among the DMs, lipids and lipid-like molecules, flavor amino acids and nucleotides were detected, which may be related to the adjustment of energy metabolism and flavor of muscle. In addition, ubiquinone and other terpenoid-quinone biosynthesis pathway and alanine, aspartate, and glutamate metabolic pathway were induced. These results will enrich our understanding of the molecular mechanism underlying the chronic low salinity tolerance in <em>E. carinicauda</em>, providing an important theoretical basis and practical guidance for the research and breeding, thereby promoting the sustainable development of aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142438198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-10DOI: 10.1016/j.cbd.2024.101338
Yixuan T. Tao, Jason P. Breves
Along the east coast of North America, mummichogs (Fundulus heteroclitus) are subjected to a broad range of salinities in their nearshore habitats. However, there is a paucity of information regarding the molecular and cellular processes that mummichogs (and other highly osmotolerant fishes) engage to survive environmental salinities greater than seawater (SW). To reveal branchial processes underlying their extraordinarily broad salinity tolerance, we performed an RNA-Seq analysis to identify differentially expressed genes (DEGs) in mummichogs residing in 3, 35, and 105 ppt conditions. We identified a series of DEGs previously associated with both freshwater (FW)- and SW-type ionocytes; however, the heightened expression of anoctamin 1a, a Ca2+-activated Cl− channel, in 35 and 105 ppt indicates that an undescribed Cl−-secretion pathway may operate within the SW-type ionocytes of mummichogs. Concerning FW-adaptive branchial processes, we identified claudin 5a as a gene whose product may limit the diffusive loss of ions between cellular tight junctions. Further, in response to hypersaline conditions, we identified DEGs linked with myo-inositol synthesis and kinase signaling. This study provides new molecular targets for future physiological investigations that promise to reveal the mechanistic bases for how mummichogs and other euryhaline species tolerate hypersaline conditions.
{"title":"Hypersalinity tolerance of mummichogs (Fundulus heteroclitus): A branchial transcriptomic analysis","authors":"Yixuan T. Tao, Jason P. Breves","doi":"10.1016/j.cbd.2024.101338","DOIUrl":"10.1016/j.cbd.2024.101338","url":null,"abstract":"<div><div>Along the east coast of North America, mummichogs (<em>Fundulus heteroclitus</em>) are subjected to a broad range of salinities in their nearshore habitats. However, there is a paucity of information regarding the molecular and cellular processes that mummichogs (and other highly osmotolerant fishes) engage to survive environmental salinities greater than seawater (SW). To reveal branchial processes underlying their extraordinarily broad salinity tolerance, we performed an RNA-Seq analysis to identify differentially expressed genes (DEGs) in mummichogs residing in 3, 35, and 105 ppt conditions. We identified a series of DEGs previously associated with both freshwater (FW)- and SW-type ionocytes; however, the heightened expression of <em>anoctamin 1a</em>, a Ca<sup>2+</sup>-activated Cl<sup>−</sup> channel, in 35 and 105 ppt indicates that an undescribed Cl<sup>−</sup>-secretion pathway may operate within the SW-type ionocytes of mummichogs. Concerning FW-adaptive branchial processes, we identified <em>claudin 5a</em> as a gene whose product may limit the diffusive loss of ions between cellular tight junctions. Further, in response to hypersaline conditions, we identified DEGs linked with <em>myo</em>-inositol synthesis and kinase signaling. This study provides new molecular targets for future physiological investigations that promise to reveal the mechanistic bases for how mummichogs and other euryhaline species tolerate hypersaline conditions.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142438199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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