Comparative biochemistry and physiology. Part D, Genomics & proteomics最新文献

{"title":"Transcriptome analysis of Chinese sucker (Myxocyprinus asiaticus) head kidney and discovery of key immune-related genes to cold stress after swimming fatigue.","authors":"Jing Xu, Chuan-Jie Qin, Jiang Xie, Jun Wang, Yang He, Junjun Tan, Xiaotao Shi","doi":"10.2139/ssrn.4379347","DOIUrl":"https://doi.org/10.2139/ssrn.4379347","url":null,"abstract":"For Chinese sucker (Myxocyprinus asiaticus), passing through a dam with fast flow and cold water are always unavoidable, and this process can cause stress, disease or even death. In this study, comparative transcriptome analysis was conducted to investigate the potential immune mechanism in head kidney of M. asiaticus with swimming fatigue stress and cold stress after fatigue. In general, a total of 181,781 unigenes were generated, and 38,545 differentially expressed genes (DEGs) were identified. In these DEGs, 22,593, 7286 and 8666 DEGs were identified among groups of fatigue vs. cold, control vs. cold, and control vs. fatigue, respectively. Enrichment analysis revealed these DEGs were involved in coagulation cascades and complement, natural killer cell mediated cytotoxicity, antigen processing and presentation, Toll-like receptor signaling pathways, and chemokine signaling pathway. Notably, immune genes including heat shock protein 4a (HSP4a), HSP70 and HSP90α genes were significantly up-regulated in fishes with cold stress after fatigue. Differently, more immune genes in control vs. cold compared with that in control vs. fatigue were significantly down-regulated expression, such as claudin-15-like, Toll-like receptor 13, antimicrobial peptide (hepcidin), immunoglobulin, CXCR4 chemokine receptor, T-cell receptor, complement factor B/C2-A3, and interleukin 8. In this study, the number of DEGs in the head kidney was less than that our previous study in the spleen, which we speculated was more sensitive to changes in water temperature than the head kidney. In summary, lots of immune-related genes in the head kidney were down-regulated under cold stress after fatigue, suggesting that M. asiaticus might have experienced severe immunosuppression in the process of passing through the dam.","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85573899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sex matters: Gamete-specific contribution of microRNA following parental exposure to hypoxia in zebrafish.","authors":"W. Heinrichs-Caldas, H. Ikert, V. M. Almeida-Val, P. M. Craig","doi":"10.2139/ssrn.4341895","DOIUrl":"https://doi.org/10.2139/ssrn.4341895","url":null,"abstract":"Oxygen availability varies among aquatic environments, and oxygen concentration has been demonstrated to drive behavioral, metabolic, and genetic adaptations in numerous aquatic species. MicroRNAs (miRNAs) are epigenetic modulators that act at the interface of the environment and the transcriptome and are known to drive plastic responses following environmental stressors. An area of miRNA that has remained underexplored is the sex specific action of miRNAs following hypoxia exposure and its effects as gene expression regulator in fishes. This study aimed to identify differences in mRNA and miRNA expression in the F1 generation of zebrafish (Danio rerio) at 1 hpf after either F0 parental male or female were exposed to 2 weeks of continuous (45 %) hypoxia. In general, F1 embryos at 1 hpf demonstrated differences in mRNA and miRNAs expression related to the stressor and to the specific sex of the F0 that was exposed to hypoxia. Bioinformatic pathway analysis of predicted miRNA:mRNA relationships indicated responses in known hypoxia signaling and mitochondrial bioenergetic pathways. This research demonstrates the importance of examining the specific male and female contributions to phenotypic variation in subsequent generations and provides evidence that there is both maternal and paternal contribution of miRNA through eggs and sperm.","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87069930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Hermetia illucens larvae meal on the Pacific white shrimp (Litopenaeus vannamei) revealed by innate immunity and 16S rRNA gene sequencing analysis.","authors":"Yongkang Chen, Zhenxiao Zhuang, Jieping Liu, Ziqiao Wang, Yucai Guo, Anqi Chen, Baoyang Chen, Wei Zhao, J. Niu","doi":"10.2139/ssrn.4372700","DOIUrl":"https://doi.org/10.2139/ssrn.4372700","url":null,"abstract":"The larvae of the black soldier fly, Hermetia illucens, are now attracting attention and becoming promising sources for aquafeed ingredient due to the nutritious substance. However, the introduction of a novel ingredient into the recipe may have unpredictable effects on the innate immune function and gut bacteria composition of crustaceans. Therefore, the present study aimed to evaluate how dietary black soldier fly larvae meal (BSFLM) affected the antioxidant ability, innate immunity and gut microbiome of shrimp (Litopenaeus vannamei) fed with a practical diet, including the gene expression of Toll and immunodeficiency (IMD) pathways. Six experimental diets were formulated by replacing gradient levels of fish meal (0 %, 10 %, 20 %, 30 %, 40 % and 50 %) based on a commercial shrimp diet. Four replicates of shrimp were fed different diets three times daily for 60 days. Growth performance linearly decreased with increasing BSFLM inclusion. Results of antioxidative enzyme activities and gene expression suggested that low dietary BSFLM levels activated the antioxidant capacity of shrimp, while dietary BSFLM levels up to 100 g/kg may induce oxidative stress and inhibit glutathione peroxidase activity. Although traf6, toll1, dorsal and relish were significantly upregulated in different BSFLM groups, the expression of tak1 was significantly downregulated in groups containing BSFLM, implying the immune susceptibility may be weakened. Gut flora analysis indicated dietary BSFLM altered both beneficial and opportunistic pathogenic bacterial abundance, with low levels of dietary BSFLM increased the abundance of bacteria that may contribute to carbohydrate utilization, while high levels of dietary BSFLM may cause intestinal disease and low intestinal immune response. To conclude, 60-80 g/kg of dietary BSFLM showed no adverse effects on the growth, antioxidant capacity and gut flora of shrimp, which was the adequate level in shrimp diet. While 100 g/kg dietary BSFLM may induce oxidative stress and potentially weaken the innate immunity of shrimp.","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84394781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HPLC-MS-based untargeted metabolomic analysis of differential plasma metabolites and their associated metabolic pathways in reproductively anosmic black porgy, Acanthopagrus schlegelii.","authors":"Xing Shen, Xian Li, Chaofeng Jia, Jun Li, Shuyin Chen, Bo Gao, Wen-Zhi Liang, Libin Zhang","doi":"10.2139/ssrn.4330797","DOIUrl":"https://doi.org/10.2139/ssrn.4330797","url":null,"abstract":"Olfaction, a universal form of chemical communication, is a powerful channel for animals to obtain social and environmental cues. The mechanisms by which fish olfaction affects reproduction, breeding and disease control are not yet clear. To evaluate metabolites profiles, plasma from anosmic and control black porgy during reproduction was analyzed by non-targeted metabolomics using ultra high-performance liquid chromatography-mass spectrometry and multivariate statistical analysis techniques, including principal component analysis and orthogonal partial least squares discriminant analysis. The metabolite profiles of anosmia and control groups were found to be significantly separated. Ten different differential metabolites, mainly including amino acids, such as isoleucine and methionine, and lipids, such as phosphatidylserine, were screened based on the combined analysis of variable importance in the projection and p values. In addition, six key differential metabolic pathways were analyzed using the Kyoto Encyclopedia of Genes and Genomes and enriched for four metabolic pathways including the citrate acid (TCA) cycle, tyrosine metabolism, arginine and proline metabolism, and arginine synthesis. The TCA cycle enhances fertility through the reduction of pyruvate kinase, and intermediate derivatives (acetyl CoA, malonyl CoA) act as signaling factors that regulate immune cell function. The tyrosine cycle can indirectly participate and promote reproduction in black porgy through melanin-concentrating hormone. Arginine and proline metabolism can promote reproduction by promoting growth hormone and enhance immunity in anosmic black porgy by stimulating T lymphocytes. Our metabolomic study revealed that anosmia in black porgy played an active role in immunity and reproduction and provided theoretical support for breeding and disease control.","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82442165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fatter or stronger: Resource allocation strategy and the underlying metabolic mechanisms in amphibian tadpoles.","authors":"Wei Zhu, Liming Chang, Guocheng Shu, Bin Wang, Jianping Jiang","doi":"10.21203/rs.3.rs-77495/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-77495/v1","url":null,"abstract":"The allocation of resources between storage and somatic growth is an essential physiological phenomenon in animals. Allocation mechanisms have broad theoretical and applied implications. The real-time resource allocation patterns in animals remain to be elucidated, and there is limited understanding of the metabolic mechanisms. We investigated the resource allocation strategy of Rana omeimontis tadpoles. Their ontogenetic fat accumulation began when body weight increased to 30-50 mg, at which time storage had a high priority in resource allocation. Beyond this weight range, somatic growth accelerated but storage investment was maintained, resulting in a positive correlation between body fat index and body weight at the population level. This pattern could be explained by assuming a positive relationship between storage abundance and growth investment, and this was supported by the prioritized increment of body fat to body weight when tadpoles were provided with increased food. At the metabolic level, hepatic fat accumulation was accompanied by upregulated utilization of fat storage, and the tadpoles presented lipid-based energy metabolism. Activating the mobilization of hepatic fat storage promoted somatic growth. In short, the liver is like a reservoir with valves that regulate energy flow for downstream developmental processes. These results provide novel mechanistic insights into resource allocation.","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89867398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and preliminary characterization of chemosensory-related proteins in the gall fly, Procecidochares utilis by transcriptomic analysis.","authors":"Lifang Li, Xi Gao, Huamin Gui, Mingxian Lan, Jiaying Zhu, Yong-hui Xie, Youguo Zhan, Zhi-jiang Wang, Li Zhengyue, M. Ye, Guo-xing Wu","doi":"10.21203/rs.3.rs-18943/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-18943/v1","url":null,"abstract":"Chemoreception is critical for insect behaviors such as foraging, host searching and oviposition. The process of chemoreception is mediated by a series of proteins, including odorant-binding proteins (OBPs), gustatory receptors (GRs), odorant receptors (ORs), ionotropic receptors (IRs), chemosensory proteins (CSPs) and sensory neuron membrane proteins (SNMPs). The tephritid stem gall fly, Procecidochares utilis Stone, is a type of egg parasitic insect, which is an effective biological control agent for the invasive weed Ageratina adenophora in many countries. However, the study of molecular components related to the olfactory system of P. utilis has not been investigated. Here, we conducted the developmental transcriptome (egg, first-third instar larva, pupa, female and male adult) of P. utilis using next-generation sequencing technology and identified a total of 133 chemosensory genes, including 40 OBPs, 29 GRs, 24 ORs, 28 IRs, 6 CSPs, and 6 SNMPs. The sequences of these candidate chemosensory genes were confirmed by BLAST, and phylogenetic analysis was performed. Quantitative real-time PCR (qRT-PCR) confirmed that the expression levels of the candidate OBPs varied at the different developmental stages of P. utilis with most OBPs expressed mainly in the pupae, female and male adults but scarcely in eggs and larvae, which was consistent with the differentially expressed genes (DEGs) analysis using the fragments per kilobase per million fragments (FPKM) value. Our results provide a significant contribution towards the knowledge of the set of chemosensory proteins and help advance the use of P. utilis as biological control agents.","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87664216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of gonadotropin-releasing hormone analog (GnRHa) immunization on the gonadal transcriptome and proteome of tilapia (Oreochromis niloticus).","authors":"Rui Wang, Luting Wen, Huawei Ma, Min Lv, Zhong Chen, Xuesong Du, Yong Lin, Huizan Yang","doi":"10.21203/rs.3.rs-18227/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-18227/v1","url":null,"abstract":"Gonadotropin releasing hormone (GnRH) plays an important role in the regulation of vertebrate reproduction. Studies have shown that immunization against GnRHa can induce sexually sterile tilapia. To explore the mechanism behind this, in this study, RNA-seq and data-independent acquisition (DIA) techniques were used to study the transcriptome and proteome of the gonad of tilapia immunized with GnRHa. 644 differentially expressed genes (80 upregulated and 564 downregulated) and 1150 differentially expressed proteins (351 upregulated and 799 downregulated) were identified. There were 209 genes with consistent differential expression patterns in the transcriptomic and proteomic analyses, of which 9 were upregulated and 200 downregulated, indicating that the gonad gene expression was inhibited by GnRHa immunization. The downregulated genes were particularly involved in the functions of single-organism process, binding, cellular process, metabolic process and catalytic activity, and associated with the pathways including ECM-receptor interaction, focal adhesion, cardiac muscle contraction and oxidative phosphorylation. The expression of six differentially expressed genes involved in the GnRH signaling pathway was all downregulated. In addition, several important functional genes related to gonadal development after GnRHa immunization were screened. This study confirmed the expression of corresponding genes was affected by GnRHa on the gonad development in tilapia at the molecular level, and laid a foundation for elucidating the mechanism of GnRHa immunization.","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88945122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early life stress causes persistent impacts on the microbiome of Atlantic salmon","authors":"T. U. Webster, S. Consuegra, C. G. de Leaniz","doi":"10.1101/2020.01.16.908939","DOIUrl":"https://doi.org/10.1101/2020.01.16.908939","url":null,"abstract":"Intensively farmed fish are commonly stressed, often leading to immune impairment and increased susceptibility to disease. Microbial communities associated with the gut and skin are vital to host immune function, but little is known about how stress affects the fish microbiome, especially during the sensitive early life stages. We compared the effects of two aquaculture-relevant stressors on the gut and skin microbiome of Atlantic salmon fry: an acute cold stress during late embryogenesis, and a chronic environmental stress during the larval stage. Acute cold stress had a lasting effect on the structure of both the gut and the skin microbiome, likely due to disruption of the egg shell microbial communities which seed the initial colonisation of the teleost microbiome upon hatching. In contrast, chronic post hatch stress altered the structure of the gut microbiome, but not that of the skin. Both types of stressors promoted similar Gammaproteobacteria ASVs, particularly within the genera Acinetobacter and Aeromonas which include several important fish pathogens and, in the gut, reduced the abundance of Lactobacillales. This suggests that there may be common signatures of stress in the salmon microbiome, which may represent useful stress biomarkers in aquaculture.","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88348122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic analysis of transferrin family from animals and plants.","authors":"Lina Bai, M. Qiao, R. Zheng, Changyan Deng, S. Mei, Wanping Chen","doi":"10.1016/j.cbd.2015.11.002","DOIUrl":"https://doi.org/10.1016/j.cbd.2015.11.002","url":null,"abstract":"","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79141940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and comparative analysis of the oriental river prawn (Macrobrachium nipponense) microRNA expression profile during hypoxia using a deep sequencing approach.","authors":"Shengming Sun, H. Fu, X. Ge, Jian Zhu, Z. Gu, Fujun Xuan","doi":"10.1016/j.cbd.2016.01.003","DOIUrl":"https://doi.org/10.1016/j.cbd.2016.01.003","url":null,"abstract":"","PeriodicalId":93949,"journal":{"name":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88945208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}