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Chen Z, Shi SH, Huang Y, Huang CQ, Liu RC, Cheng LF, Fu GH, Chen HM, Wan CH, Fu QL. Differential metabolism-associated gene expression of duck pancreatic cells in response to two strains of duck hepatitis A virus type 1. Arch Virol 2021; 166:3105-3116. [PMID: 34482448 PMCID: PMC8497338 DOI: 10.1007/s00705-021-05199-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022]
Abstract
Several outbreaks of duck hepatitis A virus type 1 (DHAV-1), which were characterized by yellow coloration and hemorrhage in pancreatic tissues, have occurred in China. The causative agent is called pancreatitis-associated DHAV-1. The mechanisms involved in pancreatitis-associated DHAV-1 infection are still unclear. Transcriptome analysis of duck pancreas infected with classical-type DHAV-1 and pancreatitis-associated DHAV-1 was carried out. Deep sequencing with Illumina-Solexa resulted in a total of 53.9 Gb of clean data from the cDNA library of the pancreas, and a total of 29,597 unigenes with an average length of 993.43 bp were generated by de novo sequence assembly. The expression levels of D-3-phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which are involved in glycine, serine, and threonine metabolism pathways, were significantly downregulated in ducks infected with pancreatitis-associated DHAV-1 compared with those infected with classical-type DHAV-1. These findings provide information regarding differences in expression levels of metabolism-associated genes between ducks infected with pancreatitis-associated DHAV-1 and those infected with classical-type DHAV-1, indicating that intensive metabolism disorders may contribute to the different phenotypes of DHAV-1-infection.
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MESH Headings
- Amino Acids/genetics
- Amino Acids/metabolism
- Animals
- Ducks/virology
- Gene Expression
- Hepatitis Virus, Duck/pathogenicity
- Hepatitis, Viral, Animal/genetics
- Hepatitis, Viral, Animal/metabolism
- Hepatitis, Viral, Animal/pathology
- Hepatitis, Viral, Animal/virology
- Host-Pathogen Interactions/genetics
- Pancreas/cytology
- Pancreas/pathology
- Pancreas/virology
- Pancreatitis/pathology
- Pancreatitis/virology
- Picornaviridae Infections/metabolism
- Picornaviridae Infections/pathology
- Picornaviridae Infections/veterinary
- Picornaviridae Infections/virology
- Poultry Diseases/genetics
- Poultry Diseases/metabolism
- Poultry Diseases/pathology
- Poultry Diseases/virology
- Real-Time Polymerase Chain Reaction
- Sequence Analysis, RNA
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Affiliation(s)
- Zhen Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, Fujian, People's Republic of China
| | - Shao-Hua Shi
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, People's Republic of China.
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou, 350013, Fujian, People's Republic of China.
- Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, Fujian, People's Republic of China.
| | - Yu Huang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, People's Republic of China.
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou, 350013, Fujian, People's Republic of China.
- Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, Fujian, People's Republic of China.
| | - Cui-Qin Huang
- College of Life Sciences, Longyan University, Longyan, 364012, Fujian, People's Republic of China
| | - Rong-Chang Liu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, Fujian, People's Republic of China
| | - Long-Fei Cheng
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, Fujian, People's Republic of China
| | - Guang-Hua Fu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, Fujian, People's Republic of China
| | - Hong-Mei Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, Fujian, People's Republic of China
| | - Chun-He Wan
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, Fujian, People's Republic of China
| | - Qiu-Ling Fu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou, 350013, Fujian, People's Republic of China
- Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, Fujian, People's Republic of China
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Riolo G, Cantara S, Ricci C. What's Wrong in a Jump? Prediction and Validation of Splice Site Variants. Methods Protoc 2021; 4:62. [PMID: 34564308 PMCID: PMC8482176 DOI: 10.3390/mps4030062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) is a crucial process to enhance gene expression driving organism development. Interestingly, more than 95% of human genes undergo AS, producing multiple protein isoforms from the same transcript. Any alteration (e.g., nucleotide substitutions, insertions, and deletions) involving consensus splicing regulatory sequences in a specific gene may result in the production of aberrant and not properly working proteins. In this review, we introduce the key steps of splicing mechanism and describe all different types of genomic variants affecting this process (splicing variants in acceptor/donor sites or branch point or polypyrimidine tract, exonic, and deep intronic changes). Then, we provide an updated approach to improve splice variants detection. First, we review the main computational tools, including the recent Machine Learning-based algorithms, for the prediction of splice site variants, in order to characterize how a genomic variant interferes with splicing process. Next, we report the experimental methods to validate the predictive analyses are defined, distinguishing between methods testing RNA (transcriptomics analysis) or proteins (proteomics experiments). For both prediction and validation steps, benefits and weaknesses of each tool/procedure are accurately reported, as well as suggestions on which approaches are more suitable in diagnostic rather than in clinical research.
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Affiliation(s)
| | | | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy; (G.R.); (S.C.)
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53
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Xie G, Zhu Y, Lin Z, Sun Y, Gu G, Wang W, Chen H. HOPMCLDA: predicting lncRNA-disease associations based on high-order proximity and matrix completion. Mol Omics 2021; 17:760-768. [PMID: 34251001 DOI: 10.1039/d1mo00138h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In recent years, emerging evidence has shown that long noncoding RNAs (lncRNAs) have important roles in the biological processes of complex diseases. However, experiments to determine the associations between diseases and lncRNAs are time consuming and costly. Therefore, there is a need to develop effective computational methods for exploring potential lncRNA-disease associations. In this study, we present a computational prediction method based on high-order proximity and matrix completion to predict lncRNA-disease associations (HOPMCLDA). HOPMCLDA integrates explicit similarity and high-order proximity information on lncRNAs and diseases and constructs a heterogeneous disease-lncRNA network to utilize similarity information. Finally, nuclear norm regularization is carried out on the heterogeneous network for the recovery of a lncRNA-disease association matrix. By implementing leave-one-out cross validation (LOOCV) and five-fold cross validation (5-fold CV), we compare HOPMCLDA with five other methods. HOPMCLDA outperforms the other methods, with area under the receiver operating characteristic curve values of 0.8755 and 0.8353 ± 0.0045 using LOOCV and 5-fold CV, respectively. Furthermore, case studies of three human diseases (gastric cancer, osteosarcoma, and hepatocellular carcinoma) confirm the reliable predictive performance of HOPMCLDA.
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Affiliation(s)
- Guobo Xie
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Yinting Zhu
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Zhiyi Lin
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Yuping Sun
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Guosheng Gu
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Weiming Wang
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Hui Chen
- School of Computers, Guangdong University of Technology, Guangzhou, China.
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Li X, Fan K, Liu Y, Liu Y, Liu PF. Administration of a recombinant ALDH7A1 (rA7) indicates potential regulation of the metabolite and immunology pathways in Atlantic salmon infected with Aeromonas salmonicida. JOURNAL OF FISH DISEASES 2021; 44:961-977. [PMID: 33645734 DOI: 10.1111/jfd.13355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The bacterium Aeromonas salmonicida is the pathogen responsible for furunculosis, which is a serious disease of salmonids. This disease has a significant economic impact on the economic benefits of the global salmon farming industry. However, the pathogenesis of this disease in fish is still unknown. Members of the aldehyde dehydrogenase gene (ALDH) superfamily play a key role in the enzyme detoxification of endogenous and exogenous aldehydes. In this study, we obtained a recombinant aldehyde dehydrogenase 7A1 (ALDH7A1) protein to find its functions on Atlantic salmon infected by A. salmonicida. The transcriptional response in the liver of Atlantic salmon (Salmo salar) with differing levels of A. salmonicida infection was analysed and compared in order to reveal mechanisms by which ALDH7A1 may confer infection resistance. With the addition of ALDH7A1 protein, it was found that a total of 13,369 genes were annotated with one or more KEGG and localized to 360 KEGG pathways in the high concentration infection group. The differential expression genes were more enriched in immune signalling pathways such as the Toll-like receptor signalling pathway, NF-kappa B signalling pathway and TNF signalling pathway. On the other hand, at low concentrations of infection, KEGG enriched a smaller number of differential expression genes. However, these differential genes were more concentrated in immune signalling pathways such as the PI3K-Akt signalling pathway, JAK-STAT signalling pathway and complement and coagulation cascades. In addition, several known immune-related genes including HSP90α, HSP70, DNA damage-inducible transcript 4, integrin alpha 5 and microtubule-associated protein 2 were among the differentially expressed transcripts. These data provide the first insights into the host-ALDH7A1 vaccine interactome. The results of this study contribute to identifying the potential resistance mechanisms of Atlantic salmon to A. salmonicida infection and determining future treatment strategies.
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Affiliation(s)
- Xiaohao Li
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, China
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, China
| | - Kunpeng Fan
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Yafang Liu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, China
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, China
| | - Ying Liu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, China
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, China
| | - Peng-Fei Liu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, China
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, China
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55
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Li X, Wu J, Xiao X, Rong Y, Yang H, Li J, Zhou Q, Zhou W, Shi J, Qi H, Du H. Characterization and complexity of transcriptome in Gymnocypris przewalskii using single-molecule long-read sequencing and RNA-seq. DNA Res 2021; 28:6275749. [PMID: 33989386 PMCID: PMC8320875 DOI: 10.1093/dnares/dsab005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/11/2021] [Indexed: 11/30/2022] Open
Abstract
The Tibetan Schizothoracinae fish Gymnocypris przewalskii has the ability to adapt to the extreme plateau environment, making it an ideal biological material for evolutionary biology research. However, the lack of well-annotated reference genomes has limited the study of the molecular genetics of G. przewalskii. To characterize its transcriptome features, we first used long-read sequencing technology in combination with RNA-seq for transcriptomic analysis. A total of 159,053 full-length (FL) transcripts were captured by Iso-Seq, having a mean length of 3,445 bp with N50 value of 4,348. Of all FL transcripts, 145,169 were well-annotated in the public database and 134,537 contained complete open reading frames. There were 4,149 pairs of alternative splicing events, of which three randomly selected were defined by RT–PCR and sequencing, and 13,293 long non-coding RNAs detected, based on all-vs.-all BLAST. A total of 118,185 perfect simple sequence repeats were identified from FL transcripts. The FL transcriptome might provide basis for further research of G. przewalskii.
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Affiliation(s)
- Xindan Li
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Jinming Wu
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Xinping Xiao
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Yifeng Rong
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Haile Yang
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Junyi Li
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Qiong Zhou
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Weiguo Zhou
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Jianquan Shi
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Hongfang Qi
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Hao Du
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China.,The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
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56
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Wang C, Luo X, Qin H, Zhao C, Yang L, Yu T, Zhang Y, Huang X, Xu X, Qin Q, Liu S. Formation of autotriploid Carassius auratus and its fertility-related genes analysis. BMC Genomics 2021; 22:435. [PMID: 34107878 PMCID: PMC8191051 DOI: 10.1186/s12864-021-07753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Background Formation of triploid organism is useful in genetics and breeding. In this study, autotriploid Carassius auratus (3nRR, 3n = 150) was generated from Carassius auratus red var. (RCC, 2n = 100) (♀) and autotetraploid Carassius auratus (4nRR, 4n = 200) (♂). The female 3nRR produced haploid, diploid and triploid eggs, whereas the male 3nRR was infertile. The aim of the present study was to explore fertility of potential candidate genes of 3nRR. Results Gonadal transcriptome profiling of four groups (3 females RCC (FRCC), 3 males 4nRR (M4nRR), 3 males 3nRR (M3nRR) and 3 females 3nRR (F3nRR)) was performed using RNA-SEq. A total of 78.90 Gb of clean short reads and 24,262 differentially expressed transcripts (DETs), including 20,155 in F3nRR vs. FRCC and 4,107 in M3nRR vs. M4nRR were identified. A total of 106 enriched pathways were identified through KEGG enrichment analysis. Out of the enriched pathways, 44 and 62 signalling pathways were identified in F3nRR vs. FRCC and M3nRR vs. M4nRR, respectively. A total of 80 and 25 potential candidate genes for fertility-related in F3nRR and M3nRR were identified, respectively, through GO, KEGG analyses and the published literature. Moreover, protein-protein interaction (PPI) network construction of these fertility-associated genes were performed. Analysis of the PPI networks showed that 6 hub genes (MYC, SOX2, BMP4, GATA4, PTEN and BMP2) were involved in female fertility of F3nRR, and 2 hub genes (TP53 and FGF2) were involved in male sterility of M3nRR. Conclusions Establishment of autotriploid fish offers an ideal model to study reproductive traits of triploid fish. RNA-Seq data revealed 6 genes, namely, MYC, SOX2, BMP4, GATA4, PTEN and BMP2, involved in the female fertility of the F3nRR. Moreover, 2 genes, namely, TP53 and FGF2, were related to the male sterility of the M3nRR. These findings provide information on reproduction and breeding in triploid fish. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07753-5.
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Affiliation(s)
- Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Xiang Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Yuxin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Xidan Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China.
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Valenzuela L, Pacheco S, Rincón G, Pavez L, Lam N, Hernández AJ, Dantagnan P, González F, Jilberto F, Ravanal MC, Ramos C, Garcia H, Araneda C, Ulloa PE. Intestinal Transcriptome Analysis Reveals Enrichment of Genes Associated with Immune and Lipid Mechanisms, Favoring Soybean Meal Tolerance in High-Growth Zebrafish ( Danio Rerio). Genes (Basel) 2021; 12:genes12050700. [PMID: 34066767 PMCID: PMC8151431 DOI: 10.3390/genes12050700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/10/2023] Open
Abstract
The molecular mechanisms underlying fish tolerance to soybean meal (SBM) remain unclear. Identifying these mechanisms would be beneficial, as this trait favors growth. Two fish replicates from 19 experimental families were fed fishmeal-(100FM) or SBM-based diets supplemented with saponin (50SBM + 2SPN) from juvenile to adult stages. Individuals were selected from families with a genotype-by-environment interaction higher (HG-50SBM + 2SPN, 170 ± 18 mg) or lower (LG-50SBM + 2SPN, 76 ± 10 mg) weight gain on 50SBM + 2SPN for intestinal transcriptomic analysis. A histological evaluation confirmed middle intestinal inflammation in the LG- vs. HG-50SBM + 2SPN group. Enrichment analysis of 665 differentially expressed genes (DEGs) identified pathways associated with immunity and lipid metabolism. Genes linked to intestinal immunity were downregulated in HG fish (mpx, cxcr3.2, cftr, irg1l, itln2, sgk1, nup61l, il22), likely dampening inflammatory responses. Conversely, genes involved in retinol signaling were upregulated (rbp4, stra6, nr2f5), potentially favoring growth by suppressing insulin responses. Genes associated with lipid metabolism were upregulated, including key components of the SREBP (mbtps1, elov5l, elov6l) and cholesterol catabolism (cyp46a1), as well as the downregulation of cyp7a1. These results strongly suggest that transcriptomic changes in lipid metabolism mediate SBM tolerance. Genotypic variations in DEGs may become biomarkers for improving early selection of fish tolerant to SMB or others plant-based diets.
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Affiliation(s)
- Luis Valenzuela
- Omics Lab, Villavicencio 378, Oficina 32, Santiago 8320164, Chile;
| | - Sebastian Pacheco
- Programa de Doctorado en Inmunología y Microbiología, Universidad San Sebastian, Lota 2465, Santiago 7510157, Chile;
| | - Gonzalo Rincón
- Zoetis, VMRD Genetics R&D, 333 Portage Street, Kalamazoo, MI 49007, USA;
| | - Leonardo Pavez
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Universidad de Las Américas, Avenida Manuel Montt 948, Santiago 7500975, Chile; (L.P.); (F.G.); (C.R.)
| | - Natalia Lam
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa 11315, Santiago 8820808, Chile; (N.L.); (F.J.); (C.A.)
| | - Adrián J. Hernández
- Laboratorio de Nutrición y Fisiología de Peces, Núcleo de Investigación en Producción Alimentaria, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco 4780000, Chile; (A.J.H.); (P.D.)
| | - Patricio Dantagnan
- Laboratorio de Nutrición y Fisiología de Peces, Núcleo de Investigación en Producción Alimentaria, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco 4780000, Chile; (A.J.H.); (P.D.)
| | - Felipe González
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Universidad de Las Américas, Avenida Manuel Montt 948, Santiago 7500975, Chile; (L.P.); (F.G.); (C.R.)
| | - Felipe Jilberto
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa 11315, Santiago 8820808, Chile; (N.L.); (F.J.); (C.A.)
| | - M. Cristina Ravanal
- Instituto de Ciencia y Tecnología de los Alimentos (ICYTAL), Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Avda. Julio Sarrazín s/n, Isla Teja, Valdivia 5090000, Chile;
| | - Cecilia Ramos
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Universidad de Las Américas, Avenida Manuel Montt 948, Santiago 7500975, Chile; (L.P.); (F.G.); (C.R.)
| | - Héctor Garcia
- Laboratorios Diagnofruit Ltd.a., Depto. Fitopatología Molecular, Santiago 7770273, Chile;
| | - Cristian Araneda
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa 11315, Santiago 8820808, Chile; (N.L.); (F.J.); (C.A.)
| | - Pilar E. Ulloa
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Universidad de Las Américas, Avenida Manuel Montt 948, Santiago 7500975, Chile; (L.P.); (F.G.); (C.R.)
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa 11315, Santiago 8820808, Chile; (N.L.); (F.J.); (C.A.)
- Correspondence: ; Tel.: +56-222-531-129
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Yang M, Lu Z, Li F, Shi F, Zhan F, Zhao L, Li Y, Li J, Lin L, Qin Z. Escherichia coli induced ferroptosis in red blood cells of grass carp (Ctenopharyngodon idella). FISH & SHELLFISH IMMUNOLOGY 2021; 112:159-167. [PMID: 33017637 DOI: 10.1016/j.fsi.2020.09.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
The red blood cells (RBCs) of fish make up around 95% of the total peripheral blood cells, and the long-held paradigm is that RBCs are mainly responsible for transporting oxygen. Previous studies have showed that the RBCs can be involved in the immune response against bacterial infection; however, this mechanism remains enigmatic. Here, we explored the structure of grass carp RBCs (GcRBCs). The results showed that the GcRBCs released a pseudopodia-like structure when grown in a 24-well plate, and the transmission electron microscopy (TEM) result showed that GcRBCs contained some organelle-like structures. To further verify the organelle-like structures might be the mitochondria and lysosome which similar to other immune cells, a fluorescent labeling assay was used to verify it. To decipher the antibacterial immunity of GcRBCs, transcriptomic profiling of grass carp RBCs after the incubation with E. coli was analyzed. The results showed that there were 4099 differently expressed genes (DEGs) of GcRBCs upon E. coli incubation, including 2041 up-regulated and 2058 down-regulated genes. In addition, to validate our transcriptomic data, we checked the expression of several cytokines, such as CCL4, CCL20, IL4, IL12 and IFN-α, and the results showed that all the selected gens were significantly up-regulated after E. coli incubation. Furthermore, E. coli incubation induced hemoglobin oxidation and increased the heme in GcRBCs, which further activated the expression of heme oxygenase 1 (HO-1), autophagy related genes 5 (ATG5), and ferritin. In contrast, E. coli incubation inhibited the expression of Ferroportin-1 (FPN1), which increased intracellular iron levels, induced Fenton reaction to release reactive oxygen species (ROS), and activated the ferroptosis signaling pathway in GcRBCs. Herein, we demonstrate that E. coli can induce teleost RBCs cell death through an iron-mediated ferroptosis pathway, which sheds new light on the interaction between bacteria and teleost RBCs.
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Affiliation(s)
- Minxuan Yang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Zhijie Lu
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Fenglin Li
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Fei Shi
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Fanbin Zhan
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Lijuan Zhao
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Yanan Li
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Jun Li
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China; School of Biological Sciences, Lake Superior State University, Sault Ste. Marie, MI, 49783, USA
| | - Li Lin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China.
| | - Zhendong Qin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China.
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Sood N, Verma DK, Paria A, Yadav SC, Yadav MK, Bedekar MK, Kumar S, Swaminathan TR, Mohan CV, Rajendran KV, Pradhan PK. Transcriptome analysis of liver elucidates key immune-related pathways in Nile tilapia Oreochromis niloticus following infection with tilapia lake virus. FISH & SHELLFISH IMMUNOLOGY 2021; 111:208-219. [PMID: 33577877 DOI: 10.1016/j.fsi.2021.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Nile tilapia (Oreochromis niloticus) is one of the most important aquaculture species farmed worldwide. However, the recent emergence of tilapia lake virus (TiLV) disease, also known as syncytial hepatitis of tilapia, has threatened the global tilapia industry. To gain more insight regarding the host response against the disease, the transcriptional profiles of liver in experimentally-infected and control tilapia were compared. Analysis of RNA-Seq data identified 4640 differentially expressed genes (DEGs), which were involved among others in antigen processing and presentation, MAPK, apoptosis, necroptosis, chemokine signaling, interferon, NF-kB, acute phase response and JAK-STAT pathways. Enhanced expression of most of the DEGs in the above pathways suggests an attempt by tilapia to resist TiLV infection. However, upregulation of some of the key genes such as BCL2L1 in apoptosis pathway; NFKBIA in NF-kB pathway; TRFC in acute phase response; and SOCS, EPOR, PI3K and AKT in JAK-STAT pathway and downregulation of the genes, namely MAP3K7 in MAPK pathway; IFIT1 in interferon; and TRIM25 in NF-kB pathway suggested that TiLV was able to subvert the host immune response to successfully establish the infection. The study offers novel insights into the cellular functions that are affected following TiLV infection and will serve as a valuable genomic resource towards our understanding of susceptibility of tilapia to TiLV infection.
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Affiliation(s)
- Neeraj Sood
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226002, Uttar Pradesh, India
| | - Dev Kumar Verma
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226002, Uttar Pradesh, India
| | - Anutosh Paria
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226002, Uttar Pradesh, India
| | - Shrish Chandra Yadav
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226002, Uttar Pradesh, India
| | - Manoj Kumar Yadav
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226002, Uttar Pradesh, India
| | - Megha Kadam Bedekar
- ICAR-Central Institute of Fisheries Education, Versova, Andheri (W), Mumbai, 400 061, Maharashtra, India
| | - Saurav Kumar
- ICAR-Central Institute of Fisheries Education, Versova, Andheri (W), Mumbai, 400 061, Maharashtra, India
| | - Thangaraj Raja Swaminathan
- Peninsular and Marine Fish Genetic Resources Centre, ICAR-NBFGR, CMFRI Campus, Kochi, 682 018, Kerala, India
| | | | - K V Rajendran
- ICAR-Central Institute of Fisheries Education, Versova, Andheri (W), Mumbai, 400 061, Maharashtra, India
| | - Pravata Kumar Pradhan
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226002, Uttar Pradesh, India.
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He J, Jia Y. Application of omics technologies in dermatological research and skin management. J Cosmet Dermatol 2021; 21:451-460. [PMID: 33759323 DOI: 10.1111/jocd.14100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/19/2021] [Accepted: 03/10/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND "Omics" are usually based on the use of high-throughput analysis methods for global analysis of biological samples and the discovery of biomarkers, and may provide new insights into biological phenomena. Over the last few years, the development of omics technologies has considerably accelerated the pace of dermatological research. AIMS The purpose of this article was to review the development of omics in recent decades and their application in dermatological research. METHODS An extensive literature search was conducted on omics technologies since the first research on omics. RESULTS This article summarizes the history and main research methods of the six omics technologies, including genomics, transcriptomics, proteomics, metabolomics, lipidomics, and microbiomics. Their application in certain skin diseases and cosmetics research and development are also summarized. CONCLUSIONS This information will help to understand the mechanism of some skin diseases and the discovery of potential biomarkers, and provide new insights for skin health management and cosmetics research and development.
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Affiliation(s)
- Jianbiao He
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,Key Laboratory of Cosmetic of China National Light Industry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,Institute of cosmetic regulatory science, Beijing Technology and Business University, Beijing, China
| | - Yan Jia
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,Key Laboratory of Cosmetic of China National Light Industry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,Institute of cosmetic regulatory science, Beijing Technology and Business University, Beijing, China
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Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq. Animals (Basel) 2021; 11:ani11030834. [PMID: 33809502 PMCID: PMC8000258 DOI: 10.3390/ani11030834] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 01/13/2023] Open
Abstract
Simple Summary Skeletal muscle is an important tissue and its development is strictly regulated by genes. In this study, in order to understand the muscle-related gene expression in Pekin duck, RNA-seq was performed to analyze and compare skeletal muscle at different growth stages. Alternative splicing, single nucleotide polymorphisms and insertion–deletions were detected, and 299 novel genes were discovered. MYL4, IGF2BP1, CSRP3, SPP1, KLHL31, LAMB2, LAMA2, ITGB1 and OPN played crucial roles in skeletal muscle development. Oxidative phosphorylation, ECM-receptor interaction, focal adhesion, carbon metabolism, and biosynthesis of amino acids participated in the regulation of skeletal muscle development in Pekin duck. This study provides an important reference for revealing the developmental mechanisms of pectoral and leg muscles in duck. Abstract Skeletal muscle, accounting for approximately 50% of body weight, is the largest and most important tissue. In this study, the gene expression profiles and pathways in skeletal muscle of Pekin duck were investigated and compared at embryonic day 17, 21, and 27 and postnatally at 6 months of age. An average of 49,555,936 reads in each sample was obtained from the transcriptome libraries. Over 70.0% of alternative splicing (AS) in each sample was mainly alternative 5′ first exon (transcription start site)—the first exon splicing (TSS) and alternative 3′ last exon (transcription terminal site)—the last exon splicing (TTS), indicating that TSS and TTS were the most common AS event in Pekin ducks, and these AS events were closely related to the regulation of muscle development at different growth stages. The results provided a valuable genomic resource for selective breeding and functional studies of genes. A total of 299 novel genes with ≥2 exons were obtained. There were 294 to 2806 differentially expressed genes (DEGs) in each pairwise comparison of Pekin duck. Notably, 90 DEGs in breast muscle and 9 DEGs in leg muscle were co-expressed at all developmental points. DEGs were validated by qPCR analysis, which confirmed the tendency of the expression. DEGs related to muscle development were involved in biological processes such as “endodermal cell differentiation”, “muscle cell cellular homeostasis”, “skeletal muscle tissue growth” and “skeletal muscle cell differentiation”, and were involved in pathways such as oxidative phosphorylation, ECM-receptor (extracellular matrix receptor) interaction, focal adhesion, carbon metabolism, and biosynthesis of amino acids. Some DEGs, including MYL4, IGF2BP1, CSRP3, SPP1 and KLHL31, as well as LAMB2, LAMA2, ITGB1 and OPN, played crucial roles in muscle growth and development. This study provides valuable information about the expression profile of mRNAs and pathways from duck skeletal muscle at different growth stages, and further functional study of these mRNAs and pathways could provide new ideas for studying the molecular networks of growth and development in duck skeletal muscle.
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Gao MM, Cui Z, Gao YL, Wang J, Liu JX. Multi-Label Fusion Collaborative Matrix Factorization for Predicting LncRNA-Disease Associations. IEEE J Biomed Health Inform 2021; 25:881-890. [PMID: 32324583 DOI: 10.1109/jbhi.2020.2988720] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
As we all know, science and technology are developing faster and faster. Many experts and scholars have demonstrated that human diseases are related to lncRNA, but only a few associations have been confirmed, and many unknown associations need to be found. In the process of finding associations, it takes a lot of time, so finding an efficient way to predict the associations between lncRNAs and diseases is particularly important. In this paper, we propose a multi-label fusion collaborative matrix factorization (MLFCMF) approach for predicting lncRNA-disease associations (LDAs). Firstly, the lncRNA space and disease space are optimized by multi-label to enhance the intrinsic link between lncRNA and disease and to tap potential information. Multi-label learning can encode a variety of data information from the sample space. Secondly, to learn multi-label information in the data space, the fusion method is used to handle the relationship between multiple labels. More comprehensive information will be obtained by weighing the effects of different labels. The addition of Gaussian interaction profile (GIP) kernel can increase the network similarity. Finally, the lncRNA-disease associations are predicted by the method of collaborative matrix factorization. The ten-fold cross-validation method is used to evaluate the MLFCMF method, and our method finally obtains an AUC value of 0.8612. Detailed analysis of ovarian cancer, colorectal cancer, and lung cancer in the simulation experiment results. So it can be seen that our method MLFCMF is an effective model for predicting lncRNA-disease associations.
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Zhou X, Zhang GR, Ji W, Shi ZC, Ma XF, Luo ZL, Wei KJ. The Dynamic Immune Response of Yellow Catfish ( Pelteobagrus fulvidraco) Infected With Edwardsiella ictaluri Presenting the Inflammation Process. Front Immunol 2021; 12:625928. [PMID: 33732247 PMCID: PMC7959794 DOI: 10.3389/fimmu.2021.625928] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
Edwardsiella ictaluri is a highly destructive pathogen in cultured yellow catfish, thus it was very necessary to study the immune response of yellow catfish against bacterial infection. In this study, RNA-Seq technology was used to study the immune response in two distinct tissues of yellow catfish at eight different time points (h) after E. ictaluri infection. The number of differentially expressed genes (DEGs) in the spleen and liver was low at 3 h and 6 h post-infection, respectively. Afterwards, the most number of DEGs in the spleen was detected at 72 h, while the number of DEGs in the liver maintained a high level from 24 h to 120 h. The GO and KEGG enrichment analyses of DEGs at different time points uncovered that cytokines were continuously transcribed at 6 h to 120 h; whereas the liver is the main organ that secretes the components of the complement system, and metabolic regulation was activated from 12 h to 120 h. Moreover, an overview of the inflammation response of yellow catfish was exhibited including pattern-recognition receptors, inflammatory cytokines, chemokines, complements, and inflammation-related signal pathways. The similar expression tendency of nine genes by qRT-PCR validated the accuracy of transcriptome analyses. The different transcriptomic profiles obtained from the spleen and liver will help to better understand the dynamic immune response of fish against bacterial infection, and will provide basic information for establishing effective measures to prevent and control diseases in fish.
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Affiliation(s)
- Xu Zhou
- National Demonstration Center for Experimental Aquaculture Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Gui-Rong Zhang
- National Demonstration Center for Experimental Aquaculture Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Wei Ji
- National Demonstration Center for Experimental Aquaculture Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Ze-Chao Shi
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Xu-Fa Ma
- National Demonstration Center for Experimental Aquaculture Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zun-Lan Luo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Kai-Jian Wei
- National Demonstration Center for Experimental Aquaculture Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan, China
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Liu Y, Wu Y, Qin G, Chen Y, Wang X, Lin Q. Bioaccumulation and reproductive toxicity of bisphenol A in male-pregnant seahorse (Hippocampus erectus) at environmentally relevant concentrations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:141805. [PMID: 32911163 DOI: 10.1016/j.scitotenv.2020.141805] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Seahorses, with brood pouch in adult males, are a bioindicator species that exhibit specialized reproductive strategy of "male pregnancy". Bisphenol A (BPA), one of the most pervasive endocrine-disrupting chemicals (EDCs), is hazardous for reproductive, immune, and neurological systems. However, no evidence of BPA toxicity to the male-pregnant animals is available. Herein, the reproductive toxicity of BPA was evaluated in lined seahorses (Hippocampus erectus) following exposure to environmentally relevant concentrations (10, 100, and 1000 μg/L) through physiological, histological, and transcriptional analyses. Our results indicated BPA bioaccumulation to be positively correlated with exposure doses in both sexes. Ovarian failure was only observed in the high-dose BPA treatment group, accompanied by the apoptosis of follicular cells and up-regulation of pro-apoptotic genes. However, brood pouches maintenance were surprisingly inhibited at low concentration, and transcriptomic analysis revealed disturbed profiles of genes involved in the extracellular matrix and cell-cell adhesion pathways. Interestingly, seahorse testes were less sensitive to BPA exposure than that in other teleosts. Thus, our study suggests that BPA at environmentally relevant concentrations might cause reproductive dysfunction in seahorses, potentially exerting adverse effects on the seahorse population since most of them inhabit shallow coastal areas with prevalent estrogenic contaminants.
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Affiliation(s)
- Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Yongli Wu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Yu Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China.
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Liu JX, Cui Z, Gao YL, Kong XZ. WGRCMF: A Weighted Graph Regularized Collaborative Matrix Factorization Method for Predicting Novel LncRNA-Disease Associations. IEEE J Biomed Health Inform 2021; 25:257-265. [PMID: 32287024 DOI: 10.1109/jbhi.2020.2985703] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In recent years, many human diseases have been determined to be associated with certain lncRNAs. Only a small percentage of all lncRNA-disease associations (LDAs) have been discovered by researchers. Predicting novel LDAs is time-consuming and costly. It is crucial to propose a method that can effectively identify potential LDAs to solve this problem based on the available datasets. Although some current methods can effectively predict potential LDAs, the prediction accuracy needs to be improved, and there are few known associations. Moreover, there are notable errors in the method of constructing the network and the bipartite graph, which interfere with the final results. A weighted graph regularized collaborative matrix factorization (WGRCMF) method is proposed to predict novel LDAs. We introduce the graph regularization terms into the collaborative matrix factorization. Considering that manifold learning can recover low-dimensional manifold structures from high-dimensional sampled data, we can find low-dimensional manifolds in high-dimensional space. In addition, a weight matrix is also introduced into the method, the significance of which is to prevent unknown associations from contributing to the final prediction matrix. Finally, the prediction accuracy of this method is better than those of other methods. In several cancer cases, we implemented the corresponding simulation experiments. According to the experimental results, the proposed method is feasible and effective.
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Feng X, Jia Y, Zhu R, Li K, Guan Z, Chen Y. Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration. BMC Genomics 2020; 21:835. [PMID: 33246415 PMCID: PMC7694923 DOI: 10.1186/s12864-020-07247-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/18/2020] [Indexed: 11/30/2022] Open
Abstract
Background The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in plateau waters with the elevation above 2500 m, is nearly esquamate and only covered with shoulder scales and anal scales, making it a good model species to study the molecular mechanism of scale degeneration. Results The transcriptomes of shoulder scaled skins (SSS), anal scaled skins (ASS) and scaleless skins (NSS) were sequenced and analyzed in G. eckloni at the age of 1 year. Histological examination showed that shoulder scale had completed its differentiation and anal scale just initiated the differentiation. A total of 578,046 unigenes were obtained from the transcriptomes, with 407,799 unigenes annotated in public databases. A total of 428 and 142 differentially expressed unigenes (DEUs) were identified between SSS and NSS, and between ASS and NSS, respectively, with 45 DEUs that were overlapped. Annotation analysis indicated that these DEUs were mainly enriched in Gene Ontology (GO) terms and KEGG pathways associated with bone and muscle formation, such as myofibril, contractile fiber, cytoskeletal protein binding, muscle structure development, cardiac muscle contraction, hypertrophic cardiomyopathy (HCM) and calcium signaling pathway. Conclusions Our results would provide insights into the molecular mechanisms of scale degeneration in G. eckloni and other congeneric fishes. In addition, the transcriptome data provides candidate genes and markers for future studies.
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Affiliation(s)
- Xiu Feng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yintao Jia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ren Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kemao Li
- QingHai Provincial Fishery Environmental Monitoring Center, Xining, 810012, China
| | - Zhongzhi Guan
- QingHai Provincial Fishery Environmental Monitoring Center, Xining, 810012, China
| | - Yifeng Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Molecular assessment and transcriptome profiling of wild fish populations of Oryzias mekongensis and O. songkhramensis (Adrianichthyidae: Beloniformes) from Thailand. PLoS One 2020; 15:e0242382. [PMID: 33211755 PMCID: PMC7676673 DOI: 10.1371/journal.pone.0242382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/01/2020] [Indexed: 11/19/2022] Open
Abstract
Among the fish of the genus Oryzias, two species are frequently used as model animals in biological research. In Thailand, Oryzias mekongensis is usually found in natural freshwater near the Mekong Basin in the northeast region, while O. songkhramensis inhabits the Songkhram Basin. For differential morphological identification, the coloured bands on the dorsal and ventral margins of the caudal fin are used to distinguish O. mekongensis from O. songkhramensis. However, these characteristics are insufficient to justify species differentiation, and little molecular evidence is available to supplement them. This study aimed to investigate the molecular population and transcriptome profiles of adult O. mekongensis and O. songkhramensis. In the molecular tree based on cytochrome b sequences, O. mekongensis exhibited four clades that were clearly distinguished from O. songkhramensis. Clade 1 of the O. mekongensis population was close to the Mekong River and lived in the eastern portion of the upper northeast region. Clade 2 was far from the Mekong River and inhabited the middle region of the Songkhram River. Clade 3 was positioned to the west of the Songkhram River, and clade 4 was to the south of the Songkhram River Basin. After RNA sequencing using an Illumina HiSeq 2500 platform, the gene category annotations hardly differentiated the species and were discussed in the text. Based on the present findings, population dispersal of these Oryzias species might be associated with geographic variations of the upper northeast region. Molecular genetics and transcriptome profiling might advance our understanding of the evolution of teleost fish.
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Molecular insights into the mechanisms of susceptibility of Labeo rohita against oomycete Aphanomyces invadans. Sci Rep 2020; 10:19531. [PMID: 33177569 PMCID: PMC7658212 DOI: 10.1038/s41598-020-76278-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/20/2020] [Indexed: 01/22/2023] Open
Abstract
Aphanomyces invadans, the causative agent of epizootic ulcerative syndrome, is one of the most destructive pathogens of freshwater fishes. To date, the disease has been reported from over 160 fish species in 20 countries and notably, this is the first non-salmonid disease that has resulted in major impacts globally. In particular, Indian major carps (IMCs) are highly susceptible to this disease. To increase our knowledge particularly with regards to host immune response against A. invadans infection in a susceptible host, the gene expression profile in head kidney of A. invadans-infected and control rohu, Labeo rohita was investigated using RNA sequencing. Time course analysis of RNA-Seq data revealed 5608 differentially expressed genes, involved among others in Antigen processing and presentation, Leukocyte transendothelial migration, IL-17 signaling, Chemokine signaling, C-type lectin receptor signaling and Toll-like receptor signaling pathways. In the affected pathways, a number of immune genes were found to be downregulated, suggesting an immune evasion strategy of A. invadans in establishing the infection. The information generated in this study offers first systematic mechanistic understanding of the host–pathogen interaction that might underpin the development of new management strategies for this economically devastating fish-pathogenic oomycete A. invadans.
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Martínez R, Codina AE, Barata C, Tauler R, Piña B, Navarro-Martín L. Transcriptomic effects of tributyltin (TBT) in zebrafish eleutheroembryos. A functional benchmark dose analysis. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122881. [PMID: 32474318 DOI: 10.1016/j.jhazmat.2020.122881] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/03/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Exposure to the antifouling tributyltin (TBT) has been related to imposex in mollusks and to obesogenicity, adipogenesis and masculinization in fish. To understand the underlying molecular mechanisms, we evaluated dose-response effects of TBT (1.7-56 nM) in zebrafish eleutheroembryos transcriptome exposed from 2 to 5 days post-fertilization. RNA-sequencing analysis identified 3238 differentially expressed transcripts in eleutheroembryos exposed to TBT. Benchmark dose analyses (BMD) showed that the point of departure (PoD) for transcriptomic effects (9.28 nM) was similar to the metabolomic PoD (11.5 nM) and about one order of magnitude lower than the morphometric PoD (67.9 nM) or the median lethal concentration (LC50: 93.6 nM). Functional analysis of BMD transcriptomic data identified steroid metabolism and cholesterol and vitamin D3 biosynthesis as the most sensitive pathways to TBT (<50% PoD). Conversely, transcripts related to general stress and DNA damage became affected only at doses above the PoD. Therefore, our results indicate that transcriptomes can act as early molecular indicators of pollutant exposure, and illustrates their usefulness for the mechanistic identification of the initial toxic events. As the estimated molecular PoDs are close to environmental levels, we concluded that TBT may represent a substantial risk in some natural environments.
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Affiliation(s)
- Rubén Martínez
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain; Universitat de Barcelona (UB), Barcelona, Catalunya 08007, Spain.
| | - Anna E Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
| | - Carlos Barata
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Romà Tauler
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Benjamin Piña
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
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Santos C, Bueno Dos Reis Martinez C. Biotransformation in the fish Prochilodus lineatus: An organ-specific approach to cyp1a gene expression and biochemical activity. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2020; 80:103467. [PMID: 32791344 DOI: 10.1016/j.etap.2020.103467] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
The biotransformation ability of the organism is the result of organ-specific responses. This paper presents a molecular and biochemical approach to elucidate the biotransformation mechanisms in different organs of Prochilodus lineatus induced at 6, 24, and 96 h after a benzo[a]pyrene (B[a]P) injection. The induction in cyp1a transcription showed an organ-specific intensity at every tested time time. The EROD (ethoxyresorufin-O-deethylase) activity increased rapidly (6 h) in the liver and the kidney; the gills and the brain showed an increase at 24 h; and the gills demonstrated the highest activity among all the organs tested. There was no increase in glutathione S-transferase (GST) activity or lipoperoxidation. The decreased hepatic glutathione content (GSH) may be due to its role as an antioxidant. B[a]P was detected in the bile, confirming the xenobiotic efflux from the metabolizing organs. The gills, liver, brain, and kidney of P. lineatus presented an integrated mechanism to deal with the xenobiotic biotransformation.
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Affiliation(s)
- Caroline Santos
- Department of Physiological Sciences, State University of Londrina, Rod. Celso Garcia Cid, km 380, Londrina, Parana, 86057-970, Brazil
| | - Claudia Bueno Dos Reis Martinez
- Department of Physiological Sciences, State University of Londrina, Rod. Celso Garcia Cid, km 380, Londrina, Parana, 86057-970, Brazil.
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Shi F, Zi Y, Lu Z, Li F, Yang M, Zhan F, Li Y, Li J, Zhao L, Lin L, Qin Z. Bacillus subtilis H2 modulates immune response, fat metabolism and bacterial flora in the gut of grass carp (Ctenopharyngodon idellus). FISH & SHELLFISH IMMUNOLOGY 2020; 106:8-20. [PMID: 32717323 DOI: 10.1016/j.fsi.2020.06.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
Functional ingredients such as Bacillus subtilis are used in aquaculture to improve fish condition, modulate microbiota and promote a healthy intestinal system. However, the underlying mechanisms of grass carp treated with B. subtilis are not fully characterized. This study investigated the gut microbes of grass carp after treated with B. subtilis H2 (106 CFU/mL) and Aeromonas hydrophila (106 CFU/mL). The intestinal flora was found that the dominant bacterial phyla identified in all samples were Proteobacteria, Actinobacteria, Fusobacteria, Bacteroidetes and Acidobacteria. Compared with the control group, the relative abundance of Proteobacteria and Bacteroidetes in B. subtilis group were significantly increased. In addition, the relative abundances of Aeromonas and Shewanella in A. hydrophila group were more than the control group. For the intestinal transcriptomic profiling of the grass carp treated with B. subtilis H2, 824 different expressed genes (DEGs) between the B. subtilis H2 treated and non-treated groups were detected, including 365 up-regulated and 459 down-regulated genes. Six DEGs were randomly selected for further validation by quantitative real-time RT-PCR (qRT-PCR) and the results were consistent with the RNA-seq data. Additionally, eight immunomodulatory genes (IL-4, IL-11, IFN-α, CSF, FOSB, MAPK12b, IGHV3-11 and IGHV3-21) were significantly up-regulated after treated with B. subtilis H2. Furthermore, almost all the lipid metabolism-associated genes were significantly up-regulated after treated with B. subtilis H2 according to the lipid metabolism pathways. Eleven lipid metabolism-associated genes were selected by qRT-PCR, which showed that the expressions of almost all the selected genes were increased, especially Apob-48, ABCG8 and DGAT. Taken together, our results support that B. subtilis could modulate the immune response, fat metabolism and bacterial assembly in the gut of grass carp.
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Affiliation(s)
- Fei Shi
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Yingjuan Zi
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Zhijie Lu
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Fenglin Li
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Minxuan Yang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Fanbin Zhan
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Yanan Li
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Jun Li
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; School of Biological Sciences, Lake Superior State University, Sault Ste. Marie, MI, 49783, USA
| | - Lijuan Zhao
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Li Lin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China.
| | - Zhendong Qin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China.
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Rasal KD, Iquebal MA, Dixit S, Vasam M, Raza M, Sahoo L, Jaiswal S, Nandi S, Mahapatra KD, Rasal A, Udit UK, Meher PK, Murmu K, Angadi UB, Rai A, Kumar D, Sundaray JK. Revealing Alteration in the Hepatic Glucose Metabolism of Genetically Improved Carp, Jayanti Rohu Labeo rohita Fed a High Carbohydrate Diet Using Transcriptome Sequencing. Int J Mol Sci 2020; 21:E8180. [PMID: 33142948 PMCID: PMC7662834 DOI: 10.3390/ijms21218180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 01/25/2023] Open
Abstract
Although feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the fish diet, and their assimilation, are still not well understood in aquaculture species. We identified molecular events that occur due to the inclusion of high carbohydrate levels in the diets of genetically improved 'Jayanti rohu' Labeo rohita. To reveal transcriptional changes in the liver of rohu, a feeding experiment was conducted with three doses of gelatinized starch (20% (control), 40%, and 60%). Transcriptome sequencing revealed totals of 15,232 (4464 up- and 4343 down-regulated) and 15,360 (4478 up- and 4171 down-regulated) differentially expressed genes. Up-regulated transcripts associated with glucose metabolisms, such as hexokinase, PHK, glycogen synthase and PGK, were found in fish fed diets with high starch levels. Interestingly, a de novo lipogenesis mechanism was found to be enriched in the livers of treated fish due to up-regulated transcripts such as FAS, ACCα, and PPARγ. The insulin signaling pathways with enriched PPAR and mTOR were identified by Kyoto Encyclopedia of Genes and Genome (KEGG) as a result of high carbohydrates. This work revealed for the first time the atypical regulation transcripts associated with glucose metabolism and lipogenesis in the livers of Jayanti rohu due to the inclusion of high carbohydrate levels in the diet. This study also encourages the exploration of early nutritional programming for enhancing glucose efficiency in carp species, for sustainable and cost-effective aquaculture production.
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Affiliation(s)
- Kiran D. Rasal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India; (M.A.I.); (M.R.); (S.J.); (U.A.); (A.R.); (D.K.)
| | - Sangita Dixit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - Manohar Vasam
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - Mustafa Raza
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India; (M.A.I.); (M.R.); (S.J.); (U.A.); (A.R.); (D.K.)
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India; (M.A.I.); (M.R.); (S.J.); (U.A.); (A.R.); (D.K.)
| | - Samiran Nandi
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - Kanta Das Mahapatra
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - Avinash Rasal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - Uday Kumar Udit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - Prem Kumar Meher
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - Khuntia Murmu
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
| | - UB Angadi
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India; (M.A.I.); (M.R.); (S.J.); (U.A.); (A.R.); (D.K.)
| | - Anil Rai
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India; (M.A.I.); (M.R.); (S.J.); (U.A.); (A.R.); (D.K.)
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India; (M.A.I.); (M.R.); (S.J.); (U.A.); (A.R.); (D.K.)
| | - Jitendra Kumar Sundaray
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751 002, India; (K.D.R.); (S.D.); (M.V.); (L.S.); (S.N.); (K.D.M.); (A.R.); (U.K.U.); (P.K.M.); (K.M.)
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Verma DK, Peruzza L, Trusch F, Yadav MK, Ravindra, Shubin SV, Morgan KL, Mohindra V, Hauton C, van West P, Pradhan PK, Sood N. Transcriptome analysis reveals immune pathways underlying resistance in the common carp Cyprinus carpio against the oomycete Aphanomyces invadans. Genomics 2020; 113:944-956. [PMID: 33127583 DOI: 10.1016/j.ygeno.2020.10.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/30/2020] [Accepted: 10/25/2020] [Indexed: 12/13/2022]
Abstract
Infection with Aphanomyces invadans is a serious fish disease with major global impacts. Despite affecting over 160 fish species, some of the species like the common carp Cyprinus carpio are resistant to A. invadans infection. In the present study, we investigated the transcriptomes of head kidney of common carp experimentally infected with A. invadans. In time course analysis, 5288 genes were found to be differentially expressed (DEGs), of which 731 were involved in 21 immune pathways. The analysis of immune-related DEGs suggested that efficient processing and presentation of A. invadans antigens, enhanced phagocytosis, recognition of pathogen-associated molecular patterns, and increased recruitment of leukocytes to the sites of infection contribute to resistance of common carp against A. invadans. Herein, we provide a systematic understanding of the disease resistance mechanisms in common carp at molecular level as a valuable resource for developing disease management strategies for this devastating fish-pathogenic oomycete.
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Affiliation(s)
- Dev Kumar Verma
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226 002, Uttar Pradesh, India
| | - Luca Peruzza
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom; Present address: Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Franziska Trusch
- International Centre for Aquaculture Research and Development, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom; Present address: University of Dundee, School of Life Sciences, Department of Plant Sciences (@ James Hutton Institute), Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - Manoj Kumar Yadav
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226 002, Uttar Pradesh, India
| | - Ravindra
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226 002, Uttar Pradesh, India
| | - Sergei V Shubin
- College of Science, Swansea University, Singleton Park, Swansea SA2 8PP, United Kingdom
| | - Kenton L Morgan
- The Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, Liverpool, United Kingdom
| | - Vindhya Mohindra
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226 002, Uttar Pradesh, India
| | - Chris Hauton
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom
| | - Pieter van West
- International Centre for Aquaculture Research and Development, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
| | - P K Pradhan
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226 002, Uttar Pradesh, India
| | - Neeraj Sood
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226 002, Uttar Pradesh, India.
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Cao D, Li J, Huang B, Zhang J, Pan C, Huang J, Zhou H, Ma Q, Chen G, Wang Z. RNA-seq analysis reveals divergent adaptive response to hyper- and hypo-salinity in cobia, Rachycentron canadum. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:1713-1727. [PMID: 32514851 DOI: 10.1007/s10695-020-00823-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
Salinity is an important abiotic stress that affects metabolic and physiological activities, breed, development, and growth of marine fish. Studies have shown that cobia (Rachycentron canadum), a euryhaline marine teleost fish, possesses the ability of rapid and effective hyper/hypo iono- and osmoregulation. However, genomic studies on this species are lacking and it has not been studied at the transcriptome level to identify the genes responsible for salinity regulation, which affects the understanding of the fundamental mechanism underlying adaptation to fluctuations in salinity. To describe the molecular response of cobia to different salinity levels, we used RNA-seq analysis to identify genes and biological processes involved in response to salinity changes. In the present study, 395,080,114 clean reads were generated and then assembled into 65,318 unigenes with an N50 size of 2758 bp. There were 20,671 significantly differentially expressed genes (DEGs) including 8805 genes adapted to hypo-salinity and 11,866 genes adapted to hyper-salinity. These DEGs were highly represented in steroid biosynthesis, unsaturated fatty acid metabolism, glutathione metabolism, energy metabolism, osmoregulation, and immune response. The candidate genes identified in cobia provide valuable information for studying the molecular mechanism of salinity adaptation in marine fish. Furthermore, the transcriptomic sequencing data acts not only as an important resource for the identification of novel genes but also for further investigations regarding cobia biology.
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Affiliation(s)
- Danyu Cao
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China
| | - Jinfeng Li
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China
| | - Baosong Huang
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China
| | - Jiandong Zhang
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China
| | - Chuanhao Pan
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China
| | - Jiansheng Huang
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China
| | - Hui Zhou
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China
| | - Qian Ma
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China
| | - Gang Chen
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China
| | - Zhongliang Wang
- Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China.
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75
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Chen D, Du Y, Fan X, Zhu Z, Jiang H, Wang J, Fan Y, Chen H, Zhou D, Xiong C, Zheng Y, Xu X, Luo Q, Guo R. Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome utilizing PacBio long reads combined with Illumina short reads. J Invertebr Pathol 2020; 176:107475. [PMID: 32976816 DOI: 10.1016/j.jip.2020.107475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 08/26/2020] [Accepted: 09/16/2020] [Indexed: 01/19/2023]
Abstract
Ascosphaera apis is a widespread fungal pathogen of honeybee larvae that results in chalkbrood disease, leading to heavy losses for the beekeeping industry in China and many other countries. This work was aimed at generating a full-length transcriptome of A. apis using PacBio single-molecule real-time (SMRT) sequencing. Here, more than 23.97 Gb of clean reads was generated from long-read sequencing of A. apis mycelia, including 464,043 circular consensus sequences (CCS) and 394,142 full-length non-chimeric (FLNC) reads. In total, we identified 174,095 high-confidence transcripts covering 5141 known genes with an average length of 2728 bp. We also discovered 2405 genic loci and 11,623 isoforms that have not been annotated yet within the current reference genome. Additionally, 16,049, 10,682, 4520 and 7253 of the discovered transcripts have annotations in the Non-redundant protein (Nr), Clusters of Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, 1205 long non-coding RNAs (lncRNAs) were identified, which have less exons, shorter exon and intron lengths, shorter transcript lengths, lower GC percent, lower expression levels, and fewer alternative splicing (AS) evens, compared with protein-coding transcripts. A total of 253 members from 17 transcription factor (TF) families were identified from our transcript datasets. Finally, the expression of A. apis isoforms was validated using a molecular approach. Overall, this is the first report of a full-length transcriptome of entomogenous fungi including A. apis. Our data offer a comprehensive set of reference transcripts and hence contributes to improving the genome annotation and transcriptomic study of A. apis.
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Affiliation(s)
- Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Yu Du
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Zhiwei Zhu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Haibin Jiang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Jie Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Yuanchan Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Huazhi Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Dingding Zhou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Cuiling Xiong
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Yanzhen Zheng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Xijian Xu
- Jiangxi Province Institute of Apiculture, 330201 Nanchang, Jiangxi, China
| | - Qun Luo
- Jiangxi Province Institute of Apiculture, 330201 Nanchang, Jiangxi, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China; Engineering Research Center of Processing and Application of Bee Products of Ministry of Education, Fuzhou 350002, Fujian Province, China.
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76
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Yuan H, Zhang X, Zhao L, Chang H, Yang C, Qiu Z, Huang Y. Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus. Sci Rep 2020; 10:14228. [PMID: 32848169 PMCID: PMC7450073 DOI: 10.1038/s41598-020-71178-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Acrididae are diverse in size, body shape, behavior, ecology and life history; widely distributed; easy to collect; and important to agriculture. They represent promising model candidates for functional genomics, but their extremely large genomes have hindered this research; establishing a reference transcriptome for a species is the primary means of obtaining genetic information. Here, two Acrididae species, Gomphocerus licenti and Mongolotettix japonicus, were selected for full-length (FL) PacBio transcriptome sequencing. For G. licenti and M. japonicus, respectively, 590,112 and 566,165 circular consensus sequences (CCS) were generated, which identified 458,131 and 428,979 full-length nonchimeric (FLNC) reads. After isoform-level clustering, next-generation sequencing (NGS) short sequences were used for error correction, and remove redundant sequences with CD-HIT, 17,970 and 16,766 unigenes were generated for G. licenti and M. japonicus. In addition, we obtained 17,495 and 16,373 coding sequences, 1,082 and 813 transcription factors, 11,840 and 10,814 simple sequence repeats, and 905 and 706 long noncoding RNAs by analyzing the transcriptomes of G. licenti and M. japonicus, respectively, and 15,803 and 14,846 unigenes were annotated in eight functional databases. This is the first study to sequence FL transcriptomes of G. licenti and M. japonicus, providing valuable genetic resources for further functional genomics research.
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Affiliation(s)
- Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Xue Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Lina Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Huihui Chang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Zhongying Qiu
- School of Basic Medical Sciences, Xi'an Medical University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
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77
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Khwatenge CN, Kimathi BM, Nahashon SN. Transcriptome Analysis and Expression of Selected Cationic Amino Acid Transporters in the Liver of Broiler Chicken Fed Diets with Varying Concentrations of Lysine. Int J Mol Sci 2020; 21:E5594. [PMID: 32764289 PMCID: PMC7460557 DOI: 10.3390/ijms21165594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 11/28/2022] Open
Abstract
Amino acids are known to play a key role in gene expression regulation. Amino acid signaling is mediated via two pathways: the mammalian target of rapamycin complex 1 (mTORC1) and the amino acid responsive (AAR) pathways. Cationic amino acid transporters (CATs) are crucial in these pathways due to their sensing, signaling and transport functions. The availability of certain amino acids plays a key role in the intake of other amino acids, hence affecting growth in young birds. However, the specific mechanism for regulating lysine transport for growth is not clear. In this study, we analyze the transcriptome profiles and mRNA expression of selected cationic amino acid transporters in the livers of broilers fed low and high lysine diets. Birds consumed high-lysine (1.42% lysine) or low-lysine (0.85% lysine) diets while the control group consumed 1.14% lysine diet. These concentrations of lysine represent 125% (high lysine), 75% (low lysine) and 100% (control), respectively, of the National Research Council's (NRC) recommendation for broiler chickens. After comparing the two groups, 210 differentially expressed genes (DEGs) were identified (fold change >1 and false discovery rate (FDR) <0.05). When comparing the high lysine and the low lysine treatments, there were 67 upregulated genes and 143 downregulated genes among these DEGs. Analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO) enrichment analysis show that cellular growth, lipid metabolism and lysine metabolism pathways were among the significantly enriched pathways. This study contributes to a better understanding of the potential molecular mechanisms underlying the correlation between lysine intake, body weight gain (BWG) and feed intake (FI) in broiler chickens. Moreover, the DEGs obtained in this study may be used as potential candidate genes for further investigation of broiler growth customized responses to individualized nutrients such as amino acids.
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Affiliation(s)
- Collins N. Khwatenge
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA; (C.N.K.); (B.M.K.)
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Boniface M. Kimathi
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA; (C.N.K.); (B.M.K.)
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Samuel N. Nahashon
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
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78
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Jiang S, Yang J, Fang DA. Transcriptome changes of Takifugu obscurus liver after acute exposure to the oxygenated-PAH 9,10-phenanthrenequione. Physiol Genomics 2020; 52:305-313. [PMID: 32538278 DOI: 10.1152/physiolgenomics.00022.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Contamination with polycyclic aromatic hydrocarbons (PAHs) causes noticeable ecological problems in aquatic ecosystems. 9,10-Phenanthrenequione (9,10-PQ) is an oxidized PAH and is highly toxic to aquatic animals. However, the effects of 9,10-PQ on the molecular metabolism of fish remain largely unknown. In this study, Takifugu obscurus juveniles were acutely exposed to 44.30 µg/L 9,10-PQ for 3 days. The transcriptome profile changes in their livers were compared between the 9,10-PQ treatment group and the control using T. rubripes as the reference genome. The results identified 22,414 genes in our transcriptome. Among them, 767 genes were differentially expressed after exposure to 9,10-PQ, which enriched 16 KEGG pathways. Among them, the glycolysis, phagosome, and FOXO signaling pathways were significantly activated in 9,10-PQ treatment compared with the control. These data indicate that 9,10-PQ increased the glycolysis capacity to produce more energy for resistance and harmed immune function. Moreover, several genes related to tumorigenesis were significantly upregulated in response to 9,10-PQ, displaying the carcinogenic toxicity of 9,10-PQ to T. obscurus. Genes in steroid biosynthesis pathways were downregulated in the 9,10-PQ treatment group, suggesting interference with the endocrine system. Overall, these findings provide information to help evaluate the environmental risks that oxygenated-PAHs present to T. obscurus.
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Affiliation(s)
- Shulun Jiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jian Yang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Di-An Fang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
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79
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Zhang H, Hong X, Yan S, Zha J, Qin J. Environmentally relevant concentrations of bifenthrin induce changes in behaviour, biomarkers, histological characteristics, and the transcriptome in Corbicula fluminea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 728:138821. [PMID: 32361119 DOI: 10.1016/j.scitotenv.2020.138821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Bifenthrin (BF) is an insecticide that is commonly used to control agricultural and domestic pests and is widespread in aquatic environments. Although previous studies have found that BF is toxic to aquatic organisms, such a comprehensive study of the mechanism of toxic effects in bivalves is not common. In this study, to assess the toxic effects of BF on bivalves, adult Corbicula fluminea (C. fluminea) were exposed to 0, 1, 5, and 25 μg/L BF for 15 days. Transcriptome analysis revealed that BF exposure significantly altered the expression of genes involved in detoxification, antioxidation, and metabolism. Moreover, the ROS content and GST activity at 25 μg/L treatments were significantly increased (p < 0.05), and significant increases of MDA concentration and CAT activity were observed at 5 and 25 μg/L treatments (p < 0.05). However, AChE activity was markedly inhibited at 25 μg/L treatments (p < 0.05). In addition, vacuolation in the digestive tubules and the hemolytic infiltration of connective tissue were observed at all treatments, and the degeneration of the digestive tubule was observed at 5 and 25 μg/L treatments. In the behavioural assay, the siphoning behaviour of C. fluminea was significantly inhibited at 25 μg/L treatments (p < 0.05), whereas no significant change in burrowing behaviour was observed. Our findings suggested that BF exposure caused changes in detoxification, antioxidation, and metabolism pathways, biomarker activity or concentrations and histopathological characteristics, resulting in changes in behaviour. Therefore, our findings provide a basis for further evaluation of the toxicity of pyrethroid insecticides in bivalves.
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Affiliation(s)
- Huan Zhang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiangsheng Hong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Saihong Yan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan 430070, China.
| | - Jianhui Qin
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan 430070, China
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80
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Identification of the novel bacterial blight resistance gene Xa46(t) by mapping and expression analysis of the rice mutant H120. Sci Rep 2020; 10:12642. [PMID: 32724216 PMCID: PMC7387522 DOI: 10.1038/s41598-020-69639-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 07/15/2020] [Indexed: 01/11/2023] Open
Abstract
Rice bacterial leaf blight is caused by Xanthomonas oryzae pv. oryzae (Xoo) and produces substantial losses in rice yields. Resistance breeding is an effective method for controlling bacterial leaf blight disease. The mutant line H120 derived from the japonica line Lijiangxintuanheigu is resistant to all Chinese Xoo races. To identify and map the Xoo resistance gene(s) of H120, we examined the association between phenotypic and genotypic variations in two F2 populations derived from crosses between H120/CO39 and H120/IR24. The segregation ratios of F2 progeny consisted with the action of a single dominant resistance gene, which we named Xa46(t). Xa46(t) was mapped between the markers RM26981 and RM26984 within an approximately 65.34-kb region on chromosome 11. The 12 genes predicted within the target region included two candidate genes encoding the serine/threonine-protein kinase Doa (Loc_Os11g37540) and Calmodulin-2/3/5 (Loc_Os11g37550). Differential expression of H120 was analyzed by RNA-seq. Four genes in the Xa46(t) target region were differentially expressed after inoculation with Xoo. Mapping and expression data suggest that Loc_Os11g37540 allele is most likely to be Xa46(t). The sequence comparison of Xa23 allele between H120 and CBB23 indicated that the Xa46(t) gene is not identical to Xa23.
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81
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Wang X, Cao C, Li Y, Hai T, Jia Q, Zhang Y, Zheng Q, Yao J, Qin G, Zhang H, Song R, Wang Y, Shui G, Lam SM, Liu Z, Wei H, Meng A, Zhou Q, Zhao J. A harlequin ichthyosis pig model with a novel ABCA12 mutation can be rescued by acitretin treatment. J Mol Cell Biol 2020; 11:1029-1041. [PMID: 30925591 PMCID: PMC6934153 DOI: 10.1093/jmcb/mjz021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/20/2019] [Accepted: 03/08/2019] [Indexed: 11/20/2022] Open
Abstract
Harlequin ichthyosis (HI) is a severe genetic skin disorder and caused by mutation in the ATP-binding cassette A12 (ABCA12) gene. The retinoid administration has dramatically improved long-term survival of HI, but improvements are still needed. However, the ABCA12 null mice failed to respond to retinoid treatment, which impedes the development of novel cure strategies for HI. Here we generated an ethylnitrosourea mutagenic HI pig model (named Z9), which carries a novel deep intronic mutation IVS49-727 A>G in the ABCA12 gene, resulting in abnormal mRNA splicing and truncated protein production. Z9 pigs exhibit significant clinical symptom as human patients with HI. Most importantly, systemic retinoid treatment significantly prolonged the life span of the mutant pigs via improving epidermal maturation, decreasing epidermal apoptosis, and triggering the expression of ABCA6. Taken together, this pig model perfectly resembles the clinical symptom and molecular pathology of patients with HI and will be useful for understanding mechanistic insight and developing therapeutic strategies.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Chunwei Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Yongshun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Tang Hai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Qitao Jia
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Qiantao Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Jing Yao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Guosong Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Hongyong Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Ruigao Song
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Yanfang Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University of China, Harbin 150030, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Anming Meng
- School of Life Sciences, Tsinghua University, Beijing 100084, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
| | - Jianguo Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Chinese Swine Mutagenesis Consortium, Beijing 100101, China
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82
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Wang M, Shi Y, Yao L, Li Q, Wang Y, Li J, Fu D. Identification of Hub Genes in Protective Effect of Astragaloside IV on Aconitine-Induced Cardiac Damage in Zebrafish Based on Bioinformatics Analysis. Front Pharmacol 2020; 11:957. [PMID: 32670070 PMCID: PMC7327619 DOI: 10.3389/fphar.2020.00957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
Accumulating evidence suggests that Astragaloside IV (AS-IV) improves cardiac function and protects the cardiovascular system. However, the molecular targets involved remain ambiguous. In this work, we report research suggesting that AS-IV can antagonize arrhythmias and reduce the cardiac damage induced by aconitine in zebrafish. Zebrafish have certain benefits with respect to studying the effect of drugs on cardiovascular disease. The possible mechanisms involved are analyzed, and hub gene targets are predicted. First, a model of cardiac damage induced by aconitine was created, and then a safe drug concentration of AS-IV was screened, and the appropriate drug dose gradient was selected within a safe drug concentration range. Second, we confirmed the protective effect of AS-IV in the cardiovascular system by observing changes in zebrafish heart rates and the cardiac and vascular structure. Third, we aimed to demonstrate the antagonistic mechanism of AS-IV on heart rate and cardiac damage induced by aconitine in zebrafish, with differentially expressed genes (DEGs) detected by RNA sequencing. The DEGs were then further analyzed by bioinformatic techniques, such as function enrichment analysis, protein-protein interaction network, and DNA-microRNA networks, for example. Next, we predicted the hub genes of the cardiac protective effects of AS-IV. Finally, we validated these genes in different transcriptome sequence datasets of cardiac damage. Thus, we conclude that miR-26b-5p/ATF3/JUN are key targets of AS-IV and play an important role in maintaining cardiac homeostasis and regulating cardiac remodeling.
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Affiliation(s)
- Mingzhu Wang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yanan Shi
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lei Yao
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qiang Li
- Children's Hospital of Fudan University, Fudan University, Shanghai, China
| | - Youhua Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jianhua Li
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Deyu Fu
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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83
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Tso CH, Wu JL, Lu MW. Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish. BMC Bioinformatics 2020; 21:174. [PMID: 32366294 PMCID: PMC7199347 DOI: 10.1186/s12859-020-3507-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/20/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Transcriptome analysis by next-generation sequencing has become a popular technique in recent years. This approach is quite suitable for non-model organism study, as de novo assembly is independent of prior genomic sequences of organisms. De novo sequencing has benefited many studies on commercially important fish species. However, to understand the functions of these assembled sequences, they still need to be annotated with existing sequence databases. By combining Basic Local Alignment Search Tool (BLAST) and Gene Ontology analysis, we were able to identify homologous sequences of assembled sequences and describe their characteristics using pre-defined tags for each gene, though the above conventional annotation results obtained for non-model assembled sequences was still associated with a lack of pre-defined tags and poorly documented records in the database. RESULTS We introduced Blast2Fish, a novel approach for performing functional enrichment analysis on non-model teleost fish transcriptome data. The Blast2Fish pipeline was designed to be a reference-based enrichment method. Instead of annotating the BLAST single top hit by a pre-defined gene-to-tag database, we included 500 hits to search related PubMed articles and parse biological terms. These descriptive terms were then sorted and recorded as annotations for the query. The results showed that Blast2Fish was capable of providing meaningful annotations on immunology topics for non-model fish transcriptome analysis. CONCLUSION Blast2Fish provides a novel approach for annotating sequences of non-model fish. The reference-based strategy allows annotation to be performed without pre-defined tags for each gene. This method strongly benefits non-model teleost fish studies for gene functional enrichment analysis.
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Affiliation(s)
- Chun-Hsi Tso
- Department of Aquaculture, National Taiwan Ocean University, No.2, Beining Rd., Zhongzheng Dist, Keelung City, 20224, Taiwan
| | - Jen-Leih Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Wei Lu
- Department of Aquaculture, National Taiwan Ocean University, No.2, Beining Rd., Zhongzheng Dist, Keelung City, 20224, Taiwan.
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84
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Amparyup P, Charoensapsri W, Samaluka N, Chumtong P, Yocawibun P, Imjongjirak C. Transcriptome analysis identifies immune-related genes and antimicrobial peptides in Siamese fighting fish (Betta splendens). FISH & SHELLFISH IMMUNOLOGY 2020; 99:403-413. [PMID: 32081810 DOI: 10.1016/j.fsi.2020.02.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/08/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
Siamese fighting fish (Betta splendens) is one of the most widely cultivated ornamental fish in global trade. However, transcriptomic data, which can reveal valuable genetic data for disease control and prevention, are extremely limited for this species. In this study, whole-body transcriptome sequencing of juvenile betta fish generated 4.457 GB of clean data and a total of 71,775 unigenes using the Illumina HiSeq4000 platform. These unigenes were functionally classified using 7 functional databases, yielding 45,316 NR (63.14%), 47,287 NT (65.88%), 39,105 Swiss-Prot (54.48%), 16,492 COG (22.98%), 37,694 KEGG (52.52%), 4,506 GO (6.28%), and 35,374 Interpro (49.28%) annotated unigenes. Furthermore, we also detected 13,834 SSRs distributed on 10,636 unigenes and 49,589 predicted CDSs. Based on KEGG analysis, five innate immune pathways (997 unigenes) were reported, including the NOD-like receptor signaling pathway, complement and coagulation cascades, toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway and cytosolic DNA-sensing pathway. Moreover, four antimicrobial peptide (AMP) families (hepcidin, piscidin, LEAP-2, and defensins) from the betta fish transcriptome were also identified. Additionally, cDNA and genomic DNA of two β-defensins was successfully isolated from four betta fish species. RT-PCR analysis showed that BsBD1 transcripts were most abundant in the muscle and kidney and BsBD2 transcripts were most abundant in the gill. The genomic organization showed that the BD1 and BD2 genes consisted of three exons and two introns according to the GT-AG rule. Most importantly, this is the first report of the betta fish whole-body transcriptome obtained by high-throughput sequencing. Our transcriptomic data and the discovery of betta fish AMPs should promote a better understanding of molecular immunology for disease prevention for further ornamental fish aquaculture.
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Affiliation(s)
- Piti Amparyup
- Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand; Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Walaiporn Charoensapsri
- Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand; Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nusree Samaluka
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand
| | - Parichat Chumtong
- Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand; Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Patchari Yocawibun
- Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand; Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chanprapa Imjongjirak
- Department of Food Technology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand.
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85
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Kemski MM, Rappleye CA, Dabrowski K, Bruno RS, Wick M. Transcriptomic response to soybean meal-based diets as the first formulated feed in juvenile yellow perch (Perca flavescens). Sci Rep 2020; 10:3998. [PMID: 32132548 PMCID: PMC7055240 DOI: 10.1038/s41598-020-59691-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/20/2020] [Indexed: 12/24/2022] Open
Abstract
With increasing levels of fish meal (FM) protein in aquafeeds being replaced with soybean meal (SBM) protein, understanding the molecular mechanisms involved in response to alternative diets has become a critical concern. Thus, the goal of this study was to examine transcriptional differences in the intestine of juvenile yellow perch through RNA-sequencing (RNA-seq), after their initial introduction to a formulated diet with 75% SBM protein inclusion for 61 days, compared to those fed a traditional FM-based diet. Transcriptomic analysis revealed a concise set of differentially expressed genes in juveniles fed the SBM-based diet, the majority of which were intrinsic to the cholesterol biosynthesis pathway. Analysis of total body lipid and cholesterol levels were also investigated, with no between-treatment differences detected. Results of this study demonstrate that in response to SBM-based diets, yellow perch juveniles up-regulate the cholesterol biosynthesis pathway in order to maintain homeostasis. These findings suggest that the upregulation of the cholesterol biosynthesis pathway may negatively impact fish growth due to its large energy expenditure, and future studies are warranted.
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Affiliation(s)
- Megan M Kemski
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, USA
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Chad A Rappleye
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Konrad Dabrowski
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Richard S Bruno
- Department of Human Sciences, The Ohio State University, Columbus, OH, USA
| | - Macdonald Wick
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA.
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86
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Ji L, Sun G, Li X, Liu Y. Comparative transcriptome analysis reveals the mechanism of β-glucan in protecting rainbow trout (Oncorhynchus mykiss) from Aeromonas salmonicida infection. FISH & SHELLFISH IMMUNOLOGY 2020; 98:87-99. [PMID: 31866453 DOI: 10.1016/j.fsi.2019.12.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
To study the mechanism of β-glucan in immune protection, rainbow trout were fed diets with or without 0.2% β-glucan for 42 days and then infected with Aeromonas salmonicida. After that, spleen tissues were sampled on 4- and 6-days post infection (dpi). Transcriptome analysis was compared between control group (CG, without β-glucan addition) and 0.2% β-glucan group (BG). In CG vs BG, 378 and 406 DEGs were identified on 4 dpi and 6 dpi respectively; furthermore, 46 DEGs were shared on 4 dpi and 6 dpi, enriching in GO terms, such as complement activation, inflammatory response, and metabolic process. KEGG pathway analysis revealed that some DEGs in CG vs BG were involved in immune or metabolic signaling pathways such as complement and coagulation cascades, toll-like receptor signaling pathway, NF-κB signaling pathway, antigen processing and presentation, and platelet activation on 4 or 6 dpi. DEGs, such as fgg, fgb, f5, c9, c3, c5, tlr5, and myd88, were analyzed in CG vs BG on 4 dpi and 6 dpi, implying their potential roles in β-glucan-modulated immunity. These results are beneficial to understand the mechanism of β-glucan in resisting bacteria in fish.
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Affiliation(s)
- Liqin Ji
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; University of Chinese Academy of Sciences, Beijing, 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Guoxiang Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xian Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ying Liu
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; School of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, China.
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87
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Kim K, Kang HE, Yook JI, Yu HS, Kim E, Cha JY, Choi YJ. Transcriptional Expression in Human Periodontal Ligament Cells Subjected to Orthodontic Force: An RNA-Sequencing Study. J Clin Med 2020; 9:jcm9020358. [PMID: 32012982 PMCID: PMC7073659 DOI: 10.3390/jcm9020358] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/23/2020] [Accepted: 01/26/2020] [Indexed: 12/11/2022] Open
Abstract
This study was performed to investigate the changes in gene expression in periodontal ligament (PDL) cells following mechanical stimulus through RNA sequencing. In this study, premolars extracted for orthodontic treatment were used. To stimulate the PDL cells, an orthodontic force of 100× g was applied to the premolar (experimental group; n = 11), whereas the tooth on the other side was left untreated (control group; n = 11). After the PDL cells were isolated from the extracted teeth, gene set enrichment analysis (GSEA), differentially expressed gene (DEG) analysis, and real-time PCR were performed to compare the two groups. GSEA demonstrated that gene sets related to the cell cycle pathway were upregulated in PDL. Thirteen upregulated and twenty downregulated genes were found through DEG analysis. Real-time PCR results confirmed that five upregulated genes (CC2D1B, CPNE3, OPHN1, TANGO2, and UAP-1) and six downregulated genes (MYOM2, PPM1F, PCDP1, ATP2A1, GPR171, and RP1-34H18.1-1) were consistent with RNA sequencing results. We suggest that, from among these eleven genes, two upregulated genes, CPNE3 and OPHN1, and one downregulated gene, PPM1F, play an important role in PDL regeneration in humans when orthodontic force is applied.
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Affiliation(s)
- Kyunam Kim
- Department of Orthodontics, The Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul 03722, Korea; (K.K.); (H.-S.Y.); (J.-Y.C.)
| | - Hee Eun Kang
- Vatech Co., Ltd. Hwaseong-si, Gyeonggi-do 18449, Korea;
| | - Jong In Yook
- Department of Oral Pathology, Oral Cancer Research Institute, Yonsei University College of Dentistry, Seoul 03722, Korea;
| | - Hyung-Seog Yu
- Department of Orthodontics, The Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul 03722, Korea; (K.K.); (H.-S.Y.); (J.-Y.C.)
| | - Euiseong Kim
- Department of Conservative Dentistry, Oral Science Research Center, Yonsei University College of Dentistry, Seoul 03722, Korea;
| | - Jung-Yul Cha
- Department of Orthodontics, The Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul 03722, Korea; (K.K.); (H.-S.Y.); (J.-Y.C.)
| | - Yoon Jeong Choi
- Department of Orthodontics, The Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul 03722, Korea; (K.K.); (H.-S.Y.); (J.-Y.C.)
- Correspondence: ; Tel.: +82-2-2228-3101; Fax: +82-2-363-3404
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Abstract
Chronic Obstructive Pulmonary Disease (COPD) and Idiopathic Pulmonary Fibrosis (IPF) have contrasting clinical and pathological characteristics and interesting whole-genome transcriptomic profiles. However, data from public repositories are difficult to reprocess and reanalyze. Here, we present PulmonDB, a web-based database (http://pulmondb.liigh.unam.mx/) and R library that facilitates exploration of gene expression profiles for these diseases by integrating transcriptomic data and curated annotation from different sources. We demonstrated the value of this resource by presenting the expression of already well-known genes of COPD and IPF across multiple experiments and the results of two differential expression analyses in which we successfully identified differences and similarities. With this first version of PulmonDB, we create a new hypothesis and compare the two diseases from a transcriptomics perspective.
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89
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Ngamniyom A, Sriyapai T, Sriyapai P. Molecular analysis of population and De Novo transcriptome sequencing of Thai medaka, Oryzias minutillus (Teleostei: Adrianichthyidae). Heliyon 2020; 6:e03079. [PMID: 31909257 PMCID: PMC6938829 DOI: 10.1016/j.heliyon.2019.e03079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/13/2019] [Accepted: 12/16/2019] [Indexed: 12/27/2022] Open
Abstract
Thai medaka (Oryzias minutillus) are alternatively known as Thai rice-fish or dwarf medaka, and they widely inhabit natural freshwater environments in all regions of Thailand. In this study, we aimed to investigate the molecular genetics of the Thai medaka population in Thailand inferred from the mitochondrial control region (D-loop) and the cytochrome c oxidase subunit 1 (coxI) sequences. Furthermore, we examined RNA sequencing (RNA-seq) of adult males and females was performed with next-generation sequencing. Together, the combination of the D-loop and coxI sequences clearly distinguished the Thai medaka populations into 2 groups, such as group 1, which generally included samples from the central, northern, western, and eastern regions of the northeastern region. In this group, the fish populations seem to be a little monophyly in which the first subpopulation comprised the main samples from the northern and central regions. The second subpopulation commonly contained fish from the eastern region and specimens from the southern part of the central region near the Gulf of Thailand. Although these subgroups related to geographical distribution, bootstrap values were low in branch considered significant for both subgroups. Group 2 consisted of almost all samples from the southern population and those from the central and southern part of the northeastern region. Group 2 was found that it was made of samples from the northeastern region and samples from the southern population. A total of 73551 unigenes were identified after gene annotation. Signal transduction was the predominant protein classification among the Thai medaka orthologous groups. A differentially expressed gene (DEG) analysis identified 6 subclusters between both sexes that were composed of 257, 131, 364, 386, 114 and 108 genes. Phototransduction was the most enriched pathway and was highly expressed in males, while viral carcinogenesis, oocyte genesis, and the complement and coagulation cascades were highly expressed in females. Further details of these DEGs are discussed below. These results suggest that Thai medaka may genetically exhibit independent populations in the geographic habitats of Thailand. Moreover, these fish also reveal the genes that are conserved in other organisms and those that may be specific to this species.
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Affiliation(s)
- Arin Ngamniyom
- Major in Environment, Faculty of Environmental Culture and Eco-tourism, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thayat Sriyapai
- Major in Environment, Faculty of Environmental Culture and Eco-tourism, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Pichapack Sriyapai
- Department of Microbiology, Faculty of Sciences, Srinakharinwirot University, Bangkok, 10110, Thailand
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90
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Zhou S, Li R, Hou W, Wang Y, Zhang S, Yu Y, Zhang L, Zhu H, Zhang Z, Fang J, Chang X, Zhang Y, Liu L, Tang L, Zhou Z. RNA-seq analysis of testes from flurochloridone-treated rats. Toxicol Mech Methods 2019; 30:219-227. [PMID: 31805805 DOI: 10.1080/15376516.2019.1701593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Flurochloridone (FLC) is a widely used herbicide in developing countries. Although the testes are a target organ for FLC in rats, the adverse effects of FLC on testes have not been fully elucidated. To clarify them, we performed RNA-seq analysis using the testes of FLC-treated rats from our previous subchronic toxicity tests. Unilateral testes of three male rats from solvent control groupand three FLC-treated groups (3 mg/kg, 31.25 mg/kg and 125 mg/kg) were used for RNA extraction. A poly A selection protocol coupled with an Illumina TruSeq RNA-Seq library protocol was used to construct RNA-Seq libraries. Principal component analysis (PCA), differentially expressed gene (DEG) analysis, and hierarchical clustering analysis (HCA) were conducted using R. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to understand the biological characteristics of the DEGs using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The results indicated that many up-regulated DEGs were enriched in pathways associated with testicular injury, such as mitogen-activated protein kinase (MAPK) signaling, lysosome and focal adhesion. Many down-regulated DEGs were enriched in pathways associated with testicular reproduction function, such as sexual reproduction, spermatogenesis and germ cell development. Moreover, we confirmed the oral no-observed-adverse-effect level (NOAEL) of 3 mg/kg in subchronic toxicity test, because the overall testicular gene expression in 3 mg/kg FLC-treated group was similar to that of the solvent control group. In 31.25 mg/kg and 125 mg/kg groups, DEGs revealed that testicular injury was related to oxidative stress.
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Affiliation(s)
- Su Zhou
- Pharmacology and Toxicology Department, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Rui Li
- Pharmacology and Toxicology Department, Shanghai Institute for Food and Drug Control, Shanghai, China.,School of Public Health, MOE Key Laboratory for Public Health Safety, Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China
| | - Wanwan Hou
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yue Wang
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Suhui Zhang
- Pharmacology and Toxicology Department, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Ying Yu
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Lei Zhang
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Hongyan Zhu
- Pharmacology and Toxicology Department, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Zhichao Zhang
- Pharmacology and Toxicology Department, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Jing Fang
- Pharmacology and Toxicology Department, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Xiuli Chang
- School of Public Health, MOE Key Laboratory for Public Health Safety, Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China
| | - Yubin Zhang
- School of Public Health, MOE Key Laboratory for Public Health Safety, Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China
| | - Luqing Liu
- School of Public Health, MOE Key Laboratory for Public Health Safety, Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China
| | - Liming Tang
- Pharmacology and Toxicology Department, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Zhijun Zhou
- School of Public Health, MOE Key Laboratory for Public Health Safety, Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China
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91
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Yang Y, Zhou H, Hou L, Xing K, Shu H. Transcriptional profiling of skeletal muscle reveals starvation response and compensatory growth in Spinibarbus hollandi. BMC Genomics 2019; 20:938. [PMID: 31805873 PMCID: PMC6896686 DOI: 10.1186/s12864-019-6345-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 11/27/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Spinibarbus hollandi is an economically important fish species in southern China. This fish is known to have nutritional and medicinal properties; however, its farming is limited by its slow growth rate. In the present study, we observed that a compensatory growth phenomenon could be induced by adequate refeeding following 7 days of fasting in S. hollandi. To understand the starvation response and compensatory growth mechanisms in this fish, the muscle transcriptomes of S. hollandi under control, fasting, and refeeding conditions were profiled using next-generation sequencing (NGS) techniques. RESULTS More than 4.45 × 108 quality-filtered 150-base-pair Illumina reads were obtained from all nine muscle samples. De novo assemblies yielded a total of 156,735 unigenes, among which 142,918 (91.18%) could be annotated in at least one available database. After 7 days of fasting, 2422 differentially expressed genes were detected, including 1510 up-regulated genes and 912 down-regulated genes. Genes involved in fat, protein, and carbohydrate metabolism were significantly up-regulated, and genes associated with the cell cycle, DNA replication, and immune and cellular structures were inhibited during fasting. After refeeding, 84 up-regulated genes and 16 down-regulated genes were identified. Many genes encoding the components of myofibers were significantly up-regulated. Histological analysis of muscle verified the important role of muscle hypertrophy in compensatory growth. CONCLUSION In the present work, we reported the transcriptome profiles of S. hollandi muscle under different conditions. During fasting, the genes involved in the mobilization of stored energy were up-regulated, while the genes associated with growth were down-regulated. After refeeding, muscle hypertrophy contributed to the recovery of growth. The results of this study may help to elucidate the mechanisms underlying the starvation response and compensatory growth.
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Affiliation(s)
- Yang Yang
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
| | - Huiqiang Zhou
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
| | - Liping Hou
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
| | - Ke Xing
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
| | - Hu Shu
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
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92
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Guo X, Zhang W, Li M, Gao P, Hei W, He Z, Wu Y, Liu J, Cai C, Li B, Cao G. Transcriptome profile of skeletal muscle at different developmental stages in Large White and Mashen pigs. CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2019-0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
From the perspectives of promoting individual growth and development, increasing pork yield, and improving feed utilization, it is desirable to screen candidate genes underlying pig muscle growth and regulation. In this study, we investigated transcriptome differences at 1, 90, and 180 d of age in Large White and Mashen pigs, characterized differentially expressed genes (DEGs), and screened candidate genes affecting skeletal muscle growth and development. RNA-seq was applied to analyze the transcriptome of the longissimus dorsi (LD) in the two breeds. In LD samples from the two breeds at three growth stages, 7215, 6332, 237, 3935, 3404, and 846 DEGs were obtained for L01 vs. L90, L01 vs. L180, L90 vs. L180, MS01 vs. MS90, MS01 vs. MS180, and MS90 vs. MS180, respectively. Significant tendencies in DEG expression could be grouped into eight profiles. Based on the functional analysis of DEGs, 16 candidate genes related to skeletal muscle growth and development were identified, including PCK2, GNAS, ADCY2, PRKAB1, PRKAB2, PRKAG1, PRKAG2, PHKA1, PHKA2, PHKG1, PHKG2, ITPR3, IGF1R, FGFR4, FGF1, and FGF18. The results of this study thus provide a theoretical basis for the mechanisms and candidate genes underlying skeletal muscle development in pigs.
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Affiliation(s)
- Xiaohong Guo
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Wanfeng Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Meng Li
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Pengfei Gao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Wei Hei
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Zhiqiang He
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Yiqi Wu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Juan Liu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Chunbo Cai
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Bugao Li
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
| | - Guoqing Cao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, People’s Republic of China
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93
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Wang Q, He Y, Li J. Conjoint Analysis of SMRT- and Illumina-Based RNA-Sequencing Data of Fenneropenaeus chinensis Provides Insight Into Sex-Biased Expression Genes Involved in Sexual Dimorphism. Front Genet 2019; 10:1175. [PMID: 31803244 PMCID: PMC6872642 DOI: 10.3389/fgene.2019.01175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022] Open
Abstract
Fenneropenaeus chinensis (F. chinensis) is one of the most commercially important cultured shrimps in China. The adult F. chinensis exhibit sexual dimorphism in growth and body color. In this research, we profiled the whole transcriptome of F. chinensis by using single molecule real-time-based full-length transcriptome sequencing. We further performed Illumina-based short reads RNA-seq on muscle and gonad of two sexes to detect the sex-biased expression genes. In muscle, we observed significantly more female-biased transcripts. With the differentially expressed transcripts (DETs) in muscle, some pathways related to the energy metabolism were enriched, which may be responsible for the difference of growth. We also digged out a pathway named porphyrin and chlorophyll metabolism. It was speculated to relevant to the difference of body color between the two sexes of shrimp. Interestingly, almost all DETs in these pathways were female-biased expression in muscle, which could explain the phenomenon of better growth performance and darker body color in female. In gonad, several pathways involved in reproduction were enriched. For instance, some female-biased DETs participated in the arachidonic acid metabolism, which was reported crucial in female reproduction. In conclusion, our studies identified abundant sex-biased expression transcripts and important pathways involved in sexual dimorphism by using the RNA-seq method. It provided a basis for future researches on the sexual dimorphism of F. chinensis.
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Affiliation(s)
- Qiong Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yuying He
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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94
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Transcriptome analysis and weighted gene co-expression network reveals potential genes responses to heat stress in turbot Scophthalmus maximus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 33:100632. [PMID: 31715507 DOI: 10.1016/j.cbd.2019.100632] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 12/12/2022]
Abstract
Turbot (Scophthalmus maximus) is an economically important marine fish cultured in China. In this study, we performed transcriptome gene expression profiling of kidney tissue in turbot exposed to heat stress (20, 23, 25 and 28 °C); control fish were maintained at 14 °C. We investigated gene relationships based on weighted gene co-expression network analysis (WGCNA). Accordingly, enrichment analyses of GO terms and KEGG pathways showed that several pathways (e.g., fat metabolism, cell apoptosis, immune system, and insulin signaling) may be involved in the response of turbot to heat stress. Moreover, via WGCNA, we identified 19 modules: the dark grey module was mainly enriched in pathways associated with fat metabolism and the FOXO and Jak-STAT signaling pathways. The ivory module was significantly enriched in the P53 signaling pathway. Furthermore, the key hub genes CBP, AKT3, CCND2, PIK3r2, SCOS3, mdm2, cyc-B, and p48 were enriched in the FOXO, Jak-STAT and P53 signaling pathways. This is the first study reporting co-expression patterns of a gene network after heat stress in marine fish. Our results may contribute to our understanding of the underlying molecular mechanism of thermal tolerance.
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95
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Wan ZY, Lin G, Yue G. Genes for sexual body size dimorphism in hybrid tilapia (Oreochromis sp. x Oreochromis mossambicus). AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2019.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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96
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Dai P, Shen D, Shen J, Tang Q, Xi M, Li Y, Li C. The roles of Nrf2 and autophagy in modulating inflammation mediated by TLR4 - NFκB in A549 cell exposed to layer house particulate matter 2.5 (PM 2.5). CHEMOSPHERE 2019; 235:1134-1145. [PMID: 31561304 DOI: 10.1016/j.chemosphere.2019.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/23/2019] [Accepted: 07/01/2019] [Indexed: 06/10/2023]
Abstract
Particulate matter (PM) from layer house has adverse effect on people and chicken respiratory health, which can further influence animal performance and reduce production efficiency. However, little study focus on the respiratory inflammation induced by PM2.5 from layer house and the underlying mechanism also unclear. In this study, human adenocarcinoma alveolar basal epithelial cells (A549 cell) was subjected to the PM2.5 from layer house to evaluate the inflammation reaction caused by PM2.5 and explore the role of Nrf2 and autophagy in regulating the inflammation. Results showed that the viability of A549 cell decreased in a time - and concentration - dependent manner after PM2.5 treatment. TNFα, IL6, and IL8 increased significantly treated with PM2.5 at 12 h. RNA sequencing indicated differentially expressed genes were enriched in immune system process, oxidative stress (OS), endoplasmic reticulum stress (ERS), and autophagy. Further studies showed TLR4 - NFκB p65 signal pathway involved in the inflammation reaction caused by PM2.5. The overexpression of Nrf2 decreased the level of TNFα, IL6, IL8 markedly as well as the level of NFκB p65 and NFκB pp65. OS and ERS were also limited under overactivation of Nrf2 in PM2.5 treated cells. Autophagy induced by PM2.5 promoted the inflammation through increasing the level of NFκB p65 and NFκB pp65. Autophagy deficient strengthened the expression of Nrf2. Collectively, our study revealed Nrf2 prevents inflammation caused by layer house PM2.5 stimulation, however, autophagy exerts a promotive role in TLR4 - NFκB p65 mediating inflammation in A549 cell.
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Affiliation(s)
- Pengyuan Dai
- College of Animal Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, PR China
| | - Dan Shen
- College of Animal Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, PR China
| | - Jiakun Shen
- College of Animal Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, PR China
| | - Qian Tang
- College of Animal Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, PR China
| | - Mengxue Xi
- College of Animal Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, PR China
| | - Yansen Li
- College of Animal Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, PR China
| | - Chunmei Li
- College of Animal Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, PR China.
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97
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Long non-coding RNA: Classification, biogenesis and functions in blood cells. Mol Immunol 2019; 112:82-92. [DOI: 10.1016/j.molimm.2019.04.011] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/16/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
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98
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Xue Y, Wei F, Jiang Y, Li L, Dong S, Tian X. Transcriptome signatures of the Pacific white shrimp Litopenaeus vannamei hepatopancreas in response to stress in biofloc culture systems. FISH & SHELLFISH IMMUNOLOGY 2019; 91:369-375. [PMID: 30999042 DOI: 10.1016/j.fsi.2019.04.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Comparative transcriptome analysis via high throughput sequencing was applied to gain knowledge on the immune response in Litopenaeus vannamei reared in biofloc technology systems (BFT). Two types of carbon sources, namely, traditional carbon sources (molasses) and biodegradable polymers [hydroxybutyric acid-co-3-hydroxyvaleric acid (PHBV)] were used in BFT systems. Clear water systems without the addition of carbon sources were treated as the control. Water quality assays showed that the average concentrations of several stress factors, including nitrite, nitrate and TSS, were the highest in molasses-based BFT systems. After sequencing and comparing the transcriptome profiles of the L. vannamei hepatopancreas, 743 and 201 genes were significantly differentially expressed in molasses- and PHBV-based BFT systems, respectively. GO enrichment analysis, which was performed using the differentially expressed genes, revealed seven significantly over-represented GO terms in molasses-based BFT systems, including catabolic process, hydrolase activity, cellular localization, organic substance metabolic process, cellular metabolic process, establishment of localization and response to stress. The captured key genes were mainly involved in the pathways including cellular stress response, immune response and pathogen recognition. However, no GO terms were significantly over-represented in PHBV-based BFT systems compared with control. This study indicates that shrimp are subject to stress in BFT systems when molasses serves as the carbon source. Thus, PHBV may be a better alternative.
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Affiliation(s)
- Yiming Xue
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China
| | - Fayi Wei
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China
| | - Yanliang Jiang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
| | - Li Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China.
| | - Shuanglin Dong
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China
| | - Xiangli Tian
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China
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99
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Hasan MS, Feugang JM, Liao SF. A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient-Gene Interactions in Agricultural Animals. Curr Dev Nutr 2019; 3:nzz082. [PMID: 31414073 PMCID: PMC6686084 DOI: 10.1093/cdn/nzz082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/08/2019] [Accepted: 07/08/2019] [Indexed: 11/15/2022] Open
Abstract
Thorough understanding of animal gene expression driven by dietary nutrients can be regarded as a bottom line of advanced animal nutrition research. Nutrigenomics (including transcriptomics) studies the effects of dietary nutrients on cellular gene expression and, ultimately, phenotypic changes in living organisms. Transcriptomics can be applied to investigate animal tissue transcriptomes at a defined nutritional state, which can provide a holistic view of intracellular RNA expression. As a novel transcriptomics approach, RNA sequencing (RNA-Seq) technology can monitor all gene expressions simultaneously in response to dietary intervention. The principle and history of RNA-Seq are briefly reviewed, and its 3 principal steps are described in this article. Application of RNA-Seq in different areas of animal nutrition research is summarized. Lastly, the application of RNA-Seq in swine science and nutrition is also reviewed. In short, RNA-Seq holds significant potential to be employed for better understanding the nutrient-gene interactions in agricultural animals.
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Affiliation(s)
- M Shamimul Hasan
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Jean M Feugang
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Shengfa F Liao
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
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100
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Yang Y, Liu D, Wu L, Huang W, Yang S, Xia J, Liu X, Meng Z. Comparative transcriptome analyses reveal changes of gene expression in fresh and cryopreserved yellow catfish (Pelteobagrus fulvidraco) sperm and the effects of Cryoprotectant Me 2SO. Int J Biol Macromol 2019; 133:457-465. [PMID: 31002905 DOI: 10.1016/j.ijbiomac.2019.04.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
Abstract
This study, for the first time in fish, compared the transcriptome of fresh and frozen-thawed sperm, and would help to better understand the effect of cryopreservation on fish sperm and then better preserve the aquatic germplasm resources. Here, we employed high-throughput sequencing technology to obtain the transcriptome of yellow catfish from fresh sperm, cryopreserved sperm with and without cryoprotectant. When cryoprotectant (Me2SO) was excluded, down-regulated genes were significantly enriched into calcium ion binding, cytoskeletal protein binding, microfilament motor activity, calmodulin binding and carnitine O-acyltransferase activity, which affected Ca2+ regulation, cellular morphology, motility and metabolism. Moreover, heat shock proteins and genes associated with regulation of cholesterol, HCO3- and protein tyrosine phosphorylation (PTP) were down-regulated, and thus would impair ability against stress, membrane rigidity, pH regulation and signal transduction of cryopreserved sperm. After Me2SO was added, the amounts of DEGs decreased significantly and down-regulation of genes were found mainly in cytoskeleton and heat shock proteins, thereby suggesting that Me2SO effectively reduced the impact caused by low temperature on gene expression. Whether adding Me2SO or not, the up-regulated genes were mainly found in ribosomal proteins genes. However, when Me2SO was added, over-expression of some genes might contribute to maintain normal function of cryopreserved sperm.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Dongqing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lina Wu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenhua Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Sen Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Junhong Xia
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Xiaochun Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Zining Meng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
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