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Li Y, Lu J, Song X, Wang Y, Li Q, Pang Y, Gou M. Conjoint transcriptomics and metabolomics analyses provide insights into the toxicity of acetamiprid to Lethenteron reissneri larvae. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116828. [PMID: 39094458 DOI: 10.1016/j.ecoenv.2024.116828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 08/04/2024]
Abstract
The neonicotinoid pesticide acetamiprid has been widely used in agricultural pest control and was frequently detected in the water environment. There have been some studies of the toxic effects of acetamiprid on fish, but studies on aquatic lower vertebrates are still very limited. As a primitive jawless vertebrate, Lethenteron reissneri has a special position in evolution and is now listed as a national second level protected animal in China. The present study aimed to investigate the toxic effect of acetamiprid on the liver of L. reissneri larvae. A conjoint analysis of the transcriptomics and metabolomics was performed to determine the responses of L. reissneri larvae liver to acetamiprid at different concentrations (L for low concentration 25 mg/L and H for high concentration 100 mg/L). Even low concentrations of acetamiprid can cause significant liver damage to L. reissneri larvae in a short period. In omics analyses, 2141 differentially expressed genes (DEGs) and 183 differentially abundant metabolites (DAMs) were identified in the H/Control group, and 229 DEGs and 144 DAMs were identified in the L/C group. Correlation analyses revealed acetamiprid affected the metabolic pathways of L. reissneri larvae liver such as the glycerophospholipid metabolism and arachidonic acid metabolism. This study not only enriches the basis for understanding the toxic effect of acetamiprid exposure to L. reissneri larvae liver and provides more information on the breeding and conservation of L. reissneri, but also further causes attention on toxicity risk from acetamiprid to aquatic lower vertebrate species.
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Affiliation(s)
- Yitong Li
- College of Life Science, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China
| | - Jiali Lu
- College of Life Science, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China
| | - Xiaoping Song
- Respiratory Medicine, Affiliated Zhong Shan Hospital of Dalian University, Dalian 116001, China
| | - Yaocen Wang
- College of Life Science, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Respiratory Medicine, Affiliated Zhong Shan Hospital of Dalian University, Dalian 116001, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China
| | - Meng Gou
- College of Life Science, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China.
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2
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Fu Y, Zhang J, Cheng W, Cheng X, Lu L, Gui L, Jiang Y, Zhang Y, Xu D. miR-124 mediates the expression of ccBax to regulate Cyprinid herpesvirus 2 (CyHV-2)-induced apoptosis and viral replication. JOURNAL OF FISH DISEASES 2023. [PMID: 37186311 DOI: 10.1111/jfd.13783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 05/17/2023]
Abstract
Cyprinid herpesvirus 2 (CyHV-2), the etiological agent of herpesvirus haematopoietic necrosis (HVHN) in carp and goldfish, has caused significant economic losses in the aquaculture industry. During viral infection, the host initiates a series of active or passive defences to regulate the process of virus infection. Apoptosis is a key component of active cellular defence, and members of the Bcl-2 family have been shown to play a critical role in the apoptotic process. However, the mechanism of action of the Bcl-2 family in inducing apoptosis during CyHV-2 infection remains unclear. In this study, we revealed the molecular mechanism of miRNA-mediated silver crucian carp BAX (ccBax) in CyHV-2-induced apoptosis for the first time and demonstrated that the overexpression of miR-124 suppressed ccBax expression and significantly down-regulated apoptosis in caudal fin cells of Carassius auratus gibelio (GiCF), while miR-124 inhibitors were the opposite. These studies indicated that miR-124 inhibits CyHV-2-induced apoptosis by reducing the expression of ccBax. Furthermore, the fact that transfection of miR-124 mimics promoted CyHV-2 replication, whereas miR-124 inhibitors inhibited CyHV-2 replication, indicated that miR-124 inhibited CyHV-2-induced apoptosis and contributed to viral replication. All these results suggested that miR-124 suppresses virus-induced apoptosis and promotes viral replication by targeting and regulating ccBax expression.
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Affiliation(s)
- Yan Fu
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Junzhe Zhang
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Wenjie Cheng
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Xingyu Cheng
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Liqun Lu
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Lang Gui
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yousheng Jiang
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Ye Zhang
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Dan Xu
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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3
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Priscilla L, Malathi E, Moses Inbaraj R. Sex steroid profile during oocyte development and maturation in the intertidal worm Marphysa madrasi (Polychaeta: Eunicidae) from the east coast of India. Gen Comp Endocrinol 2023; 331:114118. [PMID: 36037874 DOI: 10.1016/j.ygcen.2022.114118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 08/04/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
Marphysa madrasi is a commercially valuable maturation diet in crustacean aquaculture. This study presents the first detailed investigation of oogenesis in the intertidal polychaete worm M. madrasi and reports the steroid profile during oocyte growth and development. Oogenesis is extraovarian type I, originating from coelomic epithelial cells, with four stages of development - primary growth, early vitellogenic, late vitellogenic, and maturation. The primary growth phase contains oogonial cells and previtellogenic oocyte clusters in the early, mid, and late stages of development form a dispersed ovary attached to blood vessels. The late previtellogenic oocytes detach from the ovary at the onset of vitellogenesis. The detached oocytes complete vitellogenesis and final maturation in the coelomic fluid as solitary free-floating cells without any connection with follicle cells. The worms display asynchronous reproduction with a heterogeneous population of developing oocytes. Steroid extracts from the polychaete homogenates in different stages of oogenesis were identified by HPLC and confirmed by LC-MS/MS. In M. madrasi, two vertebrate-type steroids, pregnenolone (P5) and 17α-hydroxyprogesterone (17-OHP) were detected and quantified. The P5 levels were low in immature worms but increased significantly by ∼ 8.3-fold in the previtellogenic stage and peaked during oocyte maturation. 17-OHP levels were low in immature worms but gradually increase as the oogenesis progress to the primary growth and early vitellogenic phase, with a significant increase (p < 0.001) during the late vitellogenic phase. Although an increase in the concentration of P5 and 17-OHP during vitellogenesis and maturation of oocytes points to a possible role in reproduction, the absence of other vertebrate-type steroids in the investigated polychaete signifies a plausible uptake of P5 and 17-OHP from the environment.
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Affiliation(s)
- Lyndsay Priscilla
- Department of Zoology, Queen Mary's College (Autonomous), Affiliated to the University of Madras, Chennai 600004, Tamil Nadu, India; Endocrinology Unit, Department of Zoology, Madras Christian College, Affiliated to the University of Madras, Chennai, India
| | - E Malathi
- Department of Zoology, Queen Mary's College (Autonomous), Affiliated to the University of Madras, Chennai 600004, Tamil Nadu, India
| | - R Moses Inbaraj
- Endocrinology Unit, Department of Zoology, Madras Christian College, Affiliated to the University of Madras, Chennai, India.
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Ruden DM. 10 Years of Toxicogenomics section in Frontiers in Genetics: Past discoveries and Future Perspectives. Front Genet 2022; 13:979761. [PMID: 36171875 PMCID: PMC9510767 DOI: 10.3389/fgene.2022.979761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
The Frontiers Media family has over 200 journals, which are each headed by usually one Field Chief Editor, and several thousand specialty sections, which are each headed by one or more Specialty Chief Editors. The year 2021 was the 10th anniversary of the founding of the Frontiers in Genetics journal and the Frontiers in Toxicogenomics specialty section of this journal. In 2021, we also announce one of the newest of the Frontiers journals-Frontiers in Toxicology which is part of the Frontiers Media family of journals but independent of Frontiers in Genetics. Dr. Ruden is the founding, and currently sole, Specialty Chief Editor of Frontiers in Toxicogenomics and one of 9 Specialty Chief Editors of Frontiers in Toxicology. As of 2021, Frontiers in Toxicogenomics has published over 138 articles and has over 370 Editors including 90 Associate Editors and 280 Review Editors. The Frontiers in Genetics impact factor was initially approximately 2.5 when it was first listed in PubMed in 2015 and has risen steadily to its current value of 4.8, which is typical for the majority of the over 200 Frontiers journals that have established impact factors. In this overview of the first decade of Frontiers in Toxicogenomics, we discuss the top 5 articles with the highest Scopus citations, which were all written in the first few years of the journal. The article with the highest number of citations, with 353 Scopus over 600 Google Scholar citations, and the highest average number of citations (67) that steadily increased from 10 citations in 2013 to 119 citations in 2021, was written in 2012 by Dr. Ruden's laboratory and titled, "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift." The five most influential authors who published in the journal in the past 10 years based on Scopus citations of a particular paper are Dr. Ruden's laboratory, with 353 Scopus citations for the SnpSift paper mentioned above; Drs. Brock Christensen and Carmen J. Marsit, with 86 Scopus citations for their review, "Epigenomics in environmental health"; Dr. Michael Aschner and colleagues, with 61 Scopus citations for their paper "Genetic factors and manganese-induced neurotoxicity"; and Dr. Sandra C. dos Santos and colleagues, with 59 Scopus citations for their paper, "Yeast toxicogenomics: genome-wide responses to chemical stresses with impact in environmental health, pharmacology, and biotechnology." While the top 5 papers were published in the early years of the journal, we will also discuss a more recent article published in 2018 on a comparison of RNA-seq and microarray methods by Dr. Michael Liguori's laboratory, "Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies," that far exceeds the number of downloads and views of all the other articles published in the first 10 years of the journal and will likely be a top cited paper in the second decade highlights of this journal. Finally, we discuss where the Frontiers in Toxicogenomics specialty journal and the Frontiers in Toxicology journal will go to advance the field of toxicogenomics, and more generally, toxicology, in the future.
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Affiliation(s)
- Douglas M. Ruden
- Institute of Environmental Health Sciences, C. S. Mott Center for Human Health and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
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Gomes AS, Passos LS, Rocha Aride PH, Chisté B, Gomes LC, Boldrini-França J. Gene expression changes in Epinephelus marginatus (Teleostei, Serranidae) liver reveals candidate molecular biomarker of iron ore contamination. CHEMOSPHERE 2022; 303:134899. [PMID: 35561782 DOI: 10.1016/j.chemosphere.2022.134899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Wastes from iron ore mining activities are potentially damaging to adjacent aquatic ecosystems. We aimed to determine biomarkers of environmental exposure to this xenobiotic in the dusky grouper Epinephelus marginatus by differential gene expression analysis. For this, fish were exposed to iron ore (15.2 mg/L) and gene expression in liver was assessed by RNA-Seq and compared to the control group. A total of 124 differentially expressed genes were identified, from which 52 were upregulated and 72 were downregulated in response to iron ore. From these, ferritin (medium subunit), cytochrome b reductase and epoxide hydrolase genes were selected for validation by RT-qPCR that confirmed the upregulation of epoxide hydrolase in fish exposed to iron ore.
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Affiliation(s)
- Aline Silva Gomes
- Universidade Vila Velha, Rua Comissário José Dantas Melo, 21, 29102-770, Vila Velha ES, Brazil
| | - Larissa Souza Passos
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Professor Lineu Prestes, 580, 05508-000, São Paulo SP, Brazil
| | | | - Bárbara Chisté
- Universidade Vila Velha, Rua Comissário José Dantas Melo, 21, 29102-770, Vila Velha ES, Brazil
| | - Levy Carvalho Gomes
- Universidade Vila Velha, Rua Comissário José Dantas Melo, 21, 29102-770, Vila Velha ES, Brazil
| | - Johara Boldrini-França
- Universidade Vila Velha, Rua Comissário José Dantas Melo, 21, 29102-770, Vila Velha ES, Brazil; School of Biochemistry, Biomedical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom.
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Armstrong EK, Mondon J, Miller AD, Revill AT, Stephenson SA, Tan MH, Greenfield P, Tromp JJ, Corbett P, Hook SE. Transcriptomic and Histological Analysis of the Greentail Prawn (Metapenaeus bennettae) Following Light Crude Oil Exposure. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:2162-2180. [PMID: 35815472 PMCID: PMC9545365 DOI: 10.1002/etc.5413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/02/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Oil spills pose a significant threat to marine biodiversity. Crude oil can partition into sediments where it may be persistent, placing benthic species such as decapods at particular risk of exposure. Transcriptomic and histological tools are often used to investigate the effects of hydrocarbon exposure on marine organisms following oil spill events, allowing for the identification of metabolic pathways impacted by oil exposure. However, there is limited information available for decapod crustaceans, many of which carry significant economic value. In the present study, we assess the sublethal impacts of crude oil exposure in the commercially important Australian greentail prawn (Metapenaeus bennettae) using transcriptomic and histological analyses. Prawns exposed to light, unweathered crude oil "spiked" sediments for 90 h were transferred to clean sediments for a further 72 h to assess recovery. Chemical analyses indicated that polycyclic aromatic hydrocarbons increased by approximately 65% and 91% in prawn muscle following 24 and 90 h of exposure, respectively, and significantly decreased during 24- and 72-h recovery periods. Transcriptomic responses followed an exposure and recovery pattern with innate immunity and nutrient metabolism transcripts significantly lowered in abundance after 24 h of exposure and were higher in abundance after 72 h of recovery. In addition, transcription/translation, cellular responses, and DNA repair pathways were significantly impacted after 24 h of exposure and recovered after 72 h of recovery. However, histological alterations such as tubule atrophy indicated an increase in severity after 24 and 72 h of recovery. The present study provides new insights into the sublethal impacts of crude oil exposure in greentail prawns and identifies molecular pathways altered by exposure. We expect these findings to inform future management associated with oil extraction activity and spills. Environ Toxicol Chem 2022;41:2162-2180. © 2022 John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Emily K. Armstrong
- School of Life and Environmental Sciences, Centre for Integrative EcologyDeakin UniversityWaurn PondsVICAustralia
- CSIRO Oceans and AtmosphereHobartTASAustralia
| | - Julie Mondon
- School of Life and Environmental Sciences, Centre for Integrative EcologyDeakin UniversityWaurn PondsVICAustralia
| | - Adam D. Miller
- School of Life and Environmental Sciences, Centre for Integrative EcologyDeakin UniversityWaurn PondsVICAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVICAustralia
| | | | | | - Mun Hua Tan
- School of Life and Environmental Sciences, Centre for Integrative EcologyDeakin UniversityWaurn PondsVICAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVICAustralia
| | | | - Jared J. Tromp
- School of Life and Environmental Sciences, Centre for Integrative EcologyDeakin UniversityWaurn PondsVICAustralia
| | - Patricia Corbett
- School of Life and Environmental Sciences, Centre for Integrative EcologyDeakin UniversityWaurn PondsVICAustralia
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Sumithra TG, Sharma SRK, Gayathri S, Ebeneezar S, Reshma KJ, Anikuttan KK, Narasimapallavan GI, Rameshkumar P, Sakthivel M, Prabu DL, Tamilmani G, Vijayagopal P, Gopalakrishnan A. Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research. Appl Microbiol Biotechnol 2022; 106:4719-4735. [PMID: 35739345 DOI: 10.1007/s00253-022-12026-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022]
Abstract
Applications of microbiome research through metagenomics promise to generate microbiome manipulation strategies for improved larval survival in aquaculture. However, existing lacunae on the effects of sample preservation methods in metagenome profiles hinder the successful application of this technique. In this context, four preservation methods were scrutinized to identify reliable methods for fish larval microbiome research. The results showed that a total of ten metagenomics metrics, including DNA yield, taxonomic and functional microbiome profiles, and diversity measures, were significantly (P < 0.05) influenced by the preservation method. Activity ranking based on the performance and reproducibility showed that three methods, namely immediate direct freezing, room temperature preservation in absolute ethanol, and preservation at - 20 °C in lysis, storage, and transportation buffer, could be recommended for larval microbiome research. Furthermore, as there was an apparent deviation of the microbiome profiles of ethanol preserved samples at room temperature, the other methods are preferred. Detailed analysis showed that this deviation was due to the bias towards Vibrionales and Rhodobacterales. The microbial taxa responsible for the dissimilarity across different methods were identified. Altogether, the paper sheds light on the preservation protocols of fish larval microbiome research for the first time. The results can help in cross-comparison of future and past larval microbiome studies. Furthermore, this is the first report on the activity ranking of preservation methods based on metagenomics metrics. Apart from methodological perspectives, the paper provides for the first time certain insights into larval microbial profiles of Rachycentron canadum, a potential marine aquaculture species. KEY POINTS: • First report on effects of preservation methods on fish larval microbiome profiles. • First report on activity ranking of preservation methods based on metagenomics metrics. • Storage methods influenced DNA yield, taxonomic and functional microbiome profiles.
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Affiliation(s)
- T G Sumithra
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - S R Krupesha Sharma
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India.
| | - S Gayathri
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - Sanal Ebeneezar
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - K J Reshma
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - K K Anikuttan
- Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India
| | | | - P Rameshkumar
- Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India
| | - M Sakthivel
- Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India
| | - D Linga Prabu
- Tuticorin Regional Station of ICAR-CMFRI, South Beach Road, 628 001, Tuticorin, India
| | - G Tamilmani
- Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India
| | - P Vijayagopal
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
| | - A Gopalakrishnan
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India
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8
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Li PH, Wang LQ, He JY, Zhu XL, Huang W, Wang SW, Qin QW, Sun HY. MicroRNA-124 Promotes Singapore Grouper Iridovirus Replication and Negatively Regulates Innate Immune Response. Front Immunol 2021; 12:767813. [PMID: 34858424 PMCID: PMC8631330 DOI: 10.3389/fimmu.2021.767813] [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: 08/31/2021] [Accepted: 10/19/2021] [Indexed: 02/02/2023] Open
Abstract
Viral infections seriously affect the health of organisms including humans. Now, more and more researchers believe that microRNAs (miRNAs), one of the members of the non-coding RNA family, play significant roles in cell biological function, disease occurrence, and immunotherapy. However, the roles of miRNAs in virus infection (entry and replication) and cellular immune response remain poorly understood, especially in low vertebrate fish. In this study, based on the established virus-cell infection model, Singapore grouper iridovirus (SGIV)-infected cells were used to explore the roles of miR-124 of Epinephelus coioides, an economically mariculture fish in southern China and Southeast Asia, in viral infection and host immune responses. The expression level of E. coioides miR-124 was significantly upregulated after SGIV infection; miR-124 cannot significantly affect the entry of SGIV, but the upregulated miR-124 could significantly promote the SGIV-induced cytopathic effects (CPEs), the viral titer, and the expressions of viral genes. The target genes of miR-124 were JNK3/p38α mitogen-activated protein kinase (MAPK). Overexpression of miR-124 could dramatically inhibit the activation of NF-κB/activating protein-1 (AP-1), the transcription of proinflammatory factors, caspase-9/3, and the cell apoptosis. And opposite results happen when the expression of miR-124 was inhibited. The results suggest that E. coioides miR-124 could promote viral replication and negatively regulate host immune response by targeting JNK3/p38α MAPK, which furthers our understanding of virus and host immune interactions.
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Affiliation(s)
- Pin-Hong Li
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Li-Qun Wang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Jia-Yang He
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xiang-Long Zhu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Wei Huang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shao-Wen Wang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Qi-Wei Qin
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hong-Yan Sun
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
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9
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Yang C, Lim W, Song G. Immunotoxicological effects of insecticides in exposed fishes. Comp Biochem Physiol C Toxicol Pharmacol 2021; 247:109064. [PMID: 33905824 DOI: 10.1016/j.cbpc.2021.109064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/11/2021] [Accepted: 04/18/2021] [Indexed: 02/07/2023]
Abstract
Biologically active compounds used in agriculture that develop near aquatic environments easily spill into rivers or lakes. As a result, insecticides, herbicides and fungicides are observed worldwide in aquatic environments and accumulated in aquatic organism. Many insecticides, including organochlorine and organophosphate, have long been banned long ago because of their high persistence and non-target toxicity. However, previous studies have shown that persistent pesticides remain in aquatic organisms. The immune system is the first defense mechanism against exposure to persistent organic pollutants or pesticides that have been released into the aquatic environment. Many insecticides have been reported to cause immunotoxicity, which is represented by alteration of phagocytic and lysozyme activity. Recent studies show that immunotoxicity by insecticides exerts a more complex mechanism in fish. Insecticides induce immunotoxic effects, such as the release of inflammatory cytokines from head kidney macrophages and inhibition of immune cell proliferation in fish, which can lead to death in severe cases. Even currently used pesticides, such as pyrethroid, with low bioaccumulation have been shown to induce immunotoxicological effects in fish when exposed continuously. Therefore, this review describes the types and bioaccumulation of insecticides that cause immunotoxicity and detailed immunotoxicological mechanisms in fish tissues.
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Affiliation(s)
- Changwon Yang
- Institute of Animal Molecular Biotechnology and Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Whasun Lim
- Department of Food and Nutrition, Kookmin University, Seoul 02707, Republic of Korea.
| | - Gwonhwa Song
- Institute of Animal Molecular Biotechnology and Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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Zamora-Briseño JA, Améndola-Pimenta M, Ortega-Rosas DA, Pereira-Santana A, Hernández-Velázquez IM, González-Penagos CE, Pérez-Vega JA, Del Río-García M, Árcega-Cabrera F, Rodríguez-Canul R. Gill and liver transcriptomic responses of Achirus lineatus (Neopterygii: Achiridae) exposed to water-accommodated fraction (WAF) of light crude oil reveal an onset of hypoxia-like condition. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:34309-34327. [PMID: 33646544 DOI: 10.1007/s11356-021-12909-7] [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: 08/31/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Crude oil is one of the most widespread pollutants released into the marine environment, and native species have provided useful information about the effect of crude oil pollution in marine ecosystems. We consider that the lined sole Achirus lineatus can be a useful monitor of the effect of crude oil in the Gulf of Mexico (GoM) because this flounder species has a wide distribution along the GoM, and its response to oil components is relevant. The objective of this study was to compare the transcriptomic changes in liver and gill of adults lined sole fish (Achirus lineatus) exposed to a sublethal acute concentration of water-accommodated fraction (WAF) of light crude oil for 48 h. RNA-Seq was performed to assess the transcriptional changes in both organs. A total of 1073 differentially expressed genes (DEGs) were detected in gills; 662 (61.69%) were upregulated, and 411 (38.30%) were downregulated whereas in liver, 515 DEGs; 306 (59.42%) were upregulated, and 209 (40.58%) were downregulated. Xenobiotic metabolism and redox metabolism, along with DNA repair mechanisms, were activated. The induction of hypoxia-regulated genes and the generalized regulation of multiple signaling pathways support the hypothesis that WAF exposition causes a hypoxia-like condition.
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Affiliation(s)
- Jesús Alejandro Zamora-Briseño
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, CP 97310, Mérida, Yucatán, Mexico
| | - Monica Améndola-Pimenta
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, CP 97310, Mérida, Yucatán, Mexico
| | | | - Alejandro Pereira-Santana
- División de Biotecnología Industrial, CONACYT-Centro de Investigación y Asistencia en Tecnología y Diseño del estado de Jalisco, Camino Arenero 1227, El Bajío, C.P. 45019, Zapopan, Jalisco, Mexico
| | - Ioreni Margarita Hernández-Velázquez
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, CP 97310, Mérida, Yucatán, Mexico
| | - Carlos Eduardo González-Penagos
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, CP 97310, Mérida, Yucatán, Mexico
| | - Juan Antonio Pérez-Vega
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, CP 97310, Mérida, Yucatán, Mexico
| | - Marcela Del Río-García
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, CP 97310, Mérida, Yucatán, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de Abrigo S/N, 97356, Sisal, Yucatán, Mexico
| | - Rossanna Rodríguez-Canul
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, CP 97310, Mérida, Yucatán, Mexico.
- Laboratorio de Inmunología y Biología Molecular, CINVESTAV-IPN Unidad Mérida, Antigua carretera a Progreso Km 6., CP 97310, Mérida, Yucatán, Mexico.
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Loeffler CR, Tartaglione L, Friedemann M, Spielmeyer A, Kappenstein O, Bodi D. Ciguatera Mini Review: 21st Century Environmental Challenges and the Interdisciplinary Research Efforts Rising to Meet Them. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:3027. [PMID: 33804281 PMCID: PMC7999458 DOI: 10.3390/ijerph18063027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/19/2022]
Abstract
Globally, the livelihoods of over a billion people are affected by changes to marine ecosystems, both structurally and systematically. Resources and ecosystem services, provided by the marine environment, contribute nutrition, income, and health benefits for communities. One threat to these securities is ciguatera poisoning; worldwide, the most commonly reported non-bacterial seafood-related illness. Ciguatera is caused by the consumption of (primarily) finfish contaminated with ciguatoxins, potent neurotoxins produced by benthic single-cell microalgae. When consumed, ciguatoxins are biotransformed and can bioaccumulate throughout the food-web via complex pathways. Ciguatera-derived food insecurity is particularly extreme for small island-nations, where fear of intoxication can lead to fishing restrictions by region, species, or size. Exacerbating these complexities are anthropogenic or natural changes occurring in global marine habitats, e.g., climate change, greenhouse-gas induced physical oceanic changes, overfishing, invasive species, and even the international seafood trade. Here we provide an overview of the challenges and opportunities of the 21st century regarding the many facets of ciguatera, including the complex nature of this illness, the biological/environmental factors affecting the causative organisms, their toxins, vectors, detection methods, human-health oriented responses, and ultimately an outlook towards the future. Ciguatera research efforts face many social and environmental challenges this century. However, several future-oriented goals are within reach, including digital solutions for seafood supply chains, identifying novel compounds and methods with the potential for advanced diagnostics, treatments, and prediction capabilities. The advances described herein provide confidence that the tools are now available to answer many of the remaining questions surrounding ciguatera and therefore protection measures can become more accurate and routine.
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Affiliation(s)
- Christopher R. Loeffler
- National Reference Laboratory of Marine Biotoxins, Department Safety in the Food Chain, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (A.S.); (O.K.); (D.B.)
- Department of Pharmacy, School of Medicine and Surgery, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Luciana Tartaglione
- Department of Pharmacy, School of Medicine and Surgery, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy;
- CoNISMa—National Inter-University Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Miriam Friedemann
- Department Exposure, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany;
| | - Astrid Spielmeyer
- National Reference Laboratory of Marine Biotoxins, Department Safety in the Food Chain, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (A.S.); (O.K.); (D.B.)
| | - Oliver Kappenstein
- National Reference Laboratory of Marine Biotoxins, Department Safety in the Food Chain, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (A.S.); (O.K.); (D.B.)
| | - Dorina Bodi
- National Reference Laboratory of Marine Biotoxins, Department Safety in the Food Chain, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; (A.S.); (O.K.); (D.B.)
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12
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Mehinto AC, Thornton Hampton LM, Vidal-Dorsch DE, Garcia-Reyero N, Arick MA, Maruya KA, Lao W, Vulpe CD, Brown-Augustine M, Loguinov A, Bay SM. Transcriptomic response patterns of hornyhead turbot (Pleuronichthys verticalis) dosed with polychlorinated biphenyls and polybrominated diphenyl ethers. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100822. [PMID: 33684654 DOI: 10.1016/j.cbd.2021.100822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/04/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
To evaluate the impact of environmental contaminants on aquatic health, extensive surveys of fish populations have been conducted using bioaccumulation as an indicator of impairment. While these studies have reported mixtures of chemicals in fish tissues, the relationship between specific contaminants and observed adverse impacts remains poorly understood. The present study aimed to characterize the toxicological responses induced by persistent organic pollutants in wild-caught hornyhead turbot (P. verticalis). To do so, hornyhead turbot were interperitoneally injected with a single dose of PCB or PBDE congeners prepared using environmentally realistic mixture proportions. After 96-hour exposure, the livers were excised and analyzed using transcriptomic approaches and analytical chemistry. Concentrations of PCBs and PBDEs measured in the livers indicated clear differences across treatments, and congener profiles closely mirrored our expectations. Distinct gene profiles were characterized for PCB and PBDE exposed fish, with significant differences observed in the expression of genes associated with immune responses, endocrine-related functions, and lipid metabolism. Our findings highlight the key role that transcriptomics can play in monitoring programs to assess chemical-induced toxicity in heterogeneous group of fish (mixed gender and life stage) as is typically found during field surveys. Altogether, the present study provides further evidence of the potential of transcriptomic tools to improve aquatic health assessment and identify causative agents.
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Affiliation(s)
- Alvine C Mehinto
- Department of Toxicology, Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA; Department of Chemistry, Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA.
| | - Leah M Thornton Hampton
- Department of Toxicology, Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Doris E Vidal-Dorsch
- Department of Toxicology, Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS 39180, USA
| | - Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, MS 39762, USA
| | - Keith A Maruya
- Department of Chemistry, Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Wenjian Lao
- Department of Chemistry, Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Christopher D Vulpe
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Marianna Brown-Augustine
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Alex Loguinov
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Steven M Bay
- Department of Toxicology, Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
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13
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Endocrine disruptors in teleosts: Evaluating environmental risks and biomarkers. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2020.07.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Transcriptional responses in newly-hatched Japanese medaka (Oryzias latipes) associated with developmental malformations following diluted bitumen exposure. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100685. [DOI: 10.1016/j.cbd.2020.100685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 11/21/2022]
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15
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Zhou Z, Han K, Wu Y, Bai H, Ke Q, Pu F, Wang Y, Xu P. Genome-Wide Association Study of Growth and Body-Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea) Using ddRAD Sequencing. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:655-670. [PMID: 31332575 DOI: 10.1007/s10126-019-09910-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is an economically important marine fish species of China. Due to overfishing and marine pollution, the wild stocks of this croaker have collapsed in the past decades. Meanwhile, the cultured croaker is facing the difficulties of reduced genetic diversity and low growth rate. To explore the molecular markers related to the growth traits of croaker and providing the related SNPs for the marker-assisted selection, we used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic bases of growth traits in a cultured population and identify the SNPs that associated with important growth traits by GWAS. A total of 220 individuals were genotyped by ddRAD sequencing. After quality control, 27,227 SNPs were identified in 220 samples and used for GWAS analysis. We identified 13 genome-wide significant associated SNPs of growth traits on 8 chromosomes, and the beta P of these SNPs ranged from 0.01 to 0.86. Through the definition of candidate regions and gene annotation, candidate genes related to growth were identified, including important regulators such as fgf18, fgf1, nr3c1, cyp8b1, fabp2, cyp2r1, ppara, and ccm2l. We also identified SNPs and candidate genes that significantly associated with body shape, including bmp7, col1a1, col11a2, and col18a1, which are also economically important traits for large yellow croaker aquaculture. The results provided insights into the genetic basis of growth and body shape in large yellow croaker population and would provide reliable genetic markers for molecular marker-assisted selection in the future. Meanwhile, the result established a basis for our subsequent fine mapping and related gene study.
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Affiliation(s)
- Zhixiong Zhou
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Kunhuang Han
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Yidi Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Huaqiang Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Qiaozhen Ke
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Fei Pu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yilei Wang
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China.
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Jimei University, Xiamen, 361021, China.
| | - Peng Xu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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Jones J, Wellband K, Zielinski B, Heath DD. Transcriptional Basis of Copper-Induced Olfactory Impairment in the Sea Lamprey, a Primitive Invasive Fish. G3 (BETHESDA, MD.) 2019; 9:933-941. [PMID: 30670609 PMCID: PMC6404594 DOI: 10.1534/g3.118.200920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/19/2019] [Indexed: 11/18/2022]
Abstract
Olfaction mediates behaviors necessary for survival and reproduction in fishes. Anthropogenic inputs of contaminants into aquatic environments, specifically copper, are known to disrupt a broad range of olfactory-mediated behaviors and can cause long-lasting damage even at low concentrations that have profound impacts on the biology of aquatic organisms. The sea lamprey (Petromyzon marinus) is a primitive fish species invasive to the North American Great Lakes that relies on olfaction to navigate during natal homing and in mate choice during reproduction. To investigate effects of copper on sea lamprey olfaction and the potential for maintenance of olfactory function during copper exposure, we exposed juvenile sea lamprey to environmentally ecologically relevant copper concentrations (0, 5, 10 and 30 µg/L) for 24 hr and characterized gene transcription response in olfactory tissue (i.e., peripheral olfactory organ and olfactory bulb) and forebrain using whole transcriptome sequencing. Copper exposure induced a pattern of positive dose-dependent transcriptional response. Expression changes primarily reflected up-regulation of genes involved in apoptosis and wound healing. Unlike higher vertebrates, genes specifically related to the olfactory senses of the sea lamprey, e.g., olfactory receptors, exhibited little transcriptional response to copper exposure, suggesting the mechanism of copper-induced olfactory impairment is through necrosis of the olfactory bulb and not copper-selective inhibition of olfactory receptors. Fully two-thirds of the differentially expressed genes at higher doses of copper have no known function and thus represent important candidates for further study of the responses to copper-induced olfactory injury. Our results shed light on the evolution of vertebrate olfactory repair mechanisms and have important implications for the conservation and management of both invasive and native populations of lamprey.
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Affiliation(s)
- Jenna Jones
- Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Kyle Wellband
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Barbara Zielinski
- Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada N9B 3P4
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Daniel D Heath
- Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada N9B 3P4
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada N9B 3P4
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18
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Wang M, Jiang S, Wu W, Yu F, Chang W, Li P, Wang K. Non-coding RNAs Function as Immune Regulators in Teleost Fish. Front Immunol 2018; 9:2801. [PMID: 30546368 PMCID: PMC6279911 DOI: 10.3389/fimmu.2018.02801] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/13/2018] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs function as key regulators of gene expression and chromatin modification. Recently, the functional role of ncRNAs in teleost fish has been extensively studied. Teleost fish are a highly diverse group among the vertebrate lineage. Fish are also important in terms of aquatic ecosystem, food production and human life, being the source of animal proteins worldwide and models of biomedical research. However, teleost fish always suffer from the invasion of infectious pathogens including viruses and bacteria, which has resulted in a tremendous economic loss to the fishing industry worldwide. Emerging evidence suggests that ncRNAs, especially miRNAs and lncRNAs, may serve as important regulators in cytokine and chemokine signaling, antigen presentation, complement and coagulation cascades, and T cell response in teleost fish. In this review, we summarize current knowledge and understanding of the roles of both miRNAs and lncRNAs in immune regulation in teleost fish. Molecular mechanism insights into the function of ncRNAs in fish immune response may contribute to the development of potential biomarkers and therapeutic targets for the prevention and treatment of fish diseases.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Shuai Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Fei Yu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Wenguang Chang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Kun Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
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Hook SE, Mondon J, Revill AT, Greenfield PA, Stephenson SA, Strzelecki J, Corbett P, Armstrong E, Song J, Doan H, Barrett S. Monitoring sublethal changes in fish physiology following exposure to a light, unweathered crude oil. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 204:27-45. [PMID: 30173120 DOI: 10.1016/j.aquatox.2018.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 06/08/2023]
Abstract
Biomarkers are frequently used to determine the exposure of fish to petroleum hydrocarbons following an oil spill. These biomarkers must be chosen carefully if they are to be used to determine sublethal toxic impacts as well as oil exposure. Many commonly used biomarkers relate to the metabolism of high molecular weight, typically pyrogenic, polycyclic aromatic hydrocarbons (PAHs), which are not abundant in unweathered crude oil. The goal of this study was to compare the efficacy of different biomarkers, including histological examination and transcriptomic profiling, in showing exposure to oil and the potential for sublethal toxic impacts. To achieve these goals, subadults/adults of the spotted dragonet (Repomucenus calcaratus) were exposed to a representative light, unweathered Australian oil for 96 h, so that the physiological changes that occur with exposure could be documented. Fish were then transferred to clean sediment for 90 h to quantify recovery. Biomarker changes, including PAH metabolites, 7-ethoxyresorufin O-deethylase (EROD), and histopathology, are presented in this work. In addition, a de novo transcriptome for the spotted dragonet was assembled, and differential transcript abundance was determined for the gill and liver of petroleum-exposed fish relative to a control. Increased levels of some biliary phenanthrene metabolites were seen throughout the exposure period. EROD levels showed modest, but not significant, increases. Transcriptomic differences were noted in the abundances of transcripts with a role in inflammation, primary metabolism and cardiac function. The patterns of transcript abundance in the gill and the liver changed in a manner that reflected exposure and recovery. The histology showed elevated prevalence of lesions, most notably vacuolization in liver and heart tissue, multi-organ necrosis, and lamellar epithelial lifting and telangiectasia in the gill. These findings suggest that short-term exposures to low molecular weight PAHs could elicit changes in the health of fish that are well predicted by the transcriptome. Furthermore, when light oil is released into the environment, exposure and subsequent risk would be better estimated using phenanthrene metabolite levels rather than EROD. This study also adds to the weight of evidence that exposure to low molecular weight PAHs may cause cardiac problems in fish. Further study is needed to determine the impact of these changes on reproductive capacity, long-term survival, and other population specific parameters.
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Affiliation(s)
- Sharon E Hook
- CSIRO Oceans and Atmosphere, Lucas Heights, NSW, 2234, Australia.
| | - Julie Mondon
- School of Life and Environmental Sciences, Deakin University, Warrnambool, VIC, 3280, Australia
| | | | | | | | - Joanna Strzelecki
- CSIRO Oceans and Atmosphere, Indian Ocean Marine Research Centre, Crawley, WA, 6009, Australia
| | - Patricia Corbett
- School of Life and Environmental Sciences, Deakin University, Warrnambool, VIC, 3280, Australia
| | - Emily Armstrong
- CSIRO Oceans and Atmosphere, Lucas Heights, NSW, 2234, Australia; School of Life and Environmental Sciences, Deakin University, Warrnambool, VIC, 3280, Australia
| | - Jing Song
- School of Life and Environmental Sciences, Deakin University, Warrnambool, VIC, 3280, Australia; Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, Japan
| | - Hai Doan
- CSIRO Land and Water, Glen Osmond, SA, 5064, Australia
| | - Skye Barrett
- South Australian Research and Development Institute Aquatic Sciences, West Beach, SA, 5024, Australia
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20
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Hook SE, Mondon J, Revill AT, Greenfield PA, Smith RA, Turner RDR, Corbett PA, Warne MSJ. Transcriptomic, lipid, and histological profiles suggest changes in health in fish from a pesticide hot spot. MARINE ENVIRONMENTAL RESEARCH 2018; 140:299-321. [PMID: 29983192 DOI: 10.1016/j.marenvres.2018.06.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/14/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
Barramundi (Lates calcarifer) were collected at the beginning (1st sampling) and end (2nd sampling) of the wet season from Sandy Creek, an agriculturally impacted catchment in the Mackay Whitsundays region of the Great Barrier Reef catchment area, and from Repulse Creek, located approximately 100 km north in Conway National Park, to assess the impacts of pesticide exposure. Gill and liver histology, lipid class composition in muscle, and the hepatic transcriptome were examined. The first sample of Repulse Creek fish showed little tissue damage and low transcript levels of xenobiotic metabolism enzymes. Sandy Creek fish showed altered transcriptomic patterns, including those that regulate lipid metabolism, xenobiotic metabolism, and immune response; gross histological alterations including lipidosis; and differences in some lipid classes. The second sampling of Repulse Creek fish showed similar alterations in hepatic transcriptome and tissue structure as fish from Sandy Creek. These changes may indicate a decrease in health of pesticide exposed fish.
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Affiliation(s)
- Sharon E Hook
- CSIRO Oceans and Atmosphere, Lucas Heights, New South Wales, Australia.
| | - Julie Mondon
- Deakin University, Warrnambool, Victoria, Australia
| | | | | | - Rachael A Smith
- Queensland Department of Science and Environment, Brisbane, Queensland 4001, Australia
| | - Ryan D R Turner
- Queensland Department of Science and Environment, Brisbane, Queensland 4001, Australia
| | | | - Michael St J Warne
- Centre for Agroecology, Water and Resilience, Coventry University, United Kingdom; Queensland Department of Science and Environment, Brisbane, Queensland 4001, Australia; Australian Rivers Institute, Griffith University, Queensland 4111, Australia; Queensland Alliance of Environmental Health Sciences, University of Queensland, Queensland, 4108, Australia
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21
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Rodrigues PA, Ferrari RG, Conte-Junior CA. Application of molecular tools to elucidate the microbiota of seafood. J Appl Microbiol 2018; 124:1347-1365. [PMID: 29345036 DOI: 10.1111/jam.13701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 12/19/2022]
Abstract
The aim of this review is to present the methodologies currently applied to identify microbiota and pathogens transmitted to humans through seafood consumption, focusing on molecular techniques and pointing out their importance, advantages, disadvantages and applicability. Knowledge of available techniques allows researchers to identify which technique best fits their expectations. With such discernment, it will be possible to infer which disadvantages will be present and, therefore, not interfering with the final result. Two methodologies can be employed for this purpose, dependent and independent cultures. However, the dependent culture has certain limitations that can be solved through the independent cultivation techniques, such as PCR, PFGE and NGS, especially through the sequencing of the 16S rRNA region, providing a complete view of microbial diversity. These have revolutionized microbiological knowledge, mainly because they allow for the identification of uncultivable micro-organisms, which represent a substantial portion of total micro-organisms, making it possible to elucidate not yet described taxa which may display pathogenic potential, besides quantifying microbial communities, microbiota genetics, translated proteins and produced metabolites. In addition, transcriptomic and metabolomic techniques also allow for the evaluation of possible impacts that microbial communities may create in their environment, as well as the determination of potential pathogenicity to humans.
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Affiliation(s)
- P A Rodrigues
- Department of Food Technology, Faculty of Veterinary, Molecular & Analytical Laboratory Center, Universidade Federal Fluminense, Niterói, Brazil
| | - R G Ferrari
- Department of Food Technology, Faculty of Veterinary, Molecular & Analytical Laboratory Center, Universidade Federal Fluminense, Niterói, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - C A Conte-Junior
- Department of Food Technology, Faculty of Veterinary, Molecular & Analytical Laboratory Center, Universidade Federal Fluminense, Niterói, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Health Quality Control, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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22
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Kim HS, Lee BY, Han J, Jeong CB, Hwang DS, Lee MC, Kang HM, Kim DH, Lee D, Kim J, Choi IY, Lee JS. The genome of the marine medaka Oryzias melastigma. Mol Ecol Resour 2018; 18:656-665. [PMID: 29451363 DOI: 10.1111/1755-0998.12769] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/29/2018] [Accepted: 02/06/2018] [Indexed: 11/30/2022]
Abstract
Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field-based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole-genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50 = 23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish and zebrafish) were identified. Genome analyses revealed that the O. melastigma genome is highly heterozygous and contains a large number of repeat sequences. This assembly represents a useful genomic resource for fish scientists.
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Affiliation(s)
- Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Bo-Young Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
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23
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García CF, Pedrini N, Sánchez-Paz A, Reyna-Blanco CS, Lavarias S, Muhlia-Almazán A, Fernández-Giménez A, Laino A, de-la-Re-Vega E, Lukaszewicz G, López-Zavala AA, Brieba LG, Criscitello MF, Carrasco-Miranda JS, García-Orozco KD, Ochoa-Leyva A, Rudiño-Piñera E, Sanchez-Flores A, Sotelo-Mundo RR. De novo assembly and transcriptome characterization of the freshwater prawn Palaemonetes argentinus: Implications for a detoxification response. Mar Genomics 2018; 37:74-81. [DOI: 10.1016/j.margen.2017.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/25/2017] [Accepted: 08/26/2017] [Indexed: 12/14/2022]
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24
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Sudhagar A, Kumar G, El-Matbouli M. Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review. Int J Mol Sci 2018; 19:ijms19010245. [PMID: 29342931 PMCID: PMC5796193 DOI: 10.3390/ijms19010245] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/12/2022] Open
Abstract
In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.
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Affiliation(s)
- Arun Sudhagar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna 1210, Austria.
- Central Institute of Fisheries Education, Rohtak Centre, Haryana 124411, India.
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna 1210, Austria.
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna 1210, Austria.
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25
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Han J, Won EJ, Kang HM, Lee MC, Jeong CB, Kim HS, Hwang DS, Lee JS. Marine copepod cytochrome P450 genes and their applications for molecular ecotoxicological studies in response to oil pollution. MARINE POLLUTION BULLETIN 2017; 124:953-961. [PMID: 27686823 DOI: 10.1016/j.marpolbul.2016.09.048] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/20/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Abstract
Recently, accidental spills of heavy oil have caused adverse effects in marine organisms. Oil pollution can induce damages on development and reproduction, linking with detrimental effects on diverse molecular levels of genes and proteins in plankton and fish. However, most information was mainly focused on marine vertebrates and consequently, limited information was available in marine invertebrates. Furthermore, there is still a lack of knowledge bridging in vivo endpoints with the functional regulation of cytochrome P450 (CYP) genes in response to oil spill pollution in marine invertebrates. In this paper, adverse effects of oil spill pollution in marine invertebrates are summarized with the importance of CYP genes as a potential biomarker, applying for environmental monitoring to detect oil spill using marine copepods.
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Affiliation(s)
- Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Eun-Ji Won
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea; Marine Chemistry and Geochemistry Research Center, Korea Institute of Ocean Science and Technology, Ansan 15627, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea; Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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26
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Hook SE, Kroon FJ, Greenfield PA, Warne MSJ, Smith RA, Turner RD. Hepatic transcriptomic profiles from barramundi, Lates calcarifer, as a means of assessing organism health and identifying stressors in rivers in northern Queensland. MARINE ENVIRONMENTAL RESEARCH 2017; 129:166-179. [PMID: 28601346 DOI: 10.1016/j.marenvres.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/12/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Resource managers need to differentiate between sites with and without contaminants and those where contaminants cause impacts. Potentially, transcriptomes could be used to evaluate sites where contaminant-induced effects may occur, to identify causative stressors of effects and potential adverse outcomes. To test this hypothesis, the hepatic transcriptomes in Barramundi, a perciforme teleost fish, (Lates calcarifer) from two reference sites, two agriculturally impacted sites sampled during the dry season, and an impacted site sampled during the wet season were compared. The hepatic transcriptome was profiled using RNA-Seq. Multivariate analysis showed that transcriptomes were clustered based on site and by inference water quality, but not sampling time. The largest differences in transcriptomic profile were between reference sites and a site sampled during high run-off, showing that impacted sites can be identified via RNA-Seq. Transcripts with altered abundance were linked to xenobiotic metabolism, peroxisome proliferation and stress responses, indicating putative stressors with the potential for adverse outcomes in barramundi.
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Affiliation(s)
- Sharon E Hook
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere, Kirrawee, NSW 2232, Australia.
| | - Frederieke J Kroon
- Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia
| | - Paul A Greenfield
- CSIRO Oceans and Atmosphere North Ryde, New South Wales 2113, Australia
| | - Michael St J Warne
- Centre for Agroecology, Water and Resilience, Coventry University, United Kingdom; Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland 4001, Australia; Australian Rivers Institute, Griffith University, Queensland 4111, Australia; National Research Centre for Environmental Toxicology (EnTox), University of Queensland, Queensland 4108, Australia
| | - Rachael A Smith
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland 4001, Australia; Australian Rivers Institute, Griffith University, Queensland 4111, Australia
| | - Ryan D Turner
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland 4001, Australia; Australian Rivers Institute, Griffith University, Queensland 4111, Australia
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27
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Saaristo M, Wong BBM, Mincarelli L, Craig A, Johnstone CP, Allinson M, Lindström K, Craft JA. Characterisation of the transcriptome of male and female wild-type guppy brains with RNA-Seq and consequences of exposure to the pharmaceutical pollutant, 17α-ethinyl estradiol. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 186:28-39. [PMID: 28246045 DOI: 10.1016/j.aquatox.2017.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 02/09/2017] [Accepted: 02/14/2017] [Indexed: 06/06/2023]
Abstract
Waterways are increasingly being contaminated by chemical compounds that can disrupt the endocrinology of organisms. One such compound is 17α-ethinyl estradiol (EE2), a synthetic estrogen used in the contraceptive pill. Despite considerable research interest in the effects of EE2 on reproduction and gene expression, surprisingly, only a few studies have capitalised on technologies, such as next-generation sequencing (NGS), to uncover the molecular pathways related to EE2 exposure. Accordingly, using high-throughput sequencing technologies, the aim of our study was to explore the effects of EE2 on brain transcriptome in wild-type male and female guppy (Poecilia reticulata). We conducted two sets of experiments, where fish were exposed to EE2 (measured concentrations: 8ng/L and 38ng/L) in a flow-through system for 21days. The effects on the brain transcriptome on both males and females were assessed using Illumina sequencing (MiSeq and HiSeq) platform followed by bioinformatics analysis (edgeR, DESeq2). Here, we report that exposure to EE2 caused both up- and downregulation of specific transcript abundances, and affected transcript abundance in a sex-specific manner. Specifically, we found 773 transcripts, of which 60 were male-specific, 61 female-specific and 285 treatment-specific. EE2 affected expression of 165 transcripts in males, with 88 downregulated and 77 upregulated, while in females, 120 transcripts were affected with 62 downregulated and 58 upregulated. Finally, RT-qPCR validation demonstrated that expression of transcripts related to transposable elements, neuroserpin and heat shock protein were significantly affected by EE2-exposure. Our study is the first to report brain transcriptome libraries for guppies exposed to EE2. Not only does our study provide a valuable resource, it offers insights into the mechanisms underlying the feminizing effects on the brains of organisms exposed to environmentally realistic concentrations of EE2.
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Affiliation(s)
- Minna Saaristo
- School of Biological Sciences, Monash University, 3800 Victoria, Australia; Environmental and Marine Biology, Åbo Akademi University, 20500 Turku, Finland.
| | - Bob B M Wong
- School of Biological Sciences, Monash University, 3800 Victoria, Australia
| | - Laura Mincarelli
- Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, UK
| | - Allison Craig
- Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, UK
| | | | - Mayumi Allinson
- Victorian Centre for Aquatic Pollution Identification and Management (CAPIM), School of Chemistry, 3010 Victoria, Australia
| | - Kai Lindström
- Environmental and Marine Biology, Åbo Akademi University, 20500 Turku, Finland
| | - John A Craft
- Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, UK
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28
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Martyniuk CJ, Doperalski NJ, Prucha MS, Zhang JL, Kroll KJ, Conrow R, Barber DS, Denslow ND. High contaminant loads in Lake Apopka's riparian wetland disrupt gene networks involved in reproduction and immune function in largemouth bass. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 19:140-150. [DOI: 10.1016/j.cbd.2016.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 04/05/2016] [Accepted: 06/09/2016] [Indexed: 12/28/2022]
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29
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Makrinos DL, Bowden TJ. Natural environmental impacts on teleost immune function. FISH & SHELLFISH IMMUNOLOGY 2016; 53:50-57. [PMID: 26973022 DOI: 10.1016/j.fsi.2016.03.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/07/2016] [Indexed: 06/05/2023]
Abstract
The environment in which teleosts exist can experience considerable change. Short-term changes can occur in relation to tidal movements or adverse weather events. Long-term changes can be caused by anthropogenic impacts such as climate change, which can result in changes to temperature, acidity, salinity and oxygen capacity of aquatic environments. These changes can have important impacts on the physiology of an animal, including its immune system. This can have consequences on the well-being of the animal and its ability to protect against pathogens. This review will look at recent investigations of these types of environmental change on the immune response in teleosts.
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Affiliation(s)
| | - Timothy J Bowden
- School of Food & Agriculture, University of Maine, Orono, ME, USA
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30
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Kim BM, Kim J, Choi IY, Raisuddin S, Au DWT, Leung KMY, Wu RSS, Rhee JS, Lee JS. Omics of the marine medaka (Oryzias melastigma) and its relevance to marine environmental research. MARINE ENVIRONMENTAL RESEARCH 2016; 113:141-152. [PMID: 26716363 DOI: 10.1016/j.marenvres.2015.12.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/11/2015] [Accepted: 12/12/2015] [Indexed: 06/05/2023]
Abstract
In recent years, the marine medaka (Oryzias melastigma), also known as the Indian medaka or brackish medaka, has been recognized as a model fish species for ecotoxicology and environmental research in the Asian region. O. melastigma has several promising features for research, which include a short generation period (3-4 months), daily spawning, small size (3-4 cm), transparent embryos, sexual dimorphism, and ease of mass culture in the laboratory. There have been extensive transcriptome and genome studies on the marine medaka in the past decade. Such omics data can be useful in understanding the signal transduction pathways of small teleosts in response to environmental stressors. An omics-integrated approach in the study of the marine medaka is important for strengthening its role as a small fish model for marine environmental studies. In this review, we present current omics information about the marine medaka and discuss its potential applications in the study of various molecular pathways that can be targets of marine environmental stressors, such as chemical pollutants. We believe that this review will encourage the use of this small fish as a model species in marine environmental research.
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Affiliation(s)
- Bo-Mi Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jaebum Kim
- Department of Animal Biotechnology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029, South Korea
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sheikh Raisuddin
- Department of Medical Elementology & Toxicology, Hamdard University, 110062, New Delhi, India
| | - Doris W T Au
- State Key Laboratory on Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Kenneth M Y Leung
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Rudolf S S Wu
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, 22012, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
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31
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Bahamonde PA, Feswick A, Isaacs MA, Munkittrick KR, Martyniuk CJ. Defining the role of omics in assessing ecosystem health: Perspectives from the Canadian environmental monitoring program. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2016; 35:20-35. [PMID: 26771350 DOI: 10.1002/etc.3218] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/16/2015] [Accepted: 08/20/2015] [Indexed: 05/22/2023]
Abstract
Scientific reviews and studies continue to describe omics technologies as the next generation of tools for environmental monitoring, while cautioning that there are limitations and obstacles to overcome. However, omics has not yet transitioned into national environmental monitoring programs designed to assess ecosystem health. Using the example of the Canadian Environmental Effects Monitoring (EEM) program, the authors describe the steps that would be required for omics technologies to be included in such an established program. These steps include baseline collection of omics endpoints across different species and sites to generate a range of what is biologically normal within a particular ecosystem. Natural individual variability in the omes is not adequately characterized and is often not measured in the field, but is a key component to an environmental monitoring program, to determine the critical effect size or action threshold for management. Omics endpoints must develop a level of standardization, consistency, and rigor that will allow interpretation of the relevance of changes across broader scales. To date, population-level consequences of routinely measured endpoints such as reduced gonad size or intersex in fish is not entirely clear, and the significance of genome-wide molecular, proteome, or metabolic changes on organism or population health is further removed from the levels of ecological change traditionally managed. The present review is not intended to dismiss the idea that omics will play a future role in large-scale environmental monitoring studies, but rather outlines the necessary actions for its inclusion in regulatory monitoring programs focused on assessing ecosystem health.
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Affiliation(s)
- Paulina A Bahamonde
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - April Feswick
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Meghan A Isaacs
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Kelly R Munkittrick
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Christopher J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
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32
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Laporte M, Pavey SA, Rougeux C, Pierron F, Lauzent M, Budzinski H, Labadie P, Geneste E, Couture P, Baudrimont M, Bernatchez L. RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels. Mol Ecol 2015; 25:219-37. [DOI: 10.1111/mec.13466] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 11/06/2015] [Accepted: 11/06/2015] [Indexed: 12/14/2022]
Affiliation(s)
- M. Laporte
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
| | - S. A. Pavey
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- Institut National de la Recherche Scientifique (INRS); Centre Eau Terre et Environnement; 490, rue de la Couronne Québec QC G1K 9A9 Canada
- Department of Biology; University of New Brunswick; PO Box 5050 Saint-John NB E2L 4L5 Canada
| | - C. Rougeux
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
| | - F. Pierron
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - M. Lauzent
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - H. Budzinski
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - P. Labadie
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - E. Geneste
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - P. Couture
- Institut National de la Recherche Scientifique (INRS); Centre Eau Terre et Environnement; 490, rue de la Couronne Québec QC G1K 9A9 Canada
| | - M. Baudrimont
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - L. Bernatchez
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
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AlMomin S, Kumar V, Al-Amad S, Al-Hussaini M, Dashti T, Al-Enezi K, Akbar A. Draft genome sequence of the silver pomfret fish, Pampus argenteus. Genome 2015; 59:51-8. [PMID: 26692342 DOI: 10.1139/gen-2015-0056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.
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Affiliation(s)
- Sabah AlMomin
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Vinod Kumar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Sami Al-Amad
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Mohsen Al-Hussaini
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Talal Dashti
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Khaznah Al-Enezi
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Abrar Akbar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
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34
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Guo C, Cui H, Ni S, Yan Y, Qin Q. Comprehensive identification and profiling of host miRNAs in response to Singapore grouper iridovirus (SGIV) infection in grouper (Epinephelus coioides). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 52:226-235. [PMID: 26027797 DOI: 10.1016/j.dci.2015.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/25/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
microRNAs (miRNAs) are an evolutionarily conserved class of non-coding RNA molecules that participate in various biological processes. Employment of high-throughput screening strategies greatly prompts the investigation and profiling of miRNAs in diverse species. In recent years, grouper (Epinephelus spp.) aquaculture was severely affected by iridoviral diseases. However, knowledge regarding the host immune responses to viral infection, especially the miRNA-mediated immune regulatory roles, is rather limited. In this study, by employing Solexa deep sequencing approach, we identified 116 grouper miRNAs from grouper spleen-derived cells (GS). As expected, these miRNAs shared high sequence similarity with miRNAs identified in zebrafish (Danio rerio), pufferfish (Fugu rubripes), and other higher vertebrates. In the process of Singapore grouper iridovirus (SGIV) infection, 45 and 43 miRNAs with altered expression (>1.5-fold) were identified by miRNA microarray assays in grouper spleen tissues and GS cells, respectively. Furthermore, target prediction revealed 189 putative targets of these grouper miRNAs.
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Affiliation(s)
- Chuanyu Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huachun Cui
- Department of Medicine, University of Alabama at Birmingham, 901 19th Street South, Birmingham, AL 35294, USA
| | - Songwei Ni
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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35
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Simmons DBD, Benskin JP, Cosgrove JR, Duncker BP, Ekman DR, Martyniuk CJ, Sherry JP. Omics for aquatic ecotoxicology: control of extraneous variability to enhance the analysis of environmental effects. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:1693-1704. [PMID: 25827364 DOI: 10.1002/etc.3002] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/09/2015] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
There are multiple sources of biological and technical variation in a typical ecotoxicology study that may not be revealed by traditional endpoints but that become apparent in an omics dataset. As researchers increasingly apply omics technologies to environmental studies, it will be necessary to understand and control the main source(s) of variability to facilitate meaningful interpretation of such data. For instance, can variability in omics studies be addressed by changing the approach to study design and data analysis? Are there statistical methods that can be employed to correctly interpret omics data and make use of unattributed, inherent variability? The present study presents a review of experimental design and statistical considerations applicable to the use of omics methods in systems toxicology studies. In addition to highlighting potential sources that contribute to experimental variability, this review suggests strategies with which to reduce and/or control such variability so as to improve reliability, reproducibility, and ultimately the application of omics data for systems toxicology.
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Affiliation(s)
- Denina B D Simmons
- Emerging Methods Section, Aquatic Contaminants Research Division, Water Science & Technology Directorate, Environment Canada, Ontario, Canada
| | | | | | | | - Drew R Ekman
- Ecosystems Research Division, National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency, Athens, Georgia, USA
| | - Christopher J Martyniuk
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, Florida, USA
| | - James P Sherry
- Emerging Methods Section, Aquatic Contaminants Research Division, Water Science & Technology Directorate, Environment Canada, Ontario, Canada
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36
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Hook SE, Twine NA, Simpson SL, Spadaro DA, Moncuquet P, Wilkins MR. 454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 153:73-88. [PMID: 24434169 DOI: 10.1016/j.aquatox.2013.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 05/20/2023]
Abstract
Next generation sequencing using Roche's 454 pyrosequencing platform can be used to generate genomic information for non-model organisms, although there are bioinformatic challenges associated with these studies. These challenges are compounded by a lack of a standardized protocol to either assemble data or to evaluate the quality of a de novo transcriptome. This study presents an assembly of the control and toxicant responsive transcriptome of Melita plumulosa, an Australian amphipod commonly used in ecotoxicological studies. RNA was harvested from control amphipods, juvenile amphipods, and from amphipods exposed to either metal or diesel contaminated sediments. This RNA was used as the basis for a 454 based transcriptome sequencing effort. Sequencing generated 1.3 million reads from control, juvenile, metal-exposed and diesel-exposed amphipods. Different read filtering and assembly protocols were evaluated to generate an assembly that (i) had an optimal number of contigs; (ii) had long contigs; (iii) contained a suitable representation of conserved genes; and (iv) had long ortholog alignment lengths relative to the length of each contig. A final assembly, generated using fixed-length trimming based on the sequence quality scores, followed by assembly using the MIRA algorithm, produced the best results. The 26,625 contigs generated via this approach were annotated using Blast2GO, and the differential expression between treatments and control was determined by mapping with BWA followed by DESeq. Although the mapping generated low coverage, many differentially expressed contigs, including some with known developmental or toxicological function, were identified. This study demonstrated that 454 pyrosequencing is an effective means of generating reference transcriptome information for organisms, such as the amphipod M. plumulosa, that have no genomic information available in databases or in closely related sequenced species. It also demonstrated how optimization of read filtering protocols and assembly approaches changes the utility of results obtained from next generation sequencing studies, and establishes criteria to determine the quality of a de novo assembly in species lacking a reference genome. This new transcriptomic knowledge provides the genomic foundation for the creation of microarray and qPCR assays, serving as a reference transcriptome in future RNAseq studies, and allowing both the biology and ecotoxicology of this organism to be better understood. This approach will allow genomics-based methodology to be applied to a wider range of environmentally relevant species.
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Affiliation(s)
- Sharon E Hook
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW 2232, Australia.
| | - Natalie A Twine
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Stuart L Simpson
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW 2232, Australia
| | - David A Spadaro
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW 2232, Australia
| | - Philippe Moncuquet
- CSIRO Mathematics, Informatics, and Statistics, Acton, ACT, 2601, Australia
| | - Marc R Wilkins
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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37
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Hook SE, Osborn HL, Gissi F, Moncuquet P, Twine NA, Wilkins MR, Adams MS. RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium. Mar Genomics 2014; 16:45-53. [DOI: 10.1016/j.margen.2013.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/29/2013] [Accepted: 12/18/2013] [Indexed: 01/17/2023]
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38
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Williams TD, Mirbahai L, Chipman JK. The toxicological application of transcriptomics and epigenomics in zebrafish and other teleosts. Brief Funct Genomics 2014; 13:157-71. [DOI: 10.1093/bfgp/elt053] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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39
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Hook SE, Osborn HL, Spadaro DA, Simpson SL. Assessing mechanisms of toxicant response in the amphipod Melita plumulosa through transcriptomic profiling. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 146:247-57. [PMID: 24334007 DOI: 10.1016/j.aquatox.2013.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/01/2013] [Accepted: 11/04/2013] [Indexed: 05/06/2023]
Abstract
This study describes the function of transcripts with altered abundance in the epibenthic amphipod, Melita plumulosa, following whole-sediment exposure to a series of common environmental contaminants. M. plumulosa were exposed for 48 h to sediments spiked and equilibrated with the following contaminants at concentrations predicted to cause sublethal effects to reproduction: porewater ammonia 30 mg L(-1); bifenthrin at 100 μg kg(-1); fipronil at 50 μg kg(-1); 0.6% diesel; 0.3% crude oil; 250 mg Cu kg(-1); 400 mg Ni kg(-1); and 400 mg Zn kg(-1). RNA was extracted and hybridized against a custom Agilent microarray developed for this species. Although the microarray represented a partial transcriptome and not all features on the array could be annotated, unique transcriptomic profiles were generated for each of the contaminant exposures. Hierarchical clustering grouped the expression profiles together by contaminant class, with copper and zinc, the petroleum products and nickel, and the pesticides each forming a distinct cluster. Many of the transcriptional changes observed were consistent with patterns previously described in other crustaceans. The changes in the transcriptome demonstrated that contaminant exposure caused changes in digestive function, growth and moulting, and the cytoskeleton following metal exposure, whereas exposure to petroleum products caused changes in carbohydrate metabolism, xenobiotic metabolism and hormone cycling. Functional analysis of these gene expression profiles can provide a better understanding of modes of toxic action and permits the prediction of mixture effects within contaminated ecosystems.
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Affiliation(s)
- Sharon E Hook
- CSIRO Land and Water, Locked Bag 2007, Kirrawee 2232, NSW, Australia.
| | - Hannah L Osborn
- CSIRO Land and Water, Locked Bag 2007, Kirrawee 2232, NSW, Australia
| | - David A Spadaro
- CSIRO Land and Water, Locked Bag 2007, Kirrawee 2232, NSW, Australia
| | - Stuart L Simpson
- CSIRO Land and Water, Locked Bag 2007, Kirrawee 2232, NSW, Australia
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40
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Martyniuk CJ, Houlahan J. Assessing gene network stability and individual variability in the fathead minnow (Pimephales promelas) transcriptome. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2013; 8:283-91. [PMID: 24036207 DOI: 10.1016/j.cbd.2013.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 12/22/2022]
Abstract
Transcriptomics is increasingly used to assess biological responses to environmental stimuli and stressors such as aquatic pollutants. However, fundamental studies characterizing individual variability in mRNA levels are lacking, which currently limits the use of transcriptomics in environmental monitoring assessments. To address individual variability in transcript abundance, we performed a meta-analysis on 231 microarrays that were conducted in the fathead minnow (FHM), a widely used toxicological model. The mean variability for gene probes was ranked from most to least variable based upon the coefficient of variation. Transcripts that were the most variable in individual tissues included NADH dehydrogenase flavoprotein 1, GTPase IMAP family member 7-like and v-set domain-containing T-cell activation inhibitor 1-like while genes encoding ribosomal proteins (rpl24 and rpl36), basic transcription factor 3, and nascent polypeptide-associated complex alpha subunit were the least variable in individuals across a range of microarray experiments. Gene networks that showed high variability (based upon the variation in expression of individual members within the network) included cell proliferation, metabolism (steroid, lipids, and glucose), cell adhesion, vascularization, and regeneration while those that showed low variability (more stability) included mRNA and rRNA processing, regulation of translational fidelity, RNA splicing, and ribosome biogenesis. Real-time PCR was conducted on a subset of genes for comparison of variability collected from the microarrays. There was a significant positive relationship between the two methods when measuring individual variability, suggesting that variability detected in microarray data can be used to guide decisions on sample sizes for measuring transcripts in real-time PCR experiments. A power analysis revealed that measuring estrogen receptor ba (esrba) requires fewer biological replicates than that of estrogen receptor bb (esrbb) in the gonad and samples sizes required to detect a 50% change for reproductive-related transcripts is between 12 and 20. Characterizing individual variability at the molecular level will prove necessary as efforts are made toward integrating molecular tools into environmental risk assessments.
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Affiliation(s)
- Christopher J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick E2L 4L5, Canada.
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41
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Ou J, Li Y, Ding Z, Xiu Y, Wu T, Du J, Li W, Zhu H, Ren Q, Gu W, Wang W. Transcriptome-wide identification and characterization of the Procambarus clarkii microRNAs potentially related to immunity against Spiroplasma eriocheiris infection. FISH & SHELLFISH IMMUNOLOGY 2013; 35:607-617. [PMID: 23747834 DOI: 10.1016/j.fsi.2013.05.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/13/2013] [Accepted: 05/19/2013] [Indexed: 06/02/2023]
Abstract
We used the Illumina/Solexa deep sequencing technology to sequence two small RNA libraries prepared from hemocytes of Procambarus clarkii under normal and infection conditions. The high-throughput sequencing approach resulted in approximately 12,801,827 and 8,410,455 raw reads corresponding to 10,949,754 and 6,648,161 high-quality mappable reads for the normal and infected hemocyte samples, respectively. Bioinformatic analyses identified 195 unique miRNAs, including 30 that are conserved in crustaceans, 48 that are novel to crayfish but are present in other arthropods (PN-type), and 117 that are completely new (PC-type). Thirty-three miRNAs displayed significant differential expressions between the two hemocyte samples (p < 0.0001). Of these, 15 (45.5%) were significantly up-regulated and 18 (54.5%) were significantly down-regulated upon challenge with Spiroplasma eriocheiris. Integrating comparative genomic and bibliomic analysis, of the 33 significant miRNAs identified, 19 were conserved and immune-related in P. clarkii and Eriocheir sinensis infected with S. eriocheiris infection; 24 were conserved and immune-related in P. clarkii and Marsupenaeus japonicus immune response to S. eriocheiris or white spot syndrome virus (WSSV) infection. Function annotation of target genes revealed a broad range of biological processes and signal transduction pathways that regulated by crayfish miRNAs. Thereinto, pcl-miR-34, pcl-miR-7, PN-pcl-let-7, pcl-miR-1, and pcl-miR-2b are highly conserved in vertebrates and invertebrates and function in the similar pathways. To our knowledge, this is the first report of comprehensive identification of P. clarkii miRNAs and of expression analysis of P. clarkii miRNAs after exposure to S. eriocheiris in crayfish, and many miRNAs were differentially regulated under normal and infection conditions. Our results should help develop new control strategies for efficient immune protection against S. eriocheiris infections in crustaceans.
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Affiliation(s)
- Jiangtao Ou
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
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42
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Houde M, Douville M, Despatie SP, De Silva AO, Spencer C. Induction of gene responses in St. Lawrence River northern pike (Esox lucius) environmentally exposed to perfluorinated compounds. CHEMOSPHERE 2013; 92:1195-200. [PMID: 23453599 DOI: 10.1016/j.chemosphere.2013.01.099] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/31/2013] [Indexed: 05/06/2023]
Abstract
Municipal waste water effluents (MWWEs) are important sources of chemical contamination for aquatic environments. This study investigated the presence and effects of perfluorinated compounds (PFCs) in environmentally exposed northern pike (Esox lucius) collected upstream and downstream a major municipal waste water treatment plant (WWTP) in the St. Lawrence River, Canada. Twelve PFCs, including the newly detected perfluoroethylcyclohexane sulfonate (PFECHS), were quantified in fish muscle, liver, and plasma. Additionally, the expression of eight genes and the activity of three biomarkers were analyzed in fish tissues at both sites. Mean ∑PFC concentration in fish plasma collected upstream the WWTP was 185ng/g w.w. compared to 545ng/g w.w. downstream the point of release. PFECHS was quantified for the first time in St. Lawrence River fish (mean plasma concentration in MWWE fish: 5.07±4.72ng/g w.w.). Results of transcriptomic responses were tissue-specific and indicated significant up-regulation for metallothionein (MT) in blood and MT, glutathion-S-transferase (GST), superoxide dismutase (SOD), and cytochromes P450 1A1 (CYP1A1) in gill tissue of fish collected in the MWWE suggesting greater stress responses for organisms at this location. Significant relationships were found between vitellogenin (Vtg) gene expression in liver, Vtg activity in plasma and perfluorotridecanoic acid (PFTrA), perfluorotetradecanoic acid (PFTeA), and perfluorodecane sulfonate (PFDS) plasma concentrations. The possible endocrine effects of these PFCs should be further investigated.
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Affiliation(s)
- Magali Houde
- Environment Canada, Centre Saint-Laurent, 105 McGill Street, Montreal, QC, Canada H2Y 2E7.
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43
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Langlois VS, Martyniuk CJ. Genome wide analysis of Silurana (Xenopus) tropicalis development reveals dynamic expression using network enrichment analysis. Mech Dev 2013; 130:304-22. [PMID: 23295496 DOI: 10.1016/j.mod.2012.12.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/30/2012] [Accepted: 12/17/2012] [Indexed: 11/28/2022]
Abstract
Development involves precise timing of gene expression and coordinated pathways for organogenesis and morphogenesis. Functional and sub-network enrichment analysis provides an integrated approach for identifying networks underlying development. The objectives of this study were to characterize early gene regulatory networks over Silurana tropicalis development from NF stage 2 to 46 using a custom Agilent 4×44K microarray. There were >8000 unique gene probes that were differentially expressed between Nieuwkoop-Faber (NF) stage 2 and stage 16, and >2000 gene probes differentially expressed between NF 34 and 46. Gene ontology revealed that genes involved in nucleosome assembly, cell division, pattern specification, neurotransmission, and general metabolism were increasingly regulated throughout development, consistent with active development. Sub-network enrichment analysis revealed that processes such as membrane hyperpolarisation, retinoic acid, cholesterol, and dopamine metabolic gene networks were activated/inhibited over time. This study identifies RNA transcripts that are potentially maternally inherited in an anuran species, provides evidence that the expression of genes involved in retinoic acid receptor signaling may increase prior to those involved in thyroid receptor signaling, and characterizes novel gene expression networks preceding organogenesis which increases understanding of the spatiotemporal embryonic development in frogs.
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Affiliation(s)
- Valérie S Langlois
- Chemistry and Chemical Engineering Department, Royal Military College of Canada, Kingston, ON, Canada K7K 7B4.
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44
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Forbes VE, Calow P. Promises and problems for the new paradigm for risk assessment and an alternative approach involving predictive systems models. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2012; 31:2663-2671. [PMID: 23165997 DOI: 10.1002/etc.2009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The need for cost-effective risk assessment of chemicals is leading to the development of a reductionist paradigm that tries to assess impacts on humans and ecosystems from molecular changes. However, the biggest challenge for this paradigm comes from the emergence of properties that arise out of the interactions of the parts that are not included and yet which are key for assessing likely impacts. Although identifying key events and adverse outcome pathways can shed light on the involvement of important metabolic processes in toxicity, this does not mean that particular molecular initiating events are likely to be robust or accurate predictors of impacts that matter. There are even greater challenges for the new paradigm applied to ecological systems than to human health because of the need to link across more levels of biological organization. The present study argues for a predictive systems approach that makes the linkages through systems models in a mechanistic way that allows for emergence and that also has the potential for reducing the costs and use of animals in ecological risk assessments.
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Affiliation(s)
- Valery E Forbes
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
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45
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Stürzenbaum S, Aschner M, Freedman JH. Toxicogenomics in non-mammalian species-Editorial. Front Genet 2012; 3:216. [PMID: 23087709 PMCID: PMC3472458 DOI: 10.3389/fgene.2012.00216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 09/28/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Stephen Stürzenbaum
- Analytical and Environmental Science Division, School of Biomedical Sciences, King's College London London, UK
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46
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Jayapal M. Integration of next-generation sequencing based multi-omics approaches in toxicogenomics. Front Genet 2012; 3:88. [PMID: 22661985 PMCID: PMC3356856 DOI: 10.3389/fgene.2012.00088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 05/02/2012] [Indexed: 12/12/2022] Open
Affiliation(s)
- Manikandan Jayapal
- Center of Excellence in Genomic Medicine Research, King Fahd Medical Research Centre, King Abdulaziz University Jeddah, Kingdom of Saudi Arabia.
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