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Akbarzadeh A, Ming TJ, Schulze AD, Kaukinen KH, Li S, Günther OP, Houde ALS, Miller KM. Developing molecular classifiers to detect environmental stressors, smolt stages and morbidity in coho salmon, Oncorhynchus kisutch. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175626. [PMID: 39168345 DOI: 10.1016/j.scitotenv.2024.175626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/16/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Aquatic species are increasingly confronted with environmental stressors because of climate change. Although molecular technologies have advanced our understanding of how organisms respond to stressors in laboratory settings, the ability to detect physiological responses to specific stressors under complex field conditions remains underdeveloped. This research applied multi-stressor challenge trials on coho salmon, employing the "Salmon Fit-Chips" genomic tool and a random forest-based classification model to develop classifiers predictive for chronic thermal and hypoxic stress, as well as salinity acclimation, smolt stage and morbidity status. The study also examined how smolts and de-smolts (smolts not having entered SW during the smolt window) responded transcriptionally to exposure to saltwater. Using RF classifiers optimized with 4 to 12 biomarkers, we identified transcriptional signatures that accurately predicted the presence of each stressor and physiological state, achieving prediction accuracy rates between 86.8 % and 100 %, regardless of other background stressors present. Stressor recovery time was established by placing fish back into non-stressor conditions after stress exposure, providing important context to stressor detections in field applications. Recovery from thermal and hypoxic stress requires about 3 and 2 days, respectively, with >3 days needed for re-acclimation to freshwater for seawater acclimated fish. The study also found non-additive (synergistic) effects of multiple stressors on mortality risk. Importantly, osmotic stress associated with de-smolts was the most important predictor of mortality. In saltwater, de-smolts exposed to salinity, high temperature, and hypoxia experienced a 9-fold increase in mortality compared to those only exposed to saltwater, suggesting a synergistic response to multiple stressors. These findings suggest that delays in hatchery releases to support release of larger fish need to be carefully scrutinized to ensure fish are not being released as de-smolts, which are highly susceptible to additional climate-induced stressors like rising temperatures and reduced dissolved oxygen levels in the marine environment.
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Affiliation(s)
- Arash Akbarzadeh
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada; Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Oliver P Günther
- Günther Analytics, 402-5775 Hampton Place, Vancouver, BC V6T 2G6, Canada
| | - Aimee Lee S Houde
- Environmental Dynamics Inc. (EDI), 208A - 2520 Bowen Road, Nanaimo, BC V9T 3L3, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
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Koll R, Theilen J, Hauten E, Woodhouse JN, Thiel R, Möllmann C, Fabrizius A. Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173656. [PMID: 38830414 DOI: 10.1016/j.scitotenv.2024.173656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.
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Affiliation(s)
- Raphael Koll
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany.
| | - Jesse Theilen
- University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Elena Hauten
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Jason Nicholas Woodhouse
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Microbial and phytoplankton Ecology, Germany
| | - Ralf Thiel
- Leibniz Institute for the Analysis of Biodiversity Change (LIB) - Hamburg site, Centre for Taxonomy & Morphology, Zoological Museum, Germany; University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Christian Möllmann
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Andrej Fabrizius
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany
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DePasquale SW, Howell BE, Navarroli G, Jeffries KM, Cooke SJ, Wijenayake S, Jeffrey JD, Hasler CT. Are the effects of catch-and-release angling evident in changes to mRNA abundances related to metabolism, acid-base regulation and stress in lake trout ( Salvelinus namaycush) gills? CONSERVATION PHYSIOLOGY 2023; 11:coad065. [PMID: 37637261 PMCID: PMC10452961 DOI: 10.1093/conphys/coad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
Catch-and-release (C&R) angling is a conservation-oriented practice intended to reduce the impact recreational angling has on fish populations. Even though most recreationally angled fish are released, little is known about how C&R angling impacts fish at the cellular or tissue level. As the first to explore the impacts of C&R angling on mRNA abundances, our study aimed to identify how the stress of angling influenced metabolism, acid-base regulation and cellular stress in the gills of lake trout (Salvelinus namaycush). Because gills are responsible for metabolic gas exchange, are crucial sites of acid-base homeostasis and respond to stressors quickly, we hypothesized that the relative mRNA abundance of genes related to these three physiological processes would be altered after angling. We took gill samples of live lake trout at 0, 2 or 48 h after fish were angled by rod and reel, and then used quantitative PCR (qPCR) to measure the relative abundance of nine candidate mRNA transcripts. Heat shock protein 70 (hsp70) mRNA levels significantly increased over 5-fold 2 h after angling, indicating a potential activation of a cytoprotective response. However, contrary to our hypothesis, we observed no change in the relative mRNA abundance of genes related to metabolism or acid-base regulation in response to C&R angling within a 48-h period. As C&R angling can negatively impact fish populations, further use of transcript-level studies will allow us to understand the impact C&R has on specific tissues and improve our knowledge of how C&R influences overall fish health.
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Affiliation(s)
- Simon W DePasquale
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Bradley E Howell
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Giulio Navarroli
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Kenneth M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, MB, Canada R3T 2N2
| | - Steven J Cooke
- Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
| | - Sanoji Wijenayake
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Jennifer D Jeffrey
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
| | - Caleb T Hasler
- Department of Biology, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada R3B 2E9
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Wen X, Yang M, Zhou K, Huang J, Fan X, Zhang W, Luo J. Transcriptomic and proteomic analyses reveal the common and unique pathway(s) underlying different skin colors of leopard coral grouper (Plectropomus leopardus). J Proteomics 2022; 266:104671. [PMID: 35788407 DOI: 10.1016/j.jprot.2022.104671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
To gain a comprehensive and unbiased molecular understanding of the different skin colors of P. leopardus, we used Illumina HiSeq 2500 and TMT (Tandem Mass Tag) to compare transcription and protein levels between red and black skin of P. leopardus. We identified 797 upregulated and 314 downregulated genes (differentially expressed genes; DEGs) in red (RG) compared with black (BG) skin of P. leopardus. We also identified 377 differentially abundant proteins (DAPs), including 314 upregulated and 63 downregulated proteins. These DEGs and DAPs were significantly enriched in melanin synthesis (e.g., pyrimidine metabolism, Phenylalanine, tyrosine, and tryptophan biosynthesis, melanogenesis, phenylalanine metabolism, and tyrosine metabolism), oxidative phosphorylation (e.g., phosphonate and phosphinate metabolism, and oxidative phosphorylation), energy metabolism (e.g., HIF-1, glycolysis/gluconeogenesis, fatty acid biosynthesis, and fatty acid degradation), and signal transduction (e.g., Wnt, calcium, MAPK, and cGMP-PKG signaling pathways), etc. Further analysis of MAPKs showed that the activation levels of its main members JNK1 and ERK1/2 differed significantly between red and black skin colors. After RNAi was used to interfere with ERK1/2, it was found that the local skin of the tail of P. leopardus would turn black. Combined transcriptome and proteome analysis showed that most DEGs-DAPs in red skin were higher than in black skin (58 were upregulated, 1 was downregulated, and 4 were opposite). These DEGs-DAPs showed that the differences between red and black skin tissues of P. leopardus were related primarily to energy metabolism, signal transduction and cytoskeleton. These findings are not only conducive to understand the skin color regulation mechanism of P. leopardus and other coral reef fish, but also provide an important descriptive to the breeding of color strains. SIGNIFICANCE OF THE STUDY: The skin color of P. leopardus gradually darkens or blackens due to environmental factors such as changes in light intensity and human activities, and this directly affects its ornamental and economic value. In this study, RNAseq and TMT were used to conduct comparative quantitative transcriptomics and proteomics and analyze differences between red and black P. leopardus skin. The results showed that energy metabolism, signal transduction and cytoskeleton were the main metabolic pathways causing their skin color differences. These findings contribute to existing data describing fish skin color, and provide information about protein levels, which are of great significance to a deeper understanding of the skin color regulation mechanism in P. leopardus and other coral reef fishes.
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Affiliation(s)
- Xin Wen
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China.
| | - Min Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Kexin Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Jie Huang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Xin Fan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Weiwei Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Jian Luo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China.
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Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR. G3-GENES GENOMES GENETICS 2020; 10:3321-3336. [PMID: 32694198 PMCID: PMC7466982 DOI: 10.1534/g3.120.401487] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L-1] and hypoxia (DO = 4‒5 mg L-1) in 10 and 18° temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; P < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.
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Mu Y, Li W, Wei Z, He L, Zhang W, Chen X. Transcriptome analysis reveals molecular strategies in gills and heart of large yellow croaker (Larimichthys crocea) under hypoxia stress. FISH & SHELLFISH IMMUNOLOGY 2020; 104:304-313. [PMID: 32544557 DOI: 10.1016/j.fsi.2020.06.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/07/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
The gills and heart are two major targets of hypoxia in fish. However, the molecular responses in fish gills and heart to hypoxia challenge remain unclear. Here, RNA-Seq technology was used to study the gene expression profiles in gills and heart of large yellow croaker (Larimichthys crocea) at 6, 24, and 48 h after hypoxia stress. A total of 1,546 and 2,746 differentially expressed genes (DEGs) were identified in gills and heart, respectively. Expression changes of nine genes in each tissue were further validated by the qPCR. Based on KEGG and Gene ontology enrichments, we found that various innate immunity-related genes, such as complement components (C1qs, C2, C3, C6, and C7), chemokines (CCL3, CCL17, CCL19, CCL25, and CXCL8_L3), chemokine receptors (CCR9, CXCR1, and CXCR3), and nitric oxide synthase (NOS), were significantly down-regulated in gills and/or heart, suggesting that innate immune processes mediated by these genes may be inhibited by hypoxia. The genes involved in both glycolysis pathway (LDHA) and tricarboxylic acid cycle (IDH2 and OGDH) were up-regulated in gills and heart of hypoxic large yellow croakers, possibly because gill and heart tissues need enough energy to accelerate gas exchange and blood circulation. Hypoxia also affected the ion transport in gills of large yellow croaker, through down-regulating the expression levels of numerous classical ion transporters, including HVCN1, SLC20A2, SLC4A4, RHBG, RHCG, and SCN4A, suggesting an energy conservation strategy to hypoxia stress. All these results indicate that the immune processes, glycolytic pathways, and ion transport were significantly altered in gills and/or heart of large yellow croaker under hypoxia, possibly contributing to maintain cellular energy balance during hypoxia. Our data, therefore, afford new information to understand the tissue-specific molecular responses of bony fish to hypoxia stress.
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Affiliation(s)
- Yinnan Mu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Wanru Li
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Zuyun Wei
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Lianghua He
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Weini Zhang
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, PR China.
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Giraud-Billoud M, Rivera-Ingraham GA, Moreira DC, Burmester T, Castro-Vazquez A, Carvajalino-Fernández JM, Dafre A, Niu C, Tremblay N, Paital B, Rosa R, Storey JM, Vega IA, Zhang W, Yepiz-Plascencia G, Zenteno-Savin T, Storey KB, Hermes-Lima M. Twenty years of the ‘Preparation for Oxidative Stress’ (POS) theory: Ecophysiological advantages and molecular strategies. Comp Biochem Physiol A Mol Integr Physiol 2019; 234:36-49. [DOI: 10.1016/j.cbpa.2019.04.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/22/2022]
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Carruthers M, Yurchenko AA, Augley JJ, Adams CE, Herzyk P, Elmer KR. De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genomics 2018; 19:32. [PMID: 29310597 PMCID: PMC5759245 DOI: 10.1186/s12864-017-4379-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022] Open
Abstract
Background Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields. Here we generate high quality de novo transcriptomes for four salmonid species: Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and European whitefish (Coregonus lavaretus). All species except Atlantic salmon have no reference genome publicly available and few if any genomic studies to date. Results We used paired-end RNA-seq on Illumina to generate high coverage sequencing of multiple individuals, yielding between 180 and 210 M reads per species. After initial assembly, strict filtering was used to remove duplicated, redundant, and low confidence transcripts. The final assemblies consisted of 36,505 protein-coding transcripts for Atlantic salmon, 35,736 for brown trout, 33,126 for Arctic charr, and 33,697 for European whitefish and are made publicly available. Assembly completeness was assessed using three approaches, all of which supported high quality of the assemblies: 1) ~78% of Actinopterygian single-copy orthologs were successfully captured in our assemblies, 2) orthogroup inference identified high overlap in the protein sequences present across all four species (40% shared across all four and 84% shared by at least two), and 3) comparison with the published Atlantic salmon genome suggests that our assemblies represent well covered (~98%) protein-coding transcriptomes. Thorough comparison of the generated assemblies found that 84-90% of transcripts in each assembly were orthologous with at least one of the other three species. We also identified 34-37% of transcripts in each assembly as paralogs. We further compare completeness and annotation statistics of our new assemblies to available related species. Conclusion New, high-confidence protein-coding transcriptomes were generated for four ecologically and economically important species of salmonids. This offers a high quality pipeline for such complex genomes, represents a valuable contribution to the existing genomic resources for these species and provides robust tools for future investigation of gene expression and sequence evolution in these and other salmonid species. Electronic supplementary material The online version of this article (10.1186/s12864-017-4379-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Madeleine Carruthers
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Andrey A Yurchenko
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Julian J Augley
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, G61 1QH, Glasgow, UK.,Present Address: Fios Genomics Ltd., Nine Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4UX, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Pawel Herzyk
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, G61 1QH, Glasgow, UK.,Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK.
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Feng X, He D, Shan G, Tao J, Chen Y. Integrated analysis of mRNA and miRNA expression profiles in Ptychobarbus dipogon and Schizothorax oconnori , insight into genetic mechanisms of high altitude adaptation in the schizothoracine fishes. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Zhang G, Zhang J, Wen X, Zhao C, Zhang H, Li X, Yin S. Comparative iTRAQ-Based Quantitative Proteomic Analysis ofPelteobagrus vachelliLiver under Acute Hypoxia: Implications in Metabolic Responses. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700140] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/04/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Guosong Zhang
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
- Department of Life Science; Heze University; Heze Shandong P. R. China
| | - Jiajia Zhang
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province; Lianyungang Jiangsu P. R. China
| | - Xin Wen
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
| | - Cheng Zhao
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
| | - Hongye Zhang
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
| | - Xinru Li
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
| | - Shaowu Yin
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province; Lianyungang Jiangsu P. R. China
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Kwasek K, Rimoldi S, Cattaneo AG, Parker T, Dabrowski K, Terova G. The expression of hypoxia-inducible factor-1α gene is not affected by low-oxygen conditions in yellow perch (Perca flavescens) juveniles. FISH PHYSIOLOGY AND BIOCHEMISTRY 2017; 43:849-862. [PMID: 28097495 DOI: 10.1007/s10695-017-0340-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
Hypoxia can affect various fish populations, including yellow perch Perca flavescens, which is an economically and ecologically important species in Lake Erie, a freshwater system that often experiences hypoxia in the hypolimnetic part of the lake. Fish, similarly to mammals, possess molecular oxygen sensor-hypoxia-inducible factor-1 (HIF-1), a transcription factor that can affect expression of many downstream genes related to animal growth and locomotion, protein synthesis, as well as ATP and amino acid metabolism. HIF-1 is a heterodimer, which consists of two subunits: oxygen-sensitive and oxygen-insensitive subunits, α and β, respectively. In this study, we report first on the molecular cloning and sequencing of P. flavescens HIF-1α. The full-length complementary DNA (cDNA) was isolated and submitted to the GenBank with accession number KT783483. It consists of 3529 base pairs (bp) carrying a single open-reading frame that encompasses 2250 bp of the coding region, 247 bp of the 5' untranslated region (UTR), and 1032 bp of the 3' UTR. The "de novo" prediction of the 3D structure of HIF-1α protein, which consists of 749 amino acids, is presented, too. We then utilized One-Step Taqman® real-time RT-PCR technology to monitor changes in HIF-1α messenger RNA (mRNA) copies in response to chronic hypoxic stress. An experiment was conducted using 14-day post-swim-up stage yellow perch larvae with uninflated swim bladders. This experiment included three treatment groups: hypoxia, mid-hypoxia, and normoxia, in four replicates (four tanks per treatment) with the following dissolved oxygen levels: 3, 4, and >7 mg O2/L, respectively. At the end (2 weeks) and in the middle (1 week) of the experiment, fish from each tank were sampled for body measurements and molecular biology analysis. The results showed no differences in survival (∼90%) between treatment groups. Oxygen concentration was lowered to 3.02 ± 0.15 (mean ± SE) mg O2/L with no adverse effect on fish survival. The highest growth rate was observed in the normoxic group. A similar trend was observed with fish body length. The growth rate of fish declined with decreasing water-dissolved oxygen. The number of HIF-1α mRNA copies was not significantly different between hypoxic, mid-hypoxic, and normoxic conditions, and this was true for fish obtained in the middle and at the end of the experiment. Graphical abstract.
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Affiliation(s)
- Karolina Kwasek
- School of Environment and Natural Resources, Ohio State University, Columbus, OH, 43210, USA
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3, 21100, Varese, Italy
| | - Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3, 21100, Varese, Italy
| | - Anna Giulia Cattaneo
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3, 21100, Varese, Italy
| | - Timothy Parker
- School of Environment and Natural Resources, Ohio State University, Columbus, OH, 43210, USA
| | - Konrad Dabrowski
- School of Environment and Natural Resources, Ohio State University, Columbus, OH, 43210, USA
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 3, 21100, Varese, Italy.
- Inter-University Centre for Research in Protein Biotechnologies "The Protein Factory", Polytechnic University of Milan and University of Insubria, Varese, Italy.
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Pédron N, Artigaud S, Infante JLZ, Le Bayon N, Charrier G, Pichereau V, Laroche J. Proteomic responses of European flounder to temperature and hypoxia as interacting stressors: Differential sensitivities of populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 586:890-899. [PMID: 28215807 DOI: 10.1016/j.scitotenv.2017.02.068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/30/2017] [Accepted: 02/07/2017] [Indexed: 06/06/2023]
Abstract
In the context of global change, ectotherms are increasingly impacted by abiotic perturbations. Along the distribution area of a species, the populations at low latitudes are particularly exposed to temperature increase and hypoxic events. In this study, we have compared the proteomic responses in the liver of European flounder populations, by using 2-D electrophoresis. One southern peripheral population from Portugal vs two northern core populations from France, were reared in a common garden experiment. Most of the proteomic differences were observed between the two experimental conditions, a cold vs a warm and hypoxic conditions. Consistent differentiations between populations were observed in accumulation of proteins involved in the bioenergetics- and methionine-metabolisms, fatty acids transport, and amino-acid catabolism. The specific regulation of crucial enzymes like ATP-synthase and G6PDH, in the liver of the southern population, could be related to a possible local adaptation. This southern peripheral population is spatially distant from northern core populations and has experienced dissimilar ecological conditions; thus it may contain genotypes that confer resilience to climate changes.
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Affiliation(s)
- Nicolas Pédron
- Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France; Ifremer, Laboratoire Adaptation, Reproduction et Nutrition des Poissons ARN, Unité de Physiologie Fonctionnelle des Organismes Marins PFOM, Plouzané, France
| | - Sébastien Artigaud
- Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France
| | - José-Luis Zambonino Infante
- Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France; Ifremer, Laboratoire Adaptation, Reproduction et Nutrition des Poissons ARN, Unité de Physiologie Fonctionnelle des Organismes Marins PFOM, Plouzané, France
| | - Nicolas Le Bayon
- Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France; Ifremer, Laboratoire Adaptation, Reproduction et Nutrition des Poissons ARN, Unité de Physiologie Fonctionnelle des Organismes Marins PFOM, Plouzané, France
| | - Grégory Charrier
- Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France
| | - Vianney Pichereau
- Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France
| | - Jean Laroche
- Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France.
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