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Torsabo D, Ishak SD, Noordin NM, Waiho K, Koh ICC, Yazed MA, Abol-Munafi AB. Optimizing reproductive performance in pangasius catfish broodstock: A review of dietary and molecular strategies. Vet Anim Sci 2024; 25:100375. [PMID: 39005967 PMCID: PMC11245938 DOI: 10.1016/j.vas.2024.100375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024] Open
Abstract
Pangasius catfish, a significant player in the global whitefish market, encounters challenges in aquaculture production sustainability. Quality broodstock maintenance and seed production are impeded by growth, maturation, and fecundity issues. This review investigates the efficacy of strategic nutrient composition and molecular strategies in enhancing broodstock conditions and reproductive performance across various fish species. A notable knowledge gap for Pangasius catfish hampers aquaculture progress. The review assesses nutrient manipulation's impact on reproductive physiology, emphasizing pangasius broodstock. A systematic review analysis following PRISMA guidelines was conducted to identify research trends and hotspots quantitatively, revealing a focus on P. bocourti and fertilization techniques. Addressing this gap, the review offers insights into dietary nutrients manipulation and genetic tool utilization for improved seed production, contributing to pangasius catfish aquaculture sustainability.
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Affiliation(s)
- Donald Torsabo
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Department of Fisheries and Aquaculture, Joseph Sarwuan Tarka University, Makurdi, Makurdi, Benue State, Nigeria
| | - Sairatul Dahlianis Ishak
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Noordiyana Mat Noordin
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity and Conservation, College of Marine Sciences, Beibu Gulf University, Guangxi, China
- Center for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Ivan Chong Chu Koh
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Muhammad Abduh Yazed
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Ambok Bolong Abol-Munafi
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
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Wu X, Lai J, Chen Y, Liu Y, Song M, Li F, Li P, Li Q, Gong Q. Combination of metabolome and proteome analyses provides insights into the mechanism underlying growth differences in Acipenser dabryanus. iScience 2023; 26:107413. [PMID: 37559901 PMCID: PMC10407750 DOI: 10.1016/j.isci.2023.107413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/26/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023] Open
Abstract
To analyze the differences between different-sized Acipenser dabryanus, we randomly selected 600 3-month-old A. dabryanus juveniles. Four months later, the blood and white muscle of these fish were analyzed. The results showed no significant difference in the length-weight relationship (LWR) b value between the large and small A. dabryanus. The levels of serum growth hormone (gh) and insulin-like growth factor 1 (igf1) in the large A. dabryanus were significantly lower than those in the small, whereas the activity levels of Total superoxide dismutase (T-sod) and catalase (cat) were opposite to the results of gh and igf1. A total of 212 and 245 metabolites showed significant changes in the positive and negative polarity mode, respectively. Among 3,308 proteins identified, 69 proteins showed upregulated expression, and 185 proteins showed downregulated expression. These results indicated that the growth advantage of A. dabryanus was closely related to glycolysis, protein synthesis, and antioxidant function.
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Affiliation(s)
- Xiaoyun Wu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Jiansheng Lai
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Ya Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Mingjiang Song
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Feiyang Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Pengcheng Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Qingzhi Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Quan Gong
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
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Pringle BA, Duncan MI, Winkler AC, Mafwila S, Jagger C, McKeown NJ, Shaw PW, Henriques R, Potts WM. Ocean warming favours a northern Argyrosomus species over its southern congener, whereas preliminary metabolic evidence suggests that hybridization may promote their adaptation. CONSERVATION PHYSIOLOGY 2023; 11:coad026. [PMID: 37179704 PMCID: PMC10170327 DOI: 10.1093/conphys/coad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 03/21/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
Anthropogenic-induced climate change is having profound impacts on aquatic ecosystems, and the resilience of fish populations will be determined by their response to these impacts. The northern Namibian coast is an ocean warming hotspot, with temperatures rising faster than the global average. The rapid warming in Namibia has had considerable impacts on marine fauna, such as the southern extension of the distribution of Argyrosomus coronus from southern Angola into northern Namibian waters, where it now overlaps and hybridizes with the closely related Namibian species, A. inodorus. Understanding how these species (and their hybrids) perform at current and future temperatures is vital to optimize adaptive management for Argyrosomus species. Intermittent flow-through respirometry was used to quantify standard and maximum metabolic rates for Argyrosomus individuals across a range of temperatures. The modelled aerobic scope (AS) of A. inodorus was notably higher at cooler temperatures (12, 15, 18 and 21°C) compared with that of A. coronus, whereas the AS was similar at 24°C. Although only five hybrids were detected and three modelled, their AS was in the upper bounds of the models at 15, 18 and 24°C. These findings suggest that the warming conditions in northern Namibia may increasingly favour A. coronus and promote the poleward movement of the leading edge of their southern distribution. In contrast, the poor aerobic performance of both species at cold temperatures (12°C) suggests that the cold water associated with the permanent Lüderitz Upwelling Cell in the south may constrain both species to central Namibia. This is most concerning for A. inodorus because it may be subjected to a considerable coastal squeeze.
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Affiliation(s)
- Brett A Pringle
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
- Advance Africa Management Services, Johannesburg, South Africa
| | - Murray I Duncan
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
- South African Institute for Aquatic Biodiversity, Makhanda, South Africa
- University of Seychelles and Blue Economy Research Institute, Anse Royale, Mahe, Seychelles
| | - Alexander C Winkler
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
| | - Samuel Mafwila
- Department of Fisheries and Aquatic Sciences, Sam Nujoma Campus, University of Namibia, Henties Bay, Namibia
| | - Charmaine Jagger
- Department of Fisheries and Aquatic Sciences, Sam Nujoma Campus, University of Namibia, Henties Bay, Namibia
- Ministry of Fisheries and Marine Resources, Swakopmund, Namibia
| | - Niall J McKeown
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Paul W Shaw
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Romina Henriques
- Marine Genomics Group, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Warren M Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
- South African Institute for Aquatic Biodiversity, Makhanda, South Africa
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Thompson WA, Lau GY, Richards JG, Devlin RH. Rationed and satiated growth hormone transgenic Coho Salmon (Oncorhynchus kisutch) show tissue specific differences in energy stores. Comp Biochem Physiol B Biochem Mol Biol 2023; 263:110781. [PMID: 35902066 DOI: 10.1016/j.cbpb.2022.110781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
Abstract
Growth hormone transgenic coho salmon experience increased growth rates, driven primarily through elevated feed intake and feed conversion. However, neuropeptides that signal appetite stimulation have been shown to exhibit variable responses across fed states, suggesting a more complex system mediating growth in these fish. Studies have proposed that growth hormone may have a modulatory role on the energy reserves of fish, possibly through AMP-activated protein kinase (AMPK) activation. AMPK, an energy sensor in cells, has previously been shown to be upregulated in growth hormone transgenic salmon when compared to wild type, however, whether this effect is seen across fed states is unknown. Here, we tested the hypothesis that growth hormone induces an energetic deficit in metabolic tissues, leading to constitutive AMPK activation in growth hormone transgenic salmon. This study compared AMPK activity, ATP, and glycogen, of the liver, heart, and muscle of wild-type, and growth hormone transgenic salmon either fed to satiation or a wild-type ration. The results suggest that white muscle ATP levels in growth hormone salmon are elevated in satiation and rationed conditions. In the liver, growth hormone transgenic salmon fed a rationed wild-type diet experience reductions in ATP level and glycogen. In none of the tissues examined, did AMPK activity change. Taken together, these results indicate that growth hormone transgenic salmon experience metabolic duress when not fed to satiation.
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Affiliation(s)
- W A Thompson
- The University of British Columbia, Department of Zoology, 6270 University Blvd, Vancouver, British Columbia V6T 1Z4, Canada.
| | - G Y Lau
- The University of British Columbia, Department of Zoology, 6270 University Blvd, Vancouver, British Columbia V6T 1Z4, Canada
| | - J G Richards
- The University of British Columbia, Department of Zoology, 6270 University Blvd, Vancouver, British Columbia V6T 1Z4, Canada
| | - R H Devlin
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, British Columbia V7V 1N6, Canada
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5
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Taylor RS, Ruiz Daniels R, Dobie R, Naseer S, Clark TC, Henderson NC, Boudinot P, Martin SA, Macqueen DJ. Single cell transcriptomics of Atlantic salmon ( Salmo salar L.) liver reveals cellular heterogeneity and immunological responses to challenge by Aeromonas salmonicida. Front Immunol 2022; 13:984799. [PMID: 36091005 PMCID: PMC9450062 DOI: 10.3389/fimmu.2022.984799] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
The liver is a multitasking organ with essential functions for vertebrate health spanning metabolism and immunity. In contrast to mammals, our understanding of liver cellular heterogeneity and its role in regulating immunological status remains poorly defined in fishes. Addressing this knowledge gap, we generated a transcriptomic atlas of 47,432 nuclei isolated from the liver of Atlantic salmon (Salmo salar L.) contrasting control fish with those challenged with a pathogenic strain of Aeromonas salmonicida, a problematic bacterial pathogen in global aquaculture. We identified the major liver cell types and their sub-populations, revealing poor conservation of many hepatic cell marker genes utilized in mammals, while identifying novel heterogeneity within the hepatocyte, lymphoid, and myeloid lineages. This included polyploid hepatocytes, multiple T cell populations including γδ T cells, and candidate populations of monocytes/macrophages and dendritic cells. A dominant hepatocyte population radically remodeled its transcriptome following infection to activate the acute phase response and other defense functions, while repressing routine functions such as metabolism. These defense-specialized hepatocytes showed strong activation of genes controlling protein synthesis and secretion, presumably to support the release of acute phase proteins into circulation. The infection response further involved up-regulation of numerous genes in an immune-cell specific manner, reflecting functions in pathogen recognition and killing, antigen presentation, phagocytosis, regulation of inflammation, B cell differentiation and T cell activation. Overall, this study greatly enhances our understanding of the multifaceted role played by liver immune and non-immune cells in host defense and metabolic remodeling following infection and provides many novel cell-specific marker genes to empower future studies of this organ in fishes.
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Affiliation(s)
- Richard S. Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Ross Dobie
- Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Shahmir Naseer
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Thomas C. Clark
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Neil C. Henderson
- Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Samuel A.M. Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom,*Correspondence: Daniel J. Macqueen,
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Reduced physiological plasticity in a fish adapted to stable temperatures. Proc Natl Acad Sci U S A 2022; 119:e2201919119. [PMID: 35617428 DOI: 10.1073/pnas.2201919119] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Significance Plastic individuals can buffer environmental changes, maintaining a stable performance across gradients. Plasticity is therefore thought to be particularly beneficial for the survival of wild populations that experience large environmental fluctuations, such as diel and seasonal temperature changes. Maintaining plasticity is widely assumed to be costly; however, empirical evidence demonstrating this cost is scarce. Here, we predict that if plasticity is costly, it would be readily lost in a stable environment, such as a laboratory. To test this, we measured a diverse range of phenotypic traits, spanning gene expression, physiology, and behavior, in wild and laboratory zebrafish acclimated to 15 temperatures. We show that laboratory fish have lost plasticity in many traits, demonstrating that maintaining plasticity carries a cost.
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Nikolov VN, Malavia D, Kubota T. SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes. Nat Commun 2022; 13:1968. [PMID: 35413952 PMCID: PMC9005695 DOI: 10.1038/s41467-022-29591-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/23/2022] [Indexed: 12/13/2022] Open
Abstract
The Pleiotropic Drug Resistance (PDR) network is central to the drug response in fungi, and its overactivation is associated with drug resistance. However, gene regulation of the PDR network is not well understood. Here, we show that the histone chaperone Rtt106 and the chromatin remodeller SWI/SNF control expression of the PDR network genes and confer drug resistance. In Saccharomyces cerevisiae, Rtt106 specifically localises to PDR network gene promoters dependent on transcription factor Pdr3, but not Pdr1, and is essential for Pdr3-mediated basal expression of the PDR network genes, while SWI/SNF is essential for both basal and drug-induced expression. Also in the pathogenic fungus Candida glabrata, Rtt106 and SWI/SNF regulate drug-induced PDR gene expression. Consistently, loss of Rtt106 or SWI/SNF sensitises drug-resistant S. cerevisiae mutants and C. glabrata to antifungal drugs. Since they cooperatively drive PDR network gene expression, Rtt106 and SWI/SNF represent potential therapeutic targets to combat antifungal resistance.
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Affiliation(s)
- Vladislav N Nikolov
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Dhara Malavia
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- MRC Centre for Medical Mycology, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Takashi Kubota
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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Blasco J, Vélez EJ, Perelló-Amorós M, Azizi S, Capilla E, Fernández-Borràs J, Gutiérrez J. Recombinant Bovine Growth Hormone-Induced Metabolic Remodelling Enhances Growth of Gilthead Sea-Bream ( Sparus aurata): Insights from Stable Isotopes Composition and Proteomics. Int J Mol Sci 2021; 22:ijms222313107. [PMID: 34884912 PMCID: PMC8658469 DOI: 10.3390/ijms222313107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
Growth hormone and insulin-like growth factors (GH/IGF axis) regulate somatic growth in mammals and fish, although their action on metabolism is not fully understood in the latter. An intraperitoneal injection of extended-release recombinant bovine growth hormone (rbGH, Posilac®) was used in gilthead sea bream fingerlings and juveniles to analyse the metabolic response of liver and red and white muscles by enzymatic, isotopic and proteomic analyses. GH-induced lipolysis and glycogenolysis were reflected in liver composition, and metabolic and redox enzymes reported higher lipid use and lower protein oxidation. In white and red muscle reserves, rBGH increased glycogen while reducing lipid. The isotopic analysis of muscles showed a decrease in the recycling of proteins and a greater recycling of lipids and glycogen in the rBGH groups, which favoured a protein sparing effect. The protein synthesis capacity (RNA/protein) of white muscle increased, while cytochrome-c-oxidase (COX) protein expression decreased in rBGH group. Proteomic analysis of white muscle revealed only downregulation of 8 proteins, related to carbohydrate metabolic processes. The global results corroborated that GH acted by saving dietary proteins for muscle growth mainly by promoting the use of lipids as energy in the muscles of the gilthead sea bream. There was a fuel switch from carbohydrates to lipids with compensatory changes in antioxidant pathways that overall resulted in enhanced somatic growth.
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10
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Genetic composition of queen conch (Lobatus gigas) population on Pedro Bank, Jamaica and its use in fisheries management. PLoS One 2021; 16:e0245703. [PMID: 33819265 PMCID: PMC8021194 DOI: 10.1371/journal.pone.0245703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/11/2021] [Indexed: 11/19/2022] Open
Abstract
The queen conch fishery in Jamaica is sustained by Pedro Bank, which is the main harvesting site located approximately 80 km south-west from Kingston. Due to its relative size, Pedro Bank has been subdivided into zones for management purposes by the Fisheries Division and the Veterinary Services Division. Understanding whether these sub-divisions reflect different sub-populations is critical for managing exploitation levels because fisheries management must demonstrate that harvesting does not endanger the future viability of the population as queen conch are on Appendix II of the Convention in Trade in Endangered Species of Wild Fauna and Flora (CITES). This determination is essential for the continued export to international markets such as the European Union. Two hundred and eight samples were collected across the entire Pedro Bank and were genetically characterized using nine polymorphic microsatellite loci. Population structure analysis for Lobatus gigas from Pedro Bank yielded low but significant values (FST = 0.009: p = 0.006) and suggested a high magnitude of gene flow indicative of a fit and viable population throughout the bank. Analysis of molecular variance (AMOVA) indicated a 100% variation within individual samples with little variation (0.9%) between populations. In contrast pairwise genetic comparisons identified significant differences between populations located to the south eastern and eastern region of the bank to those in the central and western locations. Bayesian clustering analysis also indicated the likelihood of two population sub-divisions (K = 2) on Pedro Bank. The results provided evidence of a weak but significant population structure which has crucial implications for the fishing industry as it suggests the use of ecosystem based management (EBM) in setting quotas to promote sustainable harvesting of L. gigas within each monitoring zone on Pedro Bank.
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Bakke FK, Monte MM, Stead DA, Causey DR, Douglas A, Macqueen DJ, Dooley H. Plasma Proteome Responses in Salmonid Fish Following Immunization. Front Immunol 2020; 11:581070. [PMID: 33133099 PMCID: PMC7579410 DOI: 10.3389/fimmu.2020.581070] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/21/2020] [Indexed: 12/18/2022] Open
Abstract
Vaccination plays a critical role in the protection of humans and other animals from infectious diseases. However, the same vaccine often confers different protection levels among individuals due to variation in genetics and/or immunological histories. While this represents a well-recognized issue in humans, it has received little attention in fish. Here we address this knowledge gap in a proteomic study of rainbow trout (Oncorhynchus mykiss, Walbaum), using non-lethal repeated blood sampling to establish the plasma protein response of individual fish following immunization. Six trout were immunized with adjuvanted hen egg-white lysozyme (HEL) and peripheral blood sampled at ten time points from day 0 to day 84 post-injection. We confirm that an antigen-specific antibody response to HEL was raised, showing differences in timing and magnitude among individuals. Using label-free liquid chromatography-mass spectrometry, we quantified the abundance of 278 plasma proteins across the timecourse. As part of the analysis, we show that this approach can distinguish many (but not all) duplicated plasma proteins encoded by paralogous genes retained from the salmonid-specific whole genome duplication event. Global variation in the plasma proteome was predominantly explained by individual differences among fish. However, sampling day explained a major component of variation in abundance for a statistically defined subset of 41 proteins, representing 15% of those detected. These proteins clustered into five groups showing distinct temporal responses to HEL immunization at the population level, and include classical immune (e.g. complement system members) and acute phase molecules (e.g. apolipoproteins, haptoglobins), several enzymes and other proteins supporting the immune response, in addition to evolutionarily conserved molecules that are as yet uncharacterized. Overall, this study improves our understanding of the fish plasma proteome, provides valuable marker proteins for different phases of the immune response, and has implications for vaccine development and the design of immune challenge experiments.
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Affiliation(s)
- Fiona K Bakke
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Milena M Monte
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - David A Stead
- Aberdeen Proteomics, The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Dwight R Causey
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alex Douglas
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Helen Dooley
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology (IMET), University of Maryland School of Medicine, Baltimore, MD, United States
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12
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Little AG, Loughland I, Seebacher F. What do warming waters mean for fish physiology and fisheries? JOURNAL OF FISH BIOLOGY 2020; 97:328-340. [PMID: 32441327 DOI: 10.1111/jfb.14402] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/30/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Environmental signals act primarily on physiological systems, which then influence higher-level functions such as movement patterns and population dynamics. Increases in average temperature and temperature variability associated with global climate change are likely to have strong effects on fish physiology and thereby on populations and fisheries. Here we review the principal mechanisms that transduce temperature signals and the physiological responses to those signals in fish. Temperature has a direct, thermodynamic effect on biochemical reaction rates. Nonetheless, plastic responses to longer-term thermal signals mean that fishes can modulate their acute thermal responses to compensate at least partially for thermodynamic effects. Energetics are particularly relevant for growth and movement, and therefore for fisheries, and temperature can have pronounced effects on energy metabolism. All energy (ATP) production is ultimately linked to mitochondria, and temperature has pronounced effects on mitochondrial efficiency and maximal capacities. Mitochondria are dependent on oxygen as the ultimate electron acceptor so that cardiovascular function and oxygen delivery link environmental inputs with energy metabolism. Growth efficiency, that is the conversion of food into tissue, changes with temperature, and there are indications that warmer water leads to decreased conversion efficiencies. Moreover, movement and migration of fish relies on muscle function, which is partially dependent on ATP production but also on intracellular calcium cycling within the myocyte. Neuroendocrine processes link environmental signals to regulated responses at the level of different tissues, including muscle. These physiological processes within individuals can scale up to population responses to climate change. A mechanistic understanding of thermal responses is essential to predict the vulnerability of species and populations to climate change.
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Affiliation(s)
| | - Isabella Loughland
- School of Life and Environmental Sciences A08, University of Sydney, Sydney, Australia
| | - Frank Seebacher
- School of Life and Environmental Sciences A08, University of Sydney, Sydney, Australia
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Domestication is associated with differential expression of pikeperch egg proteins involved in metabolism, immune response and protein folding. Animal 2020; 14:2336-2350. [PMID: 32525470 DOI: 10.1017/s1751731120001184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Domestication is a condition in which the breeding, care and feeding of animals are, at least in part, controlled by humans. Information regarding the changes in the protein composition of eggs in response to domestication is very limited. Such data are prerequisite for improvements in the reproduction of domesticated fish. The aim of this study was to examine the impact of domestication on the proteome of pikeperch eggs using two-dimensional differential in-gel electrophoresis. We analysed high-quality eggs from domesticated and wild pikeperch fish to reveal proteins that were presumably only related to the domestication process and not to the quality of eggs. Here, we show that domestication has a profound impact on the protein profile of pikeperch eggs. We identified 66 differentially abundant protein spots, including 27 spots that were more abundant in wild-caught pikeperch eggs and 39 spots that were enriched in eggs collected from domesticated females. Eggs originating from wild-caught females showed higher expression levels of proteins involved in folding, apoptotic process, purine metabolism and immune response, whereas eggs of domesticated females showed higher expression levels of proteins that participated mainly in metabolism. The changes in metabolic proteins in eggs from domesticated females can reflect the adaptation of pikeperch to commercial diets, which have profoundly distinct compositions compared with natural diets. The decrease in the abundance of proteins related to immune response in eggs from the domesticated population suggests that domestication may lead to disturbances in defence mechanisms. In turn, the lower abundance of heat shock proteins in eggs of domesticated fish may indicate their adaptation to stable farming conditions and reduced environmental stressors or their better tolerance of stress from breeding. The proteins identified in this study can increase our knowledge concerning the mechanism of the pikeperch domestication process.
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Ahmed F, Kumar G, Soliman FM, Adly MA, Soliman HAM, El-Matbouli M, Saleh M. Proteomics for understanding pathogenesis, immune modulation and host pathogen interactions in aquaculture. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 32:100625. [PMID: 31639560 DOI: 10.1016/j.cbd.2019.100625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
Abstract
Proteomic analyses techniques are considered strong tools for identifying and quantifying the protein contents in different organisms, organs and secretions. In fish biotechnology, the proteomic analyses have been used for wide range of applications such as identification of immune related proteins during infections and stresses. The proteomic approach has a significant role in understanding pathogen surviving strategies, host defence responses and subsequently, the fish pathogen interactions. Proteomic analyses were employed to highlight the virulence related proteins secreted by the pathogens to invade the fish host's defence barriers and to monitor the kinetics of protein contents of different fish organs in response to infections. The immune related proteins of fish and the virulence related proteins of pathogens are up or down regulated according to their functions in defence or pathogenesis. Therefore, the proteomic analyses are useful in understanding the virulence mechanisms of microorganisms and the fish pathogen interactions thereby supporting the development of new effective therapies. In this review, we focus and summarise the recent proteomic profiling studies exploring pathogen virulence activities and fish immune responses to stressors and infections.
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Affiliation(s)
- Fatma Ahmed
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria; Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Faiza M Soliman
- Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Mohamed A Adly
- Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Hamdy A M Soliman
- Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Mona Saleh
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria.
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15
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Su H, Tang X, Zhang X, Liu L, Jing L, Pan D, Sun W, He H, Yang C, Zhao D, Zhang H, Qi B. Comparative proteomics analysis reveals the difference during antler regeneration stage between red deer and sika deer. PeerJ 2019; 7:e7299. [PMID: 31346498 PMCID: PMC6642628 DOI: 10.7717/peerj.7299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022] Open
Abstract
Deer antler, as the only mammalian regenerative appendage, provides an optimal model to study regenerative medicine. Antler harvested from red deer or sika deer were mainly study objects used to disclose the mechanism underlying antler regeneration over past decades. A previous study used proteomic technology to reveal the signaling pathways of antler stem cell derived from red deer. Moreover, transcriptome of antler tip from sika deer provide us with the essential genes, which regulated antler development and regeneration. However, antler comparison between red deer and sika deer has not been well studied. In our current study, proteomics were employed to analyze the biological difference of antler regeneration between sika deer and red deer. The proteomics profile was completed by searching the UniProt database, and differentially expressed proteins were identified by bioinformatic software. Thirty-six proteins were highly expressed in red deer antler, while 144 proteins were abundant in sika deer. GO and KEGG analysis revealed that differentially expressed proteins participated in the regulation of several pathways including oxidative phosphorylation, ribosome, extracellular matrix interaction, and PI3K-Akt pathway.
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Affiliation(s)
- Hang Su
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun, China
| | - Xiaolei Tang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Xiaocui Zhang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Li Liu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Li Jing
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun, China
| | - Daian Pan
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Weijie Sun
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Huinan He
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Chonghui Yang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Daqing Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - He Zhang
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Bin Qi
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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16
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The AMPK system of salmonid fishes was expanded through genome duplication and is regulated by growth and immune status in muscle. Sci Rep 2019; 9:9819. [PMID: 31285449 PMCID: PMC6614447 DOI: 10.1038/s41598-019-46129-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/19/2019] [Indexed: 12/25/2022] Open
Abstract
5′adenosine monophosphate-activated protein kinase (AMPK) is a master regulator of energy homeostasis in eukaryotes. This study identified expansions in the AMPK-α, -β and -γ families of salmonid fishes due to a history of genome duplication events, including five novel salmonid-specific AMPK subunit gene paralogue pairs. We tested the hypothesis that the expanded AMPK gene system of salmonids is transcriptionally regulated by growth and immunological status. As a model, we studied immune-stimulated coho salmon (Oncorhynchus kisutch) from three experiment groups sharing the same genetic background, but showing highly-divergent growth rates and nutritional status. Specifically, we compared wild-type and GH-transgenic fish, the latter achieving either enhanced or wild-type growth rate via ration manipulation. Transcript levels for the fifteen unique salmonid AMPK subunit genes were quantified in skeletal muscle after stimulation with bacterial or viral mimics to alter immune status. These analyses revealed a constitutive up-regulation of several AMPK-α and -γ subunit-encoding genes in GH-transgenic fish achieving accelerated growth. Further, immune stimulation caused a decrease in the expression of several AMPK subunit-encoding genes in GH-transgenic fish specifically. The dynamic expression responses observed suggest a role for the AMPK system in balancing energetic investment into muscle growth according to immunological status in salmonid fishes.
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Houston RD, Macqueen DJ. Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding. Anim Genet 2019; 50:3-14. [PMID: 30426521 PMCID: PMC6492011 DOI: 10.1111/age.12748] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
Abstract
Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high-quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole-genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome-wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance.
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Affiliation(s)
- R. D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianEH25 9RGUK
| | - D. J. Macqueen
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUK
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18
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Causey DR, Pohl MAN, Stead DA, Martin SAM, Secombes CJ, Macqueen DJ. High-throughput proteomic profiling of the fish liver following bacterial infection. BMC Genomics 2018; 19:719. [PMID: 30285610 PMCID: PMC6167799 DOI: 10.1186/s12864-018-5092-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023] Open
Abstract
Background High-throughput proteomics was used to determine the role of the fish liver in defense responses to bacterial infection. This was done using a rainbow trout (Oncorhynchus mykiss) model following infection with Aeromonas salmonicida, the causative agent of furunculosis. The vertebrate liver has multifaceted functions in innate immunity, metabolism, and growth; we hypothesize this tissue serves a dual role in supporting host defense in parallel to metabolic adjustments that promote effective immune function. While past studies have reported mRNA responses to A. salmonicida in salmonids, the impact of bacterial infection on the liver proteome remains uncharacterized in fish. Results Rainbow trout were injected with A. salmonicida or PBS (control) and liver extracted 48 h later for analysis on a hybrid quadrupole-Orbitrap mass spectrometer. A label-free method was used for protein abundance profiling, which revealed a strong innate immune response along with evidence to support parallel rewiring of metabolic and growth systems. 3076 proteins were initially identified against all proteins (n = 71,293 RefSeq proteins) annotated in a single high-quality rainbow trout reference genome, of which 2433 were maintained for analysis post-quality filtering. Among the 2433 proteins, 109 showed significant differential abundance following A. salmonicida challenge, including many upregulated complement system and acute phase response proteins, in addition to molecules with putative functions that may support metabolic re-adjustments. We also identified novel expansions in the complement system due to gene and whole genome duplication events in salmonid evolutionary history, including eight C3 proteins showing differential changes in abundance. Conclusions This study provides the first high-throughput proteomic examination of the fish liver in response to bacterial challenge, revealing novel markers for the host defense response, and evidence of metabolic remodeling in conjunction with activation of innate immunity. Electronic supplementary material The online version of this article (10.1186/s12864-018-5092-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dwight R Causey
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Moritz A N Pohl
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - David A Stead
- Aberdeen Proteomics, University of Aberdeen, The Rowett Institute, Aberdeen, UK
| | | | | | - Daniel J Macqueen
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK.
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