1
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Leonard EM, Porteus CS, Brink D, Milsom WK. Fish gill chemosensing: knowledge gaps and inconsistencies. J Comp Physiol B 2024:10.1007/s00360-024-01553-5. [PMID: 38758303 DOI: 10.1007/s00360-024-01553-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/04/2024] [Indexed: 05/18/2024]
Abstract
In this review, we explore the inconsistencies in the data and gaps in our knowledge that exist in what is currently known regarding gill chemosensors which drive the cardiorespiratory reflexes in fish. Although putative serotonergic neuroepithelial cells (NEC) dominate the literature, it is clear that other neurotransmitters are involved (adrenaline, noradrenaline, acetylcholine, purines, and dopamine). And although we assume that these agents act on neurons synapsing with the NECs or in the afferent or efferent limbs of the paths between chemosensors and central integration sites, this process remains elusive and may explain current discrepancies or species differences in the literature. To date it has been impossible to link the distribution of NECs to species sensitivity to different stimuli or fish lifestyles and while the gills have been shown to be the primary sensing site for respiratory gases, the location (gills, oro-branchial cavity or elsewhere) and orientation (external/water or internal/blood sensing) of the NECs are highly variable between species of water and air breathing fish. Much of what has been described so far comes from studies of hypoxic responses in fish, however, changes in CO2, ammonia and lactate have all been shown to elicit cardio-respiratory responses and all have been suggested to arise from stimulation of gill NECs. Our view of the role of NECs is broadening as we begin to understand the polymodal nature of these cells. We begin by presenting the fundamental picture of gill chemosensing that has developed, followed by some key unanswered questions about gill chemosensing in general.
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Affiliation(s)
- Erin M Leonard
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Cosima S Porteus
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.
| | - Deidre Brink
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - William K Milsom
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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2
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Li N, Xie J, Chu YM. Degradation and evaluation of myofibril proteins induced by endogenous protease in aquatic products during storage: a review. Food Sci Biotechnol 2023; 32:1005-1018. [PMID: 37215253 PMCID: PMC10195969 DOI: 10.1007/s10068-023-01291-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023] Open
Abstract
Myofibril proteins degradation constitutes an important factor in quality deterioration, procedural activation or inhibition of endogenous protease potential regulates autolytic proteolysis-induced softening of post mortem fish muscle. Based on the brief introduction of myofibril proteins degradation in fish skeletal muscle, a detailed description of the main myofibril degradation properties and the distinct role played by endogenous proteases were proposed, which reflects the limitations and challenges of the current research on myofibril hydrolysis mechanisms based on the varied surrounding conditions. In addition, the latest researches on the evaluation method of myofibril proteins degradation were comprehensively reviewed. The potential use of label-free proteomics combined with bioinformatics was also emphasized and has become an important means to in-depth understand protein degradation mechanism.
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Affiliation(s)
- Na Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306 China
- College of Food and Tourism, Shanghai Urban Construction Vocational College, Shanghai, 201415 China
| | - Jing Xie
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306 China
- National Experimental Teaching Demonstration Center for Food Science and
Engineering, Shanghai Ocean University, Shanghai, 201306 China
- Shanghai Engineering Research Center of Aquatic Product Processing and
Preservation, Shanghai, 201306 China
- Shanghai Professional Technology Service Platform on Cold Chain Equipment
Performance and Energy Saving Evaluation, Shanghai, 201306 China
| | - Yuan Ming Chu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306 China
- National Experimental Teaching Demonstration Center for Food Science and
Engineering, Shanghai Ocean University, Shanghai, 201306 China
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3
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Abstract
The skeletal muscle proteome consists of a large number of diverse protein species with a broad and dynamic concentration range. Since mature skeletal muscles are characterized by a distinctive combination of contractile cells with differing physiological and biochemical properties, it is essential to determine specific differences in the protein composition of fast, slow, and hybrid fibers. Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a powerful comparative tool to analyze fiber type-specific differences between predominantly fast contracting versus slower twitching muscles. In this chapter, the application of the 2D-DIGE method for the comparative analysis of different subtypes of skeletal muscles is outlined in detail. A standardized proteomic workflow is described, involving sample preparation, protein extraction, differential fluorescence labeling using a 3-CyDye system, first-dimension isoelectric focusing, second-dimension slab gel electrophoresis, 2D-DIGE image analysis, protein digestion, and mass spectrometry.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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4
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Nynca J, Dietrich MA, Ciereszko A. DIGE Analysis of Fish Tissues. Methods Mol Biol 2023; 2596:303-322. [PMID: 36378447 DOI: 10.1007/978-1-0716-2831-7_21] [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] [Indexed: 06/16/2023]
Abstract
Two-dimensional difference gel electrophoresis (2D-DIGE) appears to be especially useful in quantitative approaches, allowing the co-separation of proteins of control samples and proteins of treated/disease samples on the same gel, eliminating gel-to-gel variability. The principle of 2D-DIGE is to label proteins prior to isoelectric focusing and use three spectrally resolvable fluorescent dyes, allowing the independent labeling of control and experimental samples. This procedure makes it possible to reduce the number of gels in an experiment, allowing the accurate and reproducible quantification of multiple samples. 2D-DIGE has been found to be an excellent methodical tool in several areas of fish research, including environmental pollution and toxicology, the mechanisms of development and disorders, reproduction, nutrition, evolution, and ecology.
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Affiliation(s)
- Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola A Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland.
| | - Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
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5
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Li L, Liu Z, Quan J, Sun J, Lu J, Zhao G. Comprehensive proteomic analysis to elucidate the anti-heat stress effects of nano-selenium in rainbow trout (Oncorhynchus mykiss). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113736. [PMID: 35689887 DOI: 10.1016/j.ecoenv.2022.113736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/29/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Because of the continuous intensification of global warming, extreme climate fluctuations, and high-density farming, cold-water rainbow trout (Oncorhynchus mykiss) are exposed to conditions of heat stress, which has severely impacted their survival and yield. Nano-selenium (nano-Se) shows higher biological activity and lower toxicity and has emerged as an ideal and ecological Se formulation. Herein rainbow trout were fed either a basal diet (control group) or basal diet plus 5 mg/kg nano-Se (treatment group). Samples were collected before (18 °C for 9 days; CG18, Se18) and after (24 °C for 8 h; CG24, Se24) heat stress. The DIA/SWATH approach was then applied to compare changes at the proteome level. We found 223 and 269 differentially abundant proteins in the CG18-CG24 and Se18-Se24 groups, respectively, which mainly included apoptosis-, heat stress-, and lipid-related proteins. In comparison with the CG18-CG24 group, the Se18-Se24 group showed higher abundance of molecular chaperone, such as Hsp70, Hsp90a.1, Hspa8, Hsp30, DNAJA4, Dnajb1, Bag2 and Ahsa1; on nano-Se supplementation, the heat stress-induced decline in the abundance of the selenoprotein MsrB2 was partially restored. Furthermore, nano-Se supplementation downregulated the abundance of lipid-related (CYP51, EBP, DHCR7, DHCR24, and APOB) and pro-apoptotic (caspase-8 and Bad) proteins. Protein-protein interaction analyses suggested that nano-Se inhibits apoptosis by upregulating the expression of Hsp70, Hsp90a.1, Hspa8, and Dnajb1; further, Hsp70/Hspa8 and MsrB2 appear to play a synergistic role in antioxidant defense under heat stress. Overall, our findings provide novel insights into nano-Se-mediated tolerance of heat stress, demonstrating that nano-Se exerts its anti-heat stress effects in rainbow trout by promoting protein repair, enhancing recovery of antioxidant enzyme activity, and alleviating lipid metabolism and apoptosis.
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Affiliation(s)
- Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Jun Sun
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Junhao Lu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Guiyan Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
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6
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Das T, Kamle A, Kumar A, Chakravarty S. Hypoxia Induced Sex-Difference in Zebrafish Brain Proteome Profile Reveals the Crucial Role of H3K9me3 in Recovery From Acute Hypoxia. Front Genet 2022; 12:635904. [PMID: 35173759 PMCID: PMC8841817 DOI: 10.3389/fgene.2021.635904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the molecular basis of sex differences in neural response to acute hypoxic insult has profound implications for the effective prevention and treatment of ischemic stroke. Global hypoxic-ischemic induced neural damage has been studied recently under well-controlled, non-invasive, reproducible conditions using a zebrafish model. Our earlier report on sex difference in global acute hypoxia-induced neural damage and recovery in zebrafish prompted us to conduct a comprehensive study on the mechanisms underlying the recovery. An omics approach for studying quantitative changes in brain proteome upon hypoxia insult following recovery was undertaken using iTRAQ-based LC-MS/MS approach. The results shed light on the altered expression of many regulatory proteins in the zebrafish brain upon acute hypoxia following recovery. The sex difference in differentially expressed proteins along with the proteins expressed in a uniform direction in both the sexes was studied. Core expression analysis by Ingenuity Pathway Analysis (IPA) showed a distinct sex difference in the disease function heatmap. Most of the upstream regulators obtained through IPA were validated at the transcriptional level. Translational upregulation of H3K9me3 in males led us to elucidate the mechanism of recovery by confirming transcriptional targets through ChIP-qPCR. The upregulation of H3K9me3 level in males at 4 h post-hypoxia appears to affect the early neurogenic markers nestin, klf4, and sox2, which might explain the late recovery in males, compared to females. Acute hypoxia-induced sex-specific comparison of brain proteome led us to reveal many differentially expressed proteins, which can be further studied for the development of novel targets for better therapeutic strategy.
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Affiliation(s)
- Tapatee Das
- Applied Biology, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Avijeet Kamle
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Arvind Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Sumana Chakravarty
- Applied Biology, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- *Correspondence: Sumana Chakravarty,
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7
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Mandic M, Flear K, Qiu P, Pan YK, Perry SF, Gilmour KM. Aquatic surface respiration improves survival during hypoxia in zebrafish ( Danio rerio) lacking hypoxia-inducible factor 1-α. Proc Biol Sci 2022; 289:20211863. [PMID: 35016541 PMCID: PMC8753152 DOI: 10.1098/rspb.2021.1863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/03/2021] [Indexed: 01/14/2023] Open
Abstract
Hypoxia-inducible factor 1-α (Hif-1α), an important transcription factor regulating cellular responses to reductions in O2, previously was shown to improve hypoxia tolerance in zebrafish (Danio rerio). Here, we examined the contribution of Hif-1α to hypoxic survival, focusing on the benefit of aquatic surface respiration (ASR). Wild-type and Hif-1α knockout lines of adult zebrafish were exposed to two levels (moderate or severe) of intermittent hypoxia. Survival was significantly compromised in Hif-1α knockout zebrafish prevented from accessing the surface during severe (16 mmHg) but not moderate (23 mmHg) hypoxia. When allowed access to the surface in severe hypoxia, survival times did not differ between wild-type and Hif-1α knockouts. Performing ASR mitigated the negative effects of the loss of Hif-1α with the knockouts initiating ASR at a higher PO2 threshold and performing ASR for longer than wild-types. The loss of Hif-1α had little impact on survival in fish between 1 and 5 days post-fertilization, but as the larvae aged, their reliance on Hif-1α increased. Similar to adult fish, ASR compensated for the loss of Hif-1α on survival. Together, these results demonstrate that age, hypoxia severity and, in particular, the ability to perform ASR significantly modulate the impact of Hif-1α on survival in hypoxic zebrafish.
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Affiliation(s)
- Milica Mandic
- Department of Animal Science, University of California Davis, 2251 Meyer Hall, Davis, CA 95616, USA
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, Canada K1N6N5
| | - Kaitlyn Flear
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, Canada K1N6N5
| | - Pearl Qiu
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, Canada K1N6N5
| | - Yihang K. Pan
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, Canada K1N6N5
| | - Steve F. Perry
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, Canada K1N6N5
| | - Kathleen M. Gilmour
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, Canada K1N6N5
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8
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Li J, Zhang G, Yin D, Li Y, Zhang Y, Cheng J, Zhang K, Ji J, Wang T, Jia Y, Yin S. Integrated application of multi-omics strategies provides insights into the environmental hypoxia response in Pelteobagrus vachelli muscle. Mol Cell Proteomics 2022; 21:100196. [PMID: 35031490 PMCID: PMC8938323 DOI: 10.1016/j.mcpro.2022.100196] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 11/07/2021] [Accepted: 01/05/2022] [Indexed: 11/28/2022] Open
Abstract
Increasing pressures on aquatic ecosystems because of pollutants, nutrient enrichment, and global warming have severely depleted oxygen concentrations. This sudden and significant lack of oxygen has resulted in persistent increases in fish mortality rates. Revealing the molecular mechanism of fish hypoxia adaptation will help researchers to find markers for hypoxia induced by environmental stress. Here, we used a multiomics approach to identify several hypoxia-associated miRNAs, mRNAs, proteins, and metabolites involved in diverse biological pathways in the muscles of Pelteobagrus vachelli. Our findings revealed significant hypoxia-associated changes in muscles over 4 h of hypoxia exposure and discrete tissue-specific patterns. We have previously reported that P. vachelli livers exhibit increased anaerobic glycolysis, heme synthesis, erythropoiesis, and inhibit apoptosis when exposed to hypoxia for 4 h. However, the opposite was observed in muscles. According to our comprehensive analysis, fishes show an acute response to hypoxia, including activation of catabolic pathways to generate more energy, reduction of biosynthesis to decrease energy consumption, and shifting from aerobic to anaerobic metabolic contributions. Also, we found that hypoxia induced muscle dysfunction by impairing mitochondrial function, activating inflammasomes, and apoptosis. The hypoxia-induced mitochondrial dysfunction enhanced oxidative stress, apoptosis, and further triggered interleukin-1β production via inflammasome activation. In turn, interleukin-1β further impaired mitochondrial function or apoptosis by suppressing downstream mitochondrial biosynthesis–related proteins, thus resulting in a vicious cycle of inflammasome activation and mitochondrial dysfunction. Our findings contribute meaningful insights into the molecular mechanisms of hypoxia, and the methods and study design can be utilized across different fish species. First multiomics analysis of mRNA, miRNA, protein, and metabolite in fishes. Liver and muscle were tissue-specific induced by hypoxia. About 70 genes and 16 miRNAs related to hypoxia adaptation were detected. Hypoxia affects muscle function by mediating energy metabolism via HIF pathway.
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Affiliation(s)
- Jie Li
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze, 274015, China
| | - Guosong Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze, 274015, China.
| | - Danqing Yin
- School of Computer Science, University of Sydney, Sydney, 2006, Australia
| | - Yao Li
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yiran Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jinghao Cheng
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Kai Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jie Ji
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yongyi Jia
- Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China.
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9
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Xu Z, Song A, Wang F, Chen H. Sensitive and effective imaging of carbon monoxide in living systems with a near-infrared fluorescent probe. RSC Adv 2021; 11:32203-32209. [PMID: 35495506 PMCID: PMC9042026 DOI: 10.1039/d1ra06052j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/15/2021] [Indexed: 12/27/2022] Open
Abstract
CO, a gas molecule that is harmful to living organisms, has a high affinity with hemoglobin, which will cause severe hypoxia. However, in recent years, researchers have discovered that endogenous CO, similar to NO, is one of the messenger molecules, which has a certain regulatory effect in many physiological and pathological processes in the respiratory system, cardiovascular system, and nervous system. Therefore, it is urgent to explore an effective method to monitor the role of CO under physiological and pathological conditions. Herein, we designed and synthesized a near-infrared small-molecule fluorescent probe for the detection of CO in living cells. In this design, a two-site BODIPY dye was introduced as the fluorophore, and the allyl chloroformate part as the CO reactive group. The probe displays excellent sensitivity, selectivity, and a good linear relationship to CO. Furthermore, it shows good biocompatibility and low cytotoxicity. This probe has been successfully applied to the detection of CO in a variety of cells. The developed fluorescent probe can serve as a potential molecular imaging tool for in vivo imaging and detection of CO.
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Affiliation(s)
- Zhencai Xu
- Guanyun People's Hospital Lianyungang 222000 China
| | - Aibo Song
- Guanyun People's Hospital Lianyungang 222000 China
| | - Fangwu Wang
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Hainan Medical University Haikou 570102 China
| | - Hongwei Chen
- Modern Education Technology Center, Hainan Medical University Haikou 571199 China
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10
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Mandic M, Joyce W, Perry SF. The evolutionary and physiological significance of the Hif pathway in teleost fishes. J Exp Biol 2021; 224:272213. [PMID: 34533194 DOI: 10.1242/jeb.231936] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The hypoxia-inducible factor (HIF) pathway is a key regulator of cellular O2 homeostasis and an important orchestrator of the physiological responses to hypoxia (low O2) in vertebrates. Fish can be exposed to significant and frequent changes in environmental O2, and increases in Hif-α (the hypoxia-sensitive subunit of the transcription factor Hif) have been documented in a number of species as a result of a decrease in O2. Here, we discuss the impact of the Hif pathway on the hypoxic response and the contribution to hypoxia tolerance, particularly in fishes of the cyprinid lineage, which includes the zebrafish (Danio rerio). The cyprinids are of specific interest because, unlike in most other fishes, duplicated paralogs of the Hif-α isoforms arising from a teleost-specific genome duplication event have been retained. Positive selection has acted on the duplicated paralogs of the Hif-α isoforms in some cyprinid sub-families, pointing to adaptive evolutionary change in the paralogs. Thus, cyprinids are valuable models for exploring the evolutionary significance and physiological impact of the Hif pathway on the hypoxic response. Knockout in zebrafish of either paralog of Hif-1α greatly reduces hypoxia tolerance, indicating the importance of both paralogs to the hypoxic response. Here, with an emphasis on the cardiorespiratory system, we focus on the role of Hif-1α in the hypoxic ventilatory response and the regulation of cardiac function. We explore the effects of the duration of the hypoxic exposure (acute, sustained or intermittent) on the impact of Hif-1α on cardiorespiratory function and compare relevant data with those from mammalian systems.
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Affiliation(s)
- Milica Mandic
- Department of Animal Science, 2251 Meyer Hall, University of California Davis, Davis, CA 95616, USA
| | - William Joyce
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada, K1N 6N5.,Department of Biology - Zoophysiology, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark
| | - Steve F Perry
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada, K1N 6N5
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11
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Xu ZN, Zheng GD, Wu CB, Jiang XY, Zou SM. Identification of proteins differentially expressed in the gills of grass carp (Ctenopharyngodon idella) after hypoxic stress by two-dimensional gel electrophoresis analysis. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:743-752. [PMID: 30758701 DOI: 10.1007/s10695-018-0599-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Two-dimensional gel electrophoresis (2-DE) was combined with liquid chromatography-mass spectrometry (LC-MS/MS) to identify the differential proteomics of grass carp gills after hypoxic stress to better understand the roles of proteins in the hypoxic response and to explore the possible molecular mechanisms. Protein spots were obtained from a hypoxia-stressed group (372 ± 11 individuals) and a control group (406 ± 14 individuals) using the lmage Master 2D Platinum 7.0 analysis software. Fifteen protein spots were expressed differentially in the hypoxia-stressed group and varied significantly after exposure to the hypoxic conditions. In addition, these differential proteins were identified by mass spectrometry and then searched in a database. We found the expression and upregulation of the toll-like receptor 4, ephx1 protein, isocitrate dehydrogenase, L-lactate dehydrogenase, GTP-binding nuclear protein Ran, and glyceraldehyde-3-phosphate dehydrogenase; however, the expression of the keratin type II cytoskeletal 8, type I cytokeratin, ARP3 actin-related protein 3 homolog, thyroid hormone receptor alpha-A, ATP synthase subunit beta, citrate synthase, tropomyosin 2, and tropomyosin 3 were downregulated. Six proteins were found in the hypoxia-inducible factor-1 (HIF-1) signaling pathway. We concluded that the grass carp gill is involved in response processes, including energy generation, metabolic processes, cellular structure, antioxidation, immunity, and signal transduction, to hypoxic stress. To our knowledge, this is the first study to conduct a proteomics analysis of expressed proteins in the gills of grass carp, and this study will help increase the understanding of the molecular mechanisms involved in hypoxic stress responses in fish at the protein level.
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Affiliation(s)
- Zhan-Ning Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China
- Genetics and Breeding Center for Blunt Snout Bream, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China
| | - Guo-Dong Zheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China
- Genetics and Breeding Center for Blunt Snout Bream, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China
| | - Cheng-Bin Wu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China
- Genetics and Breeding Center for Blunt Snout Bream, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China
| | - Xia-Yun Jiang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China.
- Genetics and Breeding Center for Blunt Snout Bream, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| | - Shu-Ming Zou
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China.
- Genetics and Breeding Center for Blunt Snout Bream, Ministry of Agriculture, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
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12
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Huo D, Sun L, Zhang L, Ru X, Liu S, Yang X, Yang H. Global-warming-caused changes of temperature and oxygen alter the proteomic profile of sea cucumber Apostichopus japonicus. J Proteomics 2019; 193:27-43. [DOI: 10.1016/j.jprot.2018.12.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/05/2018] [Accepted: 12/14/2018] [Indexed: 12/28/2022]
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13
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Abstract
Two-dimensional difference gel electrophoresis (2D-DIGE) appears to be especially useful in quantitative approaches, allowing the co-separation of proteins of control samples from proteins of treatment/disease samples on the same gel, eliminating gel-to-gel variability. The principle of 2D-DIGE is to label proteins prior to isoelectric focusing and use three spectrally resolvable fluorescent dyes, allowing the independent labeling of control and experimental samples. This procedure makes it possible to reduce the number of gels in an experiment, allowing the accurate and reproducible quantification of multiple samples. 2D-DIGE has been found to be an excellent methodical tool in several areas of fish research, including environmental pollution and toxicology, the mechanisms of development and disorders, reproduction, nutrition, evolution, and ecology.
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Affiliation(s)
- Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Mariola A Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland.
| | - Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
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14
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Bowman LL, Kondrateva ES, Timofeyev MA, Yampolsky LY. Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species. Mol Ecol 2018; 27:2544-2559. [PMID: 29691934 DOI: 10.1111/mec.14704] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/13/2022]
Abstract
Local adaptation and phenotypic plasticity are main mechanisms of organisms' resilience in changing environments. Both are affected by gene flow and are expected to be weak in zooplankton populations inhabiting large continuous water bodies and strongly affected by currents. Lake Baikal, the deepest and one of the coldest lakes on Earth, experienced epilimnion temperature increase during the last 100 years, exposing Baikal's zooplankton to novel selective pressures. We obtained a partial transcriptome of Epischura baikalensis (Copepoda: Calanoida), the dominant component of Baikal's zooplankton, and estimated SNP allele frequencies and transcript abundances in samples from regions of Baikal that differ in multiyear average surface temperatures. The strongest signal in both SNP and transcript abundance differentiation is the SW-NE gradient along the 600+ km long axis of the lake, suggesting isolation by distance. SNP differentiation is stronger for nonsynonymous than synonymous SNPs and is paralleled by differential survival during a laboratory exposure to increased temperature, indicating directional selection operating on the temperature gradient. Transcript abundance, generally collinear with the SNP differentiation, shows samples from the warmest, less deep location clustering together with the southernmost samples. Differential expression is more frequent among transcripts orthologous to candidate thermal response genes previously identified in model arthropods, including genes encoding cytoskeleton proteins, heat-shock proteins, proteases, enzymes of central energy metabolism, lipid and antioxidant pathways. We conclude that the pivotal endemic zooplankton species in Lake Baikal exists under temperature-mediated selection and possesses both genetic variation and plasticity to respond to novel temperature-related environmental pressures.
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Affiliation(s)
- Larry L Bowman
- Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee
| | - Elizaveta S Kondrateva
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
| | - Maxim A Timofeyev
- Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk, Russia
| | - Lev Y Yampolsky
- Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee
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15
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Zhang P, Dai Y, Xiong J, Zhu S, Zhao M, Ding S, Li J. iTRAQ-based differential proteomic analysis of the brains in a rat model of delayedcarbon monoxide encephalopathy. Brain Res Bull 2018; 137:329-337. [PMID: 29355713 DOI: 10.1016/j.brainresbull.2018.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/07/2018] [Accepted: 01/12/2018] [Indexed: 11/26/2022]
Abstract
Delayed encephalopathy after acute carbon monoxide poisoning (DEACMP) is a difficult-to-manage neurological complication that can severely affect the life quality of patients. Although the central nervous system (CNS) injuries have been reported, the underlying molecular mechanisms are still unclear. Therefore, we established a rat model of DEACMP, applying isobaric tags for a relative and absolute quantification (iTRAQ)-based proteomics approach to identify differentially expressed proteins in cerebral tissue. A total of 170 proteins in the CO exposure groups were identified as differentially changed. Bioinformatics analysis suggested that these proteins are mainly involved in the biological processes, such as energy metabolism and many neurodegenerative diseases. Three proteins, Glial fibrillary acidic protein (GFAP), mitochondrial malate dehydrogenase (MDHM), and isocitrate dehydrogenase [NAD] subunit alpha (IDH3A), were identified as playing important roles in CNS injuries in DEACMP, and were successfully confirmed by immunohistochemistry analysis. Our study not only offers us new insights into the pathophysiological mechanisms of CNS injuries in DEACMP, but also may provide clinicians with important references in early prevention and treatment.
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Affiliation(s)
- Peng Zhang
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yalei Dai
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Jincheng Xiong
- Chongqing Wanzhou District Public Security Bureau, Chongqing 404000, China
| | - Shisheng Zhu
- Faculty of Medical Technology, Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Minzhu Zhao
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jianbo Li
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China.
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16
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Liu K, Kong X, Ma Y, Lin W. Rational Design of a Robust Fluorescent Probe for the Detection of Endogenous Carbon Monoxide in Living Zebrafish Embryos and Mouse Tissue. Angew Chem Int Ed Engl 2017; 56:13489-13492. [DOI: 10.1002/anie.201707518] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/23/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Keyin Liu
- Institute of Fluorescent Probes for Biological Imaging; School of Chemistry and Chemical Engineering; School of Materials Science and Engineering; University of Jinan; 250022 Jinan Shandong China
| | - Xiuqi Kong
- Institute of Fluorescent Probes for Biological Imaging; School of Chemistry and Chemical Engineering; School of Materials Science and Engineering; University of Jinan; 250022 Jinan Shandong China
| | - Yanyan Ma
- Institute of Fluorescent Probes for Biological Imaging; School of Chemistry and Chemical Engineering; School of Materials Science and Engineering; University of Jinan; 250022 Jinan Shandong China
| | - Weiying Lin
- Institute of Fluorescent Probes for Biological Imaging; School of Chemistry and Chemical Engineering; School of Materials Science and Engineering; University of Jinan; 250022 Jinan Shandong China
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17
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Liu K, Kong X, Ma Y, Lin W. Rational Design of a Robust Fluorescent Probe for the Detection of Endogenous Carbon Monoxide in Living Zebrafish Embryos and Mouse Tissue. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707518] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Keyin Liu
- Institute of Fluorescent Probes for Biological Imaging; School of Chemistry and Chemical Engineering; School of Materials Science and Engineering; University of Jinan; 250022 Jinan Shandong China
| | - Xiuqi Kong
- Institute of Fluorescent Probes for Biological Imaging; School of Chemistry and Chemical Engineering; School of Materials Science and Engineering; University of Jinan; 250022 Jinan Shandong China
| | - Yanyan Ma
- Institute of Fluorescent Probes for Biological Imaging; School of Chemistry and Chemical Engineering; School of Materials Science and Engineering; University of Jinan; 250022 Jinan Shandong China
| | - Weiying Lin
- Institute of Fluorescent Probes for Biological Imaging; School of Chemistry and Chemical Engineering; School of Materials Science and Engineering; University of Jinan; 250022 Jinan Shandong China
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18
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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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19
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Comparative proteomic study of the response to hypoxia in the muscle of oriental river prawn (Macrobrachium nipponense). J Proteomics 2016; 138:115-23. [DOI: 10.1016/j.jprot.2016.02.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/02/2016] [Accepted: 02/22/2016] [Indexed: 01/13/2023]
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20
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Wang Y, Yang L, Zhou K, Zhang Y, Song Z, He S. Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes. Genome Biol Evol 2015; 7:2970-82. [PMID: 26454018 PMCID: PMC5635588 DOI: 10.1093/gbe/evv192] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides, Triplophysa scleroptera, and Triplophysa dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes.
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Affiliation(s)
- Ying Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China University of the Chinese Academy of Sciences, Beijing, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China University of the Chinese Academy of Sciences, Beijing, China
| | - Kun Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan, China
| | - Yanping Zhang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics Breeding, Gansu Fishers Research Institute, Lanzhou, China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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21
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Cui C, Zhou T, Li J, Wang H, Li X, Xiong J, Xu P, Xue M. Proteomic analysis of the mouse brain after repetitive exposure to hypoxia. Chem Biol Interact 2015; 236:57-66. [PMID: 25937538 DOI: 10.1016/j.cbi.2015.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/04/2015] [Accepted: 04/09/2015] [Indexed: 10/23/2022]
Abstract
Hypoxic preconditioning (HPC) is known to have a protective effect against hypoxic damage; however, the precise mechanisms involved remain unknown. In this study, an acute and repetitive hypoxia mouse model, two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) coupled with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/TOF-MS), and Western blot experiments were used to identify the differential expression of key proteins in the mouse brain during HPC. Approximately 2100 2D-DIGE spots were observed following gel imaging and spot detection. Significant differences (p < 0.05) in the expression of 66 proteins were observed between the 3× HPC treatment group and the control group, 45 proteins were observed between the 6× HPC treatment group and the control group, and 70 proteins were observed between the 3× HPC treatment group and the 6× HPC group. Consistent results among Western blot, 2D-DIGE and MS methods were observed for the proteins, ATP synthase subunit alpha, malate dehydrogenase, guanine nucleotide-binding protein subunit beta-1 and proteasome subunit alpha type-2. The proteins associated with ATP synthesis and the citric acid cycle were down-regulated, while those linked to glycolysis and oxygen-binding were up-regulated. This proteomic analysis of the mouse brain after HPC furthers understanding of the molecular pathways involved in the protective effect of HPC and these findings provide new insight into the mechanisms of hypoxia and HPC.
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Affiliation(s)
- Can Cui
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing 10069, China
| | - Tao Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing 10069, China
| | - Jingyi Li
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing 10069, China
| | - Hong Wang
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing 10069, China
| | - Xiaorong Li
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing 10069, China; Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing 100069, China
| | - Jie Xiong
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing 10069, China; Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing 100069, China
| | - Pingxiang Xu
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing 10069, China; Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing 100069, China
| | - Ming Xue
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing 10069, China; Beijing Laboratory for Biomedical Detection Technology and Instrument, Beijing 100069, China.
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22
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Groh KJ, Suter MJF. Stressor-induced proteome alterations in zebrafish: a meta-analysis of response patterns. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:1-12. [PMID: 25498419 DOI: 10.1016/j.aquatox.2014.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/05/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action. We suggest that the results of any differential proteomics experiment performed with zebrafish should be interpreted keeping in mind the list of the most frequent responders that we have identified. Similar reservations should apply to any other species where proteome responses are analyzed by global proteomics methods. Careful consideration of the reliability and significance of observed changes is necessary in order not to over-interpret the experimental results and to prevent the proliferation of false positive linkages between the chemical and the cellular functions it perturbs. We further discuss the implications of the identified "top lists" of frequently responding proteins and protein families, and suggest further directions for proteomics research in ecotoxicology. Apart from improving the proteome coverage, further research should focus on defining the significance of the observed stress response patterns for organism phenotypes and on searching for common upstream regulators that can be targeted by specific assays.
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Affiliation(s)
- Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Marc J-F Suter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, 8092 Zürich, Switzerland
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23
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The hypoxia signaling pathway and hypoxic adaptation in fishes. SCIENCE CHINA-LIFE SCIENCES 2015; 58:148-55. [DOI: 10.1007/s11427-015-4801-z] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/06/2014] [Indexed: 12/17/2022]
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24
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Baral R, Ngounou Wetie AG, Darie CC, Wallace KN. Mass spectrometry for proteomics-based investigation using the zebrafish vertebrate model system. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:331-40. [PMID: 24952190 DOI: 10.1007/978-3-319-06068-2_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The zebrafish (Danio rerio) is frequently being used to investigate the genetics of human diseases as well as resulting pathologies. Ease of both forward and reverse genetic manipulation along with conservation of vertebrate organ systems and disease causing genes has made this system a popular model. Many techniques have been developed to manipulate the genome of zebrafish producing mutants in a vast array of genes. While genetic manipulation of zebrafish has progressed, proteomics have been under-utilized. This review highlights studies that have already been performed using proteomic techniques and as well as our initial proteomic work comparing changes to the proteome between the ascl1a-/- and WT intestine.
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Affiliation(s)
- Reshica Baral
- Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5810, USA
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25
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Tomanek L. Proteomics to study adaptations in marine organisms to environmental stress. J Proteomics 2014; 105:92-106. [PMID: 24788067 DOI: 10.1016/j.jprot.2014.04.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/25/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
Abstract
Comparisons of proteomic responses of closely related congeners and populations have shown which cellular processes are critical to adapt to environmental stress. For example, several proteomic species comparisons showed that increasing abundances of oxidative stress proteins indicate that reactive oxygen species (ROS) represent a ubiquitous signal and possible co-stressor of warm and cold temperature, acute hyposaline and low pH stress, possibly causing a shift from pro-oxidant NADH-producing to anti-oxidant NADPH-producing and -consuming metabolic pathways. Changes in cytoskeletal and actin-binding proteins in response to several stressors, including ROS, suggest that both are important structural and functional elements in responding to stress. Disruption of protein homeostasis, e.g., increased abundance of molecular chaperones, was severe in response to acute heat stress, inducing proteolysis, but was also observed in response to chronic heat and cold stress and was concentrated to the endoplasmic reticulum during hyposaline stress. Small GTPases affecting vesicle formation and transport, Ca(2+)-signaling and ion transport responded to salinity stress in species- and population-specific ways. Aerobic energy metabolism was in general down-regulated in response to temperature, hypoxia, hyposalinity and low pH stress, but other metabolic pathways were activated to respond to increased oxidative stress or to switch metabolic fuels. Thus, comparative proteomics is a powerful approach to identify functionally adaptive variation. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Lars Tomanek
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Sciences, Environmental Proteomics Laboratory, 1 Grand Ave., San Luis Obispo, CA 93407-0401, USA.
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Nolte H, Konzer A, Ruhs A, Jungblut B, Braun T, Krüger M. Global Protein Expression Profiling of Zebrafish Organs Based on in Vivo Incorporation of Stable Isotopes. J Proteome Res 2014; 13:2162-74. [DOI: 10.1021/pr5000335] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Hendrik Nolte
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Anne Konzer
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Aaron Ruhs
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Benno Jungblut
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Thomas Braun
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Marcus Krüger
- Max Planck Institute for
Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
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27
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Spaink HP, Cui C, Wiweger MI, Jansen HJ, Veneman WJ, Marín-Juez R, de Sonneville J, Ordas A, Torraca V, van der Ent W, Leenders WP, Meijer AH, Snaar-Jagalska BE, Dirks RP. Robotic injection of zebrafish embryos for high-throughput screening in disease models. Methods 2013; 62:246-54. [PMID: 23769806 DOI: 10.1016/j.ymeth.2013.06.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/31/2013] [Accepted: 06/03/2013] [Indexed: 12/31/2022] Open
Abstract
The increasing use of zebrafish larvae for biomedical research applications is resulting in versatile models for a variety of human diseases. These models exploit the optical transparency of zebrafish larvae and the availability of a large genetic tool box. Here we present detailed protocols for the robotic injection of zebrafish embryos at very high accuracy with a speed of up to 2000 embryos per hour. These protocols are benchmarked for several applications: (1) the injection of DNA for obtaining transgenic animals, (2) the injection of antisense morpholinos that can be used for gene knock-down, (3) the injection of microbes for studying infectious disease, and (4) the injection of human cancer cells as a model for tumor progression. We show examples of how the injected embryos can be screened at high-throughput level using fluorescence analysis. Our methods open up new avenues for the use of zebrafish larvae for large compound screens in the search for new medicines.
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Affiliation(s)
- Herman P Spaink
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, The Netherlands.
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