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Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity. BMC Ecol Evol 2021; 21:62. [PMID: 33888061 PMCID: PMC8061045 DOI: 10.1186/s12862-021-01787-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 04/08/2021] [Indexed: 12/29/2022] Open
Abstract
Background The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks. Results We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus. Conclusion This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01787-9.
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Maciuszek M, Pijanowski L, Pekala-Safinska A, Palichleb P, Błachut M, Verburg-van Kemenade BML, Chadzińska M. 17α-ethinylestradiol and 4-tert-octylphenol concurrently disrupt the immune response of common carp. FISH & SHELLFISH IMMUNOLOGY 2020; 107:238-250. [PMID: 33038508 DOI: 10.1016/j.fsi.2020.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/30/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
The aquatic environment is massively polluted with endocrine-disrupting compounds (EDCs) including synthetic estrogens (e.g. 17α-ethinylestradiol, EE2) and alkylphenols (e.g. 4-tert-octylphenol, 4t-OP). A major mechanism of action for estrogenic EDCs is their interaction with estrogen receptors and consequently their modulation of the action of enzymes involved in steroid conversion e.g. aromatase CYP19. We now studied the effects of EE2 and 4t-OP on the anti-bacterial immune response of common carp. We investigated effects on the number/composition of inflammatory leukocytes and on the gene expression of mediators that regulate inflammation and EDC binding. In vitro we found that high concentrations of both EE2 and 4t-OP down-regulated IFN-γ2 and IFN-γ-dependent immune responses in LPS-stimulated monocytes/macrophages. Similarly, during bacterial infection in fish, in vivo treated with EE2 and 4t-OP, decreased gene expression of il-12p35 and of ifn-γ2 was found in the focus of inflammation. Moreover, during A. salmonicida-induced infection in EE2-treated carp, but not in fish fed with 4t-OP-treated food, we found an enhanced inflammatory reaction manifested by high number of inflammatory peritoneal leukocytes, including phagocytes and higher expression of pro-inflammatory mediators (inos, il-1β, cxcl8_l2). Furthermore, in the liver, EE2 down-regulated the expression of acute phase proteins: CRPs and C3. Importantly, both in vitro and in vivo, EDCs altered the expression of estrogen receptors: nuclear (erα and erβ) and membrane (gpr30). EDCs also induced up-regulation of the cyp19b gene. Our findings reveal that contamination of the aquatic milieu with estrogenic EDCs, may considerably violate the subtle and particular allostatic interactions between the immune response and endogenous estrogens and this may have negative consequences for fish health.
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Affiliation(s)
- Magdalena Maciuszek
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Lukasz Pijanowski
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Agnieszka Pekala-Safinska
- Department of Fish Diseases, National Veterinary Research Institute, 57 Partyzantow Ave., 24-100, Pulawy, Poland
| | - Paulina Palichleb
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Michał Błachut
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | | | - Magdalena Chadzińska
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland.
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Martyniuk CJ, Feswick A, Munkittrick KR, Dreier DA, Denslow ND. Twenty years of transcriptomics, 17alpha-ethinylestradiol, and fish. Gen Comp Endocrinol 2020; 286:113325. [PMID: 31733209 PMCID: PMC6961817 DOI: 10.1016/j.ygcen.2019.113325] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/14/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023]
Abstract
In aquatic toxicology, perhaps no pharmaceutical has been investigated more intensely than 17alpha-ethinylestradiol (EE2), the active ingredient of the birth control pill. At the turn of the century, the fields of comparative endocrinology and endocrine disruption research witnessed the emergence of omics technologies, which were rapidly adapted to characterize potential hazards associated with exposures to environmental estrogens, such as EE2. Since then, significant advances have been made by the scientific community, and as a result, much has been learned about estrogen receptor signaling in fish from environmental xenoestrogens. Vitellogenin, the egg yolk precursor protein, was identified as a major estrogen-responsive gene, establishing itself as the premier biomarker for estrogenic exposures. Omics studies have identified a plethora of estrogen responsive genes, contributing to a wealth of knowledge on estrogen-mediated regulatory networks in teleosts. There have been ~40 studies that report on transcriptome responses to EE2 in a variety of fish species (e.g., zebrafish, fathead minnows, rainbow trout, pipefish, mummichog, stickleback, cod, and others). Data on the liver and testis transcriptomes dominate in the literature and have been the subject of many EE2 studies, yet there remain knowledge gaps for other tissues, such as the spleen, kidney, and pituitary. Inter-laboratory genomics studies have revealed transcriptional networks altered by EE2 treatment in the liver; networks related to amino acid activation and protein folding are increased by EE2 while those related to xenobiotic metabolism, immune system, circulation, and triglyceride storage are suppressed. EE2-responsive networks in other tissues are not as comprehensively defined which is a knowledge gap as regulated networks are expected to be tissue-specific. On the horizon, omics studies for estrogen-mediated effects in fish include: (1) Establishing conceptual frameworks for incorporating estrogen-responsive networks into environmental monitoring programs; (2) Leveraging in vitro and computational toxicology approaches to identify chemicals associated with estrogen receptor-mediated effects in fish (e.g., male vitellogenin production); (3) Discovering new tissue-specific estrogen receptor signaling pathways in fish; and (4) Developing quantitative adverse outcome pathway predictive models for estrogen signaling. As we look ahead, research into EE2 over the past several decades can serve as a template for the array of hormones and endocrine active substances yet to be fully characterized or discovered.
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Affiliation(s)
- Christopher J Martyniuk
- Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada; Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA; University of Florida Genetics Institute, USA; Canadian Rivers Institute, Canada.
| | - April Feswick
- Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada; Canadian Rivers Institute, Canada
| | - Kelly R Munkittrick
- Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada; Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada; Canadian Rivers Institute, Canada
| | - David A Dreier
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA; Syngenta Crop Protection, LLC, Greensboro, NC, USA
| | - Nancy D Denslow
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA; University of Florida Genetics Institute, USA
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Olsvik PA, Skjærven KH, Søfteland L. Metabolic signatures of bisphenol A and genistein in Atlantic salmon liver cells. CHEMOSPHERE 2017; 189:730-743. [PMID: 28988043 DOI: 10.1016/j.chemosphere.2017.09.076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/14/2017] [Accepted: 09/16/2017] [Indexed: 06/07/2023]
Abstract
Screening has revealed that aquafeeds with high inclusion of plant material may contain small amounts of endocrine disrupting agricultural pesticides. In this work, bisphenol A (BPA) and genistein (GEN) were selected as model endocrine disrupting toxicants with impact on DNA methylation in fish. Atlantic salmon hepatocytes were exposed in vitro to four concentrations of BPA and GEN (0.1, 1.0, 10 and 100 μM) for 48 h. Toxicity endpoints included cytotoxicity, global DNA methylation, targeted transcriptomics and metabolomic screening (100 μM). GEN was not cytotoxic in concentrations up to 100 μM, whereas one out of two cell viability assays indicated a cytotoxic response to 100 μM BPA. Compared to the control, significant global DNA hypomethylation was observed at 1.0 μM BPA. Both compounds upregulated cyp1a1 transcription at 100 μM, while estrogenic markers esr1 and vtg1 responded strongest at 10 μM. Dnmt3aa transcription was downregulated by both compounds at 100 μM. Metabolomic screening showed that BPA and GEN resulted in significant changes in numerous biochemical pathways consistent with alterations in carbohydrate metabolism, indicating perturbation in glucose homeostasis and energy generation, and glutamate metabolism. Pathway analysis showed that while the superpathway of methionine degradation was among the most strongly affected pathways by BPA, GEN induced changes to uridine and pyrimidine biosynthesis. In conclusion, this mechanistic study proposes metabolites associated with glucose and glutamate metabolism, glucuronidation detoxification, as well as cyp1a1, vtg1, esr1, ar, dnmt3aa, cdkn1b and insig1 as transcriptional markers for BPA and GEN exposure in fish liver cells.
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Affiliation(s)
- Pål A Olsvik
- National Institute of Nutrition and Seafood Research (NIFES), Bergen, Norway.
| | - Kaja H Skjærven
- National Institute of Nutrition and Seafood Research (NIFES), Bergen, Norway
| | - Liv Søfteland
- National Institute of Nutrition and Seafood Research (NIFES), Bergen, Norway
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Feswick A, Munkittrick KR, Martyniuk CJ. Estrogen-responsive gene networks in the teleost liver: What are the key molecular indicators? ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2017; 56:366-374. [PMID: 29126055 DOI: 10.1016/j.etap.2017.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 10/28/2017] [Indexed: 06/07/2023]
Abstract
An overarching goal of environmental genomics is to leverage sensitive suites of markers that are robust and reliable to assess biological responses in a range of species inhabiting variable environments. The objective of this study was to identify core groups of transcripts and molecular signaling pathways that respond to 17alpha-ethylinestadiol (EE2), a ubiquitous estrogenic contaminant, using transcriptome datasets generated from six independent laboratories. We sought to determine which biomarkers and gene networks were those most robust and reliably detected in multiple laboratories. Six laboratories conducted microarray analysis in pieces of the same liver from male fathead minnows exposed to ∼15ng/L EE2 for 96h. There were common transcriptional networks identified in every dataset. These included down-regulation of gene networks associated with blood clotting, complement activation, triglyceride storage, and xenobiotic metabolism. Noteworthy was that more than ∼85% of the gene networks were suppressed by EE2. Leveraging both these data and those mined from the Comparative Toxicogenomics Database (CTD), we narrowed in on an EE2-responsive transcriptional network. All transcripts in this network responded ∼±5-fold or more to EE2, increasing reliability of detection. This network included estrogen receptor alpha, transferrin, myeloid cell leukemia 1, insulin like growth factor 1, insulin like growth factor binding protein 2, and methionine adenosyltransferase 2A. This estrogen-responsive interactome has the advantage over single markers (e.g. vitellogenin) in that these entities are directly connected to each other based upon evidence of expression regulation and protein binding. Thus, it represents an interacting functional suite of estrogenic markers. Vitellogenin, the gold standard for estrogenic exposures, can show high individual variability in its response to estrogens, and the use of a multi-gene approach for estrogenic chemicals is expected to improve sensitivity. In our case, the coefficient of variation was significantly lowered by the gene network (∼67%) compared to Vtg alone, supporting the use of this transcriptional network as a sensitive alternative for detecting estrogenic effluents and chemicals. We propose that screening chemicals for estrogenicity using interacting genes within a defined expression network will improve sensitivity, accuracy, and reduce the number of animals required for endocrine disruption assessments.
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Affiliation(s)
- April Feswick
- Department of Biology, University of New Brunswick, Saint John, New Brunswick E2L 4L5, Canada
| | - Kelly R Munkittrick
- Executive Director of Cold Regions and Water Initiatives, Wilfred Laurier University
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA; Department of Biology, University of New Brunswick, Saint John, New Brunswick E2L 4L5, Canada.
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Pietsch C. Zearalenone (ZEN) and Its Influence on Regulation of Gene Expression in Carp (Cyprinus carpio L.) Liver Tissue. Toxins (Basel) 2017; 9:toxins9090283. [PMID: 28914814 PMCID: PMC5618216 DOI: 10.3390/toxins9090283] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/07/2017] [Accepted: 09/12/2017] [Indexed: 11/21/2022] Open
Abstract
Zearalenone (ZEN) is a frequently-occurring mycotoxin in both animal and fish feeds. In order to characterize its effects on carp, three groups of fish were fed for 28 days with feeds contaminated with three different levels of ZEN (low: 332 µg kg−1, medium: 621 µg kg−1, and high: 797 µg kg−1 feed). The reversibility of the effects of ZEN was assessed by feeding all of the groups with uncontaminated feed for a further 14 days. Gene expression of immune genes in the liver tissue of the fish was analysed, revealing reduced expressions of immune, antioxidative, and estrogen-related genes after the fish had been exposed to ZEN. However, the expression of vacuole-type H+ ATPase increased substantially with ZEN exposure, thus supporting the previously-reported sensitivity of lysosomal functions to ZEN. Feeding the fish with a ZEN-free diet for a further two weeks changed the effects of ZEN on the expression of some genes, including the expressions of the cytokines IL-1β, IL-8, IL-10, and arginase 2, which were not influenced after four weeks of treatment, but showed lower values after the recovery phase in fish previously treated with ZEN compared with the control group. In summary, this study confirmed the broad effects of ZEN on different essential functions in carp and suggests that the current maximum allowable levels in compound feed are too high to prevent damage to fish.
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Affiliation(s)
- Constanze Pietsch
- Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences (ZHAW), Grüental, P.O. Box, CH-8820 Waedenswil, Switzerland.
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Szwejser E, Verburg-van Kemenade BML, Maciuszek M, Chadzinska M. Estrogen-dependent seasonal adaptations in the immune response of fish. Horm Behav 2017; 88:15-24. [PMID: 27760301 DOI: 10.1016/j.yhbeh.2016.10.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 12/21/2022]
Abstract
Clinical and experimental evidence shows that estrogens affect immunity in mammals. Less is known about this interaction in the evolutionary older, non-mammalian, vertebrates. Fish form an excellent model to identify evolutionary conserved neuroendocrine-immune interactions: i) they are the earliest vertebrates with fully developed innate and adaptive immunity, ii) immune and endocrine parameters vary with season, and iii) physiology is constantly disrupted by increasing contamination of the aquatic environment. Neuro-immuno-endocrine interactions enable adaption to changing internal and external environment and are based on shared signaling molecules and receptors. The presence of specific estrogen receptors on/in fish leukocytes, implies direct estrogen-mediated immunoregulation. Fish leukocytes most probably are also capable to produce estrogens as they express the cyp19a and cyp19b - genes, encoding aromatase cytochrome P450, the enzyme critical for conversion of C19 steroids to estrogens. Immunoregulatory actions of estrogens, vary among animal species, and also with dose, target cell type, or physiological condition (e.g., infected/non-infected, reproductive status). They moreover are multifaceted. Interestingly, season-dependent changes in immune status correlate with changes in the levels of circulating sex hormones. Whereas E2 circulating in the bloodstream is perhaps the most likely candidate to be the physiological mediator of systemic immune-reproductive trade-offs, leukocyte-derived hormones are hypothesized to be mainly involved in local tuning of the immune response. Contamination of the aquatic environment with estrogenic EDCs may violate the delicate and precise allostatic interactions between the endogenous estrogen system and the immune system. This has negative effects on fish health, but will also affect the physiology of its consumers.
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Affiliation(s)
- Ewa Szwejser
- Department of Evolutionary Immunology, Institute of Zoology, Jagiellonian University, Gronostajowa 9, PL30-387 Krakow, Poland
| | - B M Lidy Verburg-van Kemenade
- Cell Biology and Immunology Group, Dept of Animal Sciences, Wageningen University, P.O. Box 338, 6700 AH Wageningen, The Netherlands
| | - Magdalena Maciuszek
- Department of Evolutionary Immunology, Institute of Zoology, Jagiellonian University, Gronostajowa 9, PL30-387 Krakow, Poland
| | - Magdalena Chadzinska
- Department of Evolutionary Immunology, Institute of Zoology, Jagiellonian University, Gronostajowa 9, PL30-387 Krakow, Poland.
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Genome Wide Identification, Phylogeny, and Expression of Aquaporin Genes in Common Carp (Cyprinus carpio). PLoS One 2016; 11:e0166160. [PMID: 27935978 PMCID: PMC5147823 DOI: 10.1371/journal.pone.0166160] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/24/2016] [Indexed: 12/25/2022] Open
Abstract
Background Aquaporins (Aqps) are integral membrane proteins that facilitate the transport of water and small solutes across cell membranes. Among vertebrate species, Aqps are highly conserved in both gene structure and amino acid sequence. These proteins are vital for maintaining water homeostasis in living organisms, especially for aquatic animals such as teleost fish. Studies on teleost Aqps are mainly limited to several model species with diploid genomes. Common carp, which has a tetraploidized genome, is one of the most common aquaculture species being adapted to a wide range of aquatic environments. The complete common carp genome has recently been released, providing us the possibility for gene evolution of aqp gene family after whole genome duplication. Results In this study, we identified a total of 37 aqp genes from common carp genome. Phylogenetic analysis revealed that most of aqps are highly conserved. Comparative analysis was performed across five typical vertebrate genomes. We found that almost all of the aqp genes in common carp were duplicated in the evolution of the gene family. We postulated that the expansion of the aqp gene family in common carp was the result of an additional whole genome duplication event and that the aqp gene family in other teleosts has been lost in their evolution history with the reason that the functions of genes are redundant and conservation. Expression patterns were assessed in various tissues, including brain, heart, spleen, liver, intestine, gill, muscle, and skin, which demonstrated the comprehensive expression profiles of aqp genes in the tetraploidized genome. Significant gene expression divergences have been observed, revealing substantial expression divergences or functional divergences in those duplicated aqp genes post the latest WGD event. Conclusions To some extent, the gene families are also considered as a unique source for evolutionary studies. Moreover, the whole set of common carp aqp gene family provides an essential genomic resource for future biochemical, toxicological, physiological, and evolutionary studies in common carp.
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Osachoff HL, Brown LL, Tirrul L, van Aggelen GC, Brinkman FS, Kennedy CJ. Time course of hepatic gene expression and plasma vitellogenin protein concentrations in estrone-exposed juvenile rainbow trout (Oncorhynchus mykiss). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 19:112-119. [DOI: 10.1016/j.cbd.2016.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 02/08/2016] [Accepted: 02/21/2016] [Indexed: 12/31/2022]
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Dong C, Xu J, Wang B, Feng J, Jeney Z, Sun X, Xu P. Phylogeny and Evolution of Multiple Common Carp (Cyprinus carpio L.) Populations Clarified by Phylogenetic Analysis Based on Complete Mitochondrial Genomes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:565-575. [PMID: 26054828 DOI: 10.1007/s10126-015-9639-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 05/06/2015] [Indexed: 06/04/2023]
Abstract
Common carp (Cyprinus carpio L.) is one of the oldest, most widely farmed commercially important freshwater fish in the world. However, many undetermined phylogenetic relationships and origins of common carp lineages remain, which are obstacles to conservation and genetic breeding of this species. Phylogenetic analyses based on molecular tools are helpful to distinguish the origin of species, understand and clarify their evolutionary history, and provide a genetic basis for selective breeding. In this study, we demonstrated a method to extract complete mitochondrial genome sequences from whole-genome resequencing data using the Illumina platform. The complete mitochondrial genome sequences of 26 individuals representing nine strains were obtained and subjected to a phylogenetic analysis. We reconstructed the phylogenetic topologies of the nine strains and analyzed the haplotypes. Results from both analyses suggested that the genome sequences belonged to two distinct subspecies from Europe and East Asia. We also estimated the time of divergence of the nine strains, which was up to 100 KYA. The phylogenetic results clarified the breeding history of Songpu mirror carp and suggest that this species may be hybrid of paternal European mirror carp and maternal Xingguo red carp. The results also support a previous hypothesis that koi may have originated from or have close ancestry with Oujiang color carp in China.
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Affiliation(s)
- Chuanju Dong
- CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, 100141, Beijing, China
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Arkoosh MR, Van Gaest AL, Strickland SA, Hutchinson GP, Krupkin AB, Dietrich JP. Dietary Exposure to Individual Polybrominated Diphenyl Ether Congeners BDE-47 and BDE-99 Alters Innate Immunity and Disease Susceptibility in Juvenile Chinook Salmon. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:6974-6981. [PMID: 25938634 DOI: 10.1021/acs.est.5b01076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs), used as commercial flame-retardants, are bioaccumulating in threatened Pacific salmon. However, little is known of PBDE effects on critical physiological functions required for optimal health and survival. BDE-47 and BDE-99 are the predominant PBDE congeners found in Chinook salmon collected from the Pacific Northwest. In the present study, both innate immunity (phagocytosis and production of superoxide anion) and pathogen challenge were used to evaluate health and survival in groups of juvenile Chinook salmon exposed orally to either BDE-47 or BDE-99 at environmentally relevant concentrations. Head kidney macrophages from Chinook salmon exposed to BDE-99, but not those exposed to BDE-47, were found to have a reduced ability in vitro to engulf foreign particles. However, both congeners increased the in vitro production of superoxide anion in head kidney macrophages. Salmon exposed to either congener had reduced survival during challenge with the pathogenic marine bacteria Listonella anguillarum. The concentration response curves generated for these end points were nonmonotonic and demonstrated a requirement for using multiple environmentally relevant PBDE concentrations for effect studies. Consequently, predicting risk from toxicity reference values traditionally generated with monotonic concentration responses may underestimate PBDE effect on critical physiological functions required for optimal health and survival in salmon.
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Massart S, Milla S, Redivo B, Flamion E, Mandiki SNM, Falisse E, Kestemont P. Influence of short-term exposure to low levels of 17α-ethynylestradiol on expression of genes involved in immunity and on immune parameters in rainbow trout, Oncorhynchus mykiss. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 157:57-69. [PMID: 25456220 DOI: 10.1016/j.aquatox.2014.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/29/2014] [Accepted: 10/05/2014] [Indexed: 06/04/2023]
Abstract
Fish are exposed to endocrine-disrupting chemicals (EDC), which are well known to disturb not only the reproductive system but also the immune system in vertebrates. However, the mechanisms by which these compounds are able to modify fish immunity are not well understood. In order to test the EE2 effects on immunity in selected organs, we exposed rainbow trout male juveniles for 3 weeks to EE2 concentrations ranging from 0.01 to 1 μg/L. The results of this study suggest that EE2 affects the immunity of rainbow trout in a tissue dependent manner. This molecule affects both cellular and humoral immune systems. Indeed, blood leukocyte populations, as well as hepatic and plasma lysozyme, plasma MPO and renal complement activities, are modulated by EE2. Moreover, EE2 alters the gene expression of some mucus compounds, hepatic expression of complement sub-unit and lysozyme, or genes involved in the hepatic phagocytosis and transport of immunoglobulin across the liver.
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Affiliation(s)
- Sophie Massart
- Research Unit in Environmental and Evolutionary Biology (URBE), NARILIS, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Sylvain Milla
- Unit Research Animal and Functionality of Animal Products (URAFPA), University of Lorraine, F-54003 Nancy, France
| | - Baptiste Redivo
- Research Unit in Environmental and Evolutionary Biology (URBE), NARILIS, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Enora Flamion
- Research Unit in Environmental and Evolutionary Biology (URBE), NARILIS, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - S N M Mandiki
- Research Unit in Environmental and Evolutionary Biology (URBE), NARILIS, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Elodie Falisse
- Research Unit in Environmental and Evolutionary Biology (URBE), NARILIS, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology (URBE), NARILIS, University of Namur, Rue de Bruxelles, 61, B-5000 Namur, Belgium.
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Colli-Dula RC, Martyniuk CJ, Kroll KJ, Prucha MS, Kozuch M, Barber DS, Denslow ND. Dietary exposure of 17-alpha ethinylestradiol modulates physiological endpoints and gene signaling pathways in female largemouth bass (Micropterus salmoides). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 156:148-60. [PMID: 25203422 PMCID: PMC4252624 DOI: 10.1016/j.aquatox.2014.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 05/13/2023]
Abstract
17Alpha-ethinylestradiol (EE2), used for birth control in humans, is a potent estrogen that is found in wastewater at low concentrations (ng/l). EE2 has the ability to interfere with the endocrine system of fish, affecting reproduction which can result in population level effects. The objective of this study was to determine if dietary exposure to EE2 would alter gene expression patterns and key pathways in the liver and ovary and whether these could be associated with reproductive endpoints in female largemouth bass during egg development. Female LMB received 70ng EE2/g feed (administered at 1% of body weight) for 60 days. EE2 dietary exposure significantly reduced plasma vitellogenin concentrations by 70%. Hepatosomatic and gonadosomatic indices were also decreased with EE2 feeding by 38.5% and 40%, respectively. Transcriptomic profiling revealed that there were more changes in steady state mRNA levels in the liver compared to the ovary. Genes associated with reproduction were differentially expressed, such as vitellogenin in the liver and aromatase in the gonad. In addition, a set of genes related with oxidative stress (e.g. glutathione reductase and glutathione peroxidase) were identified as altered in the liver and genes associated with the immune system (e.g. complement component 1, and macrophage-inducible C-type lectin) were altered in the gonad. In a follow-up study with 0.2ng EE2/g feed for 60 days, similar phenotypic and gene expression changes were observed that support these findings with the higher concentrations. This study provides new insights into how dietary exposure to EE2 interferes with endocrine signaling pathways in female LMB during a critical period of reproductive oogenesis.
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Affiliation(s)
- Reyna-Cristina Colli-Dula
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States
| | - Kevin J Kroll
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States
| | - Melinda S Prucha
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States
| | - Marianne Kozuch
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States
| | - David S Barber
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States
| | - Nancy D Denslow
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States.
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Vandenberg LN, Ehrlich S, Belcher SM, Ben-Jonathan N, Dolinoy DC, Hugo ER, Hunt PA, Newbold RR, Rubin BS, Saili KS, Soto AM, Wang HS, vom Saal FS. Low dose effects of bisphenol A. ACTA ACUST UNITED AC 2014. [DOI: 10.4161/endo.26490] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Effects of clofibric acid alone and in combination with 17β-estradiol on mRNA abundance in primary hepatocytes isolated from rainbow trout. Toxicol In Vitro 2014; 28:1106-16. [DOI: 10.1016/j.tiv.2014.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 05/11/2014] [Accepted: 05/14/2014] [Indexed: 12/08/2022]
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Expression of gene, protein and immunohistochemical localization of the estrogen receptor isoform ERα1 in male rainbow trout lymphoid organs; indication of the role of estrogens in the regulation of immune mechanisms. Comp Biochem Physiol B Biochem Mol Biol 2014; 174:53-61. [DOI: 10.1016/j.cbpb.2014.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 04/19/2014] [Accepted: 06/08/2014] [Indexed: 11/22/2022]
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Xu J, Zhao Z, Zhang X, Zheng X, Li J, Jiang Y, Kuang Y, Zhang Y, Feng J, Li C, Yu J, Li Q, Zhu Y, Liu Y, Xu P, Sun X. Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio). BMC Genomics 2014; 15:307. [PMID: 24762296 PMCID: PMC4234440 DOI: 10.1186/1471-2164-15-307] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 04/17/2014] [Indexed: 12/30/2022] Open
Abstract
Background A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio. Results The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster. Conclusions The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peng Xu
- Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
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Tohmé M, Prud'homme SM, Boulahtouf A, Samarut E, Brunet F, Bernard L, Bourguet W, Gibert Y, Balaguer P, Laudet V. Estrogen-related receptor γ is an in vivo receptor of bisphenol A. FASEB J 2014; 28:3124-33. [PMID: 24744145 DOI: 10.1096/fj.13-240465] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bisphenol A (BPA) is an endocrine disruptor that displays estrogenic activity. Several reports suggest that BPA may have estrogen receptor-independent effects. In zebrafish, 50 μM BPA exposure induces otic vesicle abnormalities, including otolith aggregation. The purpose of this study was to test if BPA action was mediated in vivo during zebrafish development by the orphan nuclear estrogen related receptor (ERR) γ. Combining pharmacological and functional approaches, we demonstrate that the zebrafish ERRγ mediates BPA-induced malformations in otoliths. Using different bisphenol derivatives, we show that different compounds can induce a similar otolith phenotype than BPA and that the binding affinity of these derivatives to the zebrafish ERRγ correlates with their ability to induce otolith malformations. Morpholino knockdown of ERRγ function suppresses the BPA effect on otoliths whereas overexpression of ERRγ led to a BPA-like otolith phenotype. Moreover, a subphenotypical dose of BPA (1 μM) combined with ERRγ overexpression led to a full-dose (50 μM) BPA otolith phenotype. We therefore conclude that ERRγ mediates the otic vesicle phenotype generated by BPA. Our results suggest that the range of pathways perturbed by this compound and its potential harmful effect are larger than expected.-Tohmé, M., Prud'homme, S. M., Boulahtouf, A., Samarut, E., Brunet, F., Bernard, L., Bourguet, W., Gibert, Y., Balaguer, P., Laudet, V. Estrogen-related receptor γ is an in vivo receptor of bisphenol A.
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Affiliation(s)
- Marie Tohmé
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5242, Université Lyon 1, Université de Lyon, Lyon, France
| | - Sophie M Prud'homme
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5242, Université Lyon 1, Université de Lyon, Lyon, France
| | - Abdel Boulahtouf
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM) U896, Centre Régional de la Lutte Contre le Cancer Val d'Aurelle Paul Lamarque, Montpellier, France
| | - Eric Samarut
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5242, Université Lyon 1, Université de Lyon, Lyon, France
| | - Frédéric Brunet
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5242, Université Lyon 1, Université de Lyon, Lyon, France
| | - Laure Bernard
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5242, Université Lyon 1, Université de Lyon, Lyon, France
| | - William Bourguet
- INSERM U1054, Centre de Biochimie Structurale, Montpellier, CNRS UMR5048, Universités Montpellier 1 and 2, Montpellier, France; and
| | - Yann Gibert
- Metabolic Genetic Diseases Laboratory, Metabolic Research Unit, Deakin School of Medicine, Waurn Ponds, Victoria, Australia
| | - Patrick Balaguer
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM) U896, Centre Régional de la Lutte Contre le Cancer Val d'Aurelle Paul Lamarque, Montpellier, France
| | - Vincent Laudet
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5242, Université Lyon 1, Université de Lyon, Lyon, France;
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A dense genetic linkage map for common carp and its integration with a BAC-based physical map. PLoS One 2013; 8:e63928. [PMID: 23704958 PMCID: PMC3660343 DOI: 10.1371/journal.pone.0063928] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 04/09/2013] [Indexed: 12/27/2022] Open
Abstract
Background Common carp (Cyprinus carpio) is one of the most important aquaculture species with an annual global production of 3.4 million metric tons. It is also an important ornamental species as well as an important model species for aquaculture research. To improve the economically important traits of this fish, a number of genomic resources and genetic tools have been developed, including several genetic maps and a bacterial artificial chromosome (BAC)-based physical map. However, integrated genetic and physical maps are not available to study quantitative trait loci (QTL) and assist with fine mapping, positional cloning and whole genome sequencing and assembly. The objective of this study was to integrate the currently available BAC-based physical and genetic maps. Results The genetic map was updated with 592 novel markers, including 312 BAC-anchored microsatellites and 130 SNP markers, and contained 1,209 genetic markers on 50 linkage groups, spanning 3,565.9 cM in the common carp genome. An integrated genetic and physical map of the common carp genome was then constructed, which was composed of 463 physical map contigs and 88 single BACs. Combined lengths of the contigs and single BACs covered a physical length of 498.75 Mb, or around 30% of the common carp genome. Comparative analysis between common carp and zebrafish genomes was performed based on the integrated map, providing more insights into the common carp specific whole genome duplication and segmental rearrangements in the genome. Conclusion We integrated a BAC-based physical map to a genetic linkage map of common carp by anchoring BAC-associated genetic markers. The density of the genetic linkage map was significantly increased. The integrated map provides a tool for both genetic and genomic studies of common carp, which will help us to understand the genomic architecture of common carp and facilitate fine mapping and positional cloning of economically important traits for genetic improvement and modification.
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Zheng W, Xu H, Lam SH, Luo H, Karuturi RKM, Gong Z. Transcriptomic analyses of sexual dimorphism of the zebrafish liver and the effect of sex hormones. PLoS One 2013; 8:e53562. [PMID: 23349717 PMCID: PMC3547925 DOI: 10.1371/journal.pone.0053562] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 11/29/2012] [Indexed: 01/02/2023] Open
Abstract
The liver is one of the most sex-dimorphic organs in both oviparous and viviparous animals. In order to understand the molecular basis of the difference between male and female livers, high-throughput RNA-SAGE (serial analysis of gene expression) sequencing was performed for zebrafish livers of both sexes and their transcriptomes were compared. Both sexes had abundantly expressed genes involved in translation, coagulation and lipid metabolism, consistent with the general function of the liver. For sex-biased transcripts, from in addition to the high enrichment of vitellogenin transcripts in spawning female livers, which constituted nearly 80% of total mRNA, it is apparent that the female-biased genes were mostly involved in ribosome/translation, estrogen pathway, lipid transport, etc, while the male-biased genes were enriched for oxidation reduction, carbohydrate metabolism, coagulation, protein transport and localization, etc. Sexual dimorphism on xenobiotic metabolism and anti-oxidation was also noted and it is likely that retinol x receptor (RXR) and liver x receptor (LXR) play central roles in regulating the sexual differences of lipid and cholesterol metabolisms. Consistent with high ribosomal/translational activities in the female liver, female-biased genes were significantly regulated by two important transcription factors, Myc and Mycn. In contrast, Male livers showed activation of transcription factors Ppargc1b, Hnf4a, and Stat4, which regulate lipid and glucose metabolisms and various cellular activities. The transcriptomic responses to sex hormones, 17β-estradiol (E2) or 11-keto testosterone (KT11), were also investigated in both male and female livers and we found that female livers were relatively insensitive to sex hormone disturbance, while the male livers were readily affected. E2 feminized male liver by up-regulating female-biased transcripts and down-regulating male-biased transcripts. The information obtained in this study provides comprehensive insights into the sexual dimorphism of zebrafish liver transcriptome and will facilitate further development of the zebrafish as a human liver disease model.
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Affiliation(s)
- Weiling Zheng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Hongyan Xu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Siew Hong Lam
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Huaien Luo
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | | | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
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21
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Genome-Wide SNP Discovery from Transcriptome of Four Common Carp Strains. PLoS One 2012; 7:e48140. [PMID: 23110192 PMCID: PMC3482183 DOI: 10.1371/journal.pone.0048140] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 09/20/2012] [Indexed: 01/15/2023] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) have been used as genetic marker for genome-wide association studies in many species. Gene-associated SNPs could offer sufficient coverage in trait related research and further more could themselves be causative SNPs for traits. Common carp (Cyprinus carpio) is one of the most important aquaculture species in the world accounting for nearly 14% of freshwater aquaculture production. There are various strains of common carp with different economic traits, however, the genetic mechanism underlying the different traits have not been elucidated yet. In this project, we identified a large number of gene-associated SNPs from four strains of common carp using next-generation sequencing. Results Transcriptome sequencing of four strains of common carp (mirror carp, purse red carp, Xingguo red carp, Yellow River carp) was performed with Solexa HiSeq2000 platform. De novo assembled transcriptome was used as reference for alignments, and SNP calling was done through BWA and SAMtools. A total of 712,042 Intra-strain SNPs were discovered in four strains, of which 483,276 SNPs for mirror carp, 486,629 SNPs for purse red carp, 478,028 SNPs for Xingguo red carp and 488,281 SNPs for Yellow River carp were discovered, respectively. Besides, 53,893 inter-SNPs were identified. Strain-specific SNPs of four strains were 53,938, 53,866, 48,701, 40,131 in mirror carp, purse red carp, Xingguo red carp and Yellow River carp, respectively. GO and KEGG pathway analysis were done to reveal strain-specific genes affected by strain-specific non-synonymous SNPs. Validation of selected SNPs revealed that 48% percent of SNPs (12 of 25) were tested to be true SNPs. Conclusions Transcriptome analysis of common carp using RNA-Seq is a cost-effective way of generating numerous reads for SNP discovery. After validation of identified SNPs, these data will provide a solid base for SNP array designing and genome-wide association studies.
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Martyniuk CJ, Denslow ND. Exploring androgen-regulated pathways in teleost fish using transcriptomics and proteomics. Integr Comp Biol 2012; 52:695-704. [PMID: 22596056 DOI: 10.1093/icb/ics072] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the environment, there are aquatic pollutants that disrupt androgen signaling in fish. Laboratory and field-based experiments have utilized omics technologies to characterize the molecular mechanisms underlying androgen-receptor agonism/antagonism. Transcriptomics and proteomics studies with 17β-trenbolone, a growth-promoting pharmaceutical found in water systems surrounding cattle feed lots, and androgens such as 17α-methyltestosterone and 17α-methyldihydrotestosterone, have been conducted in ovary and liver of fish that include the fathead minnow (FHM) (Pimephales promelas), common carp (Cyprinus carpio), Qurt medaka (Oryzias latipes), and zebrafish (Danio rerio). In this mini-review, we survey recent omics studies in fish and reveal that, despite the diversity of species and tissues examined, there are common cellular responses that are observed with waterborne androgenic treatments. Recurring themes in gene ontology include apoptosis, transport and oxidation of lipids, synthesis and transport of hormones, immune response, protein metabolism, and cell proliferation. However, we also discuss other mechanisms other than androgen receptor (AR) activation, such as responses to toxicant stress, estrogen receptor agonism, aromatization of androgens into estrogens, and inhibitory feedback mechanisms by high levels of androgens that may also explain molecular responses in fish. To further explore androgen-responsive protein networks, a sub-network enrichment analysis was performed on protein data collected from the livers of female FHMs exposed to 17β-trenbolone. We construct a putative AR-regulated protein/cell process network in the liver that includes B-lymphocyte differentiation, xenobiotic clearance, low-density lipoprotein oxidation, proliferation of smooth muscle cells, and permeability of blood vessels. We demonstrate that construction of protein networks can offer insight into cell processes that are potentially regulated by androgens.
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Affiliation(s)
- Christopher J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, NB E2L 4L5, Canada.
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23
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Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics. PLoS One 2012; 7:e35152. [PMID: 22514716 PMCID: PMC3325976 DOI: 10.1371/journal.pone.0035152] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/08/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Common carp (Cyprinus carpio) is one of the most important aquaculture species of Cyprinidae with an annual global production of 3.4 million tons, accounting for nearly 14% of the freshwater aquaculture production in the world. Due to the economical and ecological importance of common carp, genomic data are eagerly needed for genetic improvement purpose. However, there is still no sufficient transcriptome data available. The objective of the project is to sequence transcriptome deeply and provide well-assembled transcriptome sequences to common carp research community. RESULT Transcriptome sequencing of common carp was performed using Roche 454 platform. A total of 1,418,591 clean ESTs were collected and assembled into 36,811 cDNA contigs, with average length of 888 bp and N50 length of 1,002 bp. Annotation was performed and a total of 19,165 unique proteins were identified from assembled contigs. Gene ontology and KEGG analysis were performed and classified all contigs into functional categories for understanding gene functions and regulation pathways. Open Reading Frames (ORFs) were detected from 29,869 (81.1%) contigs with an average ORF length of 763 bp. From these contigs, 9,625 full-length cDNAs were identified with sequence length from 201 bp to 9,956 bp. Comparative analysis revealed that 27,693(75.2%) contigs have significant similarity to zebrafish Refseq proteins, and 24,371(66.2%), 24,501(66.5%) and 25,025(70.0%) to teraodon, medaka and three-spined stickleback refseq proteins. A total of 2,064 microsatellites were initially identified from 1,730 contigs, and 1,639 unique sequences had sufficient flanking sequences on both sides for primer design. CONCLUSION The transcriptome of common carp had been deep sequenced, de novo assembled and characterized, providing the valuable resource for better understanding of common carp genome. The transcriptome data will facilitate future functional studies on common carp genome, and gradually apply in breeding programs of common carp, as well as closely related other Cyprinids.
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Identification of time-dependent biomarkers by EndoTox Array in cells exposed to nonylphenol. Mol Cell Toxicol 2012. [DOI: 10.1007/s13273-011-0050-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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25
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Trudeau VL, Heyne B, Blais JM, Temussi F, Atkinson SK, Pakdel F, Popesku JT, Marlatt VL, Scaiano JC, Previtera L, Lean DRS. Lumiestrone is Photochemically Derived from Estrone and may be Released to the Environment without Detection. Front Endocrinol (Lausanne) 2011; 2:83. [PMID: 22654829 PMCID: PMC3356028 DOI: 10.3389/fendo.2011.00083] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 11/11/2011] [Indexed: 01/09/2023] Open
Abstract
Endocrine disrupting chemicals are adversely affecting the reproductive health and metabolic status of aquatic vertebrates. Estrone is often the dominant natural estrogen in urban sewage, yet little is known about its environmental fate and biological effects. Increased use of UV-B radiation for effluent treatments, and exposure of effluents to sunlight in holding ponds led us to examine the effects of environmentally relevant levels of UV-B radiation on the photodegradation potential of estrone. Surprisingly, UV-B-mediated degradation leads to the photoproduction of lumiestrone, a little known 13α-epimer form of estrone. We show for the first time that lumiestrone possesses novel biological activity. In vivo treatment with estrone stimulated estrogen receptor (ER) α mRNA production in the male goldfish liver, whereas lumiestrone was without effect, suggesting a total loss of estrogenicity. In contrast, results from in vitro ER-dependent reporter gene assays indicate that lumiestrone showed relatively higher estrogenic potency with the zebrafish ERβ2 than zfERα, suggesting that it may act through an ERβ-selectivity. Lumiestrone also activated human ERs. Microarray analysis of male goldfish liver following in vivo treatments showed that lumiestrone respectively up- and down-regulated 20 and 69 mRNAs, which was indicative of metabolic upsets and endocrine activities. As a photodegradation product from a common estrogen of both human and farm animal origin, lumiestrone is present in sewage effluent, is produced from estrone upon exposure to natural sunlight and should be considered as a new environmental contaminant.
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Affiliation(s)
- Vance L. Trudeau
- Department of Biology, Centre for Advanced Research in Environmental Genomics, University of OttawaOttawa, ON, Canada
| | - Belinda Heyne
- Department of Chemistry, University of OttawaOttawa, ON, Canada
- Department of Chemistry, University of CalgaryCalgary, AB, Canada
| | - Jules M. Blais
- Department of Biology, Centre for Advanced Research in Environmental Genomics, University of OttawaOttawa, ON, Canada
| | - Fabio Temussi
- Department of Chemistry, University of OttawaOttawa, ON, Canada
- Dipartimento Chimica Organica e Biochimica, Universita Federico II NapoliNapoli, Italia
| | - Susanna K. Atkinson
- Department of Biology, Centre for Advanced Research in Environmental Genomics, University of OttawaOttawa, ON, Canada
| | - Farzad Pakdel
- UMR CNRS 6026, IFR 140, Université de Rennes 1Rennes, France
| | - Jason T. Popesku
- Department of Biology, Centre for Advanced Research in Environmental Genomics, University of OttawaOttawa, ON, Canada
| | - Vicki L. Marlatt
- Department of Biology, Centre for Advanced Research in Environmental Genomics, University of OttawaOttawa, ON, Canada
| | - Juan C. Scaiano
- Department of Chemistry, University of OttawaOttawa, ON, Canada
| | - Lucio Previtera
- Dipartimento Chimica Organica e Biochimica, Universita Federico II NapoliNapoli, Italia
| | - David R. S. Lean
- Department of Biology, Centre for Advanced Research in Environmental Genomics, University of OttawaOttawa, ON, Canada
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Xu P, Wang J, Wang J, Cui R, Li Y, Zhao Z, Ji P, Zhang Y, Li J, Sun X. Generation of the first BAC-based physical map of the common carp genome. BMC Genomics 2011; 12:537. [PMID: 22044723 PMCID: PMC3221725 DOI: 10.1186/1471-2164-12-537] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 11/02/2011] [Indexed: 01/23/2023] Open
Abstract
Background Common carp (Cyprinus carpio), a member of Cyprinidae, is the third most important aquaculture species in the world with an annual global production of 3.4 million metric tons, accounting for nearly 14% of the all freshwater aquaculture production in the world. Apparently genomic resources are needed for this species in order to study its performance and production traits. In spite of much progress, no physical maps have been available for common carp. The objective of this project was to generate a BAC-based physical map using fluorescent restriction fingerprinting. Result The first generation of common carp physical map was constructed using four- color High Information Content Fingerprinting (HICF). A total of 72,158 BAC clones were analyzed that generated 67,493 valid fingerprints (5.5 × genome coverage). These BAC clones were assembled into 3,696 contigs with the average length of 476 kb and a N50 length of 688 kb, representing approximately 1.76 Gb of the common carp genome. The largest contig contained 171 BAC clones with the physical length of 3.12 Mb. There are 761 contigs longer than the N50, and these contigs should be the most useful resource for future integrations with linkage map and whole genome sequence assembly. The common carp physical map is available at http://genomics.cafs.ac.cn/fpc/WebAGCoL/Carp/WebFPC/. Conclusion The reported common carp physical map is the first physical map of the common carp genome. It should be a valuable genome resource facilitating whole genome sequence assembly and characterization of position-based genes important for aquaculture traits.
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Affiliation(s)
- Peng Xu
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
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Piña B, Barata C. A genomic and ecotoxicological perspective of DNA array studies in aquatic environmental risk assessment. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2011; 105:40-49. [PMID: 22099343 DOI: 10.1016/j.aquatox.2011.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 06/01/2011] [Accepted: 06/04/2011] [Indexed: 05/31/2023]
Abstract
Ecotoxicogenomics is developing into a key tool for the assessment of environmental impacts and environmental risk assessment for aquatic ecosystems. This review aims to report achievements and drawbacks of this technique and to explore potential conceptual and experimental procedures to improve future investigations. Ecotoxicogenomic literature evidences the ability of genomic technologies to characterize toxicant specific gene transcriptome patterns that can be used to identify major toxicants affecting aquatic species. They also contribute decisively to the development of new molecular biomarkers and, in many cases, to the determination of new possible gene targets. Primary transcriptomic responses obtained after short exposures provided more information of putative gene targets than secondary responses obtained after long, chronic exposures, which in turn are usually more accurate to describe actual environmental impacts in natural populations. Several problems need to be addressed in future investigations: the lack of studies (and genomic information) on key ecological species and taxa, the need to better understand the different transcriptomic responses to high and low doses and, especially, short and long exposures, and the need to improve experimental designs to minimize false transcriptome interpretations of target genes.
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Affiliation(s)
- Benjamin Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Jordi Girona, 18-26, 08034 Barcelona, Spain
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Liu CL, Sung HH. Genes are differentially expressed at transcriptional level of Neocaridina denticulata following short-term exposure to nonylphenol. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2011; 87:220-225. [PMID: 21671034 DOI: 10.1007/s00128-011-0338-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 06/02/2011] [Indexed: 05/30/2023]
Abstract
To assess the toxicity of nonylphenol towards aquatic crustaceans, Neocaridina denticulata were exposed short-term to sublethal concentration (0.001-0.5 mg/L). Following treatment, differentially expressed genes were identified using suppression subtractive hybridization on samples prepared from whole specimens. There were 20 differentially expressed sequence tags that corresponded to known genes and could be divided into six functional classes: defence, translation, metabolism, ribosomal gene expression, respiration, and genes involved in the stress response. Using semi-quantitative RT-PCR, we found that 14 of the differentially expressed sequence tags significantly responded to nonylphenol, including six at a nominal concentration of 0.01 mg/L; among them, 12 genes were down-regulated. These results suggest that under non-lethal concentrations of nonylphenol, the polluted aquatic environment may still present a potential risk to N. denticulata.
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Affiliation(s)
- Chang-Lun Liu
- Department of Microbiology, Soochow University, Taipei, Taiwan
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Li Y, Xu P, Zhao Z, Wang J, Zhang Y, Sun XW. Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:706-712. [PMID: 21088980 DOI: 10.1007/s10126-010-9332-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 11/04/2010] [Indexed: 05/30/2023]
Abstract
A bacterial artificial chromosome (BAC) library of common carp Cyprinus carpio L. was constructed as a part of ongoing common carp genome project, which is aiming assembly of common carp genome. The library, containing a total of 92,160 BAC clones with an average insert size of 141 kb, was constructed into the restriction site of Hind III on BAC vector CopyControl pCC1BAC, covering 7.7 X haploid genome equivalents. Three dimension pools and superpools of the BAC library were established and 23 positive clones of 14 targets were identified from one-fifth of the BAC library. Pilot project of BAC end sequencing was conducted on 2,688 BAC ends from 1,344 clones and harvested 2,522 high-quality Q20 sequences with average length of 677 bp. The sequencing success rate was 93.8% and pair-end success rate was 92.3%. A total of 212 microsyntenies had been established between common carp and zebrafish genomes as a trial for genome-wide comparative genomics in these two closely related species.
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Affiliation(s)
- Yan Li
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China
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Casanova-Nakayama A, Wenger M, Burki R, Eppler E, Krasnov A, Segner H. Endocrine disrupting compounds: can they target the immune system of fish? MARINE POLLUTION BULLETIN 2011; 63:412-6. [PMID: 21683417 DOI: 10.1016/j.marpolbul.2011.05.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Revised: 05/08/2011] [Accepted: 05/09/2011] [Indexed: 05/25/2023]
Abstract
Endocrine disruption, in particular disruption by estrogen-active compounds, has been identified as an important ecotoxicological hazard in the aquatic environment. Research on the impact of endocrine disrupting compounds (EDCs) on wildlife has focused on disturbances of the reproductive system. However, there is increasing evidence that EDCs affect a variety of physiological systems other than the reproductive system. Here, we discuss if EDCs may be able to affect the immune system of fish, as this would have direct implications for individual fitness and population growth. Evidence suggesting an immunomodulatory role of estrogens in fish comes from the following findings: (a) estrogen receptors are expressed in piscine immune organs, (b) immune gene expression is modulated by estrogen exposure, and (c) pathogen susceptibility of fish increases under estrogen exposure.
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Affiliation(s)
- Ayako Casanova-Nakayama
- Centre for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland.
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Martyniuk CJ, Spade DJ, Blum JL, Kroll KJ, Denslow ND. Methoxychlor affects multiple hormone signaling pathways in the largemouth bass (Micropterus salmoides) liver. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2011; 101:483-92. [PMID: 21276474 PMCID: PMC3222593 DOI: 10.1016/j.aquatox.2010.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 11/25/2010] [Accepted: 12/02/2010] [Indexed: 05/02/2023]
Abstract
Methoxychlor (MXC) is an organochlorine pesticide that has been shown to have estrogenic activity by activating estrogen receptors and inducing vitellogenin production in male fish. Previous studies report that exposure to MXC induces changes in mRNA abundance of reproductive genes in the liver and testes of largemouth bass (Micropterus salmoides). The objective of the present study was to better characterize the mode of action of MXC by measuring the global transcriptomic response in the male largemouth liver using an oligonucleotide microarray. Microarray analysis identified highly significant changes in the expression of 37 transcripts (p<0.001) (20 induced and 17 decreased) in the liver after MXC injection and a total of 900 expression changes (p<0.05) in transcripts with high homology to known genes. Largemouth bass estrogen receptor alpha (esr1) and androgen receptor (ar) were among the transcripts that were increased in the liver after MXC treatment. Functional enrichment analysis identified the molecular functions of steroid binding and androgen receptor activity as well as steroid hormone receptor activity as being significantly over-represented gene ontology terms. Pathway analysis identified c-fos signaling as being putatively affected through both estrogen and androgen signaling. This study provides evidence that MXC elicits transcriptional effects through the estrogen receptor as well as androgen receptor-mediated pathways in the liver.
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Affiliation(s)
- Christopher J. Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611 USA
| | - Daniel J. Spade
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611 USA
| | - Jason L. Blum
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611 USA
| | - Kevin J. Kroll
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611 USA
| | - Nancy D. Denslow
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611 USA
- Corresponding author – Nancy Denslow, Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, PO Box 110885, Gainesville, Florida 32611-0885, TEL: 352-294-4642, FAX: 352-392-4707
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Garcia-Reyero N, Perkins EJ. Systems biology: leading the revolution in ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2011; 30:265-273. [PMID: 21072840 DOI: 10.1002/etc.401] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The rapid development of new technologies such as transcriptomics, proteomics, and metabolomics (Omics) are changing the way ecotoxicology is practiced. The data deluge has begun with genomes of over 65 different aquatic species that are currently being sequenced, and many times that number with at least some level of transcriptome sequencing. Integrating these top-down methodologies is an essential task in the field of systems biology. Systems biology is a biology-based interdisciplinary field that focuses on complex interactions in biological systems, with the intent to model and discover emergent properties of the system. Recent studies demonstrate that Omics technologies provide valuable insight into ecotoxicity, both in laboratory exposures with model organisms and with animals exposed in the field. However, these approaches require a context of the whole animal and population to be relevant. Powerful approaches using reverse engineering to determine interacting networks of genes, proteins, or biochemical reactions are uncovering unique responses to toxicants. Modeling efforts in aquatic animals are evolving to interrelate the interacting networks of a system and the flow of information linking these elements. Just as is happening in medicine, systems biology approaches that allow the integration of many different scales of interaction and information are already driving a revolution in understanding the impacts of pollutants on aquatic systems.
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De Wit M, Keil D, van der Ven K, Vandamme S, Witters E, De Coen W. An integrated transcriptomic and proteomic approach characterizing estrogenic and metabolic effects of 17 alpha-ethinylestradiol in zebrafish (Danio rerio). Gen Comp Endocrinol 2010; 167:190-201. [PMID: 20227414 DOI: 10.1016/j.ygcen.2010.03.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 02/28/2010] [Accepted: 03/08/2010] [Indexed: 01/07/2023]
Abstract
Nowadays there is much concern about the presence of endocrine disrupting compounds (EDCs) in the environment due to their ability to interfere with the endocrine system. In the presented study, adult zebrafish (Danio rerio) were exposed to 30 ng L(-1) 17alpha-ethinylestradiol (EE2) for 4 and 28 days. The underlying molecular mechanisms of EE2 were studied in the zebrafish liver by applying a combined transcriptomics and proteomics approach. In addition, we assessed the added value of such an integrated-omics approach. Oligo microarrays, spotted with 3479 zebrafish-specific oligos, were employed to generate differential gene expression levels. The proteomic responses were evaluated by means of differential in-gel electrophoresis (DiGE), combined with MALDI-tandem mass spectrometry. Assessment of the major biological functions of the differentially expressed transcripts and proteins illustrated that both individual platforms could profile a clear estrogenic interference, next to numerous metabolism-related effects and stress responses. Cross-comparison of both transcriptomics and proteomics datasets displayed limited concordance, though, thorough revision of the results illustrated that transcriptional effects were projected on protein level as downstream effects of affected signalling pathways. Overall, this study demonstrated that a proteomics approach can lift the biological interpretation of microarrays to a higher level, and moreover, opens a window for identification of possible new biomarkers.
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Affiliation(s)
- Marijke De Wit
- Laboratory for Ecophysiology, Biochemistry and Toxicology, Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
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Effects of TCDD on Spermatogenesis Related Factor-2 (SRF-2): Gene expression in Xenopus. Toxicol Lett 2009; 191:189-94. [DOI: 10.1016/j.toxlet.2009.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 08/29/2009] [Indexed: 01/17/2023]
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Martyniuk CJ, Denslow ND. Towards functional genomics in fish using quantitative proteomics. Gen Comp Endocrinol 2009; 164:135-41. [PMID: 19523377 DOI: 10.1016/j.ygcen.2009.01.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 01/26/2009] [Accepted: 01/26/2009] [Indexed: 12/19/2022]
Abstract
Microarray and gene expression analysis have been key in our understanding of molecular pathways underlying physiological responses. Arguably, a large number of microarray based studies in fish have examined steroid nuclear receptor signaling (e.g., estrogens, androgens) in the context of both physiology and toxicology. Following close behind the advances in gene expression analysis, novel proteomic tools are available that have been under utilized in fish endocrinology studies. Quantitative proteomic approaches include both gel based (e.g., 2D gel electrophoresis, 2-D Fluorescence Difference Gel Electrophoresis; DIGE) and non-gel based methods that can be separated further into labeling approaches such as stable isotope labeling (SILAC), isotope coded affinity tags (ICAT), and isobaric tagging (iTRAQ) and label-free approaches (e.g., spectral counting and absolute quantitation). This review summarizes quantitative proteomic approaches and describes a successful application of iTRAQ) to study changes in the liver proteome in fathead minnows in response to the androgen, 17beta-trenbolone. The challenge remains to integrate molecular datasets in such a manner as to be able to consider temporal effects and complex regulation at the level of the genome and proteome.
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Affiliation(s)
- Christopher J Martyniuk
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, P.O. Box 110885, Gainesville, FL 32611-0885, USA.
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Goetz FW, Rise ML, Rise M, Goetz GW, Binkowski F, Shepherd BS. Stimulation of growth and changes in the hepatic transcriptome by 17β-estradiol in the yellow perch (Perca flavescens). Physiol Genomics 2009; 38:261-80. [DOI: 10.1152/physiolgenomics.00069.2009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The effects of dietary 17β-estradiol (E2) on growth and liver transcriptomics were investigated in the yellow perch ( Perca flavescens). After a 3-mo treatment, E2 significantly stimulated an increase in length and weight of juvenile male and female perch relative to control animals. The increase was significantly greater in females compared with males. Separate, unnormalized cDNA libraries were constructed from equal quantities of RNA from 6 male and 6 female livers of E2-treated and control perch, and 3,546 and 3,719 expressed sequence tags (ESTs) were obtained, respectively. To characterize E2-regulated transcripts, EST frequencies between libraries were calculated within contiguous sequences that were assembled from the combined ESTs of both libraries. Frequencies were also determined in EST transcript groupings produced by aligning all of the ESTs from both libraries at the nucleotide level. From these analyses, there were 28 annotated transcripts that were regulated by 75% between libraries and for which there were at least 5 ESTs of the same transcript between libraries. Regulation of a subset ( 14 ) of these transcripts was confirmed by quantitative reverse transcription-polymerase chain reaction (QPCR). Transcripts that were upregulated by E2 included reproduction-related proteins, binding proteins, and proteases and protease inhibitors. While not part of the transcript frequency analysis, QPCR showed significant upregulation of estrogen receptor esr1 and of insulin-like growth factor I (IGF-I) in E2 livers. E2-downregulated transcripts represented a variety of functional categories including components of the respiratory chain, lipid transport and metabolism, glycolysis, amino acid and nitrogen metabolism, binding proteins, a hydrolytic enzyme, and a transcriptional regulator. In perch it appears that exogenous estrogen drastically shifts liver metabolism toward the production of lipoproteins and carbohydrate binding proteins, and that the growth-promoting action may involve an increase in hepatic IGF-I production.
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Affiliation(s)
- Frederick W. Goetz
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Matthew L. Rise
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Marlies Rise
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Giles W. Goetz
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Frederick Binkowski
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Brian S. Shepherd
- Great Lakes WATER Institute/Agricultural Research Service/U.S. Department of Agriculture, Milwaukee, Wisconsin
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Lie KK, Meier S, Olsvik PA. Effects of environmental relevant doses of pollutants from offshore oil production on Atlantic cod (Gadus morhua). Comp Biochem Physiol C Toxicol Pharmacol 2009; 150:141-9. [PMID: 19379838 DOI: 10.1016/j.cbpc.2009.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 04/08/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
Abstract
The release of produced water (PW), a by-product of offshore oil production, has increased in Norwegian waters in recent years. Alkylphenols (AP), a major component of PW, have been shown to have endocrine disrupting effects on several fish species. In the present study, four groups of female Atlantic cod (Gadus morhua) were orally exposed for 20 weeks to two different concentrations of a mixture of C4-C7 APs, PW or 17beta-estradiol. The transcriptional responses in the liver of Atlantic female cod were studied using a custom-made cDNA microarray. The largest transcriptional effects were seen in cod exposed to the lowest dose of APs. Several biological processes such as glycolysis, apoptosis and the general stress response were affected by exposure to APs. In addition, genes coding for the detoxification enzymes CYP1A and sulfotransferase 2 were up-regulated in the low exposure group. Significant reduction in gonadosomatic index (GSI) and the concentration of plasma vitellogenin were seen in both AP and 17beta-estradiol exposed cod. Exposure to PW had little effect on GSI and the regulation of stress responsive genes. The findings indicate that chronic exposure to low levels of APs may cause a stress response and delayed maturation in female cod.
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Affiliation(s)
- Kai K Lie
- National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen, Norway.
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Oehlmann J, Schulte-Oehlmann U, Kloas W, Jagnytsch O, Lutz I, Kusk KO, Wollenberger L, Santos EM, Paull GC, Van Look KJW, Tyler CR. A critical analysis of the biological impacts of plasticizers on wildlife. Philos Trans R Soc Lond B Biol Sci 2009; 364:2047-62. [PMID: 19528055 PMCID: PMC2873012 DOI: 10.1098/rstb.2008.0242] [Citation(s) in RCA: 421] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This review provides a critical analysis of the biological effects of the most widely used plasticizers, including dibutyl phthalate, diethylhexyl phthalate, dimethyl phthalate, butyl benzyl phthalate and bisphenol A (BPA), on wildlife, with a focus on annelids (both aquatic and terrestrial), molluscs, crustaceans, insects, fish and amphibians. Moreover, the paper provides novel data on the biological effects of some of these plasticizers in invertebrates, fish and amphibians. Phthalates and BPA have been shown to affect reproduction in all studied animal groups, to impair development in crustaceans and amphibians and to induce genetic aberrations. Molluscs, crustaceans and amphibians appear to be especially sensitive to these compounds, and biological effects are observed at environmentally relevant exposures in the low ng l(-1) to microg l(-1) range. In contrast, most effects in fish (except for disturbance in spermatogenesis) occur at higher concentrations. Most plasticizers appear to act by interfering with the functioning of various hormone systems, but some phthalates have wider pathways of disruption. Effect concentrations of plasticizers in laboratory experiments coincide with measured environmental concentrations, and thus there is a very real potential for effects of these chemicals on some wildlife populations. The most striking gaps in our current knowledge on the impacts of plasticizers on wildlife are the lack of data for long-term exposures to environmentally relevant concentrations and their ecotoxicity when part of complex mixtures. Furthermore, the hazard of plasticizers has been investigated in annelids, molluscs and arthropods only, and given the sensitivity of some invertebrates, effects assessments are warranted in other invertebrate phyla.
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Affiliation(s)
- Jörg Oehlmann
- Department of Aquatic Ecotoxicology, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
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Levi L, Pekarski I, Gutman E, Fortina P, Hyslop T, Biran J, Levavi-Sivan B, Lubzens E. Revealing genes associated with vitellogenesis in the liver of the zebrafish (Danio rerio) by transcriptome profiling. BMC Genomics 2009; 10:141. [PMID: 19335895 PMCID: PMC2678157 DOI: 10.1186/1471-2164-10-141] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 03/31/2009] [Indexed: 11/20/2022] Open
Abstract
Background In oviparous vertebrates, including fish, vitellogenesis consists of highly regulated pathways involving 17β-estradiol (E2). Previous studies focused on a relatively small number of hepatic expressed genes during vitellogenesis. This study aims to identify hepatic genes involved in vitellogenesis and regulated by E2, by using zebrafish microarray gene expression profiling, and to provide information on functional distinctive genes expressed in the liver of a vitellogenic female, using zebrafish as a model fish. Results Genes associated with vitellogenesis were revealed by the following paired t-tests (SAM) comparisons: a) two-month old vitellogenic (Vit2) females were compared with non-vitellogenic (NV) females, showing 825 differentially expressed transcripts during early stages of vitellogenesis, b) four-month old vitellogenic (Vit4) females were compared with NV females, showing 1,046 differentially expressed transcripts during vitellogenesis and c) E2-treated males were compared with control males, showing 1,828 differentially expressed transcripts regulated by E2. A Venn diagram revealed 822 common transcripts in the three groups, indicating that these transcripts were involved in vitellogenesis and putatively regulated by E2. In addition, 431 transcripts were differentially expressed in Vit2 and Vit4 females but not in E2-treated males, indicating that they were putatively not up-regulated by E2. Correspondence analysis showed high similarity in expression profiles of Vit2 with Vit4 and of NV females with control males. The E2-treated males differed from the other groups. The repertoire of genes putatively regulated by E2 in vitellogenic females included genes associated with protein synthesis and reproduction. Genes associated with the immune system processes and biological adhesion, were among the genes that were putatively not regulated by E2. E2-treated males expressed a large array of transcripts that were not associated with vitellogenesis. The study revealed several genes that were not reported before as being regulated by E2. Also, the hepatic expression of several genes was reported here for the first time. Conclusion Gene expression profiling of liver samples revealed 1,046 differentially expressed transcripts during vitellogenesis of which at least ~64% were regulated by E2. The results raise the question on the regulation pattern and temporal pleiotropic expression of hepatic genes in vitellogenic females.
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Affiliation(s)
- Liraz Levi
- Department Marine Biology and Biotechnology, Israel Oceanographic and Limnological Research, Haifa, Israel.
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41
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Carvan MJ, Incardona JP, Rise ML. Meeting the Challenges of Aquatic Vertebrate Ecotoxicology. Bioscience 2008. [DOI: 10.1641/b581105] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Garcia-Reyero N, Griffitt RJ, Liu L, Kroll KJ, Farmerie WG, Barber DS, Denslow ND. Construction of a robust microarray from a non-model species (largemouth bass) using pyrosequencing technology. JOURNAL OF FISH BIOLOGY 2008; 72:2354-2376. [PMID: 19936325 PMCID: PMC2779536 DOI: 10.1111/j.1095-8649.2008.01904.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A novel custom microarray for largemouth bass (Micropterus salmoides) was designed with sequences obtained from a normalized cDNA library using the 454 Life Sciences GS-20 pyrosequencer. This approach yielded in excess of 58 million bases of high-quality sequence. The sequence information was combined with 2,616 reads obtained by traditional suppressive subtractive hybridizations to derive a total of 31,391 unique sequences. Annotation and coding sequences were predicted for these transcripts where possible. 16,350 annotated transcripts were selected as target sequences for the design of the custom largemouth bass oligonucleotide microarray. The microarray was validated by examining the transcriptomic response in male largemouth bass exposed to 17beta-oestradiol. Transcriptomic responses were assessed in liver and gonad, and indicated gene expression profiles typical of exposure to oestradiol. The results demonstrate the potential to rapidly create the tools necessary to assess large scale transcriptional responses in non-model species, paving the way for expanded impact of toxicogenomics in ecotoxicology.
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Affiliation(s)
- Natàlia Garcia-Reyero
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
| | - Robert J. Griffitt
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
| | - Li Liu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Kevin J. Kroll
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
| | - William G. Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - David S. Barber
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
| | - Nancy D. Denslow
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
- Corresponding author: CEHT. 471 Mowry Road. Gainesville, FL-32611. USA. Phone: +1-352-392-2243 ext 5583. Fax: +1-352-392-4707.
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Lv W, Zhang Y, Wu Z, Chu L, Koide SS, Chen Y, Yan Y, Li Y. Identification of WSB1 gene as an important regulator in the development of zebrafish embryo during midblastula transition. Acta Biochim Biophys Sin (Shanghai) 2008; 40:478-88. [PMID: 18535746 DOI: 10.1111/j.1745-7270.2008.00427.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To uncover novel genes potentially involved in embryo development, especially at the midblastula transition (MBT) phase in the developing embryo of zebrafish, Affymetrix zebrafish GeneChip microarray analysis was carried out on the expression of 14,900 gene transcripts. The results of the analysis showed that 360 genes were clearly up-regulated and 119 genes were markedly down-regulated. Many of these genes were involved in transcription factor activity, nucleic acid binding, and cell growth. The present study showed that significant changes in transcript abundance occurred during the MBT phase. The expression of eight of these 479 genes was identified by reverse transcription-polymerase chain reaction analysis, confirming the microarray results. The WSB1 gene, found to be down-regulated by the microarray and reverse transcription-polymerase chain reaction analyses, was selected for further study. Sequence analysis of the WSB1 gene showed that it encodes a protein with 75% identity to the corresponding active human orthologs. In addition, WSB1 gene expression was detected at a higher level at 2 h post fertilization and at a lower level at 4 h post fertilization, consistent with the chip results. Overexpression of the WSB1 gene can result in the formation of abnormalities in embryos, as determined by fluorescence-activated cell sorting. The present study showed unequivocally that the occurrence of WSB1 expression is an important event during the MBT phase in the development of zebrafish embryos.
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Affiliation(s)
- Wenjian Lv
- Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Shanghai 200031, China
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