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Campos A, Freitas M, de Almeida AM, Martins JC, Domínguez-Pérez D, Osório H, Vasconcelos V, Reis Costa P. OMICs Approaches in Diarrhetic Shellfish Toxins Research. Toxins (Basel) 2020; 12:E493. [PMID: 32752012 PMCID: PMC7472309 DOI: 10.3390/toxins12080493] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
Diarrhetic shellfish toxins (DSTs) are among the most prevalent marine toxins in Europe's and in other temperate coastal regions. These toxins are produced by several dinoflagellate species; however, the contamination of the marine trophic chain is often attributed to species of the genus Dinophysis. This group of toxins, constituted by okadaic acid (OA) and analogous molecules (dinophysistoxins, DTXs), are highly harmful to humans, causing severe poisoning symptoms caused by the ingestion of contaminated seafood. Knowledge on the mode of action and toxicology of OA and the chemical characterization and accumulation of DSTs in seafood species (bivalves, gastropods and crustaceans) has significantly contributed to understand the impacts of these toxins in humans. Considerable information is however missing, particularly at the molecular and metabolic levels involving toxin uptake, distribution, compartmentalization and biotransformation and the interaction of DSTs with aquatic organisms. Recent contributions to the knowledge of DSTs arise from transcriptomics and proteomics research. Indeed, OMICs constitute a research field dedicated to the systematic analysis on the organisms' metabolisms. The methodologies used in OMICs are also highly effective to identify critical metabolic pathways affecting the physiology of the organisms. In this review, we analyze the main contributions provided so far by OMICs to DSTs research and discuss the prospects of OMICs with regard to the DSTs toxicology and the significance of these toxins to public health, food safety and aquaculture.
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Affiliation(s)
- Alexandre Campos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
| | - Marisa Freitas
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
- ESS-P.Porto, School of Health, Polytechnic Institute of Porto. Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
| | - André M. de Almeida
- LEAF-Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal;
| | - José Carlos Martins
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
| | - Dany Domínguez-Pérez
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
| | - Hugo Osório
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
- Ipatimup—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Vitor Vasconcelos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro Reis Costa
- IPMA—Instituto Português do Mar da Atmosfera, Rua Alfredo Magalhães Ramalho, 6, 1495-006 Lisbon, Portugal;
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Kumar G, Denslow ND. Gene Expression Profiling in Fish Toxicology: A Review. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2017; 241:1-38. [PMID: 27464848 DOI: 10.1007/398_2016_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this review, we present an overview of transcriptomic responses to chemical exposures in a variety of fish species. We have discussed the use of several molecular approaches such as northern blotting, differential display reverse transcription-polymerase chain reaction (DDRT-PCR), suppression subtractive hybridization (SSH), real time quantitative PCR (RT-qPCR), microarrays, and next-generation sequencing (NGS) for measuring gene expression. These techniques have been mainly used to measure the toxic effects of single compounds or simple mixtures in laboratory conditions. In addition, only few studies have been conducted to examine the biological significance of differentially expressed gene sets following chemical exposure. Therefore, future studies should focus more under field conditions using a multidisciplinary approach (genomics, proteomics and metabolomics) to understand the synergetic effects of multiple environmental stressors and to determine the functional significance of differentially expressed genes. Nevertheless, recent developments in NGS technologies and decreasing costs of sequencing holds the promise to uncover the complexity of anthropogenic impacts and biological effects in wild fish populations.
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Affiliation(s)
- Girish Kumar
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic.
| | - Nancy D Denslow
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, 32611, USA
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Brinke A, Buchinger S. Toxicogenomics in Environmental Science. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 157:159-186. [DOI: 10.1007/10_2016_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Mu W, Wen H, Li J, He F. Cloning and expression analysis of a HSP70 gene from Korean rockfish (Sebastes schlegeli). FISH & SHELLFISH IMMUNOLOGY 2013; 35:1111-1121. [PMID: 23877000 DOI: 10.1016/j.fsi.2013.07.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/27/2013] [Accepted: 07/11/2013] [Indexed: 06/02/2023]
Abstract
The gene encoding HSP70 was isolated from Korean rockfish Sebastes schlegeli by homologous cloning and rapid amplification of cDNA ends (RACE). The full-length of HSP70 cDNA was composed of 2259 bp and encoded a polypeptide of 639 amino acids. BLAST analysis showed that HSP70 of S. schlegeli shared high identities with those of the Lates calcarifer, Oreochromis niloticus, Seriola quinqueradiata HSP70s (88-89%). Our current study also revealed that HSP70 of Korean rockfish was expressed in many tissues by RT-PCR under unstressed condition. Quantitative real-time PCR showed that the expression patterns of Korean rockfish HSP70 were developmental stage-dependency. The expression of HSP70 was measured by quantitative real-time PCR after different oxygen treatments. The results showed that expression of HSP70 increased significantly after exposure to hypoxia for 30 min in gill and ovary, and then decreased for 60 min, and the level in spleen and liver gradually increased and reached the highest at 60 min. In addition, in gill, spleen and liver, the HSP70 mRNA level reached the maximum in hypoxia group after one hour different oxygen concentration stress. Increased amounts of serum thyroxine (T4), and triiodothyronine (T3) were also found during 30 min hypoxia treatment and 60 min normoxia group in our study. All of the results provide information to further study the mechanism of physiology and immune function under stress conditions of ovoviviparous teleosts.
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Affiliation(s)
- Weijie Mu
- Fisheries College, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
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Mehinto AC, Martyniuk CJ, Spade DJ, Denslow ND. Applications for next-generation sequencing in fish ecotoxicogenomics. Front Genet 2012; 3:62. [PMID: 22539934 PMCID: PMC3336092 DOI: 10.3389/fgene.2012.00062] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/02/2012] [Indexed: 01/23/2023] Open
Abstract
The new technologies for next-generation sequencing (NGS) and global gene expression analyses that are widely used in molecular medicine are increasingly applied to the field of fish biology. This has facilitated new directions to address research areas that could not be previously considered due to the lack of molecular information for ecologically relevant species. Over the past decade, the cost of NGS has decreased significantly, making it possible to use non-model fish species to investigate emerging environmental issues. NGS technologies have permitted researchers to obtain large amounts of raw data in short periods of time. There have also been significant improvements in bioinformatics to assemble the sequences and annotate the genes, thus facilitating the management of these large datasets.The combination of DNA sequencing and bioinformatics has improved our abilities to design custom microarrays and study the genome and transcriptome of a wide variety of organisms. Despite the promising results obtained using these techniques in fish studies, NGS technologies are currently underused in ecotoxicogenomics and few studies have employed these methods. These issues should be addressed in order to exploit the full potential of NGS in ecotoxicological studies and expand our understanding of the biology of non-model organisms.
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Affiliation(s)
- Alvine C Mehinto
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
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Zhang Z, Wells MC, Boswell MG, Beldorth I, Kirk LM, Wang Y, Wang S, Savage M, Walter RB, Booth RE. Identification of robust hypoxia biomarker candidates from fin of medaka (Oryzias latipes). Comp Biochem Physiol C Toxicol Pharmacol 2012; 155:11-7. [PMID: 21664487 PMCID: PMC3212644 DOI: 10.1016/j.cbpc.2011.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 05/24/2011] [Accepted: 05/24/2011] [Indexed: 01/28/2023]
Abstract
Aquatic hypoxia caused by organic pollution and eutrophication is a pressing worldwide water pollution problem. Better methods for monitoring oxygen levels are needed to assist efforts to maintain and protect the health of natural aquatic environments. In this project, we used a Japanese ricefish (medaka, Oryzias latipes) 8K oligonucleotide array as a platform to identify potential hypoxic biomarkers in different organs (fin, gill, liver and brain) upon exposure to hypoxia. The microarray results were validated by qRT-PCR employing a subset of candidate biomarkers. Interestingly, the largest number and most significant of hypoxia responding array features were detected in hypoxia exposed fin tissues. We identified 173 array features that exhibited a significant response (over 2 fold change in expression) upon exposure to hypoxic conditions and validated a subset of these by quantitative RT-PCR. These gene targets were subjected to annotation and gene ontology mining. Positively identifiable gene targets that may be useful for development of a rapid and accurate biomarker test using fin clips are discussed in relation to previous reports on hypoxia responsive genes.
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Affiliation(s)
- Ziping Zhang
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Melissa C. Wells
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Mikki G. Boswell
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Ion Beldorth
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Lyndsey M. Kirk
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Yilei Wang
- Key Laboratory of Science and Technology for Aquaculture and Food Safety of Fujian Province University, Fisheries College/Fisheries Biotechnology Institute, Jimei University, Xiamen 361021, China
| | - Shulong Wang
- Key Laboratory of Science and Technology for Aquaculture and Food Safety of Fujian Province University, Fisheries College/Fisheries Biotechnology Institute, Jimei University, Xiamen 361021, China
| | - Markita Savage
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Ronald B. Walter
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Rachell E. Booth
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
- Corresponding author: Rachell E. Booth, Tel.: +1 512 245 2327; fax: +1 512 245 1922,
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Mazurais D, Darias M, Zambonino-Infante J, Cahu C. Transcriptomics for understanding marine fish larval development1This review is part of a virtual symposium on current topics in aquaculture of marine fish and shellfish. CAN J ZOOL 2011. [DOI: 10.1139/z11-036] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The larval phase is a crucial period in the life of marine fish. During this phase, the organism will acquire the phenotype of an adult fish through the development of tissues and organs and the maturation of some of the principal physiological functions. Many biological processes (differentiation, cellular proliferation, growth, etc.) are regulated during this period. These regulations take place at different biological levels and particularly concern the expression of genes involved in larval ontogenesis processes. The development of bioinformatic resources (DNA or cDNA sequences) and molecular tools enabling high throughput gene expression analysis (microarrays) have allowed the transcriptome of marine fish species to be studied. In the present review, we summarize the main findings from transcriptomic investigations of development of marine fish larvae. Special attention is paid to investigations of transcriptomic patterns during postembryonic development and to the impact of environmental or nutritional factors on the transcriptome of marine fish larvae. Transcriptomic approaches will be especially useful in the future for investigating the effect of temperature and water acidification (or pH) on the development of different fish species in the context of global climate change.
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Affiliation(s)
- D. Mazurais
- Institut Français de Recherche pour l’Exploitation de la Mer (IFREMER), Technopole Brest Iroise, BP70, 29280 Plouzané, France
| | - M. Darias
- Investigación y Tecnología Agroalimentarias – Centre de Sant Carles de la Ràpita (IRTA–SCR), Unitat de Cultius Experimentals, Carretera del Poble Nou s/n, 43540 – Sant Carles de la Ràpita, Spain
| | - J.L. Zambonino-Infante
- Institut Français de Recherche pour l’Exploitation de la Mer (IFREMER), Technopole Brest Iroise, BP70, 29280 Plouzané, France
| | - C.L. Cahu
- Institut Français de Recherche pour l’Exploitation de la Mer (IFREMER), Technopole Brest Iroise, BP70, 29280 Plouzané, France
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Li S, Pozhitkov A, Ryan RA, Manning CS, Brown-Peterson N, Brouwer M. Constructing a fish metabolic network model. Genome Biol 2010; 11:R115. [PMID: 21114829 PMCID: PMC3156954 DOI: 10.1186/gb-2010-11-11-r115] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/26/2010] [Accepted: 11/29/2010] [Indexed: 12/25/2022] Open
Abstract
We report the construction of a genome-wide fish metabolic network model, MetaFishNet, and its application to analyzing high throughput gene expression data. This model is a stepping stone to broader applications of fish systems biology, for example by guiding study design through comparison with human metabolism and the integration of multiple data types. MetaFishNet resources, including a pathway enrichment analysis tool, are accessible at http://metafishnet.appspot.com.
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Affiliation(s)
- Shuzhao Li
- Gulf Coast Research Laboratory, Department of Coastal Sciences, University of Southern Mississippi, 703 East Beach Drive, Ocean Springs, MS 39564, USA.
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Nazar RN, Chen P, Dean D, Robb J. DNA chip analysis in diverse organisms with unsequenced genomes. Mol Biotechnol 2010; 44:8-13. [PMID: 19757211 DOI: 10.1007/s12033-009-9212-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Whether for basic research or biotechnology, DNA microarrays have become indispensable tools for studying the transcriptome. Normally, analyses begin with a set of known cDNA sequences to prepare microarray chips specific for a target organism with an extensively sequenced and annotated genome. For many organisms, however, genome programs are not complete or have not been initiated. The present study demonstrates that, whether using homologous or heterologous arrays, the chances of seeing interesting differences are similar. When a specific DNA microarray is not available, the results indicate that a reverse approach based on a heterologous array can be used to probe for interesting differences in gene expression. This may be sufficient in many studies but, if necessary, the genes exhibiting the most significant changes subsequently could be identified by traditional molecular approaches. Such a reverse strategy can provide a convenient and inexpensive approach to probe for significant genetic changes in many diverse studies, to monitor or mine critical biological information for basic or applied research, long before complete sequence data are available.
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Affiliation(s)
- Ross N Nazar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Cheng F, Cho SH, Lee JK. Multi-gene expression-based statistical approaches to predicting patients' clinical outcomes and responses. Methods Mol Biol 2010; 620:471-484. [PMID: 20652516 DOI: 10.1007/978-1-60761-580-4_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Gene expression profiling technique now enables scientists to obtain a genome-wide picture of cellular functions on various human disease mechanisms which has also proven to be extremely valuable in forecasting patients' prognosis and therapeutic responses. A wide range of multivariate techniques have been employed in biomedical applications on such expression profiling data in order to identify expression biomarkers that are highly associated with patients' clinical outcome and to train multi-gene prediction models that can forecast various human disease outcome and drug toxicities. We provide here a brief overview on some of these approaches, succinctly summarizing relevant basic concepts, statistical algorithms, and several practical applications. We also introduce our recent in vitro molecular expression-based algorithm, the so-called COXEN technique, which uses specialized gene profile signatures as a Rosetta Stone for translating the information between two different biological systems or populations.
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Affiliation(s)
- Feng Cheng
- Department of Biophysics, University of Virginia, Charlottesville, VA, USA
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Gene expression profile of grass shrimp Palaemonetes pugio exposed to chronic hypoxia. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2009; 4:196-208. [DOI: 10.1016/j.cbd.2009.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 03/25/2009] [Accepted: 03/27/2009] [Indexed: 12/17/2022]
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Hinton DE, Hardman RC, Kullman SW, (Mac) Law JM, Schmale MC, Walter RB, Winn RN, Yoder JA. Aquatic animal models of human disease: selected papers and recommendations from the 4th Conference. Comp Biochem Physiol C Toxicol Pharmacol 2009; 149:121-8. [PMID: 19150511 PMCID: PMC2676715 DOI: 10.1016/j.cbpc.2008.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- David E. Hinton
- Division of Environmental Sciences and Policy, Nicholas School of the Environment, Duke University, Box 90328, A333B LSRC, Durham, NC 27708-0328, USA, Email address: , Tel.: +1 919 613 8038, Fax.: +1 919 684 8741
| | - Ron C. Hardman
- Division of Environmental Sciences and Policy, Nicholas School of the Environment, Duke University, Box 90328, A333A LSRC, Durham, NC 27708-0328, USA, Email address: , Tel.: +1 919 613 8038, Fax.: +1 919 684 8741
| | - Seth W. Kullman
- Department of Environmental and Molecular Toxicology, Box 7633, North Carolina State University, Raleigh, NC 27695-7633, Email address: , Tel.: +1 919 515 2274, Fax.: +1 919 515 7169
| | - Jerry M. (Mac) Law
- Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, Email address: , Tel.: +1 919 515 7411, Fax.: +1 919 515 3044
| | - Michael C. Schmale
- Division of Marine Biology and Fisheries, Rosentiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy. Miami, FL 33149, USA, Email address: , Tel.:+1 305 421 4140, Fax.: +1 305 421 4600
| | - Ronald B. Walter
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, Email address: , Tel.: +1 512 245 0357, Fax.: +1 512 245 1922
| | - Richard N. Winn
- Aquatic Biotechnology and Environmental Lab (ABEL), 2580 Devil’s Ford Road, Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA, Email address: , Tel.: +1 706 369 5858, Fax.: +1 706 353 2620
| | - Jeffrey A. Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606 USA, Email address: , Tel.: +1 919 515 7406, Fax.: +1 919 513 7301
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Boswell MG, Wells MC, Kirk LM, Ju Z, Zhang Z, Booth RE, Walter RB. Comparison of gene expression responses to hypoxia in viviparous (Xiphophorus) and oviparous (Oryzias) fishes using a medaka microarray. Comp Biochem Physiol C Toxicol Pharmacol 2009; 149:258-65. [PMID: 19049829 DOI: 10.1016/j.cbpc.2008.11.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 11/05/2008] [Accepted: 11/07/2008] [Indexed: 02/02/2023]
Abstract
Gene expression profiling using DNA microarray technology is a useful tool for assessing gene transcript level responses after an organism is exposed to environmental stress. Herein, we detail results from studies using an 8 k medaka (Oryzias latipes) microarray to assess modulated gene expression patterns upon hypoxia exposure of the live-bearing aquaria fish, Xiphophorus maculatus. To assess the reproducibility and reliability of using the medaka array in cross-genus hybridization, a two-factor ANOVA analysis of gene expression was employed. The data show the tissue source of the RNA used for array hybridization contributed more to the observed response of modulated gene targets than did the species source of the RNA. In addition, hierarchical clustering via heat map analyses of groupings of tissues and species (Xiphophorus and medaka) suggests that hypoxia induced similar responses in the same tissues from these two diverse aquatic model organisms. Our Xiphophorus results indicate 206 brain, 37 liver, and 925 gill gene targets exhibit hypoxia induced expression changes. Analysis of the Xiphophorus data to determine those features exhibiting a significant (p<0.05)+/-3 fold change produced only two gene targets within brain tissue and 80 features within gill tissue. Of these 82 characterized features, 39 were identified via homology searching (cut-off E-value of 1 x 10(-5)) and placed into one or more biological process gene ontology groups. Among these 39 genes, metabolic energy changes and manipulation was the most affected biological pathway (13 genes).
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Affiliation(s)
- Mikki G Boswell
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
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Broussard GW, Norris MB, Schwindt AR, Fournie JW, Winn RN, Kent ML, Ennis DG. Chronic Mycobacterium marinum infection acts as a tumor promoter in Japanese Medaka (Oryzias latipes). Comp Biochem Physiol C Toxicol Pharmacol 2009; 149:152-60. [PMID: 18929684 PMCID: PMC2700008 DOI: 10.1016/j.cbpc.2008.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 09/13/2008] [Accepted: 09/14/2008] [Indexed: 12/11/2022]
Abstract
An accumulating body of research indicates there is an increased cancer risk associated with chronic infections. The genus Mycobacterium contains a number of species, including M. tuberculosis, which mount chronic infections and have been implicated in higher cancer risk. Several non-tuberculosis mycobacterial species, including M. marinum, are known to cause chronic infections in fish and like human tuberculosis, often go undetected. The elevated carcinogenic potential for fish colonies infected with Mycobacterium spp. could have far reaching implications because fish models are widely used to study human diseases. Japanese medaka (Oryzias latipes) is an established laboratory fish model for toxicology, mutagenesis, and carcinogenesis; and produces a chronic tuberculosis-like disease when infected by M. marinum. We examined the role that chronic mycobacterial infections play in cancer risk for medaka. Experimental M. marinum infections of medaka alone did not increase the mutational loads or proliferative lesion incidence in all tissues examined. However, we showed that chronic M. marinum infections increased hepatocellular proliferative lesions in fish also exposed to low doses of the mutagen benzo[a]pyrene. These results indicate that chronic mycobacterial infections of medaka are acting as tumor promoters and thereby suggest increased human risks for cancer promotion in human populations burdened with chronic tuberculosis infections.
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Affiliation(s)
- Gregory W. Broussard
- Department of Biology, University of Louisiana, P.O. Box 42451, Lafayette, LA 70504-2451, USA
| | - Michelle B. Norris
- Warnell School of Forestry and Natural Resources, University of Georgia, Aquatic Biotechnology and Environmental Lab, 2580 Devil’s Ford Road, Athens, GA 30602, USA
| | - Adam R. Schwindt
- Center for Fish Disease Research, Department of Microbiology, 220 Nash, Oregon State University, Corvallis, OR 97331-3804, USA
| | - John W. Fournie
- U.S. Environmental Protection Agency, Gulf Ecology Division, 1 Sabine Island Drive, Gulf Breeze, FL 32561, USA
| | - Richard N. Winn
- Warnell School of Forestry and Natural Resources, University of Georgia, Aquatic Biotechnology and Environmental Lab, 2580 Devil’s Ford Road, Athens, GA 30602, USA
| | - Michael L. Kent
- Center for Fish Disease Research, Department of Microbiology, 220 Nash, Oregon State University, Corvallis, OR 97331-3804, USA
| | - Don G. Ennis
- Department of Biology, University of Louisiana, P.O. Box 42451, Lafayette, LA 70504-2451, USA
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Prunet P, Cairns MT, Winberg S, Pottinger TG. Functional Genomics of Stress Responses in Fish. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/10641260802341838] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Filanoski B, Rastogi SK, Cameron E, Mishra NN, Maki W, Maki G. A novel homogeneous bioluminescence resonance energy transfer element for biomolecular detection with CCD camera or CMOS device. LUMINESCENCE 2008; 23:22-7. [DOI: 10.1002/bio.1011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Sensitive and robust gene expression changes in fish exposed to estrogen--a microarray approach. BMC Genomics 2007; 8:149. [PMID: 17555559 PMCID: PMC1899179 DOI: 10.1186/1471-2164-8-149] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 06/07/2007] [Indexed: 01/30/2023] Open
Abstract
Background Vitellogenin is a well established biomarker for estrogenic exposure in fish. However, effects on gonadal differentiation at concentrations of estrogen not sufficient to give rise to a measurable vitellogenin response suggest that more sensitive biomarkers would be useful. Induction of zona pellucida genes may be more sensitive but their specificities are not as clear. The objective of this study was to find additional sensitive and robust candidate biomarkers of estrogenic exposure. Results Hepatic mRNA expression profiles were characterized in juvenile rainbow trout exposed to a measured concentration of 0.87 and 10 ng ethinylestradiol/L using a salmonid cDNA microarray. The higher concentration was used to guide the subsequent identification of generally more subtle responses at the low concentration not sufficient to induce vitellogenin. A meta-analysis was performed with data from the present study and three similar microarray studies using different fish species and platforms. Within the generated list of presumably robust responses, several well-known estrogen-regulated genes were identified. Two genes, confirmed by quantitative RT-PCR (qPCR), fulfilled both the criteria of high sensitivity and robustness; the induction of the genes encoding zona pellucida protein 3 and a nucleoside diphosphate kinase (nm23). Conclusion The cross-species, cross-platform meta-analysis correctly identified several robust responses. This adds confidence to our approach used for identifying candidate biomarkers. Specifically, we propose that analyses of an nm23 gene together with zona pellucida genes may increase the possibilities to detect an exposure to low levels of estrogenic compounds in fish.
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Affiliation(s)
- Michael C. Schmale
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy. Miami, FL 33149, USA, phone: 305-421-4140, fax: 305-421-4600,
| | - Rodney S. Nairn
- University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Richard N. Winn
- Aquatic Biotechnology and Environmental Lab (ABEL), 2580 Devil’s Ford Road, Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA, Phone: 706.369.5858, Fax: 706.353.2620,
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