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Charazińska S, Lochyński P, Markiewicz M, Stolte S, Burszta-Adamiak E. Treatment of electropolishing industrial wastewater and its impact on the immobilisation of Daphnia magna. ENVIRONMENTAL RESEARCH 2022; 212:113438. [PMID: 35569535 DOI: 10.1016/j.envres.2022.113438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/05/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The amount of industrial pollution entering the environment and its impact on living organisms is an ongoing concern. At the same time, due to an increasing awareness, new methods of wastewater treatment are being explored that are not only effective but also environmentally acceptable. Meeting environmental standards for permitted concentrations is a necessity, but investigating the effects of wastewater on living organisms is also an important issue. In this paper, the influence of metal ions (Fe(III), Cr(III), Ni(II), Cu(II)) in industrial wastewater from electropolishing of stainless steel on Daphnia magna has been investigated. Daphnids have been exposed to wastewater both before and after treatment (Ca(OH)2 precipitation, sorption with peat). Immobilisation in a 48-h acute toxicity test and EC50 has been determined. In the case of studied industrial wastewater, the organic content (expressed as total organic carbon) of the effluent has a positive impact in terms of the survival of D. magna and increases the range of heavy metal concentrations tolerated by them. The application of a two-stage process with Ca(OH)2 neutralisation followed by sorption with peat allows for the removal of almost 100% of metal ions from the wastewater. The reduction obtained ensured a limited impact on D. magna and a decrease in immobilisation to less than 10%. Proper execution of the wastewater treatment process ensures a reduction of its negative impact on living organisms.
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Affiliation(s)
- Sylwia Charazińska
- Wrocław University of Environmental and Life Sciences, Institute of Environmental Engineering, pl. Grunwaldzki 24 50-375, Wroclaw, Poland
| | - Paweł Lochyński
- Wrocław University of Environmental and Life Sciences, Institute of Environmental Engineering, pl. Grunwaldzki 24 50-375, Wroclaw, Poland
| | - Marta Markiewicz
- Technical University of Dresden, Institute of Water Chemistry, 01069, Dresden, Germany
| | - Stefan Stolte
- Technical University of Dresden, Institute of Water Chemistry, 01069, Dresden, Germany
| | - Ewa Burszta-Adamiak
- Wrocław University of Environmental and Life Sciences, Institute of Environmental Engineering, pl. Grunwaldzki 24 50-375, Wroclaw, Poland.
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Huang Y, Chen R, Yang S, Chen Y, Lü X. The Mechanism of Interaction Between Gold Nanoparticles and Human Dermal Fibroblasts Based on Integrative Analysis of Transcriptomics and Metabolomics Data. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The aim of this paper was to combine transcriptomics and metabolomics to analyze the mechanism of gold nanoparticles (GNPs) on human dermal fibroblasts (HDFs). First, 20-nm GNPs were prepared, and the differentially expressed genes in HDFs were subsequently screened by transcriptome
sequencing technology after 4, 8, and 24 h of treatment with GNPs. By comparing the metabolic pathways in which the metabolites obtained in a previous study were involved, the pathways involving both genes and metabolites were filtered, and the differentially expressed genes and metabolites
with upstream and downstream relationships were screened out. The gene–metabolite–metabolic pathway network was further constructed, and the functions of metabolic pathways, genes and metabolites in the important network were analyzed and experimentally verified. The results of
transcriptome sequencing experiments showed that 1904, 1216 and 489 genes were differentially expressed in HDFs after 4, 8 and 24 h of treatment with GNPs, and these genes were involved in 270, 235 and 163 biological pathways, respectively. Through the comparison and analysis of the metabolic
pathways affected by the metabolites, 7, 3 and 2 metabolic pathways with genes and metabolites exhibiting upstream and downstream relationships were identified. Through analysis of the gene–metabolite–metabolic pathway network, 4 important metabolic pathways, 9 genes and 7 metabolites
were identified. Combined with the results of verification experiments on oxidative stress, apoptosis, the cell cycle, the cytoskeleton and cell adhesion, it was found that GNPs regulated the synthesis of downstream metabolites through upstream genes in important metabolic pathways. GNPs inhibited
oxidative stress and thus did not induce significant apoptosis, but they exerted effects on several cellular functions, including arresting the cell cycle and affecting the cytoskeleton and cell adhesion.
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Affiliation(s)
- Yan Huang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, PR China
| | - Rong Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, PR China
| | - Shuci Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, PR China
| | - Ye Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, PR China
| | - Xiaoying Lü
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, PR China
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Ta HDK, Wang WJ, Phan NN, An Ton NT, Anuraga G, Ku SC, Wu YF, Wang CY, Lee KH. Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer. Cancers (Basel) 2021; 13:4902. [PMID: 34638387 PMCID: PMC8508234 DOI: 10.3390/cancers13194902] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 12/26/2022] Open
Abstract
In recent decades, breast cancer (BRCA) has become one of the most common diseases worldwide. Understanding crucial genes and their signaling pathways remain an enormous challenge in evaluating the prognosis and possible therapeutics. The "Like-Smith" (LSM) family is known as protein-coding genes, and its member play pivotal roles in the progression of several malignancies, although their roles in BRCA are less clear. To discover biological processes associated with LSM family genes in BRCA development, high-throughput techniques were applied to clarify expression levels of LSMs in The Cancer Genome Atlas (TCGA)-BRCA dataset, which was integrated with the cBioPortal database. Furthermore, we investigated prognostic values of LSM family genes in BCRA patients using the Kaplan-Meier database. Among genes of this family, LSM4 expression levels were highly associated with poor prognostic outcomes with a hazard ratio of 1.35 (95% confidence interval 1.21-1.51, p for trend = 3.4 × 10-7). MetaCore and GlueGo analyses were also conducted to examine transcript expression signatures of LSM family members and their coexpressed genes, together with their associated signaling pathways, such as "Cell cycle role of APC in cell cycle regulation" and "Immune response IL-15 signaling via MAPK and PI3K cascade" in BRCA. Results showed that LSM family members, specifically LSM4, were significantly correlated with oncogenesis in BRCA patients. In summary, our results suggested that LSM4 could be a prospective prognosticator of BRCA.
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Affiliation(s)
- Hoang Dang Khoa Ta
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Wei-Jan Wang
- Department of Biological Science and Technology, Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan;
| | - Nam Nhut Phan
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam;
| | - Nu Thuy An Ton
- NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam;
| | - Gangga Anuraga
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia
| | - Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Yung-Fu Wu
- National Defense Medical Center, Department of Medical Research, School of Medicine, Tri-Service General Hospital, Taipei 11490, Taiwan;
| | - Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Kuen-Haur Lee
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
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Dreier DA, Bowden JA, Aristizabal-Henao JJ, Denslow ND, Martyniuk CJ. Ecotoxico-lipidomics: An emerging concept to understand chemical-metabolic relationships in comparative fish models. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100742. [PMID: 32956922 DOI: 10.1016/j.cbd.2020.100742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/16/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Abstract
Lipids play an essential role in development, homeostatic functions, immune signaling, reproduction, and growth. Although it is evident that changes in lipid biosynthesis and metabolism can affect organismal physiology, few studies have determined how environmental stressors affect lipid pathways, let alone alter global lipid profiles in fish. This is a significant research gap, as a number of environmental contaminants interact with lipid signaling and metabolic pathways. In this review, we highlight the utility of lipidomics as a tool in environmental toxicology, discussing the current state of knowledge regarding chemical-lipidomic perturbations. As with most oviparous animals, the processing and storage of lipids during oocyte development is also particularly important for embryogenesis in fish. Using largemouth bass (Micropterus salmoides) as an example, transcriptomics data suggest that various chemicals alter lipid metabolism and regulation, highlighting the need for more sophisticated investigations into how toxicants impact lipid responses. We also point out the challenges ahead; these include a lack of understanding about lipid processing and signaling in fish, tissue and species-specific lipid composition, and extraneous factors (e.g., nutrition, temperature) that confound interpretation. For example, toxicant exposure can lead to oxidative stress and lipid peroxidation, resulting in complex lipid byproducts that are challenging to measure. With the emergence of lipidomics in systems toxicology, multi-omics approaches are expected to more clearly define effects on physiology, creating stronger linkages between multiple molecular entities (gene-protein-lipid/metabolite). The development and implementation of novel technologies such as ion mobility-mass spectrometry and ozone-induced dissociation support the complete structural elucidation of lipid molecules. This has implications in the adverse outcome pathway framework, which will enhance the application of lipidomics in toxicology by linking these molecular changes to effects at higher levels of biological organization.
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Affiliation(s)
- David A Dreier
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - John A Bowden
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Juan J Aristizabal-Henao
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Nancy D Denslow
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Christopher J Martyniuk
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, Genetics Institute, University of Florida, Gainesville, FL, USA.
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Diaz de Cerio O, Bilbao E, Izagirre U, Etxebarria N, Moreno G, Díez G, Cajaraville MP, Cancio I. Toxicology tailored low density oligonucleotide microarray for the thicklip grey mullets (Chelon labrosus): Biomarker gene transcription profile after caging in a polluted harbour. MARINE ENVIRONMENTAL RESEARCH 2018; 140:265-277. [PMID: 30042060 DOI: 10.1016/j.marenvres.2018.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/06/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
In aquatic organisms inhabiting polluted waters genes are activated to build an adaptive/compensatory defence against the possible effects of pollutants. Such responses can be used as biomarkers of exposure to chemical compounds, outlining the molecular mechanisms activated under specific pollution scenarios. With the aim of exploiting such approach in environmental health assessment, toxicologically relevant gene fragments were sequenced in the thicklip grey mullet (Chelon labrosus) and a toxicologically tailored low-density (160 genes) oligonucleotide microarray was customised. The tool was validated comparing organ/sex specific gene expression profiles and characterising responses under laboratory exposure to model chemicals. Finally, juvenile mullets were caged in a polluted harbour and hepatic gene expression profiles analysed after 5 and 21 days of deployment. Cages were deployed in the inner (IH) and outer (OH) Pasaia harbour, Bay of Biscay. Mussels (Mytilus galloprovincialis) were also caged as biological matrix for chemical bioaccumulation analysis and stress biomarkers measurements. Slightly higher concentrations of chemicals (metals, tributyltin, PAHs, phthalates) were quantified in IH than in OH, fish bile metabolites also revealing higher availability of PAHs in IH. Lysosome membrane stability in mussels was reduced, indicating stress condition in both sites. The developed microarray discriminated mullets showing distinctive expression profiles depending on site and deployment time. Genes related to immune and hypoxia responses were regulated comparing IH and OH at day 5. Phase I and II biotransformation genes, such as cyp2, cyp3 and ugt, were up-regulated in IH, together with the aryl hydrocarbon receptor 2 (ahr2) and the ahr repressor. Similarly, TBT-binding proteins and genes involved in lipid metabolism (pparγ, cyp7) were up-regulated with deployment time. Even if nowadays higher throughput approaches for gene expression analyses are available, the developed mullet tool constitutes a comprehensive tool to assess molecular responses of mullets exposed to pollutants, although it remains to be explored whether it can be applied to assess pollutant exposure in active pollution monitorings and in environmental health assessment.
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Affiliation(s)
- O Diaz de Cerio
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - E Bilbao
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - U Izagirre
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - N Etxebarria
- IBEA Res Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Analytical Chemistry Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - G Moreno
- International Seafood Sustainability Foundation (ISSF), 805 15th Street NW, Washington, DC, 20005, USA
| | - G Díez
- AZTI, Marine Research Division, Txatxarramendi irla z/g, 48395, Sukarrieta, Bizkaia, Spain
| | - M P Cajaraville
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - I Cancio
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain.
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Basili D, Zhang JL, Herbert J, Kroll K, Denslow ND, Martyniuk CJ, Falciani F, Antczak P. In Silico Computational Transcriptomics Reveals Novel Endocrine Disruptors in Largemouth Bass ( Micropterus salmoides). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7553-7565. [PMID: 29878769 DOI: 10.1021/acs.est.8b02805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In recent years, decreases in fish populations have been attributed, in part, to the effect of environmental chemicals on ovarian development. To understand the underlying molecular events we developed a dynamic model of ovary development linking gene transcription to key physiological end points, such as gonadosomatic index (GSI), plasma levels of estradiol (E2) and vitellogenin (VTG), in largemouth bass ( Micropterus salmoides). We were able to identify specific clusters of genes, which are affected at different stages of ovarian development. A subnetwork was identified that closely linked gene expression and physiological end points and by interrogating the Comparative Toxicogenomic Database (CTD), quercetin and tretinoin (ATRA) were identified as two potential candidates that may perturb this system. Predictions were validated by investigation of reproductive associated transcripts using qPCR in ovary and in the liver of both male and female largemouth bass treated after a single injection of quercetin and tretinoin (10 and 100 μg/kg). Both compounds were found to significantly alter the expression of some of these genes. Our findings support the use of omics and online repositories for identification of novel, yet untested, compounds. This is the first study of a dynamic model that links gene expression patterns across stages of ovarian development.
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Affiliation(s)
- Danilo Basili
- Institute for Integrative Biology, University of Liverpool , L69 7ZB , Liverpool , United Kingdom
| | - Ji-Liang Zhang
- Henan Open Laboratory of Key Subjects of Environmental and Animal Products Safety, College of Animal Science and Technology , Henan University of Science and Technology , Henan 471003 , China
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine and UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - John Herbert
- Institute for Integrative Biology, University of Liverpool , L69 7ZB , Liverpool , United Kingdom
| | - Kevin Kroll
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine and UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Nancy D Denslow
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine and UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Christopher J Martyniuk
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine and UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Francesco Falciani
- Institute for Integrative Biology, University of Liverpool , L69 7ZB , Liverpool , United Kingdom
| | - Philipp Antczak
- Institute for Integrative Biology, University of Liverpool , L69 7ZB , Liverpool , United Kingdom
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Zheng M, Lu J, Zhao D. Effects of starch-coating of magnetite nanoparticles on cellular uptake, toxicity and gene expression profiles in adult zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 622-623:930-941. [PMID: 29227944 DOI: 10.1016/j.scitotenv.2017.12.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/01/2017] [Accepted: 12/03/2017] [Indexed: 06/07/2023]
Abstract
Engineered magnetite nanoparticles (Fe3O4 NPs) have been used in many fields. To prevent particle agglomeration, stabilizers or coatings are often required. While such coatings have been shown to enhance performances, the environmental impact or toxicity of stabilized or coated Fe3O4 NPs remain poorly understood. In an effort to understand the impacts of such coatings on the toxicity of Fe3O4 NPs, we used the transcriptome sequencing (RNA-seq) technique to characterize the gill and liver transcriptomes from adult zebrafish when exposed to bare and starch-stabilized Fe3O4 NPs for 7days, demonstrating remarkable differences in gene expression profiles, also known as differentially expressed genes (DEGs) profiles, in both tissues. Bare Fe3O4 NPs exerted greater toxicity than starch-coated Fe3O4 NPs in gill; in contrast, starch-Fe3O4 NPs triggered more severe damage on liver, though both bare and stabilized NPs appeared to share similar regulatory mechanisms. Quantitative real-time polymerase chain reactions using six genes each for the two tissues verified the RNA-seq results. The surface coatings play an important role in determining the nanoparticle toxicity, which in turn modulate cell uptake and biological responses, consequently impacting the potential safety and efficacy of nanomaterials.
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Affiliation(s)
- Min Zheng
- Environmental Engineering Program, Department of Civil Engineering, Auburn University, Auburn, AL 36849, USA; School of Marine Sciences, Sun Yat-sen University, Guangdong 510275, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Guangdong 510275, China
| | - Dongye Zhao
- Environmental Engineering Program, Department of Civil Engineering, Auburn University, Auburn, AL 36849, USA; School of Environment and Energy, South China University of Technology, Guangzhou 510006, China.
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Lavelle C, Smith LC, Bisesi JH, Yu F, Silva-Sanchez C, Moraga-Amador D, Buerger AN, Garcia-Reyero N, Sabo-Attwood T, Denslow ND. Tissue-Based Mapping of the Fathead Minnow ( Pimephales promelas) Transcriptome and Proteome. Front Endocrinol (Lausanne) 2018; 9:611. [PMID: 30459712 PMCID: PMC6232228 DOI: 10.3389/fendo.2018.00611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/26/2018] [Indexed: 12/11/2022] Open
Abstract
Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The fathead minnow (Pimephales promelas) is a widely used small fish model for aquatic toxicology and regulatory testing, particularly in North America. A draft genome has been published, but the amount of available genomic or transcriptomic information is still far behind that of other more broadly studied species, such as the zebrafish. Here, we used a proteogenomics approach to survey the tissue-specific proteome and transcriptome profiles in adult male fathead minnow. To do so, we generated a draft transcriptome using short and long sequencing reads from liver, testis, brain, heart, gill, head kidney, trunk kidney, and gastrointestinal tract. We identified 30,378 different putative transcripts overall, with the assembled contigs ranging in size from 264 to over 9,720 nts. Over 17,000 transcripts were >1,000 nts, suggesting a robust transcriptome that can be used to interpret RNA sequencing data in the future. We also performed RNA sequencing and proteomics analysis on four tissues, including the telencephalon, hypothalamus, liver, and gastrointestinal tract of male fish. Transcripts ranged from 0 to 600,000 copies per gene and a large portion were expressed in a tissue-specific manner. Specifically, the telencephalon and hypothalamus shared the most expressed genes, while the gastrointestinal tract and the liver were quite distinct. Using protein profiling techniques, we identified a total of 4,045 proteins in the four tissues investigated, and their tissue-specific expression pattern correlated with the transcripts at the pathway level. Similarly to the findings with the transcriptomic data, the hypothalamus and telencephalon had the highest degree of similarity in the proteins detected. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.
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Affiliation(s)
- Candice Lavelle
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Ley Cody Smith
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
| | - Joseph H. Bisesi
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Fahong Yu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Cecilia Silva-Sanchez
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - David Moraga-Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Amanda N. Buerger
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS, United States
| | - Tara Sabo-Attwood
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Nancy D. Denslow
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
- *Correspondence: Nancy D. Denslow
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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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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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Hahn CM, Iwanowicz LR, Cornman RS, Mazik PM, Blazer VS. Transcriptome discovery in non-model wild fish species for the development of quantitative transcript abundance assays. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 20:27-40. [PMID: 27497300 DOI: 10.1016/j.cbd.2016.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/04/2016] [Accepted: 07/08/2016] [Indexed: 12/14/2022]
Abstract
Environmental studies increasingly identify the presence of both contaminants of emerging concern (CECs) and legacy contaminants in aquatic environments; however, the biological effects of these compounds on resident fishes remain largely unknown. High throughput methodologies were employed to establish partial transcriptomes for three wild-caught, non-model fish species; smallmouth bass (Micropterus dolomieu), white sucker (Catostomus commersonii) and brown bullhead (Ameiurus nebulosus). Sequences from these transcriptome databases were utilized in the development of a custom nCounter CodeSet that allowed for direct multiplexed measurement of 50 transcript abundance endpoints in liver tissue. Sequence information was also utilized in the development of quantitative real-time PCR (qPCR) primers. Cross-species hybridization allowed the smallmouth bass nCounter CodeSet to be used for quantitative transcript abundance analysis of an additional non-model species, largemouth bass (Micropterus salmoides). We validated the nCounter analysis data system with qPCR for a subset of genes and confirmed concordant results. Changes in transcript abundance biomarkers between sexes and seasons were evaluated to provide baseline data on transcript modulation for each species of interest.
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Affiliation(s)
- Cassidy M Hahn
- West Virginia University, School of Natural Resources, 322 Percival Hall, Morgantown, WV 26506, USA; US Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA.
| | - Luke R Iwanowicz
- US Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA
| | - Robert S Cornman
- US Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA
| | - Patricia M Mazik
- West Virginia University, School of Natural Resources, 322 Percival Hall, Morgantown, WV 26506, USA
| | - Vicki S Blazer
- US Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA
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12
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Molecular impacts of perfluorinated chemicals (PFASs) in the liver and testis of male largemouth bass (Micropterus salmoides) in Minnesota Lakes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 19:129-139. [PMID: 26907229 DOI: 10.1016/j.cbd.2016.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/23/2016] [Accepted: 02/05/2016] [Indexed: 12/31/2022]
Abstract
Perfluorinated chemicals (PFASs) stem from a wide range of sources and have been detected in aquatic ecosystems worldwide, including the upper Midwest and the state of Minnesota in the USA. This study investigated whether fish with high body burden levels of PFASs in the Twin Cities Metro Areas showed any evidence of adverse effects at the level of the transcriptome. We hypothesized that fish with higher body burden levels of PFASs would exhibit molecular responses in the liver and testis that were suggestive of oxidative and general stress, as well as impaired reproduction. Concentrations of PFASs in largemouth bass varied significantly across the sampled lakes, with the lowest concentrations of PFASs found in fish from Steiger and Upper Prior Lakes and the highest concentrations found in fish from Calhoun and Twin Lakes. Largemouth bass with high PFAS concentrations exhibited changes in the expression of genes related to lipid metabolism, energy production, RNA processing, protein production/degradation and contaminant detoxification, all of which are consistent with biomarker responses observed in other studies with PFASs. However, given the wide range of genes that were differentially expressed across the lakes and the variability observed in the mechanisms through which biological processes were affected, it is unlikely that PFASs are the only stressors affecting largemouth bass in the Twin Cities Metro Areas lakes. Indeed, Twin Lake is affected by the Joslyn superfund site which contains polycyclic aromatic hydrocarbons, pentachlorophenol, polychlorinated biphenyls, and dioxins. These compounds are also expected to drive the transcriptomics responses observed, but to what degree is difficult to ascertain at this time.
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13
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Brinkmann M, Koglin S, Eisner B, Wiseman S, Hecker M, Eichbaum K, Thalmann B, Buchinger S, Reifferscheid G, Hollert H. Characterisation of transcriptional responses to dioxins and dioxin-like contaminants in roach (Rutilus rutilus) using whole transcriptome analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 541:412-423. [PMID: 26410716 DOI: 10.1016/j.scitotenv.2015.09.087] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 09/16/2015] [Accepted: 09/16/2015] [Indexed: 05/10/2023]
Abstract
There is significant concern regarding the contamination of riverine sediments with dioxins and dioxin-like compounds (DLCs), including polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), polychlorinated biphenyls (PCBs) and some polycyclic aromatic hydrocarbons (PAHs). The majority of studies investigating the ecotoxicology of DLCs in fish have focused on a few standard model species. However, there is significant uncertainty as to whether these model species are representative of native river fish, particularly in Europe. In this study, the transcriptional responses following exposure to equipotent concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), PCB 156 or the dioxin-like PAH, benzo[k]fluoranthene (BkF), were investigated in juvenile roach (Rutilus rutilus), a fish species that constitutes a large proportion of the fish biomass in freshwater bodies throughout Europe. To this end, RNA sequencing analysis was used to comprehensively characterise the molecular mechanisms and pathways of toxicity of these DLCs. Whole transcriptome analyses using ClueGO software revealed that DLCs have the potential to disrupt a number of important processes, including energy metabolism, oogenesis, the immune system, apoptosis and the response to oxidative stress. However, despite using equipotent concentrations, there was very little conservation of the transcriptional responses observed in fish exposed to different DLCs. TCDD provoked significant specific changes in the levels of transcripts related to immunotoxicity and carbohydrate metabolism, while PCB 156 caused virtually no specific effects. Exposure to BkF affected the most diverse suite of molecular functions and biological processes, including blood coagulation, oxidative stress responses, unspecific responses to organic or inorganic substances/stimuli, cellular redox homeostasis and specific receptor pathways. To our knowledge, this is the first study of the transcriptome-wide effects of different classes of DLCs in fish. These findings represent an important step towards describing complete toxicity pathways of DLCs, which will be important in the context of informing risk assessments of DLC toxicity in native fish species.
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Affiliation(s)
- Markus Brinkmann
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Sven Koglin
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Bryanna Eisner
- Toxicology Centre, University of Saskatchewan, 44 Campus Drive, Saskatoon, SK S7N 5B3, Canada
| | - Steve Wiseman
- Toxicology Centre, University of Saskatchewan, 44 Campus Drive, Saskatoon, SK S7N 5B3, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, 44 Campus Drive, Saskatoon, SK S7N 5B3, Canada; School of the Environment & Sustainability, University of Saskatchewan, 44 Campus Drive, Saskatoon, SK S7N 5B3, Canada
| | - Kathrin Eichbaum
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Beat Thalmann
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Sebastian Buchinger
- Federal Institute of Hydrology (BfG), Department G3: Biochemistry, Ecotoxicology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Georg Reifferscheid
- Federal Institute of Hydrology (BfG), Department G3: Biochemistry, Ecotoxicology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Henner Hollert
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; College of Resources and Environmental Science, Chongqing University, 1 Tiansheng Road Beibei, Chongqing 400715, China; College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, 1239 Siping Road, Shanghai, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, China.
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14
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Bahamonde PA, Feswick A, Isaacs MA, Munkittrick KR, Martyniuk CJ. Defining the role of omics in assessing ecosystem health: Perspectives from the Canadian environmental monitoring program. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2016; 35:20-35. [PMID: 26771350 DOI: 10.1002/etc.3218] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/16/2015] [Accepted: 08/20/2015] [Indexed: 05/22/2023]
Abstract
Scientific reviews and studies continue to describe omics technologies as the next generation of tools for environmental monitoring, while cautioning that there are limitations and obstacles to overcome. However, omics has not yet transitioned into national environmental monitoring programs designed to assess ecosystem health. Using the example of the Canadian Environmental Effects Monitoring (EEM) program, the authors describe the steps that would be required for omics technologies to be included in such an established program. These steps include baseline collection of omics endpoints across different species and sites to generate a range of what is biologically normal within a particular ecosystem. Natural individual variability in the omes is not adequately characterized and is often not measured in the field, but is a key component to an environmental monitoring program, to determine the critical effect size or action threshold for management. Omics endpoints must develop a level of standardization, consistency, and rigor that will allow interpretation of the relevance of changes across broader scales. To date, population-level consequences of routinely measured endpoints such as reduced gonad size or intersex in fish is not entirely clear, and the significance of genome-wide molecular, proteome, or metabolic changes on organism or population health is further removed from the levels of ecological change traditionally managed. The present review is not intended to dismiss the idea that omics will play a future role in large-scale environmental monitoring studies, but rather outlines the necessary actions for its inclusion in regulatory monitoring programs focused on assessing ecosystem health.
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Affiliation(s)
- Paulina A Bahamonde
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - April Feswick
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Meghan A Isaacs
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Kelly R Munkittrick
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Christopher J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
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15
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Kim HJ, Koedrith P, Seo YR. Ecotoxicogenomic approaches for understanding molecular mechanisms of environmental chemical toxicity using aquatic invertebrate, Daphnia model organism. Int J Mol Sci 2015; 16:12261-87. [PMID: 26035755 PMCID: PMC4490443 DOI: 10.3390/ijms160612261] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 01/02/2023] Open
Abstract
Due to the rapid advent in genomics technologies and attention to ecological risk assessment, the term “ecotoxicogenomics” has recently emerged to describe integration of omics studies (i.e., transcriptomics, proteomics, metabolomics, and epigenomics) into ecotoxicological fields. Ecotoxicogenomics is defined as study of an entire set of genes or proteins expression in ecological organisms to provide insight on environmental toxicity, offering benefit in ecological risk assessment. Indeed, Daphnia is a model species to study aquatic environmental toxicity designated in the Organization for Economic Co-operation and Development’s toxicity test guideline and to investigate expression patterns using ecotoxicology-oriented genomics tools. Our main purpose is to demonstrate the potential utility of gene expression profiling in ecotoxicology by identifying novel biomarkers and relevant modes of toxicity in Daphnia magna. These approaches enable us to address adverse phenotypic outcomes linked to particular gene function(s) and mechanistic understanding of aquatic ecotoxicology as well as exploration of useful biomarkers. Furthermore, key challenges that currently face aquatic ecotoxicology (e.g., predicting toxicant responses among a broad spectrum of phytogenetic groups, predicting impact of temporal exposure on toxicant responses) necessitate the parallel use of other model organisms, both aquatic and terrestrial. By investigating gene expression profiling in an environmentally important organism, this provides viable support for the utility of ecotoxicogenomics.
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Affiliation(s)
- Hyo Jeong Kim
- Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-820, Korea.
- Department of Life Science, Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-820, Korea.
| | - Preeyaporn Koedrith
- Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-820, Korea.
- Faculty of Environment and Resource Studies, Mahidol University, 999 Phuttamonthon 4 Rd., Phuttamonthon District, Nakhon Pathom 73170, Thailand.
| | - Young Rok Seo
- Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-820, Korea.
- Department of Life Science, Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-820, Korea.
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16
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Bahamonde PA, McMaster ME, Servos MR, Martyniuk CJ, Munkittrick KR. Molecular pathways associated with the intersex condition in rainbow darter (Etheostoma caeruleum) following exposures to municipal wastewater in the Grand River basin, ON, Canada. Part B. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:302-316. [PMID: 25542366 DOI: 10.1016/j.aquatox.2014.11.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 06/04/2023]
Abstract
Rainbow darter (Etheostoma caeruleum; RBD) is a small benthic fish found in North America. This species is sensitive to sewage effluent, and intersex is found in up to 80% of males in near-field areas in the Grand River, Ontario, Canada. To learn more about the molecular signaling cascades associated with intersex, a developed customized oligonucleotide microarray (4×180 K) using next generation sequencing was developed to characterize the transcriptome in the gonad of male and female RBD. Gene expression profiling was performed in males and females from both a reference site and a polluted site. Males with and without intersex condition from the areas closest to effluent outfalls were compared to males and females from a reference site. Microarray analysis revealed that there was increased mRNA abundance for genes associated with oogenesis in intersex males (i.e. the presence of eggs within the testis), and a decrease in mRNA abundance for genes associated with spermatid development. In females exposed to effluent, cell processes related with hatching and ovulation were down-regulated, and genes involved in immune responses were increased in abundance. In the non-intersex males exposed to effluent, cell processes such as sperm cell adhesion were decreased at the transcript level relative to males from the reference site. Microarray analysis revealed that heat shock proteins (HSP) were significantly increased in non-intersex males exposed to effluent; however, HSPs were not differentially expressed in intersex males exposed to the effluent. Genes involved in sex differentiation (sox9, foxl2 and dmrt1) and reproduction (esr1, esrb, ar, vtg, cyp19a1 and cyp11a) were measured in males, females, and intersex individuals. Consistent with the intersex condition, many transcripts showed an intermediate expression level in intersex males when compared to phenotypic males and females. This study improves our knowledge regarding the molecular pathways that underlie the intersex condition and develops a suite of qPCR bioassays in RBD that are able to discriminate pollutant-exposed males without intersex from those males with intersex. Part A of this study reports on the effects of municipal wastewater effluents (MWWEs) on RBD in the Grand River and demonstrates that there are disruptions in higher level endpoints that include altered steroid levels. Here we develop a new tool for assessing and monitoring the intersex condition in RBD in polluted natural environments and begin to characterize gene networks that are associated with the condition.
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Affiliation(s)
- P A Bahamonde
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, NB, Canada E2L 4L5.
| | - M E McMaster
- Emerging Methods Branch, Aquatic Contaminant Research Division, Water Science and Technology Directorate, Environment Canada, Burlington, ON, Canada L7R 4A6
| | - M R Servos
- Canadian Rivers Institute and University of Waterloo, Department of Biology, Waterloo, ON, Canada N2L 3G1
| | - C J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, NB, Canada E2L 4L5
| | - K R Munkittrick
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, NB, Canada E2L 4L5
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17
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Houde M, Giraudo M, Douville M, Bougas B, Couture P, De Silva AO, Spencer C, Lair S, Verreault J, Bernatchez L, Gagnon C. A multi-level biological approach to evaluate impacts of a major municipal effluent in wild St. Lawrence River yellow perch (Perca flavescens). THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 497-498:307-318. [PMID: 25137380 DOI: 10.1016/j.scitotenv.2014.07.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/07/2014] [Accepted: 07/15/2014] [Indexed: 05/23/2023]
Abstract
The development of integrated ecotoxicological approaches is of great interest in the investigation of global concerns such as impacts of municipal wastewater effluents on aquatic ecosystems. The objective of this study was to investigate the effects of a major wastewater municipal effluent on fish using a multi-level biological approach, from gene transcription and enzyme activities to histological changes. Yellow perch (Perca flavescens) were selected based on their wide distribution, their commercial and recreational importance, and the availability of a customized microarray. Yellow perch were sampled upstream of a major municipal wastewater treatment plant (WWTP) and 4 km and 10 km downstream from its point of discharge in the St. Lawrence River (Quebec, Canada). Concentrations of perfluoroalkyl substances (PFASs), polybrominated diphenyl ethers (PBDEs) and metals/trace elements in whole body homogenates were comparable to those from other industrialized regions of the world. Genomic results indicated that the transcription level of 177 genes was significantly different (p<0.024) between exposed and non-exposed fish. Among these genes, 38 were found to be differentially transcribed at both downstream sites. Impacted genes were associated with biological processes and molecular functions such as immunity, detoxification, lipid metabolism/energy homeostasis (e.g., peroxisome proliferation), and retinol metabolism suggesting impact of WWTP on these systems. Moreover, antioxidant enzyme activities were more elevated in perch collected at the 4 km site. Biomarkers of lipid metabolism, biosynthetic activity, and aerobic capacities were significantly lower (p<0.05) in fish residing near the outfall of the effluent. Histological examination of the liver indicated no differences between sites. Correlations between PFAS, PBDE, and metal/trace element tissue concentrations and markers of peroxisomal proliferation, oxidative stress, and retinoid metabolism were found at the gene and cellular levels. Present results suggest that relating transcriptomic analyses to phenotypic responses is important to better understand impacts of environmental contamination on wild fish populations.
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Affiliation(s)
- Magali Houde
- Centre Saint-Laurent, Environment Canada, 105 McGill Street, Montreal, QC H2Y 2E7, Canada.
| | - Maeva Giraudo
- Centre Saint-Laurent, Environment Canada, 105 McGill Street, Montreal, QC H2Y 2E7, Canada.
| | - Mélanie Douville
- Centre Saint-Laurent, Environment Canada, 105 McGill Street, Montreal, QC H2Y 2E7, Canada.
| | - Bérénice Bougas
- Institut de biologie intégrative et des systèmes, Université Laval, 1030, avenue de la Médecine, Québec, QC G1V 0A6, Canada; Institut National de la Recherche Scientifique, Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC G1K 9A9, Canada.
| | - Patrice Couture
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC G1K 9A9, Canada.
| | - Amila O De Silva
- Canada Centre for Inland Waters, Environment Canada, 867 Lakeshore Road, P.O. Box 5050, Burlington, ON L7R 4A6, Canada.
| | - Christine Spencer
- Canada Centre for Inland Waters, Environment Canada, 867 Lakeshore Road, P.O. Box 5050, Burlington, ON L7R 4A6, Canada.
| | - Stéphane Lair
- Centre québécois sur la santé des animaux sauvages, Université de Montréal, C.P. 5000, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Jonathan Verreault
- Centre de recherche en toxicologie de l'environnement (TOXEN), Département des sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succursale Centre-ville, Montreal, QC H3C 3P8, Canada.
| | - Louis Bernatchez
- Institut de biologie intégrative et des systèmes, Université Laval, 1030, avenue de la Médecine, Québec, QC G1V 0A6, Canada.
| | - Christian Gagnon
- Centre Saint-Laurent, Environment Canada, 105 McGill Street, Montreal, QC H2Y 2E7, Canada.
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18
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Li C, Gowan S, Anil A, Beck BH, Thongda W, Kucuktas H, Kaltenboeck L, Peatman E. Discovery and validation of gene-linked diagnostic SNP markers for assessing hybridization between Largemouth bass (Micropterus salmoides) and Florida bass (M. floridanus). Mol Ecol Resour 2014; 15:395-404. [DOI: 10.1111/1755-0998.12308] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Chao Li
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Spencer Gowan
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Ammu Anil
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Benjamin H. Beck
- United States Department of Agriculture; Agricultural Research Service; Stuttgart National Aquaculture Research Center; Stuttgart AR 72160 USA
| | - Wilawan Thongda
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Huseyin Kucuktas
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Ludmilla Kaltenboeck
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Eric Peatman
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
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19
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Du F, Xu G, Nie Z, Xu P, Gu R. Transcriptome analysis gene expression in the liver of Coilia nasus during the stress response. BMC Genomics 2014; 15:558. [PMID: 24996224 PMCID: PMC4094779 DOI: 10.1186/1471-2164-15-558] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 06/26/2014] [Indexed: 12/27/2022] Open
Abstract
Background The estuarine tapertail anchovy (Coilia nasus) is widely distributed in the Yangtze River, the coastal waters of China, Korea, and the Ariake Sound of Japan. It is a commercially important species owing to its nutritional value and delicate flavor. However, Coilia nasus is strongly responsive to stress, this often results in death, which causes huge losses. In this study, we used next-generation sequencing technologies to study changes in gene expression in response to loading stress and the mechanism of death caused by loading stress in Coilia nasus. Results Using next-generation RNA-seq technologies on an Illumina HiSeq 2000 platform, we assembled a de novo transcriptome and tested for differential expression in response to stress. A total of 65,129 unigenes were generated, the mean unigene size and N50 were 607 bp and 813 bp, respectively. Of the assembled unigenes, we identified 2,990 genes that were significantly up-regulated, while 3,416 genes were significantly down-regulated in response to loading stress. Pathway enrichment analysis based on loading stress-responsive unigenes identified significantly stress related pathways. “Metabolism” and “immunity” were the two most frequently represented categories. In the “metabolism” category, “glucose metabolism” and “lipid metabolism” were major subclasses. The transcriptional expression of rate-limiting enzymes in “glucose metabolism” and “lipid metabolism” was detected by RT-qPCR, all were significantly increased after stress. Apoptosis associated proteins tumor necrosis factor alpha (TNF-α), caspase 9, cytochrome c and caspase 3 in the stress group were significantly elevated, moreover, liver injury indicators (Alanine aminotransferase, ALT, and aspartate transaminase, AST) were also significantly elevated, which indicates that loading stress induced liver injury. Conclusion This study provided abundant unigenes that could contribute greatly to the discovery of novel genes in fish. The alterations in predicted gene expression patterns reflected possible responses to stress. Loading stress may induce liver injury through the mitochondrial apoptosis pathway, which was activated by TNF-α. Taken together, our data not only provide information that will aid the identification of novel genes from fish, but also shed new light on the understanding of mechanisms by which physical stressors cause death in fish. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-558) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Ruobo Gu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No, 9 Shanshui East Road, Wuxi, Jiangsu Province, China.
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20
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Garcia-Reyero N, Tingaud-Sequeira A, Cao M, Zhu Z, Perkins EJ, Hu W. Endocrinology: advances through omics and related technologies. Gen Comp Endocrinol 2014; 203:262-73. [PMID: 24726988 DOI: 10.1016/j.ygcen.2014.03.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/20/2014] [Accepted: 03/22/2014] [Indexed: 12/27/2022]
Abstract
The rapid development of new omics technologies to measure changes at genetic, transcriptomic, proteomic, and metabolomics levels together with the evolution of methods to analyze and integrate the data at a systems level are revolutionizing the study of biological processes. Here we discuss how new approaches using omics technologies have expanded our knowledge especially in nontraditional models. Our increasing knowledge of these interactions and evolutionary pathway conservation facilitates the use of nontraditional species, both invertebrate and vertebrate, as new model species for biological and endocrinology research. The increasing availability of technology to create organisms overexpressing key genes in endocrine function allows manipulation of complex regulatory networks such as growth hormone (GH) in transgenic fish where disregulation of GH production to produce larger fish has also permitted exploration of the role that GH plays in testis development, suggesting that it does so through interactions with insulin-like growth factors. The availability of omics tools to monitor changes at nearly any level in any organism, manipulate gene expression and behavior, and integrate data across biological levels, provides novel opportunities to explore endocrine function across many species and understand the complex roles that key genes play in different aspects of the endocrine function.
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Affiliation(s)
- Natàlia Garcia-Reyero
- Institute for Genomics Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39759, USA.
| | - Angèle Tingaud-Sequeira
- Laboratoire MRMG, Maladies Rares: Génétique et Métabolisme, Université de Bordeaux, 33405 Talence Cedex, France
| | - Mengxi Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Edward J Perkins
- US Army Engineer Research and Development Center, Vicksburg, MS 39180, USA
| | - Wei Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Mehinto AC, Prucha MS, Colli-Dula RC, Kroll KJ, Lavelle CM, Barber DS, Vulpe CD, Denslow ND. Gene networks and toxicity pathways induced by acute cadmium exposure in adult largemouth bass (Micropterus salmoides). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 152:186-194. [PMID: 24794047 DOI: 10.1016/j.aquatox.2014.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 04/02/2014] [Accepted: 04/05/2014] [Indexed: 06/03/2023]
Abstract
Cadmium is a heavy metal that can accumulate to toxic levels in the environment leading to detrimental effects in animals and humans including kidney, liver and lung injuries. Using a transcriptomics approach, genes and cellular pathways affected by a low dose of cadmium were investigated. Adult largemouth bass were intraperitoneally injected with 20μg/kg of cadmium chloride (mean exposure level - 2.6μg of cadmium per fish) and microarray analyses were conducted in the liver and testis 48h after injection. Transcriptomic profiles identified in response to cadmium exposure were tissue-specific with the most differential expression changes found in the liver tissues, which also contained much higher levels of cadmium than the testis. Acute exposure to a low dose of cadmium induced oxidative stress response and oxidative damage pathways in the liver. The mRNA levels of antioxidants such as catalase increased and numerous transcripts related to DNA damage and DNA repair were significantly altered. Hepatic mRNA levels of metallothionein, a molecular marker of metal exposure, did not increase significantly after 48h exposure. Carbohydrate metabolic pathways were also disrupted with hepatic transcripts such as UDP-glucose, pyrophosphorylase 2, and sorbitol dehydrogenase highly induced. Both tissues exhibited a disruption of steroid signaling pathways. In the testis, estrogen receptor beta and transcripts linked to cholesterol metabolism were suppressed. On the contrary, genes involved in cholesterol metabolism were highly increased in the liver including genes encoding for the rate limiting steroidogenic acute regulatory protein and the catalytic enzyme 7-dehydrocholesterol reductase. Integration of the transcriptomic data using functional enrichment analyses revealed a number of enriched gene networks associated with previously reported adverse outcomes of cadmium exposure such as liver toxicity and impaired reproduction.
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Affiliation(s)
- Alvine C Mehinto
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, United States; Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States.
| | - Melinda S Prucha
- Department of Human Genetics, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, United States; Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States
| | - Reyna C Colli-Dula
- 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
| | - Candice M Lavelle
- 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
| | - Christopher D Vulpe
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, 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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Richter CA, Martyniuk CJ, Annis ML, Brumbaugh WG, Chasar LC, Denslow ND, Tillitt DE. Methylmercury-induced changes in gene transcription associated with neuroendocrine disruption in largemouth bass (Micropterus salmoides). Gen Comp Endocrinol 2014; 203:215-224. [PMID: 24694518 PMCID: PMC4145016 DOI: 10.1016/j.ygcen.2014.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/10/2014] [Accepted: 03/16/2014] [Indexed: 01/01/2023]
Abstract
Methyl-mercury (MeHg) is a potent neuroendocrine disruptor that impairs reproductive processes in fish. The objectives of this study were to (1) characterize transcriptomic changes induced by MeHg exposure in the female largemouth bass (LMB) hypothalamus under controlled laboratory conditions, (2) investigate the health and reproductive impacts of MeHg exposure on male and female largemouth bass (LMB) in the natural environment, and (3) identify MeHg-associated gene expression patterns in whole brain of female LMB from MeHg-contaminated habitats. The laboratory experiment was a single injection of 2.5 μg MeHg/g body weight for 96 h exposure. The field survey compared river systems in Florida, USA with comparably lower concentrations of MeHg (Wekiva, Santa Fe, and St. Johns Rivers) in fish and one river system with LMB that contained elevated concentrations of MeHg (St. Marys River). Microarray analysis was used to quantify transcriptomic responses to MeHg exposure. Although fish at the high-MeHg site did not show overt health or reproductive impairment, there were MeHg-responsive genes and pathways identified in the laboratory study that were also altered in fish from the high-MeHg site relative to fish at the low-MeHg sites. Gene network analysis suggested that MeHg regulated the expression targets of neuropeptide receptor and steroid signaling, as well as structural components of the cell. Disease-associated gene networks related to MeHg exposure, based upon expression data, included cerebellum ataxia, movement disorders, and hypercalcemia. Gene responses in the CNS are consistent with the documented neurotoxicological and neuroendocrine disrupting effects of MeHg in vertebrates.
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Affiliation(s)
- Catherine A. Richter
- U.S. Geological Survey, Columbia Environmental Research Center, 4200 New Haven Road, Columbia, MO 65201, USA
- Corresponding author. Fax: +1 573 876 1896.
| | - Christopher J. Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA
| | - Mandy L. Annis
- U.S. Geological Survey, Columbia Environmental Research Center, 4200 New Haven Road, Columbia, MO 65201, USA
| | - William G. Brumbaugh
- U.S. Geological Survey, Columbia Environmental Research Center, 4200 New Haven Road, Columbia, MO 65201, USA
| | - Lia C. Chasar
- U.S. Geological Survey, Florida Integrated Science Center, 2639 North Monroe Street, Suite A-200, Tallahassee, FL 32303, USA
| | - Nancy D. Denslow
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA
| | - Donald E. Tillitt
- U.S. Geological Survey, Columbia Environmental Research Center, 4200 New Haven Road, Columbia, MO 65201, USA
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Christiansen HE, Mehinto AC, Yu F, Perry RW, Denslow ND, Maule AG, Mesa MG. Correlation of gene expression and contaminant concentrations in wild largescale suckers: a field-based study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 484:379-389. [PMID: 24050789 DOI: 10.1016/j.scitotenv.2013.08.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use food resources from within the river. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant concentration suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin. The array developed in this study could also be a useful tool for studies involving endangered sucker species and other sucker species used in contaminant research.
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Affiliation(s)
- Helena E Christiansen
- U.S. Geological Survey, Western Fisheries Research Center, Columbia River Research Laboratory, 5501 Cook-Underwood Road, Cook, WA 98605, USA.
| | - Alvine C Mehinto
- University of Florida, Center for Environmental and Human Toxicology, Department of Physiological Sciences, 2187 Mowry Road, Gainesville, FL 32611, USA.
| | - Fahong Yu
- Interdisciplinary Center for Biotechnology Research, 2033 Mowry Road, P.O. Box 103622, Gainesville, FL 32610, USA.
| | - Russell W Perry
- U.S. Geological Survey, Western Fisheries Research Center, Columbia River Research Laboratory, 5501 Cook-Underwood Road, Cook, WA 98605, USA.
| | - Nancy D Denslow
- University of Florida, Center for Environmental and Human Toxicology, Department of Physiological Sciences, 2187 Mowry Road, Gainesville, FL 32611, USA.
| | - Alec G Maule
- U.S. Geological Survey, Western Fisheries Research Center, Columbia River Research Laboratory, 5501 Cook-Underwood Road, Cook, WA 98605, USA.
| | - Matthew G Mesa
- U.S. Geological Survey, Western Fisheries Research Center, Columbia River Research Laboratory, 5501 Cook-Underwood Road, Cook, WA 98605, USA.
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24
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Williams TD, Mirbahai L, Chipman JK. The toxicological application of transcriptomics and epigenomics in zebrafish and other teleosts. Brief Funct Genomics 2014; 13:157-71. [DOI: 10.1093/bfgp/elt053] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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25
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Regier N, Baerlocher L, Münsterkötter M, Farinelli L, Cosio C. Analysis of the Elodea nuttallii transcriptome in response to mercury and cadmium pollution: development of sensitive tools for rapid ecotoxicological testing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:8825-8834. [PMID: 23802634 DOI: 10.1021/es401082h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Toxic metals polluting aquatic ecosystems are taken up by inhabitants and accumulate in the food web, affecting species at all trophic levels. It is therefore important to have good tools to assess the level of risk represented by toxic metals in the environment. Macrophytes are potential organisms for the identification of metal-responsive biomarkers but are still underrepresented in ecotoxicology. In the present study, we used next-generation sequencing to investigate the transcriptomic response of Elodea nuttallii exposed to enhanced concentrations of Hg and Cd. We de novo assembled more than 60 000 contigs, of which we found 170 to be regulated dose-dependently by Hg and 212 by Cd. Functional analysis showed that these genes were notably related to energy and metal homeostasis. Expression analysis using nCounter of a subset of genes showed that the gene expression pattern was able to assess toxic metal exposure in complex environmental samples and was more sensitive than other end points (e.g., bioaccumulation, photosynthesis, etc.). In conclusion, we demonstrate the feasibility of using gene expression signatures for the assessment of environmental contamination, using an organism without previous genetic information. This is of interest to ecotoxicology in a wider sense given the possibility to develop specific and sensitive bioassays.
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Affiliation(s)
- Nicole Regier
- Institut F.-A. Forel, University of Geneva , 10 route de Suisse, CP416, 1290 Versoix, Switzerland
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26
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Gene expression networks underlying ovarian development in wild largemouth bass (Micropterus salmoides). PLoS One 2013; 8:e59093. [PMID: 23527095 PMCID: PMC3604104 DOI: 10.1371/journal.pone.0059093] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 02/12/2013] [Indexed: 01/12/2023] Open
Abstract
Background Oocyte maturation in fish involves numerous cell signaling cascades that are activated or inhibited during specific stages of oocyte development. The objectives of this study were to characterize molecular pathways and temporal gene expression patterns throughout a complete breeding cycle in wild female largemouth bass to improve understanding of the molecular sequence of events underlying oocyte maturation. Methods Transcriptomic analysis was performed on eight morphologically diverse stages of the ovary, including primary and secondary stages of oocyte growth, ovulation, and atresia. Ovary histology, plasma vitellogenin, 17β-estradiol, and testosterone were also measured to correlate with gene networks. Results Global expression patterns revealed dramatic differences across ovarian development, with 552 and 2070 genes being differentially expressed during both ovulation and atresia respectively. Gene set enrichment analysis (GSEA) revealed that early primary stages of oocyte growth involved increases in expression of genes involved in pathways of B-cell and T-cell receptor-mediated signaling cascades and fibronectin regulation. These pathways as well as pathways that included adrenergic receptor signaling, sphingolipid metabolism and natural killer cell activation were down-regulated at ovulation. At atresia, down-regulated pathways included gap junction and actin cytoskeleton regulation, gonadotrope and mast cell activation, and vasopressin receptor signaling and up-regulated pathways included oxidative phosphorylation and reactive oxygen species metabolism. Expression targets for luteinizing hormone signaling were low during vitellogenesis but increased 150% at ovulation. Other networks found to play a significant role in oocyte maturation included those with genes regulated by members of the TGF-beta superfamily (activins, inhibins, bone morphogenic protein 7 and growth differentiation factor 9), neuregulin 1, retinoid X receptor, and nerve growth factor family. Conclusions This study offers novel insight into the gene networks underlying vitellogenesis, ovulation and atresia and generates new hypotheses about the cellular pathways regulating oocyte maturation.
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27
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Malenke JR, Milash B, Miller AW, Dearing MD. Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology. Mol Ecol Resour 2013; 13:674-87. [PMID: 23496907 DOI: 10.1111/1755-0998.12092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/31/2013] [Accepted: 02/05/2013] [Indexed: 01/08/2023]
Abstract
Massively parallel sequencing has enabled the creation of novel, in-depth genetic tools for nonmodel, ecologically important organisms. We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) using the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). We tested the microarray with three experiments: one across species with similar habitat (thus, dietary) niches, one across species with different habitat niches and one across populations within a species. The resulting one-colour arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). There were a multitude of expression differences across the woodrat treatments, many of which related to biotransformation processes and activities. The pattern and function of the differences indicate shared ecological pressures, and not merely phylogenetic distance, play an important role in shaping gene expression profiles of woodrat species and populations. The quality and functionality of the woodrat transcriptome and custom microarray suggest these tools will be valuable for expanding the scope of herbivore biology, as well as the exploration of conceptual topics in ecology.
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Affiliation(s)
- J R Malenke
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
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28
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Yadetie F, Karlsen OA, Lanzén A, Berg K, Olsvik P, Hogstrand C, Goksøyr A. Global transcriptome analysis of Atlantic cod (Gadus morhua) liver after in vivo methylmercury exposure suggests effects on energy metabolism pathways. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2013; 126:314-325. [PMID: 23103053 DOI: 10.1016/j.aquatox.2012.09.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/17/2012] [Accepted: 09/23/2012] [Indexed: 06/01/2023]
Abstract
Methylmercury (MeHg) is a widely distributed contaminant polluting many aquatic environments, with health risks to humans exposed mainly through consumption of seafood. The mechanisms of toxicity of MeHg are not completely understood. In order to map the range of molecular targets and gain better insights into the mechanisms of toxicity, we prepared Atlantic cod (Gadus morhua) 135k oligonucleotide arrays and performed global analysis of transcriptional changes in the liver of fish treated with MeHg (0.5 and 2 mg/kg of body weight) for 14 days. Inferring from the observed transcriptional changes, the main pathways significantly affected by the treatment were energy metabolism, oxidative stress response, immune response and cytoskeleton remodeling. Consistent with known effects of MeHg, many transcripts for genes in oxidative stress pathways such as glutathione metabolism and Nrf2 regulation of oxidative stress response were differentially regulated. Among the differentially regulated genes, there were disproportionate numbers of genes coding for enzymes involved in metabolism of amino acids, fatty acids and glucose. In particular, many genes coding for enzymes of fatty acid beta-oxidation were up-regulated. The coordinated effects observed on many transcripts coding for enzymes of energy pathways may suggest disruption of nutrient metabolism by MeHg. Many transcripts for genes coding for enzymes in the synthetic pathways of sulphur containing amino acids were also up-regulated, suggesting adaptive responses to MeHg toxicity. By this toxicogenomics approach, we were also able to identify many potential biomarker candidate genes for monitoring environmental MeHg pollution. These results based on changes on transcript levels, however, need to be confirmed by other methods such as proteomics.
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Affiliation(s)
- Fekadu Yadetie
- Department of Molecular Biology, University of Bergen, Norway.
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29
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Marinković M, de Leeuw WC, de Jong M, Kraak MHS, Admiraal W, Breit TM, Jonker MJ. Combining next-generation sequencing and microarray technology into a transcriptomics approach for the non-model organism Chironomus riparius. PLoS One 2012; 7:e48096. [PMID: 23133553 PMCID: PMC3485019 DOI: 10.1371/journal.pone.0048096] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 09/19/2012] [Indexed: 12/22/2022] Open
Abstract
Whole-transcriptome gene-expression analyses are commonly performed in species that have a sequenced genome and for which microarrays are commercially available. To do such analyses in species with no or limited genome data, i.e. non-model organisms, necessary transcriptomics resources, i.e. an annotated transcriptome and a validated gene-expression microarray, must first be developed. The aim of the present study was to establish an advanced approach for developing transcriptomics resources for non-model organisms by combining next-generation sequencing (NGS) and microarray technology. We applied our approach to the non-biting midge Chironomus riparius, an ecologically relevant species that is widely used in sediment ecotoxicity testing. We sampled extensively covering all C. riparius developmental stages as well as toxicant exposed larvae and obtained from a normalized cDNA library 1.5 M NGS reads totalling 501 Mbp. Using the NGS data we developed transcriptomics resources in several steps. First, we designed 844 k probes directly on the NGS reads, as well as 76 k probes targeting expressed sequence tags of related species. These probes were tested for their affinity to C. riparius DNA and mRNA, by performing two biological experiments with a 1 M probe-selection microarray that contained the entire probe-library. Subsequently, the 1.5 M NGS reads were assembled into 23,709 isotigs and 135,082 singletons, which were associated to ∼55 k, respectively, ∼61 k gene ontology terms and which corresponded together to 22,593 unique protein accessions. An algorithm was developed that took the assembly and the probe affinities to DNA and mRNA into account, what resulted in 59 k highly-reliable probes that targeted uniquely 95% of the isotigs and 18% of the singletons. Concluding, our approach allowed the development of high-quality transcriptomics resources for C. riparius, and is applicable to any non-model organism. It is expected, that these resources will advance ecotoxicity testing with C. riparius as whole-transcriptome gene-expression analysis are now possible with this species.
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Affiliation(s)
- Marino Marinković
- Microarray Department and Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
- Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Wim C. de Leeuw
- Microarray Department and Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
| | - Mark de Jong
- Microarray Department and Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
| | - Michiel H. S. Kraak
- Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Wim Admiraal
- Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Timo M. Breit
- Microarray Department and Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
| | - Martijs J. Jonker
- Microarray Department and Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
- * E-mail:
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Piferrer F, Ribas L, Díaz N. Genomic approaches to study genetic and environmental influences on fish sex determination and differentiation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:591-604. [PMID: 22544374 PMCID: PMC3419836 DOI: 10.1007/s10126-012-9445-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/05/2012] [Indexed: 05/15/2023]
Abstract
The embryonic gonad is the only organ that takes two mutually exclusive differentiating pathways and hence gives rise to two different adult organs: testes or ovaries. The recent application of genomic tools including microarrays, next-generation sequencing approaches, and epigenetics can significantly contribute to decipher the molecular mechanisms involved in the processes of sex determination and sex differentiation. However, in fish, these studies are complicated by the fact that these processes depend, perhaps to a larger extent when compared to other vertebrates, on the interplay of genetic and environmental influences. Here, we review the advances made so far, taking into account different experimental approaches, and illustrate some technical complications deriving from the fact that as development progresses it becomes more and more difficult to distinguish whether changes in gene expression or DNA methylation patterns are the cause or the consequence of such developmental events. Finally, we suggest some avenues for further research in both model fish species and fish species facing specific problems within an aquaculture context.
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Affiliation(s)
- Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Passeig Marítim 37-49, Barcelona, Spain.
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31
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Pribyl AL, Schreck CB, Parker SJ, Weis VM. Identification of biomarkers indicative of barotrauma and recovery in black rockfish Sebastes melanops. JOURNAL OF FISH BIOLOGY 2012; 81:181-196. [PMID: 22747812 DOI: 10.1111/j.1095-8649.2012.03322.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A Sebastes-specific complementary DNA (cDNA) microarray was developed to identify potential biomarkers involved in the capture stress and recovery of Sebastes species if they are assisted in returning to their original depth of capture following barotrauma. Black rockfish Sebastes melanops were exposed to simulated decompression from 450 kPa (c. 35 m depth) (which resulted in barotrauma) and subsequent recompression. Sebastes melanops were sampled for liver tissue at days 3, 15 and 31 post-barotrauma. Potential candidate genes were identified from the microarray and then quantitative real-time PCR (qrt-PCR) was used to validate expression levels in biological replicates. Six potential biomarkers associated with the innate immune system were identified that were up-regulated in liver tissue at 3 days post-barotrauma: complement C1q-like protein 2, complement component C3, complement regulatory plasma protein, serum amyloid A-5, c-type lysozyme and hepcidin precursor type I. In addition, complement c1q was correlated to the presence of a ruptured swimbladder, providing further support that this gene may be a good biomarker of injury and recovery. Immune genes were no longer up-regulated at day 31 post-barotrauma, a good indication of recovery in S. melanops.
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Affiliation(s)
- A L Pribyl
- Oregon Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA.
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32
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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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33
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Pham CH, Park KS, Kim BC, Kim HN, Gu MB. Construction and characterization of Japanese medaka (Oryzias latipes) hepatic cDNA library and its implementation to biomarker screening in aquatic toxicology. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2011; 105:569-575. [PMID: 21937010 DOI: 10.1016/j.aquatox.2011.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/18/2011] [Accepted: 08/23/2011] [Indexed: 05/31/2023]
Abstract
To strengthen the toxicogenomic study, we constructed a library of hepatic cDNA from Japanese medaka under influence of specific chemical mediated stress responses. Gene expression profile analysis of the cDNA microarrays followed by real time RT-PCR assay were conducted to screen particular biomarkers for 17-beta estradiol (E2), nonylphenol (NP) and 2-chlorophenol (2CP). Information of 1509 high-quality ESTs including 260 new ESTs was added onto GenBank and dbEST. The ESTs were clustered and assembled into 159 contigs and 372 singletons. Among them, 128 contigs and 163 singletons (54.8%) were functionally characterized and 13 UniESTs (2.5%) were hypothetical proteins. Ontology analysis resulting in 282 UniESTs which involved with 2102 GOs and 93 sequences associated with 116 enzyme codes. For each test chemical, two specific biomarkers were selected from the gene expression profiling of microarrays. The expression patterns of the marker genes in real time PCR analysis were consistent with the regulated gene expression patterns in microarrays. The tentative biomarkers showed unique gene expression patterns depending on chemical concentration(s) and exposure duration in real time RT-PCR analysis. The analysis accomplished of the hepatic cDNA library and its information added to genetic and genomic resources could be sufficiently valuable specifically for aquatic toxicity studies.
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Affiliation(s)
- Chi Hoa Pham
- College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea
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Doperalski NJ, Martyniuk CJ, Prucha MS, Kroll KJ, Denslow ND, Barber DS. Cloning and expression of the translocator protein (18 kDa), voltage-dependent anion channel, and diazepam binding inhibitor in the gonad of largemouth bass (Micropterus salmoides) across the reproductive cycle. Gen Comp Endocrinol 2011; 173:86-95. [PMID: 21600210 PMCID: PMC3144257 DOI: 10.1016/j.ygcen.2011.04.027] [Citation(s) in RCA: 10] [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: 08/19/2010] [Revised: 04/30/2011] [Accepted: 04/30/2011] [Indexed: 01/14/2023]
Abstract
Cholesterol transport across the mitochondrial membrane is rate-limiting for steroidogenesis in vertebrates. Previous studies in fish have characterized expression of the steroidogenic acute regulatory protein, however the function and regulation of other genes and proteins involved in piscine cholesterol transport have not been evaluated. In the current study, mRNA sequences of the 18 kDa translocator protein (tspo; formerly peripheral benzodiazepine receptor), voltage-dependent anion channel (vdac), and diazepam binding inhibitor (dbi; also acyl-CoA binding protein) were cloned from largemouth bass. Gonadal expression was examined across reproductive stages to determine if expression is correlated with changes in steroid levels and with indicators of reproductive maturation. In testis, transcript abundance of tspo and dbi increased with reproductive maturation (6- and 23-fold maximal increase, respectively) and expression of tspo and dbi was positively correlated with reproductive stage, gonadosomatic index (GSI), and circulating levels of testosterone. Testis vdac expression was positively correlated with reproductive stage and GSI. In females, gonadal tspo and vdac expression was negatively correlated with GSI and levels of plasma testosterone and 17β-estradiol. Ovarian dbi expression was not correlated with indicators of reproductive maturation. These studies represent the first investigation of the steroidogenic role of tspo, vdac, and dbi in fish. Findings suggest that cholesterol transport in largemouth bass testis, but not in ovary, may be transcriptionally-regulated, however further investigation will be necessary to fully elucidate the role of these genes in largemouth bass steroidogenesis.
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Affiliation(s)
- Nicholas J. Doperalski
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, P. O. Box 110885, 471 Mowry Road, Gainesville, FL 32611, USA
| | - Christopher J. Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, P. O. Box 110885, 471 Mowry Road, Gainesville, FL 32611, USA
| | - Melinda S. Prucha
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, P. O. Box 110885, 471 Mowry Road, Gainesville, FL 32611, USA
| | - Kevin J. Kroll
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, P. O. Box 110885, 471 Mowry Road, Gainesville, FL 32611, USA
| | - Nancy D. Denslow
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, P. O. Box 110885, 471 Mowry Road, Gainesville, FL 32611, USA
| | - David S. Barber
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, P. O. Box 110885, 471 Mowry Road, Gainesville, FL 32611, USA
- Corresponding author; Tel.: +1 352 294-4636; fax: +1 352 392 4707;
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Ekblom R, Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) 2011; 107:1-15. [PMID: 21139633 PMCID: PMC3186121 DOI: 10.1038/hdy.2010.152] [Citation(s) in RCA: 622] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 09/10/2010] [Accepted: 11/02/2010] [Indexed: 11/09/2022] Open
Abstract
As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.
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Affiliation(s)
- R Ekblom
- Department of Animal and Plant Sciences, University of Sheffield, UK.
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Tiago DM, Laizé V, Bargelloni L, Ferraresso S, Romualdi C, Cancela ML. Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate. BMC Genomics 2011; 12:310. [PMID: 21668972 PMCID: PMC3141667 DOI: 10.1186/1471-2164-12-310] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 06/13/2011] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Fish has been deemed suitable to study the complex mechanisms of vertebrate skeletogenesis and gilthead seabream (Sparus aurata), a marine teleost with acellular bone, has been successfully used in recent years to study the function and regulation of bone and cartilage related genes during development and in adult animals. Tools recently developed for gilthead seabream, e.g. mineralogenic cell lines and a 4 × 44K Agilent oligo-array, were used to identify molecular determinants of in vitro mineralization and genes involved in anti-mineralogenic action of vanadate. RESULTS Global analysis of gene expression identified 4,223 and 4,147 genes differentially expressed (fold change - FC > 1.5) during in vitro mineralization of VSa13 (pre-chondrocyte) and VSa16 (pre-osteoblast) cells, respectively. Comparative analysis indicated that nearly 45% of these genes are common to both cell lines and gene ontology (GO) classification is also similar for both cell types. Up-regulated genes (FC > 10) were mainly associated with transport, matrix/membrane, metabolism and signaling, while down-regulated genes were mainly associated with metabolism, calcium binding, transport and signaling. Analysis of gene expression in proliferative and mineralizing cells exposed to vanadate revealed 1,779 and 1,136 differentially expressed genes, respectively. Of these genes, 67 exhibited reverse patterns of expression upon vanadate treatment during proliferation or mineralization. CONCLUSIONS Comparative analysis of expression data from fish and data available in the literature for mammalian cell systems (bone-derived cells undergoing differentiation) indicate that the same type of genes, and in some cases the same orthologs, are involved in mechanisms of in vitro mineralization, suggesting their conservation throughout vertebrate evolution and across cell types. Array technology also allowed identification of genes differentially expressed upon exposure of fish cell lines to vanadate and likely involved in its anti-mineralogenic activity. Many were found to be unknown or they were never associated to bone homeostasis previously, thus providing a set of potential candidates whose study will likely bring insights into the complex mechanisms of tissue mineralization and bone formation.
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Affiliation(s)
- Daniel M Tiago
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
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Angeloni F, Wagemaker CAM, Jetten MSM, Op den Camp HJM, Janssen-Megens EM, Francoijs KJ, Stunnenberg HG, Ouborg NJ. De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques. Mol Ecol Resour 2011; 11:662-74. [PMID: 21676196 DOI: 10.1111/j.1755-0998.2011.02990.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Next-generation sequencing (NGS) technologies are increasingly applied in many organisms, including nonmodel organisms that are important for ecological and conservation purposes. Illumina and 454 sequencing are among the most used NGS technologies and have been shown to produce optimal results at reasonable costs when used together. Here, we describe the combined application of these two NGS technologies to characterize the transcriptome of a plant species of ecological and conservation relevance for which no genomic resource is available, Scabiosa columbaria. We obtained 528,557 reads from a 454 GS-FLX run and a total of 28,993,627 reads from two lanes of an Illumina GAII single run. After read trimming, the de novo assembly of both types of reads produced 109,630 contigs. Both the contigs and the >75 bp remaining singletons were blasted against the Uniprot/Swissprot database, resulting in 29,676 and 10,515 significant hits, respectively. Based on sequence similarity with known gene products, these sequences represent at least 12,516 unique genes, most of which are well covered by contig sequences. In addition, we identified 4320 microsatellite loci, of which 856 had flanking sequences suitable for PCR primer design. We also identified 75,054 putative SNPs. This annotated sequence collection and the relative molecular markers represent a main genomic resource for S. columbaria which should contribute to future research in conservation and population biology studies. Our results demonstrate the utility of NGS technologies as starting point for the development of genomic tools in nonmodel but ecologically important species.
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Affiliation(s)
- F Angeloni
- Department of Molecular Ecology, Radboud University Nijmegen, Institute for Water and Wetland Research, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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Fernandino JI, Popesku JT, Paul-Prasanth B, Xiong H, Hattori RS, Oura M, Strüssmann CA, Somoza GM, Matsuda M, Nagahama Y, Trudeau VL. Analysis of sexually dimorphic expression of genes at early gonadogenesis of pejerrey Odontesthes bonariensis using a heterologous microarray. Sex Dev 2011; 5:89-101. [PMID: 21325793 DOI: 10.1159/000324423] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2010] [Indexed: 12/29/2022] Open
Abstract
The process of morphological development of a differentiated gonad from an undifferentiated primordium is a very important step of gonadogenesis. Studies on sexually dimorphic gene expression are important to increase our understanding of this process and to investigate how environmental factors such as temperature can regulate gonadal development. The aim of this study was to identify putative genes involved in sex differentiation in pejerrey (Odontesthes bonariensis) reared at male- and female-producing temperatures (MPT and FPT, respectively) using a microarray heterologous from the medaka (Oryzias latipes), a closely phylogenetic species. Genes related to numerous processes presented higher expression at MPT, including those involved in muscular contraction, metabolic pathways, developmental processes, and reproduction. Genes induced by FPT were classified under the gene ontology terms of response to stimulus, transport and proteolysis. From genes selected for validation, at MPT ndrg3 expression was observed in the somatic cells, whereas pen-2 was detected in germ cells in the caudal portion of the gonads, where no apoptotic signals were observed. Finally, hsp90 was highly expressed in somatic cells of the gonads at the FPT. The results suggest that the interplay of pro-apoptotic and anti-apoptotic genes is important during the masculinization process and for the prevention of sterility following exposure to warm temperatures.
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Affiliation(s)
- J I Fernandino
- Laboratorio de Ictiofisiología y Acuicultura, Instituto de Investigaciones Biotecnológicas, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús, Argentina. fernandino @ intech.gov.ar
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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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Ewen-Campen B, Shaner N, Panfilio KA, Suzuki Y, Roth S, Extavour CG. The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 2011; 12:61. [PMID: 21266083 PMCID: PMC3040728 DOI: 10.1186/1471-2164-12-61] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 01/25/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Most evolutionary developmental biology ("evo-devo") studies of emerging model organisms focus on small numbers of candidate genes cloned individually using degenerate PCR. However, newly available sequencing technologies such as 454 pyrosequencing have recently begun to allow for massive gene discovery in animals without sequenced genomes. Within insects, although large volumes of sequence data are available for holometabolous insects, developmental studies of basally branching hemimetabolous insects typically suffer from low rates of gene discovery. RESULTS We used 454 pyrosequencing to sequence over 500 million bases of cDNA from the ovaries and embryos of the milkweed bug Oncopeltus fasciatus, which lacks a sequenced genome. This indirectly developing insect occupies an important phylogenetic position, branching basal to Diptera (including fruit flies) and Hymenoptera (including honeybees), and is an experimentally tractable model for short-germ development. 2,087,410 reads from both normalized and non-normalized cDNA assembled into 21,097 sequences (isotigs) and 112,531 singletons. The assembled sequences fell into 16,617 unique gene models, and included predictions of splicing isoforms, which we examined experimentally. Discovery of new genes plateaued after assembly of ~1.5 million reads, suggesting that we have sequenced nearly all transcripts present in the cDNA sampled. Many transcripts have been assembled at close to full length, and there is a net gain of sequence data for over half of the pre-existing O. fasciatus accessions for developmental genes in GenBank. We identified 10,775 unique genes, including members of all major conserved metazoan signaling pathways and genes involved in several major categories of early developmental processes. We also specifically address the effects of cDNA normalization on gene discovery in de novo transcriptome analyses. CONCLUSIONS Our sequencing, assembly and annotation framework provide a simple and effective way to achieve high-throughput gene discovery for organisms lacking a sequenced genome. These data will have applications to the study of the evolution of arthropod genes and genetic pathways, and to the wider evolution, development and genomics communities working with emerging model organisms.[The sequence data from this study have been submitted to GenBank under study accession number SRP002610 (http://www.ncbi.nlm.nih.gov/sra?term=SRP002610). Custom scripts generated are available at http://www.extavourlab.com/protocols/index.html. Seven Additional files are available.].
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Affiliation(s)
- Ben Ewen-Campen
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Li CJ, Gan F, Chen XH, Liu ZG, Li LX, Wei QW, Tang YK. Molecular and expression analysis of apolipoprotein E gene in the Chinese sturgeon, Acipenser sinensis. Comp Biochem Physiol B Biochem Mol Biol 2011; 158:64-70. [DOI: 10.1016/j.cbpb.2010.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 09/14/2010] [Accepted: 09/17/2010] [Indexed: 01/15/2023]
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Salem M, Rexroad CE, Wang J, Thorgaard GH, Yao J. Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 2010; 11:564. [PMID: 20942956 PMCID: PMC3091713 DOI: 10.1186/1471-2164-11-564] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 10/13/2010] [Indexed: 12/28/2022] Open
Abstract
Background Rainbow trout are important fish for aquaculture and recreational fisheries and serves as a model species for research investigations associated with carcinogenesis, comparative immunology, toxicology and evolutionary biology. However, to date there is no genome reference sequence to facilitate the development of molecular technologies that utilize high-throughput characterizations of gene expression and genetic variation. Alternatively, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Although a large number (258,973) of EST sequences are publicly available, the nature of rainbow trout duplicated genome hinders assembly and complicates annotation. Results High-throughput deep sequencing of the Swanson rainbow trout doubled-haploid transcriptome using 454-pyrosequencing technology yielded ~1.3 million reads with an average length of 344 bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus (TC) sequences (average length of 662 bp) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing sequences resulted in 161,818 TCs (average length of 758 bp) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed high similarities to transcriptomes of other fish species with known genome sequences. Conclusion The 454 library significantly increased the suite of ESTs available for rainbow trout, allowing improved assembly and annotation of the transcriptome. Furthermore, the 454 sequencing enables functional genome research in rainbow trout, providing a wealth of sequence data to serve as a reference transcriptome for future studies including identification of paralogous sequences and/or allelic variation, digital gene expression and proteomic research.
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Affiliation(s)
- Mohamed Salem
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
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Spade DJ, Griffitt RJ, Liu L, Brown-Peterson NJ, Kroll KJ, Feswick A, Glazer RA, Barber DS, Denslow ND. Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the Florida Keys. PLoS One 2010; 5:e12737. [PMID: 20856805 PMCID: PMC2939879 DOI: 10.1371/journal.pone.0012737] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 08/02/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Queen conch (Strombus gigas) reproduction is inhibited in nearshore areas of the Florida Keys, relative to the offshore environment where conchs reproduce successfully. Nearshore reproductive failure is possibly a result of exposure to environmental factors, including heavy metals, which are likely to accumulate close to shore. Metals such as Cu and Zn are detrimental to reproduction in many mollusks. METHODOLOGY/PRINCIPAL FINDINGS Histology shows gonadal atrophy in nearshore conchs as compared to reproductively healthy offshore conchs. In order to determine molecular mechanisms leading to tissue changes and reproductive failure, a microarray was developed. A normalized cDNA library for queen conch was constructed and sequenced using the 454 Life Sciences GS-FLX pyrosequencer, producing 27,723 assembled contigs and 7,740 annotated transcript sequences. The resulting sequences were used to design the microarray. Microarray analysis of conch testis indicated differential regulation of 255 genes (p<0.01) in nearshore conch, relative to offshore. Changes in expression for three of four transcripts of interest were confirmed using real-time reverse transcription polymerase chain reaction. Gene Ontology enrichment analysis indicated changes in biological processes: respiratory chain (GO:0015992), spermatogenesis (GO:0007283), small GTPase-mediated signal transduction (GO:0007264), and others. Inductively coupled plasma-mass spectrometry analysis indicated that Zn and possibly Cu were elevated in some nearshore conch tissues. CONCLUSIONS/SIGNIFICANCE Congruence between testis histology and microarray data suggests that nearshore conch testes regress during the reproductive season, while offshore conch testes develop normally. Possible mechanisms underlying the testis regression observed in queen conch in the nearshore Florida Keys include a disruption of small GTPase (Ras)-mediated signaling in testis development. Additionally, elevated tissue levels of Cu (34.77 ng/mg in testis) and Zn (831.85 ng/mg in digestive gland, 83.96 ng/mg in testis) nearshore are similar to reported levels resulting in reproductive inhibition in other gastropods, indicating that these metals possibly contribute to NS conch reproductive failure.
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Affiliation(s)
- Daniel J. Spade
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Robert J. Griffitt
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Li Liu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
| | - Nancy J. Brown-Peterson
- Department of Coastal Sciences, University of Southern Mississippi, Ocean Springs, Mississippi, United States of America
| | - Kevin J. Kroll
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - April Feswick
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Robert A. Glazer
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Marathon, Florida, United States of America
| | - David S. Barber
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Nancy D. Denslow
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Rawat A, Gust KA, Deng Y, Garcia-Reyero N, Quinn MJ, Johnson MS, Indest KJ, Elasri MO, Perkins EJ. From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite. Physiol Genomics 2010; 42:219-35. [PMID: 20406850 PMCID: PMC3032282 DOI: 10.1152/physiolgenomics.00022.2010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 04/16/2010] [Indexed: 01/02/2023] Open
Abstract
The limited availability of genomic tools and data for nonmodel species impedes computational and systems biology approaches in nonmodel organisms. Here we describe the development, functional annotation, and utilization of genomic tools for the avian wildlife species Northern bobwhite (Colinus virginianus) to determine the molecular impacts of exposure to 2,6-dinitrotoluene (2,6-DNT), a field contaminant of military concern. Massively parallel pyrosequencing of a normalized multitissue library of Northern bobwhite cDNAs yielded 71,384 unique transcripts that were annotated with gene ontology (GO), pathway information, and protein domain analysis. Comparative genome analyses with model organisms revealed functional homologies in 8,825 unique Northern bobwhite genes that are orthologous to 48% of Gallus gallus protein-coding genes. Pathway analysis and GO enrichment of genes differentially expressed in livers of birds exposed for 60 days (d) to 10 and 60 mg/kg/d 2,6-DNT revealed several impacts validated by RT-qPCR including: prostaglandin pathway-mediated inflammation, increased expression of a heme synthesis pathway in response to anemia, and a shift in energy metabolism toward protein catabolism via inhibition of control points for glucose and lipid metabolic pathways, PCK1 and PPARGC1, respectively. This research effort provides the first comprehensive annotated gene library for Northern bobwhite. Transcript expression analysis provided insights into the metabolic perturbations underlying several observed toxicological phenotypes in a 2,6-DNT exposure case study. Furthermore, the systemic impact of dinitrotoluenes on liver function appears conserved across species as PPAR signaling is similarly affected in fathead minnow liver tissue after exposure to 2,4-DNT.
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Affiliation(s)
- Arun Rawat
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, USA
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Martyniuk CJ, Kroll KJ, Doperalski NJ, Barber DS, Denslow ND. Genomic and proteomic responses to environmentally relevant exposures to dieldrin: indicators of neurodegeneration? Toxicol Sci 2010; 117:190-9. [PMID: 20584760 DOI: 10.1093/toxsci/kfq192] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dieldrin is a persistent organochlorine pesticide that induces neurotoxicity in the vertebrate central nervous system and impairs reproductive processes in fish. This study examined the molecular events produced by subchronic dietary exposures to 2.95 mg dieldrin/kg feed in the neuroendocrine brain of largemouth bass, an apex predator. Microarrays, proteomics, and pathway analysis were performed to identify genes, proteins, and cell processes altered in the male hypothalamus. Fifty-four genes were induced, and 220 genes were reduced in steady-state levels (p < 0.001; fold change greater than +/- 1.5). Functional enrichment analysis revealed that the biological gene ontology categories of stress response, nucleotide base excision repair, response to toxin, and metabolic processes were significantly impacted by dieldrin. Using isobaric tagging for relative and absolute quantitation, 90 proteins in the male hypothalamus were statistically evaluated for changes in protein abundance. Several proteins altered by dieldrin are known to be associated with human neurodegenerative diseases, including apolipoprotein E, microtubule-associated tau protein, enolase 1, stathmin 1a, myelin basic protein, and parvalbumin. Proteins altered by dieldrin were involved in oxidative phosphorylation, differentiation, proliferation, and cell survival. This study demonstrates that a subchronic exposure to dieldrin alters the abundance of messenger RNAs and proteins in the hypothalamus that are associated with cell metabolism, cell stability and integrity, stress, and DNA repair.
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Affiliation(s)
- Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida 32611, USA.
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Ferraresso S, Milan M, Pellizzari C, Vitulo N, Reinhardt R, Canario AVM, Patarnello T, Bargelloni L. Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity. BMC Genomics 2010; 11:354. [PMID: 20525278 PMCID: PMC2889902 DOI: 10.1186/1471-2164-11-354] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 06/03/2010] [Indexed: 11/10/2022] Open
Abstract
Background The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for D. labrax. Results A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant. Conclusions The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon.
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Affiliation(s)
- Serena Ferraresso
- Department of Public Health, Comparative Pathology, and Veterinary Hygiene, Faculty of Veterinary Medicine, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
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Effects of acute dieldrin exposure on neurotransmitters and global gene transcription in largemouth bass (Micropterus salmoides) hypothalamus. Neurotoxicology 2010; 31:356-66. [PMID: 20438755 DOI: 10.1016/j.neuro.2010.04.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/30/2010] [Accepted: 04/26/2010] [Indexed: 12/29/2022]
Abstract
Exposure to dieldrin induces neurotoxic effects in the vertebrate CNS and disrupts reproductive processes in teleost fish. Reproductive impairment observed in fish by dieldrin is likely the result of multiple effects along the hypothalamic-pituitary-gonadal axis, but the molecular signaling cascades are not well characterized. To better elucidate the mode of action of dieldrin in the hypothalamus, this study measured neurotransmitter levels and examined the transcriptomic response in female largemouth bass (LMB) to an acute treatment of dieldrin. Male and female LMB were injected with either vehicle or 10 mg dieldrin/kg and sacrificed after 7 days. There were no significant changes in dopamine or DOPAC concentrations in the neuroendocrine brain of males and females after treatment but GABA levels in females were moderately increased 20-30% in the hypothalamus and cerebellum. In the female hypothalamus, there were 227 transcripts (p<0.001) identified as being differentially regulated by dieldrin. Functional enrichment analysis revealed transcription, DNA repair, ubiquitin-proteasome pathway, and cell communication, as biological processes over-represented in the microarray analysis. Pathway analysis identified DNA damage, inflammation, regeneration, and Alzheimer's disease as major cell processes and diseases affected by dieldrin. Using multiple bioinformatics approaches, this study demonstrates that the teleostean hypothalamus is a target for dieldrin-induced neurotoxicity and provides mechanistic evidence that dieldrin activates similar cell pathways and biological processes that are also associated with the etiology of human neurological disorders.
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Schirmer K, Fischer BB, Madureira DJ, Pillai S. Transcriptomics in ecotoxicology. Anal Bioanal Chem 2010; 397:917-23. [PMID: 20369230 PMCID: PMC2868166 DOI: 10.1007/s00216-010-3662-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 01/08/2023]
Abstract
The emergence of analytical tools for high-throughput screening of biomolecules has revolutionized the way in which toxicologists explore the impact of chemicals or other stressors on organisms. One of the most developed and routinely applied high-throughput analysis approaches is transcriptomics, also often referred to as gene expression profiling. The transcriptome represents all RNA molecules, including the messenger RNA (mRNA), which constitutes the building blocks for translating DNA into amino acids to form proteins. The entirety of mRNA is a mirror of the genes that are actively expressed in a cell or an organism at a given time. This in turn allows one to deduce how organisms respond to changes in the external environment. In this article we explore how transcriptomics is currently applied in ecotoxicology and highlight challenges and trends. The transcriptome (RNA) is a mirror of the genes that are actively expressed in a cell or organism at a given time, providing information on how organisms respond to chemicals or other stressors in the environment ![]()
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Affiliation(s)
- Kristin Schirmer
- Department of Environmental Toxicology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Uberlandstrasse 133, 8600 Dübendorf, Switzerland.
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Abstract
Natural populations v. inbred stocks provide a much richer resource for identifying the effects of nucleotide substitutions because natural populations have greater polymorphism. Additionally, natural populations offer an advantage over most common research organisms because they are subject to natural selection, and analyses of these adaptations can be used to identify biologically important changes. Among fishes, these analyses are enhanced by having a wide diversity of species (>28 000 species, more than any other group of vertebrates) living in a huge range of environments (from below freezing to > 46 degrees C, in fresh water to salinities >40 ppt.). Moreover, fishes exhibit many different life-history and reproductive strategies and have many different phenotypes and social structures. Although fishes provide numerous advantages over other vertebrate models, there is still a dearth of available genomic tools for fishes. Fishes make up approximately half of all known vertebrate species, yet <0.2% of fish species have significant genomic resources. Nonetheless, genomic approaches with fishes have provided some of the first measures of individual variation in gene expression and insights into environmental and ecological adaptations. Thus, genomic approaches with natural fish populations have the potential to revolutionize fundamental studies of diverse fish species that offer myriad ecological and evolutionary questions.
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Affiliation(s)
- M F Oleksiak
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL 33149, USA.
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