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Su X, Wang X, Zhou Z, Zeng X, Wu Q, Leung JYS. Can antimony contamination in soil undermine the ecological contributions of earthworms? THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166305. [PMID: 37586541 DOI: 10.1016/j.scitotenv.2023.166305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/30/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
As antimony (Sb) has been increasingly used in manufacturing industries (e.g., alloy, polymer and electronics industries), Sb contamination in the soil environment becomes widely reported and has drawn growing attention due to the toxicity of Sb to living organisms. Whether soil-dwelling organisms can tolerate Sb toxicity and maintain their ecological functions remains poorly understood. Using a cosmopolitan, ecologically important earthworm species (Eisenia fetida) as an ideal model organism, we examine the effects of Sb on the physiological, molecular and behavioural responses of earthworms to different levels of Sb contamination in soil (0, 10, 50, 100, 250 and 500 mg/kg). We found that earthworms could tolerate heavy Sb contamination (100 mg/kg) by boosting their antioxidant defence (POD and GST) and immune systems (ACP) so that their body weight and survival rate were sustained (c.f. control). However, these systems were compromised under extreme Sb contamination (500 mg/kg), leading to mortality. As such, earthworms exhibited avoidance behaviour to escape from the Sb-contaminated soil, implying the loss of their ecological contributions to the environment (e.g., increase in soil aeration and maintenance of soil structure). By measuring various types of biomarkers along a concentration gradient, this study provides a mechanistic understanding of how earthworms resist or succumb to Sb toxicity. Since extreme Sb contamination in soil (>100 mg/kg) is rarely found in nature, we are optimistic that the health and performance of earthworms are not influenced by Sb in most circumstances, but regular monitoring of Sb in soil is recommended to ensure the integrity and functioning of soil environment. Further studies are recommended to evaluate the long-term impact of Sb in the soil ecosystem through bioaccumulation and trophic transfer among soil-dwelling organisms.
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Affiliation(s)
- Xiaotong Su
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta (Ministry of Education), School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Xiaolan Wang
- School of Life Sciences, Guangzhou University, Guangzhou 510655, China
| | - Zhiqian Zhou
- School of Life Sciences, Guangzhou University, Guangzhou 510655, China
| | - Xuan Zeng
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta (Ministry of Education), School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Qihang Wu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta (Ministry of Education), School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China.
| | - Jonathan Y S Leung
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China; School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia.
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Zhao W, Teng M, Zhang J, Wang K, Zhang J, Xu Y, Wang C. Insights into the mechanisms of organic pollutant toxicity to earthworms: Advances and perspectives. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 303:119120. [PMID: 35283202 DOI: 10.1016/j.envpol.2022.119120] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Earthworms play positive ecological roles in soil formation, structure, and fertility, environmental protection, and terrestrial food chains. For this review, we searched the Web of Science database for articles published from 2011 to 2021 using the keywords "toxic" and "earthworm" and retrieved 632 publications. From the perspective of bibliometric analysis, we conducted a co-occurrence network analysis using the keywords "toxic" and "earthworm" to identify the most and least reported topics. "Eisenia fetida," "bioaccumulation," "heavy metals," "oxidative stress," and "pesticides" were the most common terms, and "microbial community," "bacteria," "PFOS," "bioaugmentation," "potentially toxic elements," "celomic fluid," "neurotoxicity," "joint toxicity," "apoptosis," and "nanoparticles" were uncommon terms. Additionally, in this review we highlight the main routes of organic pollutant entry into soil, and discuss the adverse effects on the soil ecosystem. We then systematically review the mechanisms underlying organic pollutant toxicity to earthworms, including oxidative stress, energy and lipid metabolism disturbances, neurological toxicity, intestinal inflammation and injury, gut microbiota dysbiosis, and reproductive toxicity. We conclude by discussing future research perspectives, focusing on environmentally relevant concentrations and conditions, novel data processing approaches, technologies, and detoxification and mitigation methods. This review has implications for soil management in the context of environmental pollution.
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Affiliation(s)
- Wentian Zhao
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - Miaomiao Teng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jie Zhang
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, 570228, China
| | - Kai Wang
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling Road, Shenyang, People's Republic Of China
| | - Jialu Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - Yong Xu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - Chengju Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China.
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Jacobsen J, Adomako-Bonsu AG, Maser E. Induction of carbonyl reductase 1 (CR1) gene expression in Daphnia magna by TNT, but not its key metabolites 2-ADNT and 4-ADNT. Chem Biol Interact 2022; 351:109752. [PMID: 34801537 DOI: 10.1016/j.cbi.2021.109752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/16/2021] [Accepted: 11/16/2021] [Indexed: 11/03/2022]
Abstract
2,4,6-trinitrotoluene (TNT) is a known source of reactive oxygen species (ROS), which cause oxidative stress in aquatic ecosystems. Carbonyl reductases (CRs) are one of several possible defense mechanisms induced against ROS products, especially those that result in the 'so-called' carbonyl stress. Daphnia magna, a freshwater organism living in stagnant freshwater bodies, expresses four copies of the CR gene (Dma_CR1, Dma_CR2, Dma_CR3 and Dma_CR4). In this study, induction of all four copies of Dma_CR by 2-amino-4,6-dinitrotoluene (2-ADNT) and 4-amino-2,6-dinitrotoluene (4-ADNT), was investigated. Reverse transcription polymerase chain reaction (RT-PCR) analysis of treated daphnids revealed up-regulation of Dma_CR1 alone in response to TNT, but not 2-ADNT and 4-ADNT (which are key metabolites of TNT). This concentration- and time-dependent up-regulation in mRNA-expression was observed both in the presence and absence of light, in the same magnitude. Moreover, significant change in mRNA-expression could be observed 8 h after treatment with TNT. In the presence of TNT, the antioxidant N-acetylcysteine (NAc) could not reverse TNT-induced up-regulation of Dma_CR1 mRNA-expression. On the other hand, withdrawal of TNT from the culture medium caused a significant reduction in the TNT-induced mRNA-expression of Dma_CR1 within 24 h. These findings highlight the potential of Dma_CR1 as a biomarker for biomonitoring of TNT levels in freshwater bodies.
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Affiliation(s)
- Jana Jacobsen
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany
| | - Amma G Adomako-Bonsu
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany
| | - Edmund Maser
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany.
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Schüttler A, Jakobs G, Fix J, Krauss M, Krüger J, Leuthold D, Altenburger R, Busch W. Transcriptome-Wide Prediction and Measurement of Combined Effects Induced by Chemical Mixture Exposure in Zebrafish Embryos. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:47006. [PMID: 33826412 PMCID: PMC8041271 DOI: 10.1289/ehp7773] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
BACKGROUND Humans and environmental organisms are constantly exposed to complex mixtures of chemicals. Extending our knowledge about the combined effects of chemicals is thus essential for assessing the potential consequences of these exposures. In this context, comprehensive molecular readouts as retrieved by omics techniques are advancing our understanding of the diversity of effects upon chemical exposure. This is especially true for effects induced by chemical concentrations that do not instantaneously lead to mortality, as is commonly the case for environmental exposures. However, omics profiles induced by chemical exposures have rarely been systematically considered in mixture contexts. OBJECTIVES In this study, we aimed to investigate the predictability of chemical mixture effects on the whole-transcriptome scale. METHODS We predicted and measured the toxicogenomic effects of a synthetic mixture on zebrafish embryos. The mixture contained the compounds diuron, diclofenac, and naproxen. To predict concentration- and time-resolved whole-transcriptome responses to the mixture exposure, we adopted the mixture concept of concentration addition. Predictions were based on the transcriptome profiles obtained for the individual mixture components in a previous study. Finally, concentration- and time-resolved mixture exposures and subsequent toxicogenomic measurements were performed and the results were compared with the predictions. RESULTS This comparison of the predictions with the observations showed that the concept of concentration addition provided reasonable estimates for the effects induced by the mixture exposure on the whole transcriptome. Although nonadditive effects were observed only occasionally, combined, that is, multicomponent-driven, effects were found for mixture components with anticipated similar, as well as dissimilar, modes of action. DISCUSSION Overall, this study demonstrates that using a concentration- and time-resolved approach, the occurrence and size of combined effects of chemicals may be predicted at the whole-transcriptome scale. This allows improving effect assessment of mixture exposures on the molecular scale that might not only be of relevance in terms of risk assessment but also for pharmacological applications. https://doi.org/10.1289/EHP7773.
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Affiliation(s)
- A. Schüttler
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
- Institute for Environmental Research, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - G. Jakobs
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - J.M. Fix
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - M. Krauss
- Department Effect-Directed Analysis, UFZ, Leipzig, Germany
| | - J. Krüger
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - D. Leuthold
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - R. Altenburger
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
- Institute for Environmental Research, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - W. Busch
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
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Gong P, Donohue KB, Mayo AM, Wang Y, Hong H, Wilbanks MS, Barker ND, Guan X, Gust KA. Comparative toxicogenomics of three insensitive munitions constituents 2,4-dinitroanisole, nitroguanidine and nitrotriazolone in the soil nematode Caenorhabditis elegans. BMC SYSTEMS BIOLOGY 2018; 12:92. [PMID: 30547801 PMCID: PMC6293504 DOI: 10.1186/s12918-018-0636-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Ecotoxicological studies on the insensitive munitions formulation IMX-101 and its components 2,4-dinitroanisole (DNAN), nitroguanidine (NQ) and nitrotriazolone (NTO) in various organisms showed that DNAN was the main contributor to the overall toxicity of IMX-101 and suggested that the three compounds acted independently. These results motivated this toxicogenomics study to discern toxicological mechanisms for these compounds at the molecular level. METHODS Here we used the soil nematode Caenorhabditis elegans, a well-characterized genomics model, as the test organism and a species-specific, transcriptome-wide 44 K-oligo probe microarray for gene expression analysis. In addition to the control treatment, C. elegans were exposed for 24 h to 6 concentrations of DNAN (1.95-62.5 ppm) or NQ (83-2667 ppm) or 5 concentrations of NTO (187-3000 ppm) with ten replicates per treatment. The nematodes were transferred to a clean environment after exposure. Reproduction endpoints (egg and larvae counts) were measured at three time points (i.e., 24-, 48- and 72-h). Gene expression profiling was performed immediately after 24-h exposure to each chemical at the lowest, medium and highest concentrations plus the control with four replicates per treatment. RESULTS Statistical analyses indicated that chemical treatment did not significantly affect nematode reproduction but did induce 2175, 378, and 118 differentially expressed genes (DEGs) in NQ-, DNAN-, and NTO-treated nematodes, respectively. Bioinformatic analysis indicated that the three compounds shared both DEGs and DEG-mapped Reactome pathways. Gene set enrichment analysis further demonstrated that DNAN and NTO significantly altered 12 and 6 KEGG pathways, separately, with three pathways in common. NTO mainly affected carbohydrate, amino acid and xenobiotics metabolism while DNAN disrupted protein processing, ABC transporters and several signal transduction pathways. NQ-induced DEGs were mapped to a wide variety of metabolism, cell cycle, immune system and extracellular matrix organization pathways. CONCLUSION Despite the absence of significant effects on apical reproduction endpoints, DNAN, NTO and NQ caused significant alterations in gene expression and pathways at 1.95 ppm, 187 ppm and 83 ppm, respectively. This study provided supporting evidence that the three chemicals may exert independent toxicity by acting on distinct molecular targets and pathways.
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Affiliation(s)
- Ping Gong
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA.
| | - Keri B Donohue
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA
| | - Anne M Mayo
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA
| | - Yuping Wang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Mitchell S Wilbanks
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA
| | - Natalie D Barker
- Bennett Aerospace Inc., 1249 Kildaire Farm Road, Cary, NC, 27511, USA
| | - Xin Guan
- Bennett Aerospace Inc., 1249 Kildaire Farm Road, Cary, NC, 27511, USA
| | - Kurt A Gust
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS, 39180, USA
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Mayilswami S, Krishnan K, Megharaj M, Naidu R. Gene expression profile changes in Eisenia fetida chronically exposed to PFOA. ECOTOXICOLOGY (LONDON, ENGLAND) 2016; 25:759-769. [PMID: 26942927 DOI: 10.1007/s10646-016-1634-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/16/2016] [Indexed: 06/05/2023]
Abstract
Eisenia fetida is a terrestrial organism, which can be used to diagnose sub-lethal concentrations of PFOA by using molecular biomarkers. In order to identify potential molecular biomarkers, we have exposed E. fetida to 10 mg/kg of PFOA in soil for 8 months. The mRNA isolation, sequencing, transcriptome assembly followed by differential gene expression studies have revealed that genes that are involved in apoptotic process, reproduction, calcium signalling, neuronal development and lipid metabolism are predominantly affected. Highly specific genes that are altered by PFOA can be further validated and used as biomarker to detect sub-lethal concentrations of PFOA in the soil.
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Affiliation(s)
- Srinithi Mayilswami
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, Adelaide, SA, 5095, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC-CARE), Mawson Lakes, Adelaide, SA, 5095, Australia
| | - Kannan Krishnan
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC-CARE), Mawson Lakes, Adelaide, SA, 5095, Australia.
- Global Centre for Environmental Remediation, Faculty of Science and Information Technology, The University of Newcastle, Callaghan, NSW, 2308, Australia.
| | - Mallavarapu Megharaj
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC-CARE), Mawson Lakes, Adelaide, SA, 5095, Australia
- Global Centre for Environmental Remediation, Faculty of Science and Information Technology, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Ravi Naidu
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC-CARE), Mawson Lakes, Adelaide, SA, 5095, Australia
- Global Centre for Environmental Remediation, Faculty of Science and Information Technology, The University of Newcastle, Callaghan, NSW, 2308, Australia
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Bernard F, Brulle F, Dumez S, Lemiere S, Platel A, Nesslany F, Cuny D, Deram A, Vandenbulcke F. Antioxidant responses of Annelids, Brassicaceae and Fabaceae to pollutants: a review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 114:273-303. [PMID: 24951273 DOI: 10.1016/j.ecoenv.2014.04.024] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 04/15/2014] [Accepted: 04/20/2014] [Indexed: 06/03/2023]
Abstract
Pollutants, such as Metal Trace Elements (MTEs) and organic compounds (polycyclic aromatic hydrocarbons, pesticides), can impact DNA structure of living organisms and thus generate damage. For instance, cadmium is a well-known genotoxic and mechanisms explaining its clastogenicity are mainly indirect: inhibition of DNA repair mechanisms and/or induction of Reactive Oxygen Species (ROS). Animal or vegetal cells use antioxidant defense systems to protect themselves against ROS produced during oxidative stress. Because tolerance of organisms depends, at least partially, on their ability to cope with ROS, the mechanisms of production and management of ROS were investigated a lot in Ecotoxicology as markers of biotic and abiotic stress. This was mainly done through the measurement of enzyme activities The present Review focuses on 3 test species living in close contact with soil that are often used in soil ecotoxicology: the worm Eisenia fetida, and two plant species, Trifolium repens (white clover) and Brassica oleracea (cabbage). E. fetida is a soil-dwelling organism commonly used for biomonitoring. T. repens is a symbiotic plant species which forms root nodule with soil bacteria, while B. oleracea is a non-symbiotic plant. In literature, some oxidative stress enzyme activities have already been measured in those species but such analyses do not allow distinction between individual enzyme involvements in oxidative stress. Gene expression studies would allow this distinction at the transcriptomic level. A literature review and a data search in molecular database were carried out on the basis of keywords in Scopus, in PubMed and in Genbank™ for each species. Molecular data regarding E. fetida were already available in databases, but a lack of data regarding oxidative stress related genes was observed for T. repens and B. oleracea. By exploiting the conservation observed between species and using molecular biology techniques, we partially cloned missing candidates involved in oxidative stress and in metal detoxification in E. fetida, T. repens and B. oleracea.
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Affiliation(s)
- F Bernard
- Université Lille Nord de France, F-59000 Lille, France; Laboratoire de Génie Civil et géo-Environnement EA4515 - Université Lille Nord de France - Lille 1, Ecologie Numérique et Ecotoxicologie, F-59655 Villeneuve d'Ascq, France; Laboratoire des Sciences Végétales et Fongiques - Université de Lille 2, EA4483, F-59006 Lille Cedex, France
| | - F Brulle
- Université Lille Nord de France, F-59000 Lille, France; Laboratoire des Sciences Végétales et Fongiques - Université de Lille 2, EA4483, F-59006 Lille Cedex, France
| | - S Dumez
- Université Lille Nord de France, F-59000 Lille, France; Laboratoire des Sciences Végétales et Fongiques - Université de Lille 2, EA4483, F-59006 Lille Cedex, France
| | - S Lemiere
- Université Lille Nord de France, F-59000 Lille, France; Laboratoire de Génie Civil et géo-Environnement EA4515 - Université Lille Nord de France - Lille 1, Ecologie Numérique et Ecotoxicologie, F-59655 Villeneuve d'Ascq, France
| | - A Platel
- Université Lille Nord de France, F-59000 Lille, France; Laboratoire de Toxicologie - Institut Pasteur de Lille, EA 4483, F-59800 Lille, France
| | - F Nesslany
- Université Lille Nord de France, F-59000 Lille, France; Laboratoire de Toxicologie - Institut Pasteur de Lille, EA 4483, F-59800 Lille, France
| | - D Cuny
- Université Lille Nord de France, F-59000 Lille, France; Laboratoire des Sciences Végétales et Fongiques - Université de Lille 2, EA4483, F-59006 Lille Cedex, France
| | - A Deram
- Université Lille Nord de France, F-59000 Lille, France; Laboratoire des Sciences Végétales et Fongiques - Université de Lille 2, EA4483, F-59006 Lille Cedex, France; Faculté de Management de la Santé (ILIS) - Université de Lille 2, EA4483, F-59120 Loos, France
| | - F Vandenbulcke
- Université Lille Nord de France, F-59000 Lille, France; Laboratoire de Génie Civil et géo-Environnement EA4515 - Université Lille Nord de France - Lille 1, Ecologie Numérique et Ecotoxicologie, F-59655 Villeneuve d'Ascq, France.
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Pan X, Ochoa KM, Francisco MJS, Cox SB, Dixon K, Anderson TA, Cobb GP. Absorption, distribution, and biotransformation of hexahydro-1,3,5-trinitro-1,3,5-triazine in B6C3F1 mice (Mus musculus). ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2013; 32:1295-1303. [PMID: 23423972 DOI: 10.1002/etc.2188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/14/2013] [Accepted: 01/21/2013] [Indexed: 06/01/2023]
Abstract
Absorption, distribution, and biotransformation are 3 critical aspects affecting toxicant action in animals. In the present study, B6C3F1 mice (Mus musculus) were exposed for 28 d to contaminated feed that contained 1 of 5 different hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) concentrations: 0 mg/kg, 0.5 mg/kg, 5 mg/kg, 50 mg/kg, and 500 mg/kg. The authors quantified RDX and its reductive transformation products hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine (DNX), and hexahydro-1,3,5-trinitroso-1,3,5-triazine (TNX) in the stomach, intestine, plasma, liver, and brain of these mice. Average RDX concentrations followed a dose-dependent pattern for all matrices tested. No controls had concentrations above limits of detection. Average RDX concentrations in tissues of exposed mice ranged from 11.1 ng/mL to 182 ng/mL, 25.6 ng/g to 3319 ng/g, 123 ng/g to 233 ng/g, 144 ng/g to 35 900 ng/g, and 51.1 ng/g to 2697 ng/g in the plasma, brain, liver, stomach, and intestine, respectively. A considerable amount of RDX was present in the brain, especially in the highest-exposure group. This is consistent with the widely observed central nervous system effects caused by γ-aminobutyric acid inhibition associated with RDX exposure. N-nitroso metabolites of RDX were also present in tested tissues in a dose-dependent pattern. Average MNX concentrations in the stomachs of mice exposed to RDX ranged from nondetectable in control exposures to 490 ng/g in the highest-exposure groups. In the brain, MNX accumulated at a maximum average concentration of 165.1 ng/g, suggesting the potential formation of MNX from RDX within the brain. At higher exposures, DNX and TNX were present in the stomach, plasma, and brain of mice. The presence of RDX metabolites at notable amounts in different tissues suggests that RDX can transform into its N-nitroso metabolites in vivo by an undefined mechanism.
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Affiliation(s)
- Xiaoping Pan
- Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas, USA
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Steinberg CEW, Pietsch K, Saul N, Menzel S, Swain SC, Stürzenbaum SR, Menzel R. Transcript expression patterns illuminate the mechanistic background of hormesis in caenorhabditis elegans maupas. Dose Response 2013; 11:558-76. [PMID: 24298231 DOI: 10.2203/dose-response.12-024.steinberg] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The animal model Caenorhabditis elegans was employed to study polyphenol- and humic substances-induced hormetic changes in lifespan. A detailed insight into the underlying mechanism of hormesis was uncovered by applying whole genome DNA microarray experimentation over a range of quercetin (Q), tannic acid (TA), and humic substances (HuminFeed(®), HF) concentrations. The transcriptional response to all exposures followed a non-linear mode which highlighted differential signaling and metabolic pathways. While low Q concentrations regulated processes improving the health of the nematodes, higher concentrations extended lifespan and modulated substantially the global transcriptional response. Over-represented transcripts were notably part of the biotransformation process: enhanced catabolism of toxic intermediates possibly contributes to the lifespan extension. The regulation of transcription, Dauer entry, and nucleosome suggests the presence of distinct exposure dependent differences in transcription and signaling pathways. TA- and HF-mediated transcript expression patterns were overall similar to each other, but changed across the concentration range indicating that their transcriptional dynamics are complex and cannot be attributed to a simple adaptive response. In contrast, Q-mediated hormesis was well aligned to fit the definition of an adaptive response. Simple molecules are more likely to induce an adaptive response than more complex molecules.
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Warner CM, Gust KA, Stanley JK, Habib T, Wilbanks MS, Garcia-Reyero N, Perkins EJ. A systems toxicology approach to elucidate the mechanisms involved in RDX species-specific sensitivity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:7790-7798. [PMID: 22697906 DOI: 10.1021/es300495c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Interspecies uncertainty factors in ecological risk assessment provide conservative estimates of risk where limited or no toxicity data is available. We quantitatively examined the validity of interspecies uncertainty factors by comparing the responses of zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) to the energetic compound 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), a known neurotoxicant. Relative toxicity was measured through transcriptional, morphological, and behavioral end points in zebrafish and fathead minnow fry exposed for 96 h to RDX concentrations ranging from 0.9 to 27.7 mg/L. Spinal deformities and lethality occurred at 1.8 and 3.5 mg/L RDX respectively for fathead minnow and at 13.8 and 27.7 mg/L for zebrafish, indicating that zebrafish have an 8-fold greater tolerance for RDX than fathead minnow fry. The number and magnitude of differentially expressed transcripts increased with increasing RDX concentration for both species. Differentially expressed genes were enriched in functions related to neurological disease, oxidative-stress, acute-phase response, vitamin/mineral metabolism and skeletal/muscular disorders. Decreased expression of collagen-coding transcripts were associated with spinal deformity and likely involved in sensitivity to RDX. Our work provides a mechanistic explanation for species-specific sensitivity to RDX where zebrafish responded at lower concentrations with greater numbers of functions related to RDX tolerance than fathead minnow. While the 10-fold interspecies uncertainty factor does provide a reasonable cross-species estimate of toxicity in the present study, the observation that the responses between ZF and FHM are markedly different does initiate a call for concern regarding establishment of broad ecotoxicological conclusions based on model species such as zebrafish.
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Affiliation(s)
- Christopher M Warner
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi, United States
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11
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Roelofs D, de Boer M, Agamennone V, Bouchier P, Legler J, van Straalen N. Functional environmental genomics of a municipal landfill soil. Front Genet 2012; 3:85. [PMID: 22623925 PMCID: PMC3353140 DOI: 10.3389/fgene.2012.00085] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 04/28/2012] [Indexed: 11/13/2022] Open
Abstract
We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardized Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II, and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects.
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Affiliation(s)
- Dick Roelofs
- Department of Ecological Science, VU University Amsterdam, Netherlands
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12
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Hawliczek A, Nota B, Cenijn P, Kamstra J, Pieterse B, Winter R, Winkens K, Hollert H, Segner H, Legler J. Developmental toxicity and endocrine disrupting potency of 4-azapyrene, benzo[b]fluorene and retene in the zebrafish Danio rerio. Reprod Toxicol 2012; 33:213-23. [DOI: 10.1016/j.reprotox.2011.11.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 11/01/2011] [Accepted: 11/04/2011] [Indexed: 10/15/2022]
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13
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Gong P, Guan X, Pirooznia M, Liang C, Perkins EJ. Gene expression analysis of CL-20-induced reversible neurotoxicity reveals GABA(A) receptors as potential targets in the earthworm Eisenia fetida. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:1223-1232. [PMID: 22191394 PMCID: PMC3332050 DOI: 10.1021/es203642e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The earthworm Eisenia fetida is one of the most used species in standardized soil ecotoxicity tests. End points such as survival, growth, and reproduction are eco-toxicologically relevant but provide little mechanistic insight into toxicity pathways, especially at the molecular level. Here we apply a toxicogenomic approach to investigate the mode of action underlying the reversible neurotoxicity of hexanitrohexaazaisowurtzitane (CL-20), a cyclic nitroamine explosives compound. We developed an E. fetida-specific shotgun microarray targeting 15119 unique E. fetida transcripts. Using this array we profiled gene expression in E. fetida in response to exposure to CL-20. Eighteen earthworms were exposed for 6 days to 0.2 μg/cm(2) of CL-20 on filter paper, half of which were allowed to recover in a clean environment for 7 days. Nine vehicle control earthworms were sacrificed at days 6 and 13, separately. Electrophysiological measurements indicated that the conduction velocity of earthworm medial giant nerve fiber decreased significantly after 6-day exposure to CL-20, but was restored after 7 days of recovery. Total RNA was isolated from the four treatment groups including 6-day control, 6-day exposed, 13-day control, and 13-day exposed (i.e., 6-day exposure followed by 7-day recovery), and was hybridized to the 15K shotgun oligo array. Statistical and bioinformatic analyses suggest that CL-20 initiated neurotoxicity by noncompetitively blocking the ligand-gated GABA(A) receptor ion channel, leading to altered expression of genes involved in GABAergic, cholinergic, and Agrin-MuSK pathways. In the recovery phase, expression of affected genes returned to normality, possibly as a result of autophagy and CL-20 dissociation/metabolism. This study provides significant insights into potential mechanisms of CL-20-induced neurotoxicity and the recovery of earthworms from transient neurotoxicity stress.
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Affiliation(s)
- Ping Gong
- Environmental Services, SpecPro Inc., San Antonio, Texas 78216, United States.
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14
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van Straalen NM, Feder ME. Ecological and evolutionary functional genomics--how can it contribute to the risk assessment of chemicals? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:3-9. [PMID: 22043966 DOI: 10.1021/es2034153] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Nico M van Straalen
- Department of Ecological Science, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands.
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15
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Novais SC, Howcroft CF, Carreto L, Pereira PM, Santos MAS, De Coen W, Soares AMVM, Amorim MJB. Differential gene expression analysis in Enchytraeus albidus exposed to natural and chemical stressors at different exposure periods. ECOTOXICOLOGY (LONDON, ENGLAND) 2012; 21:213-224. [PMID: 21892792 DOI: 10.1007/s10646-011-0780-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/20/2011] [Indexed: 05/31/2023]
Abstract
The soil oligochaete Enchytraeus albidus is a standard test organism used in biological testing for Environmental Risk Assessment (ERA). Although effects are known at acute and chronic level through survival, reproduction and avoidance behaviour endpoints, very little is known at the sub-cellular and molecular levels. In this study, the effects of soil properties (clay, organic matter and pH) and of the chemicals copper and phenmedipham were studied on E. albidus gene expression, during exposure periods of 2, 4 and 21 days, using DNA microarrays based on a normalised cDNA library for this test species (Amorim et al. 2011). The main objectives of this study were: (1) to assess changes in gene expression of E. albidus over time, and (2) to identify molecular markers for natural and chemical exposures. Results showed an influence of exposure time on gene expression. Transcriptional responses to phenmedipham were seen at 2 days while the responses to copper and the different soils were more pronounced at 4 days of exposure. Some genes were differentially expressed in a stress specific manner and, in general, the responses were related with effects in the energy metabolism and cell growth.
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Affiliation(s)
- Sara C Novais
- Department of Biology & CESAM, University of Aveiro, 3810-193 Aveiro, Portugal.
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16
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Belden JB, Lotufo GR, Chambliss CK, Fisher JC, Johnson DR, Boyd RE, Sims JG. Accumulation of 14C-trinitrotoluene and related nonextractable (bound) residues in Eisenia fetida. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:1363-1368. [PMID: 21295392 DOI: 10.1016/j.envpol.2011.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 01/04/2011] [Accepted: 01/06/2011] [Indexed: 05/30/2023]
Abstract
To determine if trinitrotoluene (TNT) forms nonextractable residues in earthworms and to measure the relative degree of accumulation as compared to TNT and its deaminated metabolites, Eisenia fetida was exposed to 14C-TNT using dermal contact to filter paper or exposure to soil. Nonextractable residues made up 32-68% of total body burden depending on exposure media and depuration time. Parent TNT accounted for less than 3% of radioactivity, while ADNTs accounted for 7-38%. Elimination half-lives were 61-120 h for TNT, ADNTs, and DANTs, which was significantly lower than the half-lives found for nonextractable residues, 201-240 h. However, over 80% of the nonextractable residue was solubilized using weak acid (pH 2). Based on our findings that TNT accumulation occurs primarily as nonextractable residues, which have a longer half-life, and that nonextractable residues can be solubilized, we propose that nonextractable residues could be used as a selective biomarker for assessing TNT contamination.
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Affiliation(s)
- Jason B Belden
- Department of Zoology, Oklahoma State University, Stillwater, OK 74078, USA.
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17
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Garcia-Reyero N, Habib T, Pirooznia M, Gust KA, Gong P, Warner C, Wilbanks M, Perkins E. Conserved toxic responses across divergent phylogenetic lineages: a meta-analysis of the neurotoxic effects of RDX among multiple species using toxicogenomics. ECOTOXICOLOGY (LONDON, ENGLAND) 2011; 20:580-594. [PMID: 21516383 DOI: 10.1007/s10646-011-0623-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/14/2011] [Indexed: 05/28/2023]
Abstract
At military training sites, a variety of pollutants such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), may contaminate the area originating from used munitions. Studies investigating the mechanism of toxicity of RDX have shown that it affects the central nervous system causing seizures in humans and animals. Environmental pollutants such as RDX have the potential to affect many different species, therefore it is important to establish how phylogenetically distant species may respond to these types of emerging pollutants. In this paper, we have used a transcriptional network approach to compare and contrast the neurotoxic effects of RDX among five phylogenetically disparate species: rat (Sprague-Dawley), Northern bobwhite quail (Colinus virginianus), fathead minnow (Pimephales promelas), earthworm (Eisenia fetida), and coral (Acropora formosa). Pathway enrichment analysis indicated a conservation of RDX impacts on pathways related to neuronal function in rat, Northern bobwhite quail, fathead minnows and earthworm, but not in coral. As evolutionary distance increased common responses decreased with impacts on energy and metabolism dominating effects in coral. A neurotransmission related transcriptional network based on whole rat brain responses to RDX exposure was used to identify functionally related modules of genes, components of which were conserved across species depending upon evolutionary distance. Overall, the meta-analysis using genomic data of the effects of RDX on several species suggested a common and conserved mode of action of the chemical throughout phylogenetically remote organisms.
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Gong P, Pirooznia M, Guan X, Perkins EJ. Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida. PLoS One 2010; 5:e14266. [PMID: 21170345 PMCID: PMC2999564 DOI: 10.1371/journal.pone.0014266] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 11/14/2010] [Indexed: 11/24/2022] Open
Abstract
High density oligonucleotide probe arrays have increasingly become an important tool in genomics studies. In organisms with incomplete genome sequence, one strategy for oligo probe design is to reduce the number of unique probes that target every non-redundant transcript through bioinformatic analysis and experimental testing. Here we adopted this strategy in making oligo probes for the earthworm Eisenia fetida, a species for which we have sequenced transcriptome-scale expressed sequence tags (ESTs). Our objectives were to identify unique transcripts as targets, to select an optimal and non-redundant oligo probe for each of these target ESTs, and to annotate the selected target sequences. We developed a streamlined and easy-to-follow approach to the design, validation and annotation of species-specific array probes. Four 244K-formatted oligo arrays were designed using eArray and were hybridized to a pooled E. fetida cRNA sample. We identified 63,541 probes with unsaturated signal intensities consistently above the background level. Target transcripts of these probes were annotated using several sequence alignment algorithms. Significant hits were obtained for 37,439 (59%) probed targets. We validated and made publicly available 63.5K oligo probes so the earthworm research community can use them to pursue ecological, toxicological, and other functional genomics questions. Our approach is efficient, cost-effective and robust because it (1) does not require a major genomics core facility; (2) allows new probes to be easily added and old probes modified or eliminated when new sequence information becomes available, (3) is not bioinformatics-intensive upfront but does provide opportunities for more in-depth annotation of biological functions for target genes; and (4) if desired, EST orthologs to the UniGene clusters of a reference genome can be identified and selected in order to improve the target gene specificity of designed probes. This approach is particularly applicable to organisms with a wealth of EST sequences but unfinished genome.
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Affiliation(s)
- Ping Gong
- Environmental Services, SpecPro Inc., Vicksburg, Mississippi, United States of America.
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19
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Chowbina S, Deng Y, Ai J, Wu X, Guan X, Wilbanks MS, Escalon BL, Meyer SA, Perkins EJ, Chen JY. A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNT. BMC Genomics 2010; 11 Suppl 3:S4. [PMID: 21143786 PMCID: PMC2999349 DOI: 10.1186/1471-2164-11-s3-s4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract Background Military and industrial activities have lead to reported release of 2,4-dinitrotoluene (2,4DNT) into soil, groundwater or surface water. It has been reported that 2,4DNT can induce toxic effects on humans and other organisms. However the mechanism of 2,4DNT induced toxicity is still unclear. Although a series of methods for gene network construction have been developed, few instances of applying such technology to generate pathway connected networks have been reported. Results Microarray analyses were conducted using liver tissue of rats collected 24h after exposure to a single oral gavage with one of five concentrations of 2,4DNT. We observed a strong dose response of differentially expressed genes after 2,4DNT treatment. The most affected pathways included: long term depression, breast cancer regulation by stathmin1, WNT Signaling; and PI3K signaling pathways. In addition, we propose a new approach to construct pathway connected networks regulated by 2,4DNT. We also observed clear dose response pathway networks regulated by 2,4DNT. Conclusions We developed a new method for constructing pathway connected networks. This new method was successfully applied to microarray data from liver tissue of 2,4DNT exposed animals and resulted in the identification of unique dose responsive biomarkers in regards to affected pathways.
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Affiliation(s)
- Sudhir Chowbina
- Indiana University School of Informatics, Indianapolis, IN 46202, USA.
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20
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Deng Y, Johnson DR, Guan X, Ang CY, Ai J, Perkins EJ. In vitro gene regulatory networks predict in vivo function of liver. BMC SYSTEMS BIOLOGY 2010; 4:153. [PMID: 21073692 PMCID: PMC2998496 DOI: 10.1186/1752-0509-4-153] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 11/12/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Evolution of toxicity testing is predicated upon using in vitro cell based systems to rapidly screen and predict how a chemical might cause toxicity to an organ in vivo. However, the degree to which we can extend in vitro results to in vivo activity and possible mechanisms of action remains to be fully addressed. RESULTS Here we use the nitroaromatic 2,4,6-trinitrotoluene (TNT) as a model chemical to compare and determine how we might extrapolate from in vitro data to in vivo effects. We found 341 transcripts differentially expressed in common among in vitro and in vivo assays in response to TNT. The major functional term corresponding to these transcripts was cell cycle. Similarly modulated common pathways were identified between in vitro and in vivo. Furthermore, we uncovered the conserved common transcriptional gene regulatory networks between in vitro and in vivo cellular liver systems that responded to TNT exposure, which mainly contain 2 subnetwork modules: PTTG1 and PIR centered networks. Interestingly, all 7 genes in the PTTG1 module were involved in cell cycle and downregulated by TNT both in vitro and in vivo. CONCLUSIONS The results of our investigation of TNT effects on gene expression in liver suggest that gene regulatory networks obtained from an in vitro system can predict in vivo function and mechanisms. Inhibiting PTTG1 and its targeted cell cycle related genes could be key mechanism for TNT induced liver toxicity.
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Affiliation(s)
- Youping Deng
- Rush University Medical Center, Chicago, IL 60612, USA.
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21
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Identification and optimization of classifier genes from multi-class earthworm microarray dataset. PLoS One 2010; 5:e13715. [PMID: 21060837 PMCID: PMC2965664 DOI: 10.1371/journal.pone.0013715] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 10/06/2010] [Indexed: 11/19/2022] Open
Abstract
Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT and RDX. One important goal of microarray experiments is to discover novel biomarkers for toxicity evaluation. We have developed an earthworm microarray containing 15,208 unique oligo probes and have used it to profile gene expression in 248 earthworms exposed to TNT, RDX or neither. We assembled a new machine learning pipeline consisting of several well-established feature filtering/selection and classification techniques to analyze the 248-array dataset in order to construct classifier models that can separate earthworm samples into three groups: control, TNT-treated, and RDX-treated. First, a total of 869 genes differentially expressed in response to TNT or RDX exposure were identified using a univariate statistical algorithm of class comparison. Then, decision tree-based algorithms were applied to select a subset of 354 classifier genes, which were ranked by their overall weight of significance. A multiclass support vector machine (MC-SVM) method and an unsupervised K-mean clustering method were applied to independently refine the classifier, producing a smaller subset of 39 and 30 classifier genes, separately, with 11 common genes being potential biomarkers. The combined 58 genes were considered the refined subset and used to build MC-SVM and clustering models with classification accuracy of 83.5% and 56.9%, respectively. This study demonstrates that the machine learning approach can be used to identify and optimize a small subset of classifier/biomarker genes from high dimensional datasets and generate classification models of acceptable precision for multiple classes.
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Brulle F, Morgan AJ, Cocquerelle C, Vandenbulcke F. Transcriptomic underpinning of toxicant-mediated physiological function alterations in three terrestrial invertebrate taxa: a review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2010; 158:2793-2808. [PMID: 20619942 DOI: 10.1016/j.envpol.2010.06.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 06/09/2010] [Accepted: 06/12/2010] [Indexed: 05/29/2023]
Abstract
Diverse anthropogenic activities often lead to the accumulation of inorganic and organic residues in topsoils. Biota living in close contact with contaminated soils may experience stress at different levels of biological organisation throughout the continuum from the molecular-genetic to ecological and community levels. To date, the relationship between changes at the molecular (mRNA expression) and biochemical/physiological levels evoked by exposures to chemical compounds has been partially established in a limited number of terrestrial invertebrate species. Recently, the advent of a family of transcriptomic tools (e.g. Real-time PCR, Subtractive Suppressive Hybridization, Expressed Sequence Tag sequencing, pyro-sequencing technologies, Microarray chips), together with supporting informatic and statistical procedures, have permitted the robust analyses of global gene expression changes within an ecotoxicological context. This review focuses on how transcriptomics is enlightening our understanding of the molecular-genetic responses of three contrasting terrestrial macroinvertebrate taxa (nematodes, earthworms, and springtails) to inorganics, organics, and agrochemicals.
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Nota B, Verweij RA, Molenaar D, Ylstra B, van Straalen NM, Roelofs D. Gene expression analysis reveals a gene set discriminatory to different metals in soil. Toxicol Sci 2010; 115:34-40. [PMID: 20133373 DOI: 10.1093/toxsci/kfq043] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Environmental pollution is a worldwide problem, and metals are the largest group of contaminants in soil. Microarray toxicogenomic studies with ecologically relevant organisms, such as springtails, supplement traditional ecotoxicological research but are presently rather descriptive. Classifier analysis, a more analytical application of the microarray technique, is able to predict biological classes of unknown samples. We used the uncorrelated shrunken centroid method to classify gene expression profiles of the springtail Folsomia candida exposed to soil spiked with six different metals (barium, cadmium, cobalt, chromium, lead, and zinc). We identified a gene set (classifier) of 188 genes that can discriminate between six different metals present in soil, which allowed us to predict the correct classes for samples of an independent test set with an accuracy of 83% (error rate = 0.17). This study shows further that in order to apply classifier analysis to actual contaminated field soil samples, more insight and information is needed on the transcriptional responses of soil organisms to different soil types (properties) and mixtures of contaminants.
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Affiliation(s)
- Benjamin Nota
- Department of Animal Ecology, Institute of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands.
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Hodgins-Davis A, Townsend JP. Evolving gene expression: from G to E to GxE. Trends Ecol Evol 2009; 24:649-58. [PMID: 19699549 PMCID: PMC2805859 DOI: 10.1016/j.tree.2009.06.011] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 06/05/2009] [Accepted: 06/08/2009] [Indexed: 12/21/2022]
Abstract
Analyses of gene expression data sets for multiple individuals and species promise to shed light on the mode of evolution of gene expression. However, complementary complexities challenge this goal. Characterization of the genetic variation underlying gene expression can easily be compromised by lack of environmental control. Conversely, the breadth of conclusions from studies of environmental effects has been limited by the use of single strains. Controlled studies have hinted at extensive genexenvironment interaction. Thus, both genetics and environment are key components in models of the evolution of gene expression. We review the literature on the evolution of gene expression in terms of genetics (G), environmental response (E) and GxE interactions to make this conceptual point.
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Affiliation(s)
- Andrea Hodgins-Davis
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
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25
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Garcia-Reyero N, Poynton HC, Kennedy AJ, Guan X, Escalon BL, Chang B, Varshavsky J, Loguinov AV, Vulpe CD, Perkins EJ. Biomarker discovery and transcriptomic responses in Daphnia magna exposed to munitions constituents. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2009; 43:4188-4193. [PMID: 19569350 DOI: 10.1021/es803702a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Ecotoxicogenomic approaches are emerging as alternative methods in environmental monitoring because they allow insight into pollutant modes of action and help assess the causal agents and potential toxicity beyond the traditional end points of death, growth, and reproduction. Gene expression analysis has shown particular promise for identifying gene expression biomarkers of chemical exposure that can be further used to monitor specific chemical exposures in the environment. We focused on the development of gene expression markers to detect and discriminate between chemical exposures. Using a custom cDNA microarray for Daphnia magna, we identified distinct expression fingerprints in response to exposure at sublethal concentrations of Cu, Zn, Pb, and munitions constituents. Using the results obtained from microarray analysis, we chose a suite of potential biomarkers for each of the specific exposures. The selected potential biomarkers were tested in independent chemical exposures for specificity using quantitative reverse transcription polymerase chain reaction. Six genes were confirmed as differentially regulated bythe selected chemical exposures. Furthermore, each exposure was identified by response of a unique combination (suite) of individual gene expression biomarkers. These results demonstrate the potential for discovery and validation of novel biomarkers of chemical exposures using gene expression analysis, which could have broad applicability in environmental monitoring.
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26
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Nota B, Bosse M, Ylstra B, van Straalen NM, Roelofs D. Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene. BMC Genomics 2009; 10:236. [PMID: 19457238 PMCID: PMC2688526 DOI: 10.1186/1471-2164-10-236] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 05/20/2009] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons are common pollutants in soil, have negative effects on soil ecosystems, and are potentially carcinogenic. The Springtail (Collembola) Folsomia candida is often used as an indicator species for soil toxicity. Here we report a toxicogenomic study that translates the ecological effects of the polycyclic aromatic hydrocarbon phenanthrene in soil to the early transcriptomic responses in Folsomia candida. RESULTS Microarrays were used to examine two different exposure concentrations of phenanthrene, namely the EC10 (24.95 mg kg-1 soil) and EC50 (45.80 mg kg-1 soil) on reproduction of this springtail, which evoked 405 and 251 differentially expressed transcripts, respectively. Fifty transcripts were differential in response to either concentration. Many transcripts encoding xenobiotic detoxification and biotransformation enzymes (phases I, II, and III) were upregulated in response to either concentration. Furthermore, indications of general and oxidative stress were found in response to phenanthrene. Chitin metabolism appeared to be disrupted particularly at the low concentration, and protein translation appeared suppressed at the high concentration of phenanthrene; most likely in order to reallocate energy budgets for the detoxification process. Finally, an immune response was evoked especially in response to the high effect concentration, which was also described in a previous transcriptomic study using the same effect concentration (EC50) of cadmium. CONCLUSION Our study provides new insights in the molecular mode of action of the important polluting class of polycyclic aromatic hydrocarbons in soil animals. Furthermore, we present a fast, sensitive, and specific soil toxicity test which enhances traditional tests and may help to improve current environmental risk assessments and monitoring of potentially polluted sites.
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Affiliation(s)
- Benjamin Nota
- VU University Amsterdam, Institute of Ecological Science, Department of Animal Ecology, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Mirte Bosse
- VU University Amsterdam, Institute of Ecological Science, Department of Animal Ecology, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Bauke Ylstra
- VU University Medical Center, Department of Pathology, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Nico M van Straalen
- VU University Amsterdam, Institute of Ecological Science, Department of Animal Ecology, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Dick Roelofs
- VU University Amsterdam, Institute of Ecological Science, Department of Animal Ecology, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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Stürzenbaum SR, Andre J, Kille P, Morgan AJ. Earthworm genomes, genes and proteins: the (re)discovery of Darwin's worms. Proc Biol Sci 2009; 276:789-97. [PMID: 19129111 PMCID: PMC2664377 DOI: 10.1098/rspb.2008.1510] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Small incremental biological change, winnowed by natural selection over geological time scales to produce large consequences, was Darwin's singular insight that revolutionized the life sciences. His publications after 1859, including the ‘earthworm book’, were all written to amplify and support the evolutionary theory presented in the Origin. Darwin was unable to provide a physical basis for the inheritance of favoured traits because of the absence of genetic knowledge that much later led to the ‘modern synthesis’. Mistaken though he was in advocating systemic ‘gemmules’ as agents of inheritance, Darwin was perceptive in seeking to underpin his core vision with concrete factors that both determine the nature of a trait in one generation and convey it to subsequent generations. This brief review evaluates the molecular genetic literature on earthworms published during the last decade, and casts light on the specific aspects of earthworm evolutionary biology that more or less engaged Darwin: (i) biogeography, (ii) species diversity, (iii) local adaptations and (iv) sensitivity. We predict that the current understanding will deepen with the announcement of a draft earthworm genome in Darwin's bicentenary year, 2009. Subsequently, the earthworm may be elevated from the status of a soil sentinel to that elusive entity, an ecologically relevant genetic model organism.
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Affiliation(s)
- S R Stürzenbaum
- School of Biomedical & Health Sciences, King's College London, London SE1 9NH, UK.
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Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research. BMC Genomics 2008; 9 Suppl 2:I1. [PMID: 18831773 PMCID: PMC3226104 DOI: 10.1186/1471-2164-9-s2-i1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and International Journal of Functional Informatics and Personalized Medicine, IEEE 7th Bioinformatics and Bioengineering attracted more than 600 papers and 500 researchers and medical doctors. It was the only synergistic inter/multidisciplinary IEEE conference with 24 Keynote Lectures, 7 Tutorials, 5 Cutting-Edge Research Workshops and 32 Scientific Sessions including 11 Special Research Interest Sessions that were designed dynamically at Harvard in response to the current research trends and advances. The committee was very grateful for the IEEE Plenary Keynote Lectures given by: Dr. A. Keith Dunker (Indiana), Dr. Jun Liu (Harvard), Dr. Brian Athey (Michigan), Dr. Mark Borodovsky (Georgia Tech and President of ISIBM), Dr. Hamid Arabnia (Georgia and Vice-President of ISIBM), Dr. Ruzena Bajcsy (Berkeley and Member of United States National Academy of Engineering and Member of United States Institute of Medicine of the National Academies), Dr. Mary Yang (United States National Institutes of Health and Oak Ridge, DOE), Dr. Chih-Ming Ho (UCLA and Member of United States National Academy of Engineering and Academician of Academia Sinica), Dr. Andy Baxevanis (United States National Institutes of Health), Dr. Arif Ghafoor (Purdue), Dr. John Quackenbush (Harvard), Dr. Eric Jakobsson (UIUC), Dr. Vladimir Uversky (Indiana), Dr. Laura Elnitski (United States National Institutes of Health) and other world-class scientific leaders. The Harvard meeting was a large academic event 100% full-sponsored by IEEE financially and academically. After a rigorous peer-review process, the committee selected 27 high-quality research papers from 600 submissions. The committee is grateful for contributions from keynote speakers Dr. Russ Altman (IEEE BIBM conference keynote lecturer on combining simulation and machine learning to recognize function in 4D), Dr. Mary Qu Yang (IEEE BIBM workshop keynote lecturer on new initiatives of detecting microscopic disease using machine learning and molecular biology, http://ieeexplore.ieee.org/servlet/opac?punumber=4425386) and Dr. Jack Y. Yang (IEEE BIBM workshop keynote lecturer on data mining and knowledge discovery in translational medicine) from the first IEEE Computer Society BioInformatics and BioMedicine (IEEE BIBM) international conference and workshops, November 2-4, 2007, Silicon Valley, California, USA.
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Abstract
Transcription and metabolite analysis is a powerful way to reveal physiological shifts in response to environmental pollution. Recent studies on earthworms, including one in BMC Biology, show that the type of pollution and its availability for uptake by organisms can differentially affect transcription and metabolism.
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Affiliation(s)
- Nico M van Straalen
- Institute of Ecological Science, VU University, 1081 HV Amsterdam, The Netherlands.
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Yang JY, Yang MQ, Zhu MM, Arabnia HR, Deng Y. Promoting synergistic research and education in genomics and bioinformatics. BMC Genomics 2008; 9 Suppl 1:I1. [PMID: 18366597 PMCID: PMC3226105 DOI: 10.1186/1471-2164-9-s1-i1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology. High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to handle the massive bioinformatics and personalized healthcare data, which will obviously have a profound effect on how biomedical research will be conducted toward the improvement of human health and prolonging of human life in the future. The International Society of Intelligent Biological Medicine (http://www.isibm.org) and its official journals, the International Journal of Functional Informatics and Personalized Medicine (http://www.inderscience.com/ijfipm) and the International Journal of Computational Biology and Drug Design (http://www.inderscience.com/ijcbdd) in collaboration with International Conference on Bioinformatics and Computational Biology (Biocomp), touch tomorrow's bioinformatics and personalized medicine throughout today's efforts in promoting the research, education and awareness of the upcoming integrated inter/multidisciplinary field. The 2007 international conference on Bioinformatics and Computational Biology (BIOCOMP07) was held in Las Vegas, the United States of American on June 25-28, 2007. The conference attracted over 400 papers, covering broad research areas in the genomics, biomedicine and bioinformatics. The Biocomp 2007 provides a common platform for the cross fertilization of ideas, and to help shape knowledge and scientific achievements by bridging these two very important disciplines into an interactive and attractive forum. Keeping this objective in mind, Biocomp 2007 aims to promote interdisciplinary and multidisciplinary education and research. 25 high quality peer-reviewed papers were selected from 400+ submissions for this supplementary issue of BMC Genomics. Those papers contributed to a wide-range of important research fields including gene expression data analysis and applications, high-throughput genome mapping, sequence analysis, gene regulation, protein structure prediction, disease prediction by machine learning techniques, systems biology, database and biological software development. We always encourage participants submitting proposals for genomics sessions, special interest research sessions, workshops and tutorials to Professor Hamid R. Arabnia (hra@cs.uga.edu) in order to ensure that Biocomp continuously plays the leadership role in promoting inter/multidisciplinary research and education in the fields. Biocomp received top conference ranking with a high score of 0.95/1.00. Biocomp is academically co-sponsored by the International Society of Intelligent Biological Medicine and the Research Laboratories and Centers of Harvard University – Massachusetts Institute of Technology, Indiana University - Purdue University, Georgia Tech – Emory University, UIUC, UCLA, Columbia University, University of Texas at Austin and University of Iowa etc. Biocomp - Worldcomp brings leading scientists together across the nation and all over the world and aims to promote synergistic components such as keynote lectures, special interest sessions, workshops and tutorials in response to the advances of cutting-edge research.
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Affiliation(s)
- Jack Y Yang
- Harvard University, PO Box 400888, Cambridge, Massachusetts 02140-0888, USA.
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