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Nguyen TD, Itayama T, Tran QV, Dao TS, Iqbal MS, Pham TL. Ecotoxicity of the fluoroquinolone antibiotic delafloxacin to the water flea Simocephalus vetulus and its offspring under the influence of calcium modulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171450. [PMID: 38438028 DOI: 10.1016/j.scitotenv.2024.171450] [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: 10/12/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Delafloxacin (DFX), one of the latest additions to the fluoroquinolone antibiotics, is gaining heightened recognition in human therapy due to its potential antibacterial efficacy in a wide range of applications. Concerns have arisen regarding its presence in the environment and its potential interactions with multivalent metals, such as calcium (Ca). The present study investigated the trans- and multigenerational effects of environmentally projected concentrations of DFX (100-400 μg DFX L-1) on individual- and population-level responses of parental S. vetulus (F0) and its descendants (F1) under normal (26 mg L-1) and high (78 mg L-1) Ca conditions. Exposure of the F0 generation to DFX under the normal Ca condition resulted in reduced juvenile body length (JBL), increased age-specific survival rate (lx), indicating prolonged developmental time, reduced age-specific fecundity rate (mx), and decreased population growth rate (rm). Under the high Ca condition, JBL, mx, and rm were adversely affected. Transgenerational effects of DFX existed, as F1 individuals exhibited persistent suppressions in at least one endpoint under both Ca conditions even after being transferred to a clear medium. Continuous exposure of the F1 generation to DFX had negative impacts on JBL, mx, and rm under the normal Ca condition, and on JBL and rm under the high Ca condition. However, cumulative effects were not observed, suggesting the potential development of tolerance to DFX in the F1 organisms. These findings suggest that DFX is a harmful compound for the non-target model organism S. vetulus and reveal a potential antagonism between DFX and Ca. Nevertheless, the interaction between other (fluoro)quinolones and Ca remains unclear, necessitating further research to establish this phenomenon more comprehensively, including understanding the interaction mechanism in ecotoxicological contexts.
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Affiliation(s)
- Tan-Duc Nguyen
- Department of Science and Technology, Nagasaki University, Nagasaki City, Japan; Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Protection, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China.
| | - Tomoaki Itayama
- Department of Science and Technology, Nagasaki University, Nagasaki City, Japan
| | - Quang Vinh Tran
- Asian Centre for Water Research (CARE), Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Viet Nam
| | - Thanh-Son Dao
- Faculty of Environment and Natural Resources, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Viet Nam; Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | | | - Thanh Luu Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology (VAST), Hanoi City, Viet Nam; Institute of Tropical Biology, Vietnam Academy of Science and Technology (VAST), Ho Chi Minh City, Viet Nam
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Ishimota M, Kodama M, Tomiyama N, Ohyama K. Chemical tolerance related to the ABC transporter gene and DNA methylation in cladocera (Daphnia magna). ENVIRONMENTAL TOXICOLOGY 2024; 39:1978-1988. [PMID: 38073494 DOI: 10.1002/tox.24077] [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: 12/05/2022] [Revised: 10/10/2023] [Accepted: 11/28/2023] [Indexed: 03/09/2024]
Abstract
We performed multigenerational tests to clarify the chemical tolerance mechanisms of a nontarget aquatic organism, Daphnia magna. We continuously exposed D. magna to a carbamate insecticide (pirimicarb) at lethal or sublethal concentrations (0, 3.8, 7.5, and 15 μg/L) for 15 generations (F0-F14). We then determined the 48 h-EC50 values and mRNA expression levels of acetylcholinesterase, glutathione S-transferase, and ATP (Adenosine triphosphate)-binding cassette transporter (ABCt) in neonates (<24 h old) from F0, F4, F9, and F14. To ascertain the effects of DNA methylation on pirimicarb sensitivity, we measured 5-methylcytosine levels (DNA methylation levels) in neonates of parents in the last generation (F14). In addition, we cultured groups exposed to 0 and 7.5 μg/L (the latter of which acquired chemical tolerance to pirimicarb) with or without 5-azacytidine (de-methylating agent) and determined methylation levels and 48 h-EC50 values in neonates (<24 h old) from the treated parents. The EC50 values (30.3-31.6 μg/L) in F14 of the 7.5 and 15 μg/L groups were approximately two times higher than that in the control (16.0 μg/L). A linear mixed model analysis showed that EC50 and ABCt mRNA levels were significantly increased with generational alterations; further analysis showed that the ABCt mRNA level was positively related to the EC50 . Therefore, ABCt may be associated with altered pirimicarb sensitivity. In addition, the EC50 value and DNA methylation levels in pirimicarb-tolerant clones decreased after exposure to 5-azacytidine, suggesting that DNA methylation contributes to chemical tolerance. These findings improved our knowledge regarding the acquisition of chemical tolerance in aquatic organisms.
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Affiliation(s)
- Makoto Ishimota
- The Institute of Environmental Toxicology, Laboratory of Residue Analysis II, Chemistry Division, Joso-shi, Ibaraki, Japan
| | - Mebuki Kodama
- The Institute of Environmental Toxicology, Laboratory of Residue Analysis II, Chemistry Division, Joso-shi, Ibaraki, Japan
| | - Naruto Tomiyama
- The Institute of Environmental Toxicology, Laboratory of Residue Analysis II, Chemistry Division, Joso-shi, Ibaraki, Japan
| | - Kazutoshi Ohyama
- The Institute of Environmental Toxicology, Laboratory of Residue Analysis II, Chemistry Division, Joso-shi, Ibaraki, Japan
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Fedoseeva EV, Tereshina VM, Danilova OA, Ianutsevich EA, Yakimenko OS, Terekhova VA. Effect of humic acid on the composition of osmolytes and lipids in a melanin-containing phytopathogenic fungus Alternaria alternata. ENVIRONMENTAL RESEARCH 2021; 193:110395. [PMID: 33127397 DOI: 10.1016/j.envres.2020.110395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/12/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Humic substances (HS) have a direct impact on living cells, causing a wide range of various biological effects, and stimulating or inhibiting fungal growth. Therefore, it is important to reveal cellular indicators that could indicate the nature and level of HS' effects on living organisms. Paying attention to the important role of lipid and osmolytes in adaptation to stress, the aim of this work was to study the composition of osmolytes and lipids in the growth dynamics of the phytopathogenic melanin-containing fungus Alternaria alternata under the influence of humic acid (HA). HA was isolated from a commercial peat humic product. For cultivation, liquid Czapek medium with the addition of 200 mg/l HA (HA variant) was used, and with no HA for the control variant. The main osmolytes of the fungal mycelium were glucose, mannitol, and trehalose. Both in the control and in HA variants, a general pattern was observed during the growth process; the amount of glucose increased against the background of a decrease of mannitol. In the control, the amount of trehalose increased significantly by the stage of active melanin formation (day 4), while under the influence of HA, such an increase was not observed. Membrane lipids were represented by phospholipids, sphingolipids, and sterols. A characteristic feature of A. alternata was a high proportion of phosphatidic acids (PA) in the composition of membrane lipids. The amount and proportion of PA decreased during growth in the control, while under the influence of HA such decline was not observed. The influence of HA induced the increase in the amount of sterols (St) and phosphatidylcholines (PC) that were able to stabilise the membrane lipid bilayer. We can assume that general cellular response of A. alternata to HA influence, being expressed as a higher amount of PA, PC, St and a lower level of trehalose in comparison with the control, indicates the an absence of inhibition of growth processes of this phytopathogenic melanin-producing fungus. The effect of HA on the qualitative and quantitative composition of the osmolytes and membrane lipids of A. alternata may cause changes of virulence and stress resistance of this phytopathogen.
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Affiliation(s)
- E V Fedoseeva
- Pirogov Russian National Research Medical University, 1, Ostrovityanova st., Moscow, 117997, Russian Federation.
| | - V M Tereshina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Prospect, Moscow, 119071, Russian Federation.
| | - O A Danilova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Prospect, Moscow, 119071, Russian Federation.
| | - E A Ianutsevich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Prospect, Moscow, 119071, Russian Federation.
| | - O S Yakimenko
- Faculty of Soil Science, Lomonosov Moscow State University, 1, bld. 12, Leninskie Gory, Moscow, 119991, Russian Federation.
| | - V A Terekhova
- Faculty of Soil Science, Lomonosov Moscow State University, 1, bld. 12, Leninskie Gory, Moscow, 119991, Russian Federation; A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, 33, Leninsky Prospekt, Moscow, 119071, Russian Federation.
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Aydin M, Arslan E, Yigider E, Taspinar MS, Agar G. Protection of Phaseolus vulgaris L. from Herbicide 2,4-D Results from Exposing Seeds to Humic Acid. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2021. [DOI: 10.1007/s13369-020-04893-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Misaki K, Matsuda S, Matsuda T, Kusakabe T, Shimizu Y. Detection of DNA damage formation by natural organic matter using EGFP-fused MDC1-expressing cells. CHEMOSPHERE 2019; 235:169-174. [PMID: 31255757 DOI: 10.1016/j.chemosphere.2019.06.126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 06/09/2023]
Abstract
Studies have been conducted on the genotoxicity and carcinogenicity of disinfection by-products formed from natural organic matter (NOM) and mitigation effect for mutagens and clastogens by NOM. Whereas, reportedly, synthetic humic acid in high concentration has induced genotoxicity in human cells, and NOM samples have provoked mild oxidative and other physiological responses in aquatic organisms. Our group developed a novel detection method for DNA damage formation, namely enhanced green fluorescent protein (EGFP)-fused mediator of DNA damage checkpoint 1 (MDC1)-expressing human cells as simple and high-sensitive system. By using this method, a significant increase in the foci area was observed after 3 h, but not 24 h for 130 mgC L-1 Suwannee River fulvic acid (SRFA), 38 mgC L-1 humic acid (SRHA), and 19 mgC L-1 NOM (SRNOM). The SRNOM concentration is the original environmental one; therefore, it was suggested that the formation and repair of DNA damage associated with γ-H2AX, a biomarker for DNA double-strand breaks by mild oxidative stress, in Suwannee River (SR) were detected for the first time. The increase in the foci area was not observed for 18 mgC L-1 Lake Biwa fulvic acid (LBFA) and 50 mg L-1 catechin after both 3 h and 24 h. The difference between the SR and Lake Biwa (LB) samples may result from the differences in their electron-accepting capacity. The application of this methodology is expected to elucidate oxidative stress and toxicological effects shortly and in detail for many water samples.
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Affiliation(s)
- Kentaro Misaki
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan; School of Nursing, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Japan.
| | - Shun Matsuda
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan
| | - Taketoshi Kusakabe
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan
| | - Yoshihisa Shimizu
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan
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Lindeman LC, Thaulow J, Song Y, Kamstra JH, Xie L, Asselman J, Aleström P, Tollefsen KE. Epigenetic, transcriptional and phenotypic responses in two generations of Daphnia magna exposed to the DNA methylation inhibitor 5-azacytidine. ENVIRONMENTAL EPIGENETICS 2019; 5:dvz016. [PMID: 31528364 PMCID: PMC6736351 DOI: 10.1093/eep/dvz016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 07/20/2019] [Accepted: 07/25/2019] [Indexed: 05/16/2023]
Abstract
The water flea Daphnia magna is a keystone species in freshwater ecosystems and has been widely used as a model organism in environmental ecotoxicology. This aquatic crustacean is sensitive to environmental stressors and displays considerable plasticity in adapting to changing environmental conditions. Part of this plasticity may be due to epigenetic regulation of gene expression, including changes to DNA methylation and histone modifications. Because of the generally hypomethylated genome of this species, we hypothesized that the histone code may have an essential role in the epigenetic control and that histone modifications might be an early marker for stress. This study aims to characterize the epigenetic, transcriptional and phenotypic responses and their causal linkages in directly exposed adult (F0) Daphnia and peritoneal exposed neonates (F1) after a chronic (7-day) exposure to a sublethal concentration (10 mg/l) of 5-azacytidine, a well-studied vertebrate DNA methylation inhibitor. Exposure of the F0 generation significantly reduced the cumulative fecundity, accompanied with differential expression of genes in the one-carbon-cycle metabolic pathway. In the epigenome of the F0 generation, a decrease in global DNA methylation, but no significant changes on H3K4me3 or H3K27me3, were observed. In the F1 offspring generation, changes in gene expression, a significant reduction in global DNA methylation and changes in histone modifications were identified. The results indicate that exposure during adulthood may result in more pronounced effects on early development in the offspring generation, though interpretation of the data should be carefully done since both the exposure regime and developmental period is different in the two generations examined. The obtained results improve our understanding of crustacean epigenetics and the tools developed may promote use of epigenetic markers in hazard assessment of environmental stressors.
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Affiliation(s)
- Leif Christopher Lindeman
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, PO Box 1432 Ås, Norway
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
- Correspondence address. Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, PO Box 1432 Ås, Norway. Tel: +47 67232039; Fax: +47 67230691; E-mail:
| | - Jens Thaulow
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
- Norwegian Institute for Water Research, N-0349 Oslo, Norway
| | - You Song
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
- Norwegian Institute for Water Research, N-0349 Oslo, Norway
| | - Jorke H Kamstra
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, PO Box 369 Sentrum, N-0454 Oslo, Norway
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Li Xie
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
- Norwegian Institute for Water Research, N-0349 Oslo, Norway
| | - Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University, 9000 Ghent, Belgium
| | - Peter Aleström
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, PO Box 369 Sentrum, N-0454 Oslo, Norway
| | - Knut Erik Tollefsen
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, PO Box 1432 Ås, Norway
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
- Norwegian Institute for Water Research, N-0349 Oslo, Norway
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Barbosa DS, Barbosa DS, Espíndola ELG, Daam MA. The direct effects of a tropical natural humic substance to three aquatic species and its influence on their sensitivity to copper. ECOTOXICOLOGY (LONDON, ENGLAND) 2019; 28:550-558. [PMID: 31119590 DOI: 10.1007/s10646-019-02031-3] [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] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
Few studies have been conducted so far into the effects of humic substances (HS) on aquatic organisms and their influence on the toxicity of chemical pollutants in the tropics. The aim of the present study was therefore to evaluate the direct effects of locally-derived tropical natural HS on the cladoceran Daphnia similis, the midge Chironomus xanthus and the fish Danio rerio. The influence of a HS concentration series on the acute toxicity of copper to these organisms was also assessed through laboratory toxicity testing. The HS did not exert direct acute effects on the test organisms, but long-term exposure to higher HS concentrations provoked a stress response (increase in feces production) to D. rerio and exerted effects on chironomid adult emergence and sex ratio. The biotic ligand model proved to be a useful tool in converting total copper concentrations to the appropriate bio-available fraction to which tropical aquatic organisms are exposed.
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Affiliation(s)
- Domingos S Barbosa
- NEEA/CRHEA/SHS, São Carlos Engineering School, University of São Paulo, Av. Trabalhador São Carlense, 400, São Carlos, 13.560-970, Brazil
- Environmental Technology and Management Laboratory (LTGA), Federal University of Mato Grosso, Av. dos Estudantes 5055, Rondonópolis, 78735-901, Brazil
| | - Danilo S Barbosa
- NEEA/CRHEA/SHS, São Carlos Engineering School, University of São Paulo, Av. Trabalhador São Carlense, 400, São Carlos, 13.560-970, Brazil
- Federal Institute of Paraná (IFPR), Rodovia PR 323, km 310, Umuarama, 87.507-014, Brazil
| | - Evaldo L G Espíndola
- NEEA/CRHEA/SHS, São Carlos Engineering School, University of São Paulo, Av. Trabalhador São Carlense, 400, São Carlos, 13.560-970, Brazil
| | - Michiel A Daam
- CENSE, Department of Environmental Sciences and Engineering, Faculty of Sciences and Technology, New University of Lisbon, Quinta da Torre, Caparica, 2829-516, Portugal.
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Misaki K, Morita Y, Kobayashi K, Sugawara Y, Shimizu Y, Kusakabe T. Evaluation of algal photosynthesis inhibition activity for dissolved organic matter with the consideration of inorganic and coloring constituents. CHEMOSPHERE 2019; 224:333-342. [PMID: 30826703 DOI: 10.1016/j.chemosphere.2019.02.106] [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: 11/28/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
The effect of waterborne ingredient on ecosystem has been of great interest. In the present study, the evaluation method using algal photosynthesis inhibition assay with dual-channel pulse amplitude modulation (PAM) system was established for a series of water samples to elucidate the potential effect of the total body of organic compounds including natural organic matter (NOM) on aquatic ecosystems. The more sensitive and less time-consuming monitoring method compared with algal growth inhibition assay was suggested, especially considering inorganic and coloring constituents. Algal photosynthesis inhibition activity was detected with high sensitivity for photosystem II (PSII) inhibitors, whereas the IC10 of the other chemicals was over the environmental standard concentration for Chlamydomonas moewusii (Chlorophyceae) and Pheodactylum tricornutum (Diatomea). The photosynthesis inhibition activity of Lake Biwa dissolved organic matter (LBDOM) and fulvic acid (LBFA) was significantly detected at ≥10 times the concentration and >10 mgC L-1, respectively, whereas prominent activity was confirmed for Suwannee River NOM (SRNOM) on the river original concentration (>30 mgC L-1) for both algae. Significant inhibition activity was detected in both algae at least in twice-concentration for water samples from a wastewater treatment pilot plant. There was no great difference in the activity between sewage secondary effluent and its filtrate with ultrafiltration (UF), and physically washing water for the UF membrane.
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Affiliation(s)
- Kentaro Misaki
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan; School of Nursing, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Japan.
| | - Yuhei Morita
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan
| | - Kentaro Kobayashi
- Global Environmental Research Laboratories, Toray Industries, Inc., 3-2-1 Sonoyama, Otsu, Shiga, Japan
| | - Yuichi Sugawara
- Water Treatment Technical Dept., Toray Industries, Inc., 3-3-3 Sonoyama, Otsu, Shiga, Japan
| | - Yoshihisa Shimizu
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan.
| | - Taketoshi Kusakabe
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan.
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Chatterjee N, Choi S, Kwon OK, Lee S, Choi J. Multi-generational impacts of organic contaminated stream water on Daphnia magna: A combined proteomics, epigenetics and ecotoxicity approach. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 249:217-224. [PMID: 30893634 DOI: 10.1016/j.envpol.2019.03.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/28/2019] [Accepted: 03/10/2019] [Indexed: 06/09/2023]
Abstract
The present study aimed to elucidate the mechanisms of organismal sensitivity and/or physiological adaptation in the contaminated water environment. Multigenerational cultures (F0, F1, F2) of Daphnia magna in collected stream water (OCSW), contaminated with high fecal coliform, altered the reproductive scenario (changes in first brood size timing, clutch numbers, clutch size etc.), compromised fitness (increase hemoglobin, alteration in behavior), and affected global DNA methylation (hypermethylation) without affecting survival. Using proteomics approach, we found 288 proteins in F0 and 139 proteins in F2 that were significantly differentially upregulated after OCSW exposure. The individual protein expressions, biological processes and molecular functions were mainly related to metabolic processes, development and reproduction, transport (protein/lipid/oxygen), antioxidant activity, increased globin and S-adenosylmethionine synthase protein level etc., which was further found to be connected to phenotype-dependent endpoints. The proteomics pathway analysis evoked proteasome, chaperone family proteins, neuronal disease pathways (such as, Parkinson's disease) and apoptosis signaling pathways in OCSW-F0, which might be the cause of behavioral and developmental alterations in OCSW-F0. Finally, chronic multigenerational exposure to OCSW exhibited slow physiological adaptation in most of the measured effects, including proteomics analysis, from the F0 to F2 generations. The common upregulated proteins in both generations (F0 & F2), such as, globin, vitellinogen, lipid transport proteins etc., were possibly play the pivotal role in the organism's physiological adaptation. Taken together, our results, obtained with a multilevel approach, provide new insight of the molecular mechanism in fecal coliform-induced phenotypic plasticity in Daphnia magna.
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Affiliation(s)
- Nivedita Chatterjee
- School of Environmental Engineering, University of Seoul, 163 Siripdaero, Dongdaemun-gu, Seoul, 130-743, South Korea
| | - Suhyon Choi
- School of Environmental Engineering, University of Seoul, 163 Siripdaero, Dongdaemun-gu, Seoul, 130-743, South Korea
| | - Oh Kwang Kwon
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Sangkyu Lee
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Siripdaero, Dongdaemun-gu, Seoul, 130-743, South Korea.
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Chatterjee N, Gim J, Choi J. Epigenetic profiling to environmental stressors in model and non-model organisms: Ecotoxicology perspective. ENVIRONMENTAL HEALTH AND TOXICOLOGY 2018; 33:e2018015-0. [PMID: 30286591 PMCID: PMC6182246 DOI: 10.5620/eht.e2018015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/19/2018] [Indexed: 05/16/2023]
Abstract
Epigenetics, potentially heritable changes in genome function that occur without alterations to DNA sequence, is an important but understudied component of ecotoxicology studies. A wide spectrum of environmental challenge, such as temperature, stress, diet, toxic chemicals, are known to impact on epigenetic regulatory mechanisms. Although the role of epigenetic factors in certain biological processes, such as tumourigenesis, has been heavily investigated, in ecotoxicology field, epigenetics still have attracted little attention. In ecotoxicology, potential role of epigenetics in multi- and transgenerational phenomenon to environmental stressors needs to be unrevealed. Natural variation in the epigenetic profiles of species in responses to environmental stressors, nature of dose-response relationships for epigenetic effects, and how to incorporate this information into ecological risk assessment should also require attentions. In this review, we presented the available information on epigenetics in ecotoxicological context. For this, we have conducted a systemic review on epigenetic profiling in response to environmental stressors, mostly chemical exposure, in model organisms, as well as, in ecotoxicologically relevant wildlife species.
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Affiliation(s)
- Nivedita Chatterjee
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dondaemun-gu, Seoul 02504, Republic of Korea
| | - Jiwan Gim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dondaemun-gu, Seoul 02504, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dondaemun-gu, Seoul 02504, Republic of Korea
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Hu L, Xiao P, Jiang Y, Dong M, Chen Z, Li H, Hu Z, Lei A, Wang J. Transgenerational Epigenetic Inheritance Under Environmental Stress by Genome-Wide DNA Methylation Profiling in Cyanobacterium. Front Microbiol 2018; 9:1479. [PMID: 30022974 PMCID: PMC6039552 DOI: 10.3389/fmicb.2018.01479] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/13/2018] [Indexed: 11/19/2022] Open
Abstract
Epigenetic modifications such as DNA methylation are well known as connected with many important biological processes. Rapid accumulating evidence shows environmental stress can generate particular defense epigenetic changes across generations in eukaryotes. This transgenerational epigenetic inheritance in animals and plants has gained interest over the last years. Cyanobacteria play very crucial role in the earth, and as the primary producer they can adapt to nearly all diverse environments. However, few knowledge about the genome wide epigenetic information such as methylome information in cyanobacteria, especially under any environment stress, was reported so far. In this study we profiled the genome-wide cytosine methylation from a model cyanobacterium Synechocystis sp. PCC 6803, and explored the possibility of transgenerational epigenetic process in this ancient single-celled prokaryote by comparing the DNA methylomes among normal nitrogen medium cultivation, nitrogen starvation for 72 h and nitrogen recovery for about 12 generations. Our results shows that DNA methylation patterns in nitrogen starvation and nitrogen recovery are much more similar with each other, significantly different from that of the normal nitrogen. This study reveals the difference in global DNA methylation pattern of cyanobacteria between normal and nutrient stress conditions and reports the evidence of transgenerational epigenetic process in cyanobacteria. The results of this study may contribute to a better understanding of epigenetic regulation in prokaryotic adaptation to and survive in the ever changing environment.
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Affiliation(s)
- Lang Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Nanshan District Key Lab for Biopolymers and Safety Evaluation, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China
| | - Peng Xiao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yongguang Jiang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Mingjie Dong
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zixi Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hui Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Anping Lei
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiangxin Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Nanshan District Key Lab for Biopolymers and Safety Evaluation, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China
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Yang J, Chatterjee N, Kim Y, Roh JY, Kwon JH, Park MS, Choi J. Histone methylation-associated transgenerational inheritance of reproductive defects in Caenorhabditis elegans exposed to crude oil under various exposure scenarios. CHEMOSPHERE 2018; 200:358-365. [PMID: 29494917 DOI: 10.1016/j.chemosphere.2018.02.080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 02/11/2018] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
As part of a study to explore the long-term effects of the Hebei Spirit oil spill accident, transgenerational toxicity and associated epigenetic changes were investigated in the nematode Caenorhabditis elegans. Under experimental conditions, worms were exposed to Iranian heavy crude oil (IHC) under three different scenarios: partial early-life exposure (PE), partial late-life exposure (PL), and whole-life exposure (WE). Growth, reproduction, and histone methylation were monitored in the exposed parental worms (P0) and in three consecutive unexposed offspring generations (F1-3). Reproductive potential in the exposed P0 generation in the WE treatment group was reduced; additionally, it was inhibited in the unexposed offspring generations of the P0 worms. This suggests that there was transgenerational inheritance of defective reproduction. Comparison of developmental periods of exposure showed that IHC-treated worms in the PL group had a greater reduction in reproductive capacity than those in the PE group. Decreased methylation of histone H3 (H3K9) was found in the IHC-exposed parental generation. A heritable reduction in reproductive capacity occurred in wildtype N2 but was not found in a H3K9 histone methyltransferase (HMT) mutant, met-2(n4256), suggesting a potential role for HMT in transgenerational toxicity. Our results suggest that the reproductive toxicity after IHC exposure could be heritable and that histone methylation is associated with the transmission of the inherited phenotype.
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Affiliation(s)
- Jisu Yang
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Nivedita Chatterjee
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Youngho Kim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Ji-Yeon Roh
- Division of Environmental Science and Ecological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jung-Hwan Kwon
- Division of Environmental Science and Ecological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Myung-Sook Park
- Taean Environmental Health Center, 1952-16 Seohae-ro, Taean-eup, Taean-gun, Chungcheongnam-do, 32148, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea.
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Reitsema RE, Meire P, Schoelynck J. The Future of Freshwater Macrophytes in a Changing World: Dissolved Organic Carbon Quantity and Quality and Its Interactions With Macrophytes. FRONTIERS IN PLANT SCIENCE 2018; 9:629. [PMID: 29868084 PMCID: PMC5960680 DOI: 10.3389/fpls.2018.00629] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 04/20/2018] [Indexed: 05/22/2023]
Abstract
Freshwater ecosystems are confronted with the effects of climate change. One of the major changes is an increased concentration of aquatic carbon. Macrophytes are important in the aquatic carbon cycle and play as primary producers a crucial role in carbon storage in aquatic systems. However, macrophytes are affected by increasing carbon concentrations. The focus of this review lies on dissolved organic carbon (DOC), one of the most abundant forms of carbon in aquatic ecosystems which has many effects on macrophytes. DOC concentrations are rising; the exact cause of this increase is not known, although it is hypothesized that climate change is one of the drivers. The quality of DOC is also changing; for example, in urban areas DOC composition is different from the composition in natural watersheds, resulting in DOC that is more resistant to photo-degradation. Plants can benefit from DOC as it attenuates UV-B radiation, it binds potentially harmful heavy metals and provides CO2 as it breaks down. Yet plant growth can also be impaired under high DOC concentrations, especially by humic substances (HS). HS turn the water brown and attenuate light, which limits macrophyte photosynthesis at greater depths. This leads to lower macrophyte abundance and lower species diversity. HS form a wide class of chemicals with many different functional groups and they therefore have the ability to interfere with many biochemical processes that occur in freshwater organisms. Few studies have looked into the direct effects of HS on macrophytes, but there is evidence that HS can interfere with photosynthesis by entering macrophyte cells and causing damage. DOC can also affect reactivity of heavy metals, water and sediment chemistry. This indirectly affects macrophytes too, so they are exposed to multiple stressors that may have contradictive effects. Finally, macrophytes can affect DOC quality and quantity as they produce DOC themselves and provide a substrate to heterotrophic bacteria that degrade DOC. Because macrophytes take a key position in the aquatic ecosystem, it is essential to understand to what extent DOC quantity and quality in surface water are changing and how this will affect macrophyte growth and species diversity in the future.
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Saebelfeld M, Minguez L, Griebel J, Gessner MO, Wolinska J. Humic dissolved organic carbon drives oxidative stress and severe fitness impairments in Daphnia. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 182:31-38. [PMID: 27846396 DOI: 10.1016/j.aquatox.2016.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/03/2016] [Accepted: 11/06/2016] [Indexed: 06/06/2023]
Abstract
Increases in dissolved organic carbon (DOC) in the form of humic substances, causing browning of surface water, have been reported worldwide. Field surveys indicate that higher DOC levels can influence primary production and thus plankton composition. Experimental studies on the direct effects of humic DOC on aquatic organisms have shown varying results depending on concentration and additional environmental factors. Moreover, changes in life-histories and stress responses have usually been tested separately, rather than in combination. We experimentally tested the impact of a sudden increase in humic DOC on two species of the zooplankton cladoceran Daphnia, across several levels of biological organisation, from cellular to population responses. In D. magna, strong impacts on reproduction (delayed maturity and reduced number of offspring) were coupled with overall stress induction (increases in antioxidant capacity and oxidative damage, combined with a reduced amount of available energy). In D. longispina, increased mortality and lowered fecundity were observed. We conclude that a strong input of humic DOC into aquatic systems can have severe negative impacts on zooplankton species, and has the potential to alter zooplankton community structures.
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Affiliation(s)
- Manja Saebelfeld
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Ecosystem Research, Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin (FU), Germany.
| | - Laëtitia Minguez
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, Stechlin, Germany.
| | - Johanna Griebel
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Ecosystem Research, Berlin, Germany
| | - Mark O Gessner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, Stechlin, Germany; Department of Ecology, Berlin Institute of Technology, Technische Universität Berlin (TU), Germany
| | - Justyna Wolinska
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Ecosystem Research, Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin (FU), Germany
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Wolf R, Andersen T, Hessen DO, Hylland K. The influence of dissolved organic carbon and ultraviolet radiation on the genomic integrity of
Daphnia magna. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12730] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Raoul Wolf
- Department of Biosciences University of Oslo 0316 Oslo Norway
| | - Tom Andersen
- Department of Biosciences University of Oslo 0316 Oslo Norway
| | - Dag O. Hessen
- Department of Biosciences University of Oslo 0316 Oslo Norway
| | - Ketil Hylland
- Department of Biosciences University of Oslo 0316 Oslo Norway
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16
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Amara Korba R, Alayat MS, Bouiba L, Boudrissa A, Bouslama Z, Boukraa S, Francis F, Failloux AB, Boubidi SC. Ecological differentiation of members of the Culex pipiens complex, potential vectors of West Nile virus and Rift Valley fever virus in Algeria. Parasit Vectors 2016; 9:455. [PMID: 27534938 PMCID: PMC4989528 DOI: 10.1186/s13071-016-1725-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/25/2016] [Indexed: 12/24/2022] Open
Abstract
Background We investigated the ecological differentiation of two members of the Culex pipiens complex, Cx. p. pipiens form pipiens and Cx. p. pipiens form molestus in three sites, El-Kala, M'Sila and Tinerkouk in Algeria. These two forms are the most widespread mosquito vectors in temperate regions exhibiting important behavioural and physiological differences. Nevertheless, this group of potential vectors has been poorly studied, particularly in North Africa. Methods Ten larval populations of Cx. p. pipiens were sampled from various above- and underground habitats in three zones representing the three bioclimatic regions in Algeria. The reproduction characteristics were also investigated in the laboratory to define the rates of autogeny and stenogamy. Identification of Cx. p. pipiens members present in Algeria was achieved using a molecular analysis with the microsatellite CQ11 locus. Results We detected larvae of Cx. p. pipiens in all areas suggesting that the species is a ubiquitous mosquito well adapted to various environments. To our knowledge, this study provides the first molecular evidence of the presence of the Cx. p. pipiens form molestus and hybrids (molestus/pipiens) in Algeria with a high proportion of molestus form (48.3 %) in comparison with hybrids (36.8 %) and pipiens form (14.9 %). Conclusions Some unexpected correlations between the proportion of forms pipiens, molestus and hybrids, and mosquito biological characteristics were observed suggesting some epigenetic effects controlling Cx. p. pipiens mating and reproduction. Consequences for pathogen transmission are discussed. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1725-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raouf Amara Korba
- Laboratoire Ecologie des Systèmes Terrestres et Aquatiques, Département de Biologie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie. .,Institut Pasteur d'Alger, Unité d'Entomologie Médicale, Service d'Eco-épidémiologie parasitaire et génétique des populations, Alger, Algérie.
| | - Moufida Saoucen Alayat
- Laboratoire de Biologie Animale Appliquée, Faculté des Sciences, Département de Biologie, Université Badji Mokhtar, Annaba, Algérie
| | - Lazhari Bouiba
- Institut Pasteur d'Alger, Unité d'Entomologie Médicale, Service d'Eco-épidémiologie parasitaire et génétique des populations, Alger, Algérie
| | - Abdelkarim Boudrissa
- Institut Pasteur d'Alger, Unité d'Entomologie Médicale, Service d'Eco-épidémiologie parasitaire et génétique des populations, Alger, Algérie
| | - Zihad Bouslama
- Laboratoire Ecologie des Systèmes Terrestres et Aquatiques, Département de Biologie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie
| | - Slimane Boukraa
- Unit of Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Frederic Francis
- Unit of Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Anna-Bella Failloux
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, Paris, France
| | - Saïd Chaouki Boubidi
- Institut Pasteur d'Alger, Unité d'Entomologie Médicale, Service d'Eco-épidémiologie parasitaire et génétique des populations, Alger, Algérie
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17
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Athanasio CG, Chipman JK, Viant MR, Mirbahai L. Optimisation of DNA extraction from the crustacean Daphnia. PeerJ 2016; 4:e2004. [PMID: 27190714 PMCID: PMC4867708 DOI: 10.7717/peerj.2004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/12/2016] [Indexed: 11/20/2022] Open
Abstract
Daphnia are key model organisms for mechanistic studies of phenotypic plasticity, adaptation and microevolution, which have led to an increasing demand for genomics resources. A key step in any genomics analysis, such as high-throughput sequencing, is the availability of sufficient and high quality DNA. Although commercial kits exist to extract genomic DNA from several species, preparation of high quality DNA from Daphnia spp. and other chitinous species can be challenging. Here, we optimise methods for tissue homogenisation, DNA extraction and quantification customised for different downstream analyses (e.g., LC-MS/MS, Hiseq, mate pair sequencing or Nanopore). We demonstrate that if Daphnia magna are homogenised as whole animals (including the carapace), absorbance-based DNA quantification methods significantly over-estimate the amount of DNA, resulting in using insufficient starting material for experiments, such as preparation of sequencing libraries. This is attributed to the high refractive index of chitin in Daphnia's carapace at 260 nm. Therefore, unless the carapace is removed by overnight proteinase digestion, the extracted DNA should be quantified with fluorescence-based methods. However, overnight proteinase digestion will result in partial fragmentation of DNA therefore the prepared DNA is not suitable for downstream methods that require high molecular weight DNA, such as PacBio, mate pair sequencing and Nanopore. In conclusion, we found that the MasterPure DNA purification kit, coupled with grinding of frozen tissue, is the best method for extraction of high molecular weight DNA as long as the extracted DNA is quantified with fluorescence-based methods. This method generated high yield and high molecular weight DNA (3.10 ± 0.63 ng/µg dry mass, fragments >60 kb), free of organic contaminants (phenol, chloroform) and is suitable for large number of downstream analyses.
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Affiliation(s)
| | - James K Chipman
- School of Biosciences, University of Birmingham , Birmingham , United Kingdom
| | - Mark R Viant
- School of Biosciences, University of Birmingham , Birmingham , United Kingdom
| | - Leda Mirbahai
- School of Biosciences, University of Birmingham , Birmingham , United Kingdom
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Taylor NS, Kirwan JA, Yan ND, Viant MR, Gunn JM, McGeer JC. Metabolomics confirms that dissolved organic carbon mitigates copper toxicity. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2016; 35:635-644. [PMID: 26274843 DOI: 10.1002/etc.3206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/11/2015] [Accepted: 08/11/2015] [Indexed: 06/04/2023]
Abstract
Reductions in atmospheric emissions from the metal smelters in Sudbury, Canada, produced major improvements in acid and metal contamination of local lakes and indirectly increased dissolved organic carbon (DOC) concentrations. Metal toxicity, however, has remained a persistent problem for aquatic biota. Integrating high-throughput, nontargeted mass spectrometry metabolomics with conventional toxicological measures elucidated the mediating effects of dissolved organic matter (DOM) on the toxicity of Cu to Daphnia pulex-pulicaria, a hybrid isolated from these soft water lakes. Two generations of daphniids were exposed to Cu (0-20 μg/L) at increasing levels of natural DOM (0-4 mg DOC/L). Added DOM reduced Cu toxicity monotonically with median lethal concentration values increasing from 2.3 μg/L Cu without DOM to 22.7 μg/L Cu at 4 mg DOC/L. Reproductive output similarly benefited, increasing with DOM, yet falling with increases in Cu. Second generation reproduction was more impaired than the first generation. Dissolved organic matter had a greater influence than Cu on the metabolic status of the daphniids. Putative identification of metabolite peaks indicated that DOM elevation increased the metabolic energy status of the first generation animals, but this benefit was reduced in the second generation, although evidence of increased oxidative stress was detected. These results indicate that Sudbury's terrestrial ecosystems should be managed to increase aquatic DOM supply to enable daphniid colonists to both survive and foster stable populations.
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Affiliation(s)
- Nadine S Taylor
- Department of Biology and Institute for Water Science, Wilfrid Laurier University, Waterloo, Ontario, Canada
- Living with Lakes Centre, Laurentian University, Sudbury, Ontario, Canada
| | - Jennifer A Kirwan
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Norman D Yan
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - John M Gunn
- Living with Lakes Centre, Laurentian University, Sudbury, Ontario, Canada
| | - James C McGeer
- Department of Biology and Institute for Water Science, Wilfrid Laurier University, Waterloo, Ontario, Canada
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Epigenetics in an ecotoxicological context. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 764-765:36-45. [DOI: 10.1016/j.mrgentox.2013.08.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 08/22/2013] [Indexed: 11/23/2022]
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Hofmann S, Timofeyev MA, Putschew A, Saul N, Menzel R, Steinberg CEW. Leaf litter leachates have the potential to increase lifespan, body size, and offspring numbers in a clone of Moina macrocopa. CHEMOSPHERE 2012; 86:883-890. [PMID: 22115468 DOI: 10.1016/j.chemosphere.2011.10.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 10/19/2011] [Accepted: 10/24/2011] [Indexed: 05/31/2023]
Abstract
Leaf litter processing is one major pathway of the global organic carbon cycle. During this process, a variety of small reactive organic compounds are released and transported to the aquatic environment, and may directly impact aquatic organisms as natural xenobiotics. We hypothesize that different forest stockings produce different leachate qualities, which in turn, stress the aquatic communities and, eventually, separate sensitive from tolerant species. Particularly, leachates from coniferous trees are suspected to have strongly adverse impacts on sensitive species. We exposed individuals of a clone of the model organism, Moina macrocopa, to comparable concentrations (approximately 2mM) of litter leachates of Norway spruce, Picea abies, Colorado blue spruce, Picea pungens, black poplar, Populus nigra, and sessile oak, Quercus petraea. The animals were fed ad libitum. The following life trait variables were recorded: growth, lifespan, and lifetime offspring. To identify, whether or not exposure to litter leachates provokes an internal oxidative stress in the exposed animals we measured the superoxide anion radical scavenging capacity via photoluminescence. Except of P. abies, exposure to the leachates reduced this antioxidant capacity by approximately 50%. Leachate exposures, except that of Quercus, increased body size and extended lifespan; furthermore, particularly the leachates of both Picea species significantly increased the offspring numbers. This unexpected behavior of exposed Moina may be based on food supplements (e.g., high carbohydrate contents) in the leachates or on yet to be identified regulatory pathways of energy allocation. Overall, our results suggest that the potentially adverse effects of litter leachates can be overruled by either bacterial-growth supporting fractions in the leachates or an internal compensation mechanism in the Moina individuals.
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Affiliation(s)
- Sylva Hofmann
- Humboldt-Universität zu Berlin, Department of Biology, Laboratory of Freshwater and Stress Ecology, Arboretum, 12437 Berlin, Germany
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