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de la Fuente M, Novo M. Understanding Diversity, Evolution, and Structure of Small Heat Shock Proteins in Annelida Through in Silico Analyses. Front Physiol 2022; 13:817272. [PMID: 35530508 PMCID: PMC9075518 DOI: 10.3389/fphys.2022.817272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/22/2022] [Indexed: 12/04/2022] Open
Abstract
Small heat shock proteins (sHsps) are oligomeric stress proteins characterized by an α-crystallin domain (ACD). These proteins are localized in different subcellular compartments and play critical roles in the stress physiology of tissues, organs, and whole multicellular eukaryotes. They are ubiquitous proteins found in all living organisms, from bacteria to mammals, but they have never been studied in annelids. Here, a data set of 23 species spanning the annelid tree of life, including mostly transcriptomes but also two genomes, was interrogated and 228 novel putative sHsps were identified and manually curated. The analysis revealed very high protein diversity and showed that a significant number of sHsps have a particular dimeric architecture consisting of two tandemly repeated ACDs. The phylogenetic analysis distinguished three main clusters, two of them containing both monomeric sHsps, and ACDs located downstream in the dimeric sHsps, and the other one comprising the upstream ACDs from those dimeric forms. Our results support an evolutionary history of these proteins based on duplication events prior to the Spiralia split. Monomeric sHsps 76) were further divided into five subclusters. Physicochemical properties, subcellular location predictions, and sequence conservation analyses provided insights into the differentiating elements of these putative functional groups. Strikingly, three of those subclusters included sHsps with features typical of metazoans, while the other two presented characteristics resembling non-metazoan proteins. This study provides a solid background for further research on the diversity, evolution, and function in the family of the sHsps. The characterized annelid sHsps are disclosed as essential for improving our understanding of this important family of proteins and their pleotropic functions. The features and the great diversity of annelid sHsps position them as potential powerful molecular biomarkers of environmental stress for acting as prognostic tool in a diverse range of environments.
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Affiliation(s)
- Mercedes de la Fuente
- Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), Las Rozas, Spain
- *Correspondence: Mercedes de la Fuente,
| | - Marta Novo
- Faculty of Biology, Biodiversity, Ecology and Evolution Department, Complutense University of Madrid, Madrid, Spain
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Chironomus riparius Proteome Responses to Spinosad Exposure. TOXICS 2020; 8:toxics8040117. [PMID: 33322338 PMCID: PMC7768432 DOI: 10.3390/toxics8040117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 01/27/2023]
Abstract
The potential of proteome responses as early-warning indicators of insecticide exposure was evaluated using the non-biting midge Chironomus riparius (Meigen) as the model organism. Chironomus riparius larvae were exposed to environmentally relevant concentrations of the neurotoxic pesticide spinosad to uncover molecular events that may provide insights on the long-term individual and population level consequences. The iTRAQ labeling method was performed to quantify protein abundance changes between exposed and non-exposed organisms. Data analysis revealed a general dose-dependent decrease in the abundance of globin proteins as a result of spinosad exposure. Additionally, the downregulation of actin and a larval cuticle protein was also observed after spinosad exposure, which may be related to previously determined C. riparius life-history traits impairment and biochemical responses. Present results suggest that protein profile changes can be used as early warning biomarkers of pesticide exposure and may provide a better mechanistic interpretation of the toxic response of organisms, aiding in the assessment of the ecological effects of environmental contamination. This work also contributes to the understanding of the sublethal effects of insecticides in invertebrates and their molecular targets.
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Niemuth NJ, Zhang Y, Mohaimani AA, Schmoldt A, Laudadio ED, Hamers RJ, Klaper RD. Protein Fe-S Centers as a Molecular Target of Toxicity of a Complex Transition Metal Oxide Nanomaterial with Downstream Impacts on Metabolism and Growth. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15257-15266. [PMID: 33166448 DOI: 10.1021/acs.est.0c04779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Oxidative stress is frequently identified as a mechanism of toxicity of nanomaterials. However, rarely have the specific underlying molecular targets responsible for these impacts been identified. We previously demonstrated significant negative impacts of transition metal oxide (TMO) lithium-ion battery cathode nanomaterial, lithium cobalt oxide (LCO), on the growth, development, hemoglobin, and heme synthesis gene expression in the larvae of a model sediment invertebrate Chironomus riparius. Here, we propose that alteration of the Fe-S protein function by LCO is a molecular initiating event leading to these changes. A 10 mg/L LCO exposure causes significant oxidation of the aconitase 4Fe-4S center after 7 d as determined from the electron paramagnetic resonance spectroscopy measurements of intact larvae and a significant reduction in the aconitase activity of larval protein after 48 h (p < 0.05). Next-generation RNA sequencing identified significant changes in the expression of genes involved in 4Fe-4S center binding, Fe-S center synthesis, iron ion binding, and metabolism for 10 mg/L LCO at 48 h (FDR-adjusted, p < 0.1). We propose an adverse outcome pathway, where the oxidation of metabolic and regulatory Fe-S centers of proteins by LCO disrupts metabolic homeostasis, which negatively impacts the growth and development, a mechanism that may apply for these conserved proteins across species and for other TMO nanomaterials.
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Affiliation(s)
- Nicholas J Niemuth
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Avenue, Milwaukee, Wisconsin 53204, United States
| | - Yonqian Zhang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Aurash A Mohaimani
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Avenue, Milwaukee, Wisconsin 53204, United States
| | - Angela Schmoldt
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Avenue, Milwaukee, Wisconsin 53204, United States
| | - Elizabeth D Laudadio
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Robert J Hamers
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Rebecca D Klaper
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Avenue, Milwaukee, Wisconsin 53204, United States
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Planelló R, Herrero O, García P, Beltrán EM, Llorente L, Sánchez-Argüello P. Developmental/reproductive effects and gene expression variations in Chironomus riparius after exposure to reclaimed water and its fortification with carbamazepine and triclosan. WATER RESEARCH 2020; 178:115790. [PMID: 32334179 DOI: 10.1016/j.watres.2020.115790] [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: 11/29/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
The potential benefits of reclaimed water (RW) uses for environmental enhancement and restoration could become adverse impacts if RW does not meet the quality criteria that ensure wildlife preservation. RW can contain complex mixtures of micropollutants that may accumulate in sediment after environmental uses and affect benthic fauna. Therefore, we designed this study to assess the effects of RW on a sediment insect species used mainly in ecotoxicology (Chironomus riparius). Whole organism effects and gene expression were measured in a water sediment system after spiking RW as overlying water, which was renewed 3 times during the test. Development rate, emergence rate and fecundity were monitored after the 21-day exposure. Endocrine-related genes (EcR, ERR, E75, Vtg), cellular stress genes (hsp70, hsc70, hsp24, hsp10) and biotransformation genes (gp93, GSTd3, GPx, cyp4g) were assessed in larvae after the 10-day exposure. The experimental design also included single or binary fortifications of both test medium and RW, obtained by adding two emerging pollutants: carbamazepine (100 μg/L CBZ) and triclosan (20 μg/L TCS). The chemical characterisation of RW showed that 20 of the 23 screened emerging pollutants fell within the detection limit, 10 exceeded 0.01 μg/L (including CBZ) and three exceeded 0.1 μg/L (hydrochlorothiazide, atenolol, ibuprofen). The analytical measures of sediment (day 21) and overlying water (days 7, 14 and 21) were taken to know the water-sediment distribution of CBZ and TCS added to fortifications. CBZ distributed mainly in overlying water (110-164 μg/L and 73-100 μg/kg), while TCS showed a higher affinity to sediment (2.8-5.1 μg/L and 36-55 μg/kg). RW had significant effects in molecular terms (Vtg, hsp70, hsc70), but had no significant effects on the whole organism. Nevertheless, the single RW fortifications impaired both the development rate and fecundity, while the binary RW fortification impaired only fecundity. The most marked increase in EcR expression was observed for the binary RW fortification. Hsps, GSTd3 and cyp4g showed a similar tendency to that observed for EcR and Vtg in the binary and single RW fortifications. The binary mixture (CBZ and TCS together) in RW was toxic, but not in the medium tests. Therefore, the major concern of RW uses is apparently related to the interactivity between this complex matrix and any other pollutants possibly present in the environment where RW is applied. Our results underscore the need for raising awareness about RW effects, which can be achieved by ecotoxicological testing.
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Affiliation(s)
- Rosario Planelló
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Senda del Rey 9, 28040, Madrid, Spain
| | - Oscar Herrero
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Senda del Rey 9, 28040, Madrid, Spain
| | - Pilar García
- Laboratorio de Ecotoxicología, Departamento de Medio Ambiente, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Crta A Coruña Km 7, 28040, Madrid, Spain
| | - Eulalia María Beltrán
- Laboratorio de Ecotoxicología, Departamento de Medio Ambiente, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Crta A Coruña Km 7, 28040, Madrid, Spain
| | - Lola Llorente
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Senda del Rey 9, 28040, Madrid, Spain
| | - Paloma Sánchez-Argüello
- Laboratorio de Ecotoxicología, Departamento de Medio Ambiente, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Crta A Coruña Km 7, 28040, Madrid, Spain.
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A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera). G3-GENES GENOMES GENETICS 2020; 10:1151-1157. [PMID: 32060047 PMCID: PMC7144091 DOI: 10.1534/g3.119.400710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Making use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species, and the respective recombination rate among the first insect recombination rates at all. The genome assembly and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in particular. The estimated recombination rate will help evolutionary biologists gaining a better understanding of commonalities and differences of genomic patterns in insects.
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Carvajal-Lopez P, Von Borstel FD, Torres A, Rustici G, Gutierrez J, Romero-Vivas E. Microarray-Based Quality Assessment as a Supporting Criterion for de novo Transcriptome Assembly Selection. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:198-206. [PMID: 30059314 DOI: 10.1109/tcbb.2018.2860997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
RNA-Sequencing and de novo assembly have enabled the analysis of species with non-available reference transcriptomes, although intrinsic features (biological and technical) induce errors in the reconstruction. A strategy to resolve these errors consists of varying assembling process parameters to generate multiple reconstructions. However, the best assembly selection remains a challenge. Quantitative metrics for quality assessment have been inconsistent when compared with pertinent references. In this paper, a criterion for supporting assembly selection based on mapping DNA microarray hybridized probes to assembly sets is proposed. Mouse and fruit fly RNA-Seq datasets were assembled with standard de novo procedures. Quality assessment was estimated using quantitative metrics and the proposed criterion. The assembly that best mapped to the available reference transcriptomes of these model species provided the highest quality assembly. The hybridized probes identified the best assemblies, whereas quantitative metrics remained inconsistent. For example, subtle probe mapping difference of 0.25 percent, but statistically significant (ANOVA, p < 0.05), enabled the assembly selection that led to identify 3,719 more contigs and led to 1,049 further mapped contigs to the mouse reference transcriptome. The microarray data availability for non-model species makes the proposed criterion suitable for quality assessment of multiple de novo assembly strategies.
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Monteiro HR, Pestana JLT, Novais SC, Leston S, Ramos F, Soares AMVM, Devreese B, Lemos MFL. Assessment of fipronil toxicity to the freshwater midge Chironomus riparius: Molecular, biochemical, and organismal responses. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 216:105292. [PMID: 31546069 DOI: 10.1016/j.aquatox.2019.105292] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 08/01/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Fipronil is a phenylpyrazole insecticide that entered the market to replace organochlorides and organophosphates. Fipronil impairs the regular inhibition of nerve impulses that ultimately result in paralysis and death of insects. Because of its use as a pest control, and due to runoff events, fipronil has been detected in freshwater systems near agricultural areas, and therefore might represent a threat to non-target aquatic organisms. In this study, the toxicity of fipronil to the freshwater midge Chironomus riparius was investigated at biochemical, molecular, and whole organism (e.g. growth, emergence, and behavior) levels. At the individual level, chronic (28 days) exposure to fipronil resulted in reduced larval growth and emergence with a lowest observed effect concentration (LOEC) of 0.081 μg L-1. Adult weight, which is directly linked to the flying performance and fecundity of midges, was also affected (LOEC = 0.040 μg L-1). Additionally, behavioral changes such as irregular burrowing behavior of C. riparius larvae (EC50 = 0.084 μg L-1) and impairment of adult flying performance were observed. At a biochemical level, acute (48 h) exposure to fipronil increased cellular oxygen consumption (as indicated by the increase of electron transport system (ETS) activity) and decreased antioxidant and detoxification defenses (as suggested by the decrease in catalase (CAT) and glutathione S-transferase (GST) activities). Exposure to fipronil also caused alterations in the fatty acid profile of C. riparius, since high levels of stearidonic acid (SDA) were observed. A comparison between exposed and non-exposed larvae also revealed alterations in the expression of globins, cytoskeleton and motor proteins, and proteins involved in protein biosynthesis. These alterations may aid in the interpretation of potential mechanisms of action that lead to the effects observed at the organism level. Present results show that environmentally relevant concentrations of fipronil are toxic to chironomid populations which call for monitoring of phenylpyrazole insecticides and of their ecological effects in freshwaters. Present results also emphasize the importance of complementing ecotoxicological data with molecular approaches such as proteomics, for a better interpretation of the mode of action of insecticides in aquatic invertebrates.
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Affiliation(s)
- Hugo R Monteiro
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal; MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Peniche, Portugal; Department of Biochemistry and Microbiology, Laboratory for Microbiology, Ghent University, Ghent, Belgium.
| | - João L T Pestana
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Sara C Novais
- MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Peniche, Portugal
| | - Sara Leston
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Pharmacy Faculty, University of Coimbra, Coimbra, Portugal
| | - Fernando Ramos
- REQUIMTE/LAQV, Pharmacy Faculty, University of Coimbra, Coimbra, Portugal
| | | | - Bart Devreese
- Department of Biochemistry and Microbiology, Laboratory for Microbiology, Ghent University, Ghent, Belgium
| | - Marco F L Lemos
- MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Peniche, Portugal
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Lafuente E, Beldade P. Genomics of Developmental Plasticity in Animals. Front Genet 2019; 10:720. [PMID: 31481970 PMCID: PMC6709652 DOI: 10.3389/fgene.2019.00720] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
Developmental plasticity refers to the property by which the same genotype produces distinct phenotypes depending on the environmental conditions under which development takes place. By allowing organisms to produce phenotypes adjusted to the conditions that adults will experience, developmental plasticity can provide the means to cope with environmental heterogeneity. Developmental plasticity can be adaptive and its evolution can be shaped by natural selection. It has also been suggested that developmental plasticity can facilitate adaptation and promote diversification. Here, we summarize current knowledge on the evolution of plasticity and on the impact of plasticity on adaptive evolution, and we identify recent advances and important open questions about the genomics of developmental plasticity in animals. We give special attention to studies using transcriptomics to identify genes whose expression changes across developmental environments and studies using genetic mapping to identify loci that contribute to variation in plasticity and can fuel its evolution.
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Affiliation(s)
| | - Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- CNRS-UMR5174, Université Paul Sabatier, Toulouse, France
- Centre for Ecology, Evolution, and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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Muñiz-González AB, Martínez-Guitarte JL. Effects of single exposure and binary mixtures of ultraviolet filters octocrylene and 2-ethylhexyl 4-(dimethylamino) benzoate on gene expression in the freshwater insect Chironomus riparius. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:35501-35514. [PMID: 30350147 DOI: 10.1007/s11356-018-3516-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 10/17/2018] [Indexed: 06/08/2023]
Abstract
Ultraviolet filters are used extensively in the production of many personal care and industrial products. These products can inadvertently pollute the environment through recreational activities. They have been associated with endocrine disruption in vertebrates but their effects in invertebrates are poorly understood. Chironomus riparius is a species of the dipteran order, with aquatic larvae that are frequently used in toxicity tests. Previously, we showed that octocrylene (OC) and 2-ethylhexyl 4-(dimethylamino) benzoate (OD-PABA) differentially affected the mRNA levels of the ecdysone receptor and Hsp70 genes. For a better understanding of their mode of action, transcriptional activity by real-time PCR was analyzed in fourth instar larvae exposed to OC, OD-PABA, or a binary mixture of both. We studied 16 genes related to the endocrine system, stress, the immune system, and biotransformation mechanisms to elucidate the putative interactions between these compounds. No response was observed for the genes involved in biotransformation, suggesting that enzymes other than cytochromes P450 and glutathione-S-transferases (GSTs) could get involved in transformation of these compounds. Similarly, no response was observed for endocrine-related genes while the stress gene HYOU1 was inhibited by OD-PABA, suggesting an effect in response to hypoxia. In addition, no significant interactions were observed following exposure to a binary mixture of these compounds. Overall, the results suggest a weak, acute response in different metabolic pathways and a lack of interaction between the compounds. Finally, new genes are identified in this organism, opening the possibility to analyze new cellular pathways as targets of toxicants.
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Affiliation(s)
- Ana-Belén Muñiz-González
- Grupo de Biología y Toxicología Ambiental, Departamento de Física Matemática y de Fluidos, Universidad Nacional de Educación a Distancia, UNED, Senda del Rey 9, 28040, Madrid, Spain
| | - José-Luis Martínez-Guitarte
- Grupo de Biología y Toxicología Ambiental, Departamento de Física Matemática y de Fluidos, Universidad Nacional de Educación a Distancia, UNED, Senda del Rey 9, 28040, Madrid, Spain.
- Facultad de Ciencias, UNED, Paseo de la Senda del Rey 9, 28040, Madrid, Spain.
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Mantilla JG, Gomes L, Cristancho MA. The differential expression of Chironomus spp genes as useful tools in the search for pollution biomarkers in freshwater ecosystems. Brief Funct Genomics 2018; 17:151-156. [PMID: 28968626 DOI: 10.1093/bfgp/elx021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Insects of the Chironomidae family are characterized by a wide ecological diversity in freshwater ecosystems. The larvae have the physiological potential to tolerate environmental stress even when there is a low concentration of oxygen, the presence of toxic substances or when there are changes in temperature and salinity. On the other hand, it is important to consider that at a cellular level, when individual insects are exposed to environmental changes, it induces responses of groups of genes that govern the molecular mechanisms related to such tolerance. In this review, using fourth instar larvae of Chironomus spp. in natural conditions and of Chironomus columbiensis under controlled conditions, we will discuss the genetic expression of a group of genes that respond to detoxification and also the biological functions involved and impacted on by mining stressors. The study of macroinvertebrate bioindicator species and their gene expression as a result of mining activity opens a window on the search for genetic biomarkers that could be used in environmental pollution assessments in freshwater ecosystems.
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Martínez-Guitarte JL. Transcriptional activity of detoxification genes is altered by ultraviolet filters in Chironomus riparius. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 149:64-71. [PMID: 29154136 DOI: 10.1016/j.ecoenv.2017.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 11/01/2017] [Accepted: 11/09/2017] [Indexed: 06/07/2023]
Abstract
Ultraviolet (UV) filters are compounds used to prevent the damage produced by UV radiation in personal care products, plastics, etc. They have been associated with endocrine disruption, showing anti-estrogen activity in vertebrates and altering the ecdysone pathway in invertebrates. Although they have attracted the attention of multiple research teams there is a lack of data about how animals activate detoxification systems, especially in invertebrates. Here, analysis of the effects of two UV filters, benzophenone-3 (BP3) and 4-methylbenzylidene camphor (4MBC), on the transcriptional activity of nine genes covering the three steps of the detoxification process has been performed. Four cytochrome P450 genes belonging to different members of this family, five GST genes, and the multidrug resistance protein 1 (MRP1) gene were studied by RT-PCR to analyze their transcriptional activity in fourth instar larvae exposed to the UV filters for 8 and 24h. The obtained results show a differential response with downregulation of the different Cyp450s tested by 4MBC while BP3 seems not to modify their expression. On the other hand, some of the GST genes were affected by one or other of the filters, showing a less homogenous response. Finally, MRP1 was activated by both filters but at different times. These results demonstrate for first time that UV filters alter the expression of genes involved in the different steps of the detoxification process and that they can be processed by phase I enzymes other than Cyp450s. They also suggest that UV filters affect biotransformation processes, compromising the ability of the individual to respond to chemical stress, so further research is needed to know the extent of the damage that they can produce in the resistance of the cell to chemicals.
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Affiliation(s)
- José-Luis Martínez-Guitarte
- Grupo de Biología y Toxicología Ambiental, Departamento de Física Matemática y de Fluidos, Universidad Nacional de Educación a Distancia, UNED, Senda del Rey 9, 28040 Madrid, Spain
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12
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Martín-Folgar R, Aquilino M, Ozáez I, Martínez-Guitarte JL. Ultraviolet filters and heat shock proteins: effects in Chironomus riparius by benzophenone-3 and 4-methylbenzylidene camphor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:333-344. [PMID: 29034430 DOI: 10.1007/s11356-017-0416-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/03/2017] [Indexed: 06/07/2023]
Abstract
Benzophenone-3 (BP3) and 4-methylbenzylidene camphor (4MBC) are common ultraviolet filters (UV filters), compounds considered as emergent contaminants, used in different products like plastics and personal care products. The levels of these compounds are rising in the wild, but the effects they have on invertebrates are poorly understood. Chironomus riparius is a benthic insect widely used in toxicology, and several studies have been previously performed in our laboratory to determine the effects these compounds have on this organism at the molecular level. We have shown that UV filters can alter the mRNA levels of heat shock protein 70 (Hsp70), one of the most studied heat shock proteins. Although these proteins are crucial for the survival of organisms, little data is available on the effects these emergent contaminants have on them, especially in invertebrates. Here, we analyzed the transcriptional activity of 12 genes covering the different groups of heat shock protein [Hsp10, Hsp17, Hsp21, Hsp22, Hsp23, Hsp24, Hsp27, Hsp34, Hsp40, Hsp60, Hsc70 (3), and Hsc70 (4)] in response to 0.1 and 1 mg/L concentrations of BP3 and 4MBC at 8 and 24 h. The results showed that some small Hsp (sHsp) genes were altered by these compounds, while the genes of proteins present in mitochondria, Hsp10 and Hsp60, did not change. sHsps are also involved in developmental processes, so the observed variations could be due to the endocrine disruption activity described for these compounds rather than to a stress response.
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Affiliation(s)
- Raquel Martín-Folgar
- Grupo de Biología y Toxicología Ambiental, Departamento de Física Matemática y de Fluidos, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Paseo de la Senda del Rey 9, 28040, Madrid, Spain
| | - Mónica Aquilino
- Grupo de Biología y Toxicología Ambiental, Departamento de Física Matemática y de Fluidos, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Paseo de la Senda del Rey 9, 28040, Madrid, Spain
| | - Irene Ozáez
- Grupo de Biología y Toxicología Ambiental, Departamento de Física Matemática y de Fluidos, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Paseo de la Senda del Rey 9, 28040, Madrid, Spain
| | - José-Luis Martínez-Guitarte
- Grupo de Biología y Toxicología Ambiental, Departamento de Física Matemática y de Fluidos, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Paseo de la Senda del Rey 9, 28040, Madrid, Spain.
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Aquilino M, Sánchez-Argüello P, Martínez-Guitarte JL. Genotoxic effects of vinclozolin on the aquatic insect Chironomus riparius (Diptera, Chironomidae). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 232:563-570. [PMID: 28987565 DOI: 10.1016/j.envpol.2017.09.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/26/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Vinclozolin (Vz) is a pollutant found in aquatic environments whose antiandrogenic effects in reproduction are well known in mammals. Although its reproductive effects have been less studied in invertebrates, other effects, including genotoxicity, have been described. Therefore, in this work, we studied the genotoxic effects of Vz in the freshwater benthic invertebrate Chironomus riparius. DNA damage was evaluated with the comet assay (tail area, olive moment, tail moment and % DNA in tail), and the transcriptional levels of different genes involved in DNA repair (ATM, NLK and XRCC1) and apoptosis (DECAY) were measured by RT-PCR. Fourth instar larvae of C. riparius, were exposed to Vz for 24 h at 20 and 200 μg/L. The Vz exposures affected the DNA integrity in this organism, since a dose-response relationship occurred, with DNA strand breaks significantly increased with increased dose for tail area, olive moment and tail moment parameters. Additionally, the lower concentration of Vz produced a significant induction of the transcripts of three genes under study (ATM, NLK and XRCC1) showing the activation of the cellular repair mechanism. In contrast, the expression of these genes with the highest concentration were downregulated, indicating failure of the cellular repair mechanism, which would explain the higher DNA damage. These data report for the first time the alterations of Vz on gene transcription of an insect and confirm the potential genotoxicity of this compound on freshwater invertebrates.
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Affiliation(s)
- Mónica Aquilino
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Senda del Rey 9, 28040 Madrid, Spain.
| | - Paloma Sánchez-Argüello
- Laboratorio de Ecotoxicología, Departamento de Medio Ambiente, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. La Coruña km 7, 28040 Madrid, Spain
| | - José-Luis Martínez-Guitarte
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Senda del Rey 9, 28040 Madrid, Spain
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14
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Park SY, Choi J. Molecular Characterization and Expression Analysis of P38 MAPK Gene and Protein in Aquatic Midge, Chironomus riparius (Diptera: Chironomidae), Exposed to Environmental Contaminants. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2017; 72:428-438. [PMID: 28144697 DOI: 10.1007/s00244-017-0366-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/12/2017] [Indexed: 06/06/2023]
Abstract
P38 Mitogen-activated protein kinase (MAPK), an important signaling protein involved in various cellular processes, including stress responses, has been well characterized in model organisms. P38 has been identified in a number of insects, including the genus Drosophila; however, its homologue in Chironomus riparius has not yet been identified. In this study, we identified and characterized p38 MAPK (Crp38) gene in C. riparius using a transcriptome database that was previously generated 454 GS-FLX pyrosequencing. Comparative and phylogenetic analyses were performed using the p38 homologue of other species, such as Drosophila melanogaster, Aedes aegypti, Bombyx mori, Caenorhabditis elegans, Homo sapiens, etc. Furthermore, to test its potential as a biomarker of environmental contamination, Crp38 gene expression was analyzed upon exposure to nonylphenol (NP), silver nanoparticles (AgNPs), and cadmium (Cd). Crp38 gene expression was up- or down-regulated depending on the concentration and exposure duration of chemicals. These results show the role of Crp38 gene in defense against environmental stresses, as well as its potential use as a biomarker for various environmental pollutants. We further synthesized p38 antibody based on the predicted amino acid sequence deduced from Crp38 cDNA and, using this customized antibody, examined p38 protein expression in Cd exposed C. riparius. Although transcriptional alteration was not translated to the protein level, this result showed the possible application of a protein level functional study using cDNA sequence information from next-generation sequencing database in nonmodel organisms.
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Affiliation(s)
- Sun-Young Park
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, 02504, Republic of Korea
- Risk Assessment Division, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, 02504, Republic of Korea.
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15
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Jeppe KJ, Carew ME, Pettigrove V, Hoffmann AA. Toxicant mixtures in sediment alter gene expression in the cysteine metabolism of Chironomus tepperi. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2017; 36:691-698. [PMID: 27474893 DOI: 10.1002/etc.3570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 04/11/2016] [Accepted: 07/28/2016] [Indexed: 06/06/2023]
Abstract
Sediment contamination can pose risks to the environment, and sediment toxicity tests have been developed to isolate the impact of sediment from other factors. Mixtures of contaminants often occur in sediments, and traditional endpoints used in toxicity testing, such as growth, reproduction, and survival, cannot discern the cause of toxicity from chemical mixtures because of complex interactions. In urban waterways, the synthetic pyrethroid bifenthrin and the metal copper are commonly found in mixtures, so the present study was designed to investigate how these contaminants cause toxicity in mixtures. To investigate this, Chironomus tepperi was exposed to environmentally relevant concentrations of copper and bifenthrin-spiked sediments in a 2-way factorial mixture for 5 d. Growth and expression profiles of cysteine metabolism genes were measured after exposure. Growth increased at low copper concentrations, decreased at high copper concentrations, and was unaffected by bifenthrin exposures. Copper exposures induced possible cellular repair by upregulating S-adenosylmethionine synthetase expression and downregulating expression of S-adenosylhomocysteine hydrolase and cystathionine-β-synthase. Metallothionein upregulation was also observed. Bifenthrin exposure altered cysteine metabolism to a lesser extent, downregulating cystathionine-β-synthase and γ-glutamylcysteine synthase. Synergistic, antagonistic, and dose-dependent interactions were observed, and there was evidence of conflicting modes of action and limited substrate production. These findings demonstrate how contextual gene expression changes can be sensitive and specific identifiers of toxicant exposure in mixtures. Environ Toxicol Chem 2017;36:691-698. © 2016 SETAC.
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Affiliation(s)
- Katherine J Jeppe
- Centre for Aquatic Pollution Identification and Management, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Melissa E Carew
- Bio21 Molecular Science and Biotechnology Institute, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Vincent Pettigrove
- Centre for Aquatic Pollution Identification and Management, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ary A Hoffmann
- Bio21 Molecular Science and Biotechnology Institute, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
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16
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Ozáez I, Aquilino M, Morcillo G, Martínez-Guitarte JL. UV filters induce transcriptional changes of different hormonal receptors in Chironomus riparius embryos and larvae. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 214:239-247. [PMID: 27089421 DOI: 10.1016/j.envpol.2016.04.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 06/05/2023]
Abstract
Organic ultraviolet (UV) filters are emerging contaminants that are ubiquitous in fresh and marine aquatic systems due to their extensive use in cosmetics, plastics, paints, textiles, and many other industrial products. The estrogenic effects of organic UV filters have been long demonstrated in vertebrates, and other hormonal activities may be altered, according to more recent reports. The impact of UV filters on the endocrine system of invertebrates is largely unknown. We have previously reported that some UV filters may affect ecdysone-related genes in the aquatic insect Chironomus riparius, an ecotoxicologically important model organism. To further analyze other possible effects on endocrine pathways, we first characterized four pivotal genes related with hormonal pathways in insects; thereafter, these genes were assessed for alterations in transcriptional activity after exposure to 4-methylbenzylidene camphor (4MBC) or benzophenone-3 (BP-3), two extensively used sunscreens. We found that both chemicals disturbed the expression of all four genes analyzed: hormonal receptor 38 (HR38), methoprene-tolerant (Met), membrane-associate progesterone receptor (MAPR) and insulin-like receptor (INSR), measured by changes in mRNA levels by real-time PCR. An upregulatory effect at the genomic level was detected in different developmental stages. Interestingly, embryos appeared to be more sensitive to the action of the UV filters than larvae. Our results suggest that the risk of disruption through different endocrine routes is not negligible, considering the significant effects of UV filters on key hormonal receptor and regulatory genes. Further effort is needed to develop environmental risk assessment studies on these pollutants, particularly for aquatic invertebrate model organisms.
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Affiliation(s)
- Irene Ozáez
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Senda del Rey 9, 28040 Madrid, Spain
| | - Mónica Aquilino
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Senda del Rey 9, 28040 Madrid, Spain
| | - Gloria Morcillo
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Senda del Rey 9, 28040 Madrid, Spain
| | - José-Luis Martínez-Guitarte
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Senda del Rey 9, 28040 Madrid, Spain.
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17
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Aquilino M, Sánchez-Argüello P, Martínez-Guitarte JL. Vinclozolin alters the expression of hormonal and stress genes in the midge Chironomus riparius. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 174:179-187. [PMID: 26966872 DOI: 10.1016/j.aquatox.2016.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
Vinclozolin is a fungicide used in agriculture that can reach aquatic ecosystems and affect the organisms living there. Its effects have been intensively studied in vertebrates, where it acts as an antiandrogen, but there is a lack of information about its mechanistic effects on invertebrates. In this work, we analyzed the response of genes related to the endocrine system, the stress response, and the detoxification mechanisms of Chironomus riparius fourth instar larvae after 24h and 48h exposures to 20 (69.9nM), 200 (699nM), and 2000μg/L (6.99μM) of Vinclozolin. Survival analysis showed that this compound has low toxicity, as it was not lethal for this organism at the concentrations used. However, this fungicide was shown to modify the transcriptional activity of the ecdysone response pathway genes EcR, E74, and Kr-h1 by increasing their mRNA levels. While no changes were observed in disembodied, a gene related with the ecdysone synthesis metabolic pathway, Cyp18A1, which is involved in the inactivation of the active form of ecdysone, was upregulated. Additionally, the expression of two genes related to other hormones, FOXO and MAPR, did not show any changes when Vinclozolin was present. The analysis of stress response genes showed significant changes in the mRNA levels of Hsp70, Hsp24, and Gp93, indicating that Vinclozolin activates the cellular stress mechanisms. Finally, the expressions of the genes Cyp4G and GstD3, which encode enzymes involved in phase I and phase II detoxification, respectively, were analyzed. It was found that their mRNA levels were altered by Vinclozolin, suggesting their involvement in the degradation of this compound. For the first time, these results show evidence that Vinclozolin can modulate gene expression, leading to possible significant endocrine alterations of the insect endocrine system. These results also offer new clues about the mode of action of this compound in invertebrates.
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Affiliation(s)
- Mónica Aquilino
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Senda del Rey 9, 28040 Madrid, Spain
| | - Paloma Sánchez-Argüello
- Laboratorio de Ecotoxicología, Departamento de Medioambiente, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. La Coruña km 7, 28040 Madrid, Spain
| | - José-Luis Martínez-Guitarte
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Senda del Rey 9, 28040 Madrid, Spain.
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18
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Martín-Folgar R, de la Fuente M, Morcillo G, Martínez-Guitarte JL. Characterization of six small HSP genes from Chironomus riparius (Diptera, Chironomidae): Differential expression under conditions of normal growth and heat-induced stress. Comp Biochem Physiol A Mol Integr Physiol 2015; 188:76-86. [DOI: 10.1016/j.cbpa.2015.06.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 04/17/2015] [Accepted: 06/19/2015] [Indexed: 10/23/2022]
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19
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Caroti F, Urbansky S, Wosch M, Lemke S. Germ line transformation and in vivo labeling of nuclei in Diptera: report on Megaselia abdita (Phoridae) and Chironomus riparius (Chironomidae). Dev Genes Evol 2015; 225:179-86. [PMID: 26044750 PMCID: PMC4460289 DOI: 10.1007/s00427-015-0504-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/20/2015] [Indexed: 11/28/2022]
Abstract
To understand how and when developmental traits of the fruit fly Drosophila melanogaster originated during the course of insect evolution, similar traits are functionally studied in variably related satellite species. The experimental toolkit available for relevant fly models typically comprises gene expression and loss as well as gain-of-function analyses. Here, we extend the set of available molecular tools to piggyBac-based germ line transformation in two satellite fly models, Megaselia abdita and Chironomus riparius. As proof-of-concept application, we used a Gateway variant of the piggyBac transposon vector pBac{3xP3-eGFPafm} to generate a transgenic line that expresses His2Av-mCherry as fluorescent nuclear reporter ubiquitously in the gastrulating embryo of M. abdita. Our results open two phylogenetically important nodes of the insect order Diptera for advanced developmental evolutionary genetics.
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Affiliation(s)
- Francesca Caroti
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Silvia Urbansky
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Maike Wosch
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Steffen Lemke
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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20
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Trapp J, Armengaud J, Salvador A, Chaumot A, Geffard O. Next-generation proteomics: toward customized biomarkers for environmental biomonitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13560-13572. [PMID: 25345346 DOI: 10.1021/es501673s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Because of their ecological representativeness, invertebrates are commonly employed as test organisms in ecotoxicological assessment; however, to date, biomarkers employed for these species were the result of a direct transposition from vertebrates, despite deep evolutionary divergence. To gain efficiency in the diagnostics of ecosystem health, specific biomarkers must be developed. In this sense, next-generation proteomics enables the specific identification of proteins involved in key physiological functions or defense mechanisms, which are responsive to ecotoxicological challenges. However, the analytical investment required restricts use in biomarker discovery. Routine biomarker validation and assays rely on more conventional mass spectrometers. Here, we describe how proteomics remains a challenge for ecotoxicological test organisms because of the lack of appropriate protein sequences databases, thus restricting the analysis on conserved and ubiquitous proteins. These limits and some strategies used to overcome them are discussed. These new tools, such as proteogenomics and targeted proteomics, should result in new biomarkers specific to relevant environmental organisms and applicable to routine ecotoxicological assessment.
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Affiliation(s)
- Judith Trapp
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France
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21
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Harrisson KA, Pavlova A, Telonis-Scott M, Sunnucks P. Using genomics to characterize evolutionary potential for conservation of wild populations. Evol Appl 2014; 7:1008-25. [PMID: 25553064 PMCID: PMC4231592 DOI: 10.1111/eva.12149] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/10/2014] [Indexed: 12/16/2022] Open
Abstract
Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.
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Affiliation(s)
| | - Alexandra Pavlova
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
| | | | - Paul Sunnucks
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
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22
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Torto-Alalibo T, Purwantini E, Lomax J, Setubal JC, Mukhopadhyay B, Tyler BM. Genetic resources for advanced biofuel production described with the Gene Ontology. Front Microbiol 2014; 5:528. [PMID: 25346727 PMCID: PMC4193338 DOI: 10.3389/fmicb.2014.00528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/22/2014] [Indexed: 12/12/2022] Open
Abstract
Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary. The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology () project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. Here we review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.
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Affiliation(s)
- Trudy Torto-Alalibo
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Endang Purwantini
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Jane Lomax
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome CampusCambridge, UK
| | - João C. Setubal
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Department of Biological Sciences, Oregon State UniversityCorvallis, OR, USA
| | - Brett M. Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Center for Genome Research and Biocomputing, Oregon State UniversityCorvallis, OR, USA
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23
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Jeppe KJ, Carew ME, Long SM, Lee SF, Pettigrove V, Hoffmann AA. Genes involved in cysteine metabolism of Chironomus tepperi are regulated differently by copper and by cadmium. Comp Biochem Physiol C Toxicol Pharmacol 2014; 162:1-6. [PMID: 24603357 DOI: 10.1016/j.cbpc.2014.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 02/19/2014] [Accepted: 02/20/2014] [Indexed: 10/25/2022]
Abstract
Freshwater invertebrates are often exposed to metal contamination, and changes in gene expression patterns can help understand mechanisms underlying toxicity and act as pollutant-specific biomarkers. In this study the expressions of genes involved in cysteine metabolism are characterized in the midge Chironomus tepperi during exposures to sublethal concentrations of cadmium and copper. These metals altered gene expression of the cysteine metabolism differently. Both metals decreased S-adenosylhomocysteine hydrolase expression and did not change the expression of S-adenosylmethionine synthetase. Cadmium exposure likely increased cystathionine production by up-regulating cystathionine-β-synthase (CβS) expression, while maintaining control level cysteine production via cystathionine-γ-lyase (CγL) expression. Conversely, copper down-regulated CβS expression and up-regulated CγL expression, which in turn could diminish cystathionine to favor cysteine production. Both metals up-regulated glutathione related expression (γ-glutamylcysteine synthase and glutathione synthetase). Only cadmium up-regulated metallothionein expression and glutathione S-transferase d1 expression was up-regulated only by copper exposure. These different transcription responses of genes involved in cysteine metabolism in C. tepperi point to metal-specific detoxification pathways and suggest that the transsulfuration pathway could provide biomarkers for identifying specific metals.
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Affiliation(s)
- Katherine J Jeppe
- Centre for Aquatic Pollution Identification and Management (CAPIM), Department of Zoology, The University of Melbourne, Royal Pde, Parkville 3010, Australia.
| | - Melissa E Carew
- Department of Zoology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville 3010, Australia
| | - Sara M Long
- Centre for Aquatic Pollution Identification and Management (CAPIM), Department of Zoology, The University of Melbourne, Royal Pde, Parkville 3010, Australia
| | - Siu F Lee
- Department of Genetics, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville 3010, Australia
| | - Vincent Pettigrove
- Centre for Aquatic Pollution Identification and Management (CAPIM), Department of Zoology, The University of Melbourne, Royal Pde, Parkville 3010, Australia
| | - Ary A Hoffmann
- Centre for Aquatic Pollution Identification and Management (CAPIM), Department of Zoology, The University of Melbourne, Royal Pde, Parkville 3010, Australia; Department of Zoology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville 3010, Australia; Department of Genetics, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Rd, Parkville 3010, Australia
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24
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Jonker MJ, de Leeuw WC, Marinković M, Wittink FRA, Rauwerda H, Bruning O, Ensink WA, Fluit AC, Boel CH, Jong MD, Breit TM. Absence/presence calling in microarray-based CGH experiments with non-model organisms. Nucleic Acids Res 2014; 42:e94. [PMID: 24771343 PMCID: PMC4066771 DOI: 10.1093/nar/gku343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknown order of probe targets. We therefore present an additional analysis approach, which does not depend on the structural information of a reference genome, and quantifies the presence or absence of a probe target in an unknown genome. The principle is that intensity values of target probes are compared with the intensities of negative-control probes and positive-control probes from a control hybridization, to determine if a probe target is absent or present. In a test, analyzing the genome content of a known bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful, demonstrated by receiver operating characteristic area under the curve values larger than 0.9995. We show its usability in various applications, such as comparing genome content and validating next-generation sequencing reads from eukaryotic non-model organisms.
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Affiliation(s)
- Martijs J Jonker
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Wim C de Leeuw
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Marino Marinković
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - Floyd R A Wittink
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Han Rauwerda
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Oskar Bruning
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Wim A Ensink
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Ad C Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - C H Boel
- Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mark de Jong
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Timo M Breit
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
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Park K, Kwak IS. The effect of temperature gradients on endocrine signaling and antioxidant gene expression during Chironomus riparius development. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 470-471:1003-1011. [PMID: 24239821 DOI: 10.1016/j.scitotenv.2013.10.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 10/12/2013] [Accepted: 10/15/2013] [Indexed: 06/02/2023]
Abstract
Temperature is one of the most important environmental factors affecting the biological processes of aquatic species. To investigate the potential effects of temperature on the developmental processes of aquatic invertebrates, we analyzed biological and molecular transcriptional responses during Chironomus riparius development, including five stages spanning from embryo to adult stages. We assessed the temperature change-induced reduction of survival rate, changes in biological development including the male:female ratio in emerged adults, the success rates of pupation and emergence, and the developmental timing of pupation and emergence. The increased temperature induced expression of endocrine signaling genes, such as the ecdysone receptor, ultraspiracle (ortholog of the RXR), and the estrogen-related receptor in the fourth-instar larval and pupal stages of C. riparius development. Altered temperature also affected the activity of antioxidant genes, including catalase, peroxidase, glutathione peroxidase, and superoxide dismutase during the fourth-instar larval to adult stages of C. riparius development, as a result of altered development. Increased temperature during the fourth-instar larval stage increased oxidative stress in pupae and adults. Responses of antioxidant genes to increased temperature occurred in a developmental stage-dependent manner. However, reduced temperature did not induce the expression of antioxidant genes in a developmental stage-dependent manner, although it did induce oxidative stress during C. riparius development. Increased temperature also caused greater toxicity of di-ethylhexyl phthalate (DEHP) in fourth-instar larvae. Our findings suggest that altered temperatures may disturb the invertebrate hormone system and developmental processes by inducing oxidative stress in aquatic environments.
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Affiliation(s)
- Kiyun Park
- Department of Fisheries and Ocean Science, Chonnam National University, San 96-1, Dundeok-dong, Yeosu, Jeonnam 550-749, Republic of Korea
| | - Ihn-Sil Kwak
- Department of Fisheries and Ocean Science, Chonnam National University, San 96-1, Dundeok-dong, Yeosu, Jeonnam 550-749, Republic of Korea.
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Cook S, Chung BYW, Bass D, Moureau G, Tang S, McAlister E, Culverwell CL, Glücksman E, Wang H, Brown TDK, Gould EA, Harbach RE, de Lamballerie X, Firth AE. Novel virus discovery and genome reconstruction from field RNA samples reveals highly divergent viruses in dipteran hosts. PLoS One 2013; 8:e80720. [PMID: 24260463 PMCID: PMC3832450 DOI: 10.1371/journal.pone.0080720] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/07/2013] [Indexed: 12/17/2022] Open
Abstract
We investigated whether small RNA (sRNA) sequenced from field-collected mosquitoes and chironomids (Diptera) can be used as a proxy signature of viral prevalence within a range of species and viral groups, using sRNAs sequenced from wild-caught specimens, to inform total RNA deep sequencing of samples of particular interest. Using this strategy, we sequenced from adult Anopheles maculipennis s.l. mosquitoes the apparently nearly complete genome of one previously undescribed virus related to chronic bee paralysis virus, and, from a pool of Ochlerotatus caspius and Oc. detritus mosquitoes, a nearly complete entomobirnavirus genome. We also reconstructed long sequences (1503-6557 nt) related to at least nine other viruses. Crucially, several of the sequences detected were reconstructed from host organisms highly divergent from those in which related viruses have been previously isolated or discovered. It is clear that viral transmission and maintenance cycles in nature are likely to be significantly more complex and taxonomically diverse than previously expected.
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Affiliation(s)
- Shelley Cook
- Department of Life Sciences, Natural History Museum, London, United Kingdom
- * E-mail: (SC); (AEF)
| | - Betty Y.-W. Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Gregory Moureau
- UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille, France
| | - Shuoya Tang
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Erica McAlister
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | | | - Edvard Glücksman
- Department of General Botany, University Duisburg-Essen, Essen, Germany
| | - Hui Wang
- Centre for Ecology & Hydrology, Wallingford, Oxfordshire, United Kingdom
| | - T. David K. Brown
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Ernest A. Gould
- UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille, France
- Centre for Ecology & Hydrology, Wallingford, Oxfordshire, United Kingdom
| | - Ralph E. Harbach
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Xavier de Lamballerie
- UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille, France
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (SC); (AEF)
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Ledón-Rettig CC. Ecological epigenetics: an introduction to the symposium. Integr Comp Biol 2013; 53:307-18. [PMID: 23696554 DOI: 10.1093/icb/ict053] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phenotypic variation arises from interactions between environmental and genetic variation, and the emergence of such variation is, in part, mediated by epigenetic mechanisms: factors that modify gene expression but do not change the gene sequence, per se. The role of epigenetic variation and inheritance in natural populations, however, remains poorly understood. The budding field of Ecological Epigenetics seeks to extend our knowledge of epigenetic mechanisms and processes to natural populations, and recent conceptual and technical advances have made progress toward this goal more feasible. In light of these breakthroughs, now is a particularly opportune time to develop a framework that will guide and facilitate exceptional studies in Ecological Epigenetics. Toward this goal, the Ecological Epigenetics symposium brought together researchers with diverse strengths in theory, developmental genetics, ecology, and evolution, and the proceedings from their talks are presented in this issue. By characterizing environmentally dependent epigenetic variation in natural populations, we will enhance our understanding of developmental, ecological, and evolutionary phenomena. In particular, ecological epigenetics has the potential to explain how populations endure (or fail to endure) profound and rapid environmental change. Here, my goal is to introduce some of the common goals and challenges shared by those pursuing this critical field.
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Affiliation(s)
- Cris C Ledón-Rettig
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27606, USA.
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Marinković M, de Leeuw WC, Ensink WA, de Jong M, Breit TM, Admiraal W, Kraak MHS, Jonker MJ. Gene expression patterns and life cycle responses of toxicant-exposed chironomids. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:12679-12686. [PMID: 23126638 DOI: 10.1021/es3033617] [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
Cellular stress responses are frequently presumed to be more sensitive than traditional ecotoxicological life cycle end points such as survival and growth. Yet, the focus to reduce test duration and to generate more sensitive end points has caused transcriptomics studies to be performed at low doses during short exposures, separately and independently from traditional ecotoxicity tests, making comparisons with life cycle end points indirect. Therefore we aimed to directly compare the effects on growth, survival, and gene expression of the nonbiting midge Chironomus riparius. To this purpose, we simultaneously analyzed life cycle and transcriptomics responses of chironomid larvae exposed to four model toxicants. We observed that already at the lowest test concentrations many transcripts were significantly differentially expressed, while the life cycle end points of C. riparius were hardly affected. Analysis of the differentially expressed transcripts showed that at the lowest test concentrations substantial and biologically relevant cellular stress was induced and that many transcripts responded already maximally at these lowest test concentrations. The direct comparison between molecular end life cycle responses after fourteen days of exposure revealed that gene expression is more sensitive to toxicant exposure than life cycle end points, underlining the potential of transcriptomics for ecotoxicity testing and environmental risk assessment.
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Affiliation(s)
- Marino Marinković
- Microarray Department and Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands.
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