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Chu L, Hou X, Song X, Zhao X, Hu S, Shen G. Toxicity of ionic liquids against earthworms (Eisenia fetida). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162411. [PMID: 36870498 DOI: 10.1016/j.scitotenv.2023.162411] [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: 12/20/2022] [Revised: 02/18/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Ionic liquids (ILs) are widely used in frontier fields because of their highly tunable properties. Although ILs may have adverse effects on organisms, few studies have focused on their effect on earthworm gene expression. Herein we investigated the toxicity mechanism of different ILs towards Eisenia fetida using transcriptomics. Earthworms were exposed to soil containing different concentrations and types of ILs, and behavior, weight, enzymatic activity and transcriptome were analyzed. Earthworms exhibited avoidance behavior towards ILs and growth was inhibited. ILs also affected antioxidant and detoxifying enzymatic activity. These effects were concentration and alkyl chain length-dependent. Analysis of intrasample expression levels and differences in transcriptome expression levels showed good parallelism within groups and large differences between groups. Based on functional classification analysis, we speculate that toxicity mainly occurs through translation and modification of proteins and intracellular transport functions, which affect protein-related binding functions and catalytic activity. KEGG pathway analysis revealed that ILs may damage the digestive system of earthworms, among other possible pathological effects. Transcriptome analysis reveals mechanisms that cannot be observed by conventional toxicity endpoints. This is useful to evaluate the potential environmental adverse effects of the industrial use of ILs.
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Affiliation(s)
- Linglong Chu
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaoxiao Hou
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xinshan Song
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaoxiang Zhao
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
| | - Shuangqing Hu
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China; Shanghai Academy of Environmental Sciences, Shanghai 200233, China
| | - Genxiang Shen
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China; Shanghai Academy of Environmental Sciences, Shanghai 200233, China
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Rao Tatta E, Paul S, Kumavath R. Transcriptome Analysis revealed the Synergism of Novel Rhodethrin inhibition on Biofilm architecture, Antibiotic Resistance and Quorum sensing inEnterococcus faecalis. Gene 2023; 871:147436. [PMID: 37075926 DOI: 10.1016/j.gene.2023.147436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/31/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023]
Abstract
Enterococcus sp. emerged as an opportunistic nosocomial pathogen with the highest antibiotic resistance and mortality rate. Biofilm is problematic primarily since it is regulated by the global bacterial cell to cell communication mediated by the quorum sensing system. sing system. Thus, potential natural antagonists in a novel drug formulation against biofilm-forming Enterococcus faecalis is critical. We used RNA-Seq to evaluate the effects of the novel molecule rhodethrin with chloramphenicol induced on Enterococcus faecalis and DEGs were identified. In transcriptome sequence analysis, a total of 448 with control Vs rhodethrin, 1591 were in control Vs chloramphenicol, 379 genes were DEGs from control Vs synergies, in rhodethrin with chloramphenicol, 379 genes were differentially expressed, whereas 264 genes were significantly downregulated, indicating that 69.69% ofE. faecaliswas altered. The transcriptional sequence data further expression analysis qRT-PCR, and the results shed that the expression profiles of five significant biofilm formation responsible genes such as, Ace, AtpB, lepA, bopD, and typA, 3 genes involved in quorum sensing are sylA, fsrC and camE, and 4 genes involved in resistance were among including liaX, typA, EfrA, and lepA, were significantly suppressed expressions of the biofilm, quorum sensing, and resistance that are supported by transcriptome analysis.
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Affiliation(s)
- Eswar Rao Tatta
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO), Kasaragod, Kerala 671320, India
| | - Sayan Paul
- Department of Biochemistry & Molecular Biology, the University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO), Kasaragod, Kerala 671320, India; Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
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Lathakumari S, Seenipandian S, Balakrishnan S, Raj APMS, Sugiyama H, Namasivayam GP, Sivasubramaniam S. Identification of genes responsible for the social skill in the earthworm, Eudrilus eugeniae. GENE REPORTS 2023. [DOI: 10.1016/j.genrep.2023.101774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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de Sosa I, Verdes A, Tilikj N, Marchán DF, Planelló R, Herrero Ó, Almodóvar A, Cosín DD, Novo M. How to thrive in unstable environments: Gene expression profile of a riparian earthworm under abiotic stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152749. [PMID: 34990683 DOI: 10.1016/j.scitotenv.2021.152749] [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: 11/09/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Nowadays, extreme weather events caused by climate change are becoming more frequent. This leads to the occurrence of extreme habitats to which species must adapt. This challenge becomes crucial for species living in unstable environments, such as the riparian earthworm Eiseniella tetraedra. Its cosmopolitan distribution exposes it to various environmental changes, such as freezing in subarctic regions or droughts in Mediterranean areas. Transcriptional changes under cold and desiccation conditions could therefore shed light on the adaptive mechanisms of this species. An experiment was performed for each condition. In the cold experiment, the temperature was lowered to -14 °C ± 2 °C (compared to 8 °C for control samples), and in the desiccation treatment, humidity was lowered from 60% to 15%. Comparisons of gene expression levels between earthworms under freezing conditions and control earthworms revealed a total of 84 differentially expressed genes and comparisons between the desiccation experiment and the control yielded 163 differentially expressed genes. However, no common responses were found between the two treatments. The results suggest that E. tetraedra can acclimate to low temperatures due to the upregulation of genes involved in glucose accumulation. However, downregulation of the respiratory chain suggests that this earthworm does not tolerate freezing conditions. Under desiccation conditions, genes involved in cell protection from apoptosis and DNA repair were upregulated. In contrast, lipid metabolism was downregulated, presumably to conserve resources by reducing the rate at which they are consumed.
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Affiliation(s)
- Irene de Sosa
- Biodiversity, Ecology and Evolution Department, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 12, 28040 Madrid, Spain.
| | - Aída Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, C/Jose Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Natasha Tilikj
- Biodiversity, Ecology and Evolution Department, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 12, 28040 Madrid, Spain
| | - Daniel F Marchán
- CEFE, UMR 5175, CNRS-Univ Montpellier-Univ Paul-Valéry-EPHE-SupAgro Montpellier-INRA-IRD, Montpellier, France
| | - Rosario Planelló
- Biology and Environmental Toxicology Group, Faculty of Science, Universidad Nacional de Educación a Distancia (UNED), Campus UNED Las Rozas, Avda. Esparta s/n, 28232, Las Rozas de Madrid, Madrid, Spain
| | - Óscar Herrero
- Biology and Environmental Toxicology Group, Faculty of Science, Universidad Nacional de Educación a Distancia (UNED), Campus UNED Las Rozas, Avda. Esparta s/n, 28232, Las Rozas de Madrid, Madrid, Spain
| | - Ana Almodóvar
- Biodiversity, Ecology and Evolution Department, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 12, 28040 Madrid, Spain
| | - Darío Díaz Cosín
- Biodiversity, Ecology and Evolution Department, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 12, 28040 Madrid, Spain
| | - Marta Novo
- Biodiversity, Ecology and Evolution Department, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 12, 28040 Madrid, Spain
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Paul S, Balakrishnan S, Arumugaperumal A, Lathakumari S, Syamala SS, Vijayan V, Durairaj SCJ, Arumugaswami V, Sivasubramaniam S. Importance of clitellar tissue in the regeneration ability of earthworm Eudrilus eugeniae. Funct Integr Genomics 2022; 22:1-32. [PMID: 35416560 DOI: 10.1007/s10142-022-00849-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/04/2022]
Abstract
Among the annelids, earthworms are renowned for their phenomenal ability to regenerate the lost segments. The adult earthworm Eudrilus eugeniae contains 120 segments and the body segments of the earthworm are divided into pre-clitellar, clitellar and post-clitellar segments. The present study denoted that clitellum plays vital role in the successful regeneration of the species. We have performed histological studies to identify among the three skin layers of the earthworm, which cellular layer supports the blastema formation and regeneration of the species. The histological evidences denoted that the proliferation of the longitudinal cell layer at the amputation site is crucial for the successful regeneration of the earthworm and it takes place only in the presence of an intact clitellum. Besides we have performed clitellar transcriptome analysis of the earthworm Eudrilus eugeniae to monitor the key differentially expressed genes and their associated functions and pathways controlling the clitellar tissue changes during both anterior and posterior regeneration of the earthworm. A total of 4707 differentially expressed genes (DEGs) were identified between the control clitellum and clitellum of anterior regenerated earthworms and 4343 DEGs were detected between the control clitellum and clitellum of posterior regenerated earthworms. The functional enrichment analysis confirmed the genes regulating the muscle mass shape and structure were significantly downregulated and the genes associated with response to starvation and anterior-posterior axis specification were significantly upregulated in the clitellar tissue during both anterior and posterior regeneration of the earthworm. The RNA sequencing data of clitellum and the comparative transcriptomic analysis were helpful to understand the complex regeneration process of the earthworm.
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Affiliation(s)
- Sayan Paul
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India.,Centre for Cardiovascular Biology and Disease, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | | | - Arun Arumugaperumal
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India
| | - Saranya Lathakumari
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India
| | - Sandhya Soman Syamala
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India
| | - Vijithkumar Vijayan
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India
| | - Selvan Christyraj Jackson Durairaj
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India.,Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, 600 119, India
| | | | - Sudhakar Sivasubramaniam
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India.
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The transcriptome of anterior regeneration in earthworm Eudrilus eugeniae. Mol Biol Rep 2020; 48:259-283. [PMID: 33306150 DOI: 10.1007/s11033-020-06044-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/28/2020] [Indexed: 12/25/2022]
Abstract
The oligochaete earthworm, Eudrilus eugeniae is capable of regenerating both anterior and posterior segments. The present study focuses on the transcriptome analysis of earthworm E. eugeniae to identify and functionally annotate the key genes supporting the anterior blastema formation and regulating the anterior regeneration of the worm. The Illumina sequencing generated a total of 91,593,182 raw reads which were assembled into 105,193 contigs using CLC genomics workbench. In total, 40,946 contigs were annotated against the NCBI nr and SwissProt database and among them, 15,702 contigs were assigned to 14,575 GO terms. Besides a total of 9389 contigs were mapped to 416 KEGG biological pathways. The RNA-Seq comparison study identified 10,868 differentially expressed genes (DEGs) and of them, 3986 genes were significantly upregulated in the anterior regenerated blastema tissue samples of the worm. The GO enrichment analysis showed angiogenesis and unfolded protein binding as the top enriched functions and the pathway enrichment analysis denoted TCA cycle as the most significantly enriched pathway associated with the upregulated gene dataset of the worm. The identified DEGs and their function and pathway information can be effectively utilized further to interpret the key cellular, genetic and molecular events associated with the regeneration of the worm.
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