Loading...
edu-logo

2023-1-BG01-KA220-HED-000155777 – DigiOmica

Welcome to CLP6 “Integrated environmental omics in aquatic toxicology”

In Brief

 

CLP6 is foreseen for:

      • Postgraduates: Ph.D. students; EQF 7
      • Postdoctoral researchers & Research associates; EQF 8

CLP6 Summary

The advancement of DNA-based approaches for genome data generation and interpretation encompasses, among others, the study of the genomes at an environmental scale using environmental DNA (eDNA). eDNA is the genetic material of nuclear and mitochondrial origin released from an organism in the environment. It is obtained directly from environmental samples (terrestrial or aquatic) without the necessity of biomaterial availability and used as an efficient, easy-to-manipulate, and standardized, non-invasive sampling approach. Thus, eDNA sampling is applied for species distribution monitoring and operates through sensitive and cost-effective protocols. Although the current technical challenges and drawbacks that scientists face are related mainly to the pitfalls in eDNA obtaining, sequencing, and data interpretation, the potential of eDNA applications is undoubtful. The perspectives on eDNA applications cover the field methods and laboratory protocols improvement for its detection and technical advancements in eDNA application as a biodiversity inventory and monitoring tool.

Aquatic ecosystems are under increasing pressure from a variety of environmental stressors, including chemical pollutants, habitat degradation, climate change, and invasive species. It is essential to comprehend how aquatic organisms respond molecularly to various stresses in order to evaluate the condition of aquatic ecosystems and create efficient plans for environmental preservation and management. Omics, which includes genomics, transcriptomics, proteomics, and metabolomics, transforms aquatic toxicology by providing thorough understanding of how contaminants affect aquatic life. Evaluation of genomic methods in aquatic toxicology, possibilities and limitations of the microarray and quantitative polymerase chain reaction (PCR) methodologies, proteomics, metabolomics, RNA sequencing, and DNA methylation studies are discussed in details. Together, these omics approaches provide a holistic understanding of the molecular mechanisms underlying toxicity, facilitating the identification of novel biomarkers for early detection of pollution, assessment of environmental risk, and development of more effective mitigation strategies to safeguard aquatic ecosystems and human health. This learning outcome focuses on comprehensive look for omics in aquatic toxicology with approaches of cases studies, covering their principles, applications, challenges, and future directions.

Environmental proteomics is a proteomics application area studying the effects of growth environments on organism development in natural, non-controlled conditions. This proteomics branch contributes to the proteins expressed in the cell, identification and quantitative determination, the discovery of the mechanisms of essential cellular processes, and the elucidation of phenomena like syntrophy, gene exchange, and cell-to-cell communication at the molecular level. Environmental proteomics investigates microbial-dominated organisms’ assemblages and designs differential protein production and expression patterns that reflect physiological responses to environmental changes (in norma and under stress). It performs laboratory surveys with model environmental microorganisms and studies natural microbial communities, analysing their collective proteome (metaproteomics). Environmental proteomics has diverse research and application areas (e.g., metabolic engineering, microbial ecology, environmental stress tolerance, etc.) due to the methodological and technical innovations (e.g., 2D PAGE, LC, ICAT, MS, phage display, bioinformatics. etc.) that allow protein identification and structural characterization.

Environmental mRNA (environmental transcriptomics) retrieves transcriptomes of microbial assemblages lacking information on the kinds of genes expressed at the community level. It links microbial genetic potential with their biogeochemical activity. However, the vision of using this approach for various applications in environmental science at the molecular level is hampered by technical difficulties of working with mRNA, such as lacking polyadenylation mechanism, very short half-lives of mRNAs, and lack of abundance of mRNA molecules within the total RNA pool in the microbial cell resulting in poor detection signals. Protocols have been developed to overcome these difficulties and facilitate the analyses of partial environmental transcriptomes. Among the promising studies, the retrieval of community-specific sequences of functional genes essential for quantitative ecological surveys, the generation of new hypotheses for known microbial processes, or the assessment (with the aid of environmental genomics) of the genetic potential and activities patterns of natural microbial assemblages can be listed.

Authors

  • Aysel Çağlan Günal, Gazi University
  • Gamze Yücel Işıldar, Gazi University
  • Iliyana Rasheva, Sofia University “St. Kliment Ohridski”
  • Maria Vassileva,University of Granada
  • Nikolay Vassilev, University of Granada
  • Trayana Nedeva, Sofia University “St. Kliment Ohridski”

Educational Goals

This CLP6 offers new knowledge and skills about:

  • eDNA as a tool for monitoring species, populations and communities at molecular level
  • eDNA sampling and its technical challenges and drawbacks
  • eDNA application areas and future potential
  • Provision of background knowledge about utilizing omics techniques in aquatic toxicology including genomics, transcriptomics, proteomics, and metabolomics.  
  • Emphasis on significance for developing the skills to effectively interpreting omics data generated from studies of aquatic toxicology.
  • Highlighting the omics approaches to enhance risk assessment strategies with case studies in aquatic toxicology
  • Proteomics and Environmental proteomics essentials
  • Main categories of environmental proteomics and the relevant to them methodological and technical innovations
  • Challenges, frontiers, and perspective of environmental proteomics applications
  • Environmental transcriptomics linking genetic potential with microbial biogeochemical activity
  • Basic steps in the protocol for analysis of partial environmental transcriptomes
  • Different approaches and solutions to overcome the difficulties of transcriptional heterogeneity

Learning Outcomes

Upon completion of this CLP the learners will be able to:

  • Define eDNA as a tool for monitoring species, populations and communities at molecular level
  • Explain the application areas of eDNA of microbial origin and macro-organisms in different habitats and time frames
  • Recognize and apply eDNA sampling protocols for monitoring species distribution
  • Explain the technical challenges and drawbacks of eDNA sampling and data interpretation
  • Understand the eDNA applications potential
  • Gain knowledge of how pollutants interact with aquatic organisms at the molecular level through genomics, transcriptomics, proteomics, and metabolomics, elucidating the pathways and processes affected by toxicants.
  • Identify of biomarkers and characterize molecular biomarkers indicative of exposure to aquatic pollutants, enabling more sensitive and reliable monitoring of environmental contamination and early detection of potential risks to aquatic ecosystems.
  • Integrate of omics data into risk assessment frameworks, allowing for a more comprehensive evaluation of the potential impacts of pollutants on aquatic organisms and ecosystems, and informing evidence-based regulatory decisions.
  • Apply of omics in aquatic toxicology with designing and conducting omics-based experiments to investigate the effects of pollutants on aquatic organisms, including the selection of appropriate omics techniques, sample preparation, data analysis, and interpretation.
  • Understand the principles and applications of omics techniques in interdisciplinary research approach with case studies to develop innovative strategies for the protection and conservation of aquatic ecosystems.
  • Describe the principles of transcriptomics / landscape transcriptomics
  • Apply Landscape transcriptomics approaches in ecology, evolution, and conservation
  • Define the main categories of Landscape transcriptomics studies of wild systems in natural environments
  • Explain the approaches for collection, analysis, and explanation of transcriptomics data from natural environments
  • Understand the gene expression as a time-based and tissue specific process
  • Present the core of environmental mRNA (environmental transcriptomics)
  • Explain the technical difficulties of working with mRNA
  • Know and apply the basic steps in the protocol for analysis of partial environmental transcriptomes
  • Understand the major promising applications of environmental mRNA approach in microbial ecology
  • Apply the good practices in the state of art in single-cell transcriptomics and single-cell RNA-sequencing

Composition

This CLP6 comprises two Units of Learning Outcomes (ULO 2 & ULO 9)

  • ULO 2:
    • Module 1 Genomics: environmental DNA and sampling
    • Module 9 Omics in aquatic toxicology
  • ULO 9
    • Module 3 Advanced environmental proteomics
    • Module 7 Microbial gene transcripts in environmental samples

Learning Content

Access here the CLP6 learning content!

>> Genomics: environmental DNA and sampling

>> Omics in aquatic toxicology

>> Advanced environmental proteomics

>> Microbial gene transcripts in environmental samples

Knowledge Assessment

Check your knowledge!

ECTS Credit Points & Certificate

Get your certificate!