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

Welcome to CLP 2: “Environmental genomics and proteomics – water habitats”

In Brief

 

CLP2 is foreseen for:

  • Undergraduates: B.Sc. students; EQF 6
  • Graduates: M.Sc. students; EQF 7

CLP2 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 biotechnology is the application of biotechnology principles and techniques to study and manage the natural environment. It involves microorganisms and other biological agents’ usage for the performance of environmentally beneficial tasks such as cleaning up contaminated sites, enhancing soil health, and reducing greenhouse gas emissions. Examples of environmental biotechnology applications include the use of bacteria to break down pollutants in water and soil, the use of algae to absorb excess nutrients from wastewater, and the use of fungi to decompose organic matter in landfills. Environmental biotechnology has the potential to contribute to finding sustainable solutions to environmental problems, and it is an area of active research and development. Environmental database provides access to international scientific literature relating to all aspects of environmental quality, monitoring, resource management, and conservation. Bioinformatics is essential for understanding ecological processes, managing data, and developing tools to address global challenges.

Authors

  • Aleksandar Dolashki, IOCCP-BAS
  • Aysel Çağlan Günal, Gazi University
  • Gamze Yücel Işıldar, Gazi University
  • Iliana Rasheva, Sofia University “St. Kliment Ohridski”
  • Lyudmila Velkova, IOCCP-BAS
  • Maria Vassileva,University of Granada
  • Nikolay Vassilev, University of Granada
  • Pavlina Dolashka, IOCCP-BAS
  • Trayana Nedeva, Sofia University “St. Kliment Ohridski”

Educational Goals

This CLP2 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 significant 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
  • Bioinformatics’ methods and software tools for understanding biological data
  • Data science – environmental databases that provide access to a wealth of information related to environmental science
  • Environmental science – field that study the environment and solve environmental problems
  • Challenges and perspective of environmental bioinformatics

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 proteomics / environmental proteomics
  • Apply proteiomics studies for assessment of protein diversity of ecosystems and communities
  • Define the main categories of environmental proteomics studies
  • Explain the application of environmental proteomics for metabolic engineering, microbial ecology surveys and environmental stress tolerance assessment
  • Specify the challenges, frontiers, and perspective of environmental proteomics
  • Describe the principles and key aspects of environmental bioinformatics and its methods and software tools
  • Use different environmental databases that cover all aspects of human impact on the environment.
  • Define the major categories of environmental science
  • Explain the application of environmental bioinformatics
  • Define the challenges, limits and perspective of environmental bioinformatics

Composition

This CLP2 comprises two Units of Learning Outcomes (ULO2 & ULO 6)

  • ULO 2:
    • Module 1 Genomics: environmental DNA and sampling
    • Module 9 Omics in aquatic toxicology
  • ULO 6
    • Module 3 Advanced environmental proteomics
    • Module 6 Environmental database and bioinformatics

Learning Content

Access here the CLP2 learning content!

>> Genomics: environmental DNA and sampling

>> Omics in aquatic toxicology

>> Advanced environmental proteomics

>> Environmental database and bioinformatics

Knowledge Assessment

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ECTS Credit Points & Certificate

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