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

Welcome to CLP7 “Integrated environmental omics for air pollution assessment”

In Brief

 

CLP7 is foreseen for:

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

CLP7 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.

Omics approaches to study the air pollutant exposure’s health effects comprise systematic investigations at the genomic level. Genomics and epigenomics contribute to the assessment of the response to air pollutant exposure through studies based on single-nucleotide polymorphisms (SNP) in DNA (genome-wide) and epigenomic changes like differences in DNA methylation and post-translational histones modifications (epigenome-wide). The genome/epigenome changes that result from gene-environment interaction influence protein expression and function at the metabolic level, thus impacting cellular functions in response to air pollution. The appraisal of these changes through genomics/epigenomics tools facilitates the adverse effects of air pollutants’ understanding. This case study presents data about the state-of-the-art in genome-wide association studies of SNP, changes in DNA methylation, and post-translational histone modifications that occur with air pollutant exposure. The material also reveals GWIS and conceptual models for air pollution epigenetic epidemiologic studies as advantageous research perspectives.

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.

Contemporary environmental protection has emphasized how molecular and “omics” technologies can be used to determine the nature, behavior, and functions of microbial communities present in ecosystems to limit and eliminate pollution. Environmental “omics” aim to understand better the metabolic processes of a wide range of organisms and/or complex microbial communities to improve phenotype-genotype relationships, thereby providing new insights into the key molecules and processes responsible for the adaptation of organisms in response to environmental changes. Advances in new omics approaches (metagenomics, metatranscriptomics, metaproteomics, metabolomics, and fluxomics) and the applied multi-omics approach have led to invaluable information on microbial communities and essential biotechnological applications – from pollutant bioremediation to the design of innovative biosensors, screening for new catalysts or biological production of materials and products. The progress in “omics” technologies will allow us to explore and characterize new environments and processes to develop and optimize new biotechnological applications.

Authors

  • Aleksander Dolashki, IOCCP-BAS
  • Alexander Savov, R&D Center Biointech Ltd.
  • Boryana Angelova, R&D Center Biointech Ltd.
  • Lyudmila Velkova, IOCCP-BAS
  • Maria Vassileva,University of Granada
  • Nikolay Vassilev, University of Granada
  • Pavlina Dolashka, IOCCP-BAS
  • Valentin Savov, R&D Center Biointech Ltd.

Educational Goals

This CLP7 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
  • ‘Omics’ (especially, genomics and epigenomics) approaches to study the negative effects of air pollutant exposure
  • Genome-wide association studies (GWAS) Genome-wide interaction studies (GWIS) of air pollution exposure
  • Impact of epigenomic modifications in air pollution research
  • 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
  • Мultiomics holistical approach in ecological research by using omics technologies
  • Omics techniques and approaches for biotechnological applications: biodegradation, bioremediation, sustainable agriculture, reduction/mitigation environmental damage
  • Prospects and challenges in bio-technological application of ”оmics“ techniques

    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
    • Describe how the genome-wide association studies can improve our understanding of the adverse effects of air pollutants
    • Understand the links between air pollutant exposure and the epigenome
    • Present the principles of ‘candidate gene’ and the ‘genome-wide’ (‘hypothesis-independent’) approaches as tools for assessment of the biological response to air pollutants exposure
    • Examine the causative role for the epigenome in the adverse effects of environmental exposures, using air pollution as a model
    • Define the main perspectives and challenges in the application of Omics techniques for biotechnological applications in an environmental context.
    • 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
    • Know the essence of the approach for use of GWAS to measure controlled air pollutants exposures in healthy individuals
    • Describe the omics approaches in ecological research
    • Present the role of a holistic multiomics approach for bioremediation and environmental protection.
    • Reveal the potential of multiomics techniques and approaches for biotechnological applications in an environmental context
    • Explain a multimix solution for developing biotechnology to reduce oil pollution and mitigate environmental damage

      Composition

      This CLP7 comprises two Units of Learning Outcomes (ULO 3 & ULO 10)

      • ULO 3:
        • Module 1 Genomics: environmental DNA and sampling
        • Module 10 Air pollution genomics
      • ULO 10
        • Module 6 Environmental database and bioinformatics
        • Module 11 Omics techniques for biotechnological applications

      Learning Content

      Access here the CLP7 learning content!

      >> Genomics: environmental DNA and sampling

      >> Air pollution genomics

      >> Environmental database and bioinformatics

      >> Omics techniques for biotechnological applications

      Knowledge Assessment

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      ECTS Credit Points & Certificate

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