How the Environment Changes Our Cells
A Look at the Molecular Impact of Environmental Factors Using Omics Techniques
In a world where temperatures break records year after year 1 and where millions of tons of plastic end up in the oceans 1 , understanding how these environmental changes affect us at the deepest level has become a crucial question. Today, science has powerful tools to decipher this mystery: omics methodologies and chemometrics.
Record Temperatures
Global warming continues to break historical records annually
Plastic Pollution
Millions of tons of plastic waste enter marine ecosystems each year
Molecular Footprints
Environmental stressors leave detectable molecular signatures in organisms
These technologies allow us to read the molecular fingerprints that pollution leaves in living beings, as if they were open books telling a story of changes invisible to the naked eye.
This article will take you into the fascinating world of cutting-edge environmental research, where scientists observe model organisms—such as zebrafish—to decipher how environmental aggressions alter their internal functioning, from their genes to their metabolites.
The Tools of Scientific Revolution
Three technologies revolutionizing our understanding of environmental impact
Genomics
Studies the totality of an organism's DNA (its genome). When an organism is exposed to a contaminant, some of its genes may "activate" or "deactivate." Genomics allows researchers to see which genes change their behavior, revealing how the organism tries to adapt or how damage begins 1 .
Proteomics
Analyzes the set of proteins (the proteome) present in a cell or tissue at a given time. Proteins are the molecular machines that execute the functions of the cell. Proteomics shows how the abundance and type of proteins change under environmental stress, indicating which cellular process is being affected.
Metabolomics
Examines the complete set of metabolites (metabolome), which are the small molecules resulting from metabolism, such as sugars, fatty acids, or amino acids. Metabolites are the fastest and most direct response to an environmental aggression; they are the immediate chemical fingerprint that pollution leaves in the organism.
To understand the immense amount of data generated by these omics techniques, chemometrics comes into play. This discipline applies statistical and mathematical methods to extract patterns and meaningful information from these large, complex datasets. Without it, it would be like having all the pieces of a puzzle without the reference image.
The Experiment: Zebrafish and Microplastics
Investigating the impact of microplastics on zebrafish (Danio rerio), a model organism
Why Zebrafish?
Zebrafish (Danio rerio) are widely used in biological research due to their:
- Transparency during embryonic development
- Rapid growth and reproduction
- Genetic similarity to humans (approximately 70% of human genes have at least one zebrafish counterpart)
- Well-characterized genome
These characteristics make them an ideal model organism for studying the effects of environmental contaminants at the molecular level.
Methodology Step by Step
1 Controlled Exposure
Adult zebrafish are distributed in several aquariums. One group serves as control (with clean water), while other groups are exposed to different concentrations of microplastics for a determined period (for example, 28 days).
2 Sampling
At the end of the exposure period, samples of liver tissue are collected from the fish. The liver is the main detoxification organ and, therefore, a key indicator of metabolic stress.
3 Omics Analysis
Transcriptomics (part of genomics): Messenger RNA from the liver is analyzed to identify which genes have been overexpressed or underexpressed in response to microplastics.
Metabolomics: Metabolites from the liver tissue are extracted and analyzed using techniques such as mass spectrometry to detect changes in the metabolic profile.
4 Chemometric Analysis
Data from all samples and groups are compiled and analyzed with statistical tools. A principal component analysis (PCA) is performed to see if the exposed fish clearly differ from the controls. It also searches for which metabolites or genes are the main responsible for this differentiation.
Results and Analysis
Microplastic exposure causes significant oxidative stress in zebrafish
The results reveal that exposure to microplastics causes significant oxidative stress in zebrafish. This means that the cells suffer an imbalance between free radicals (harmful molecules) and antioxidants, leading to cellular damage.
What is Oxidative Stress?
Oxidative stress occurs when there's an imbalance between the production of free radicals and the ability of the body to counteract their harmful effects through neutralization by antioxidants. This can damage cells, proteins, and DNA.
Metabolite Changes
The following table shows an example of the types of metabolites that could be altered and their biological function:
| Metabolite | Change (vs. Control) | Biological Function | Interpretation |
|---|---|---|---|
| Glutathione | Decrease | Key antioxidant | Consumed to combat oxidative stress, indicating cellular damage. |
| Malondialdehyde | Increase | Marker of lipid peroxidation | Confirms damage to cell membranes from oxidative stress. |
| Lactate | Increase | Product of anaerobic metabolism | Possible change in energy production towards less efficient pathways. |
| Phosphatidylcholine | Decrease | Component of membranes | Reflects degradation or alteration of cell membranes. |
Gene Expression Changes
At the genomic level, transcriptomic analysis would show that genes related to detoxification and stress response have been significantly activated.
| Gene | Change (vs. Control) | Gene Function | Interpretation |
|---|---|---|---|
| CYP1A | Overexpression | Detoxification enzyme (Cytochrome P450) | The organism attempts to metabolize the contaminant. |
| SOD | Overexpression | Superoxide dismutase (antioxidant) | Response to increased free radicals. |
| HSP70 | Overexpression | Heat shock protein | Indicates general cellular stress and protein damage. |
Chemometric Analysis
Chemometric analysis, using a tool like principal component analysis, would allow clear visualization of these changes. In a graph, the control fish and the exposed ones would group in clearly differentiated areas, and the biomarkers from the tables above would be the ones that contribute most to this separation.
| Principal Component | Variance Explained | Biomarkers with Most Weight (Contribution) |
|---|---|---|
| PC1 | 65% | Malondialdehyde, Glutathione, CYP1A Expression |
| PC2 | 18% | Lactate, HSP70 Expression |
Simulated PCA plot showing separation between control and microplastic-exposed zebrafish based on molecular profiles
The Researcher's Toolkit
Essential materials and reagents for environmental omics research
To carry out this type of study, scientists have a set of essential materials and reagents. The following table describes some of the key elements of the "toolkit" in such an experiment.
| Element | Function in the Experiment |
|---|---|
| Model organism (e.g., Zebrafish) | Biological system of study; its biology is well understood and it is representative of other species. |
| Contaminant of interest (e.g., Microplastics, PFAS) | The environmental stressor to be investigated. PFAS are "forever chemicals" linked to reproductive damage and cancer 3 4 . |
| Mass spectrometer | Analytical instrument that identifies and quantifies compounds (such as metabolites or proteins) based on their mass-to-charge ratio. |
| RNA/DNA extraction reagents | Chemicals used to isolate genetic molecules from tissue samples for genomic analysis. |
| Oxidative stress analysis kits | Commercial assays that allow specific measurement of markers such as malondialdehyde or glutathione activity. |
| Statistical analysis software (e.g., R, Python) | Chemometric tools to process omics data, perform multivariate analyses and visualize results. |
Laboratory Techniques
Modern environmental research relies on sophisticated laboratory techniques including:
- High-performance liquid chromatography (HPLC)
- Gas chromatography-mass spectrometry (GC-MS)
- Liquid chromatography-mass spectrometry (LC-MS)
- Next-generation sequencing (NGS)
- Nuclear magnetic resonance (NMR) spectroscopy
Data Analysis Approaches
The complex data generated requires advanced analytical approaches:
- Multivariate statistical analysis
- Machine learning algorithms
- Pathway analysis and enrichment
- Network analysis
- Integration of multi-omics data
A Future Marked by Molecular Footprints
The evolution of environmental assessment using omic methodologies and chemometrics
The field of environmental assessment using omic methodologies and chemometrics is constantly evolving. Future research will focus on understanding the effects of complex mixtures of contaminants, moving away from the study of isolated substances. Furthermore, the creation of large public databases with the molecular footprints of hundreds of contaminants will allow, in the near future, to quickly diagnose what types of environmental pressures an ecosystem suffers simply by analyzing its organisms.
Complex Mixtures
Moving beyond single contaminants to study realistic environmental mixtures
Reference Databases
Creating comprehensive molecular signature databases for rapid environmental diagnostics
AI Integration
Applying artificial intelligence for predictive modeling of environmental impacts
Environmental Challenges
In a context where environmental challenges are increasingly complex—from biodiversity loss, which has accelerated the sixth mass extinction 1 , to policies that threaten to weaken environmental protection laws 3 4 —these technologies are not just a scientific tool. They are a beacon of hope that offers us the ability to detect, understand, and ultimately prevent damage before it becomes irreversible, ensuring a healthier environment for future generations.