EQO's lab is at the forefront of leveraging eRNA and eDNA to support owners, operators, or consultants in their efforts to detect, diagnose, and monitor their freshwater and marine aquatic ecosystem challenges.
eRNA vs eDNA
Both eRNA and eDNA are powerful tools in environmental sciences. eDNA, a robust molecule, serves as the archival record of all genetic information within a species, indicating its past or present existence in an environment. Conversely, the less stable eRNA offers a fleeting glimpse into the active processes of a cell, much like a culinary recipe in action. Leveraging these molecular insights, we provide real-time snapshots and comprehensive archives of aquatic ecosystems, enabling actionable, informed decisions.
Quantitative PCR (qPCR) is a method that involves designing a specific gene probe to amplify a section of DNA or RNA in order to perform high-specificity measurements. Using a fluorescence system, qPCR copies the target sequence and measures the abundance of certain DNA or RNA sequences, with the more common sequences resulting in earlier fluorescence. This technique is valuable for its precision and sensitivity and can measure the expression of specific genes to give insight into metabolism, stress response, and other functions of an organism. In environmental science, qPCR can provide an understanding of the past presence and current state of specific species, including their stress levels and biological activities.
PhyloChip is a type of microchip composed of thousands of small wells, each containing DNA sequences specific to different prokaryotic organisms. By amplifying a gene common to all prokaryotes, like the 16s gene, and allowing these amplified fragments to bind to the sequences in the wells, scientists can determine which organisms are present. While this method doesn't provide the depth of data possible with metagenomics or the quantitative specificity of qPCR, it can give a broad-spectrum view of all known bacteria and archaea present in a sample. This makes PhyloChip a useful tool in environmental science for assessing microbial biodiversity.
Metabarcoding is a method within next generation sequencing (NGS) which involves taking DNA or RNA, breaking it into fragments, and attaching a barcode, a known sequence of DNA, to each fragment. This barcode only binds to specific fragments, allowing us to selectively amplify and analyze genetic data from target species or genes. In an environmental context, metabarcoding can provide relative abundance of different species based on the frequency of their DNA or RNA sequences. However, due to many variable factors during the process, the results are not entirely reproducible, which makes it useful for understanding biodiversity and general trends rather than for precise diagnostic purposes.