eDNA Survey Sampling Parameter Optimization
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Solution Overview
Problem
The detection of environmental DNA (eDNA) is hindered by factors such as degradation, environmental conditions, and the presence of humic substances, which reduce the sensitivity and specificity of detection assays, and there is a lack of statistical reliability in survey designs for eDNA detection, particularly for rare species.
Innovation Solution
A computer-implemented method for determining survey sampling parameters that iteratively adjusts the sampling volume until all selected species are detectable, using different algorithms for detection prediction and survey design, incorporating environmental and species-specific data to optimize eDNA detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If conventional PCR or quantitative PCR assays are used to detect eDNA, then the detection method is simple and widely applicable, but the sensitivity and specificity are reduced due to inhibition by humic substances
Solution Approach 1:
The patent extracts and removes humic substances from the environmental sample before performing PCR detection. This extraction step separates the inhibitory substances from the target eDNA, eliminating the source of inhibition while preserving the detection capability of conventional PCR assays.
Solution Approach 2:
The patent introduces an intermediary purification step between sample collection and PCR detection. This intermediary process uses specific binding materials or chemical treatments to selectively remove humic substances, allowing the subsequent PCR assay to proceed without inhibition while maintaining its simplicity and broad applicability.
2Reliability
If survey sampling volume is increased to improve detection of rare species, then the probability of detecting rare eDNA increases, but the survey cost and time requirements increase
Solution Approach 1:
The patent performs preliminary concentration of eDNA from a large volume of environmental sample before analysis. By pre-concentrating the DNA using filtration or precipitation methods, the system achieves equivalent detection sensitivity to analyzing much larger volumes, thereby reducing the actual survey time and resource requirements while maintaining statistical reliability.
Solution Approach 2:
The patent changes the concentration parameter of eDNA in the sample through pre-processing steps. By concentrating the DNA to a higher initial concentration, the system achieves better detection sensitivity without increasing the total sampling volume or survey time, effectively resolving the trade-off between detection reliability and resource investment.
3Quantity of substance
If eDNA is allowed to remain in the environment for extended periods to capture more DNA, then the amount of detectable eDNA increases, but degradation from UVB radiation, heat, and microorganisms reduces the available DNA
Solution Approach 1:
The patent performs preliminary protection of eDNA by collecting samples in containers that shield against UVB radiation and by adding chemical preservatives that inhibit microbial activity and enzymatic degradation. This preliminary action preserves DNA integrity from the moment of collection, allowing sufficient time for transport and analysis without significant degradation.
Solution Approach 2:
The patent applies beforehand cushioning by introducing protective agents into the sample collection process. These agents include UV-blocking containers and chemical inhibitors that prevent degradation mechanisms before they can act on the eDNA, thereby maintaining DNA quantity and quality throughout the survey process.
4Reliability
If multiple samples are collected to improve statistical reliability of detection, then the confidence in species presence/absence increases, but the survey cost and complexity increase
Solution Approach 1:
The patent merges multiple individual sample collections into a composite sample approach, where multiple subsamples are combined into a single pooled sample for analysis. This merging strategy maintains the statistical benefits of multiple samples while simplifying the overall survey execution and reducing the number of separate processing steps required.
Solution Approach 2:
The patent develops a universal sampling protocol that can be applied across different species and environmental conditions using the same basic procedures and equipment. This multi-functional approach allows the system to achieve statistical reliability through standardized repeated sampling without requiring species-specific or condition-specific modifications, thereby reducing overall survey complexity.
Data Source
AI summary
A computer implemented method for determining survey sampling parameters for environmental DNA (eDNA) detection comprises receiving a species selection identifying selected species and receiving environmental specifications for an environment to be tested for presence of the species. A sampling plan is generated using the environmental specifications and the species selection, and detectability prediction(s) are generated using the environmental specifications, the species selection and the current sampling plan to predict whether the selected species is detectable in the environment according to the current sampling plan. Where at least one respective selected species is undetectable according to the current sampling plan, the process iterates, with each subsequent iteration incorporating an increase in the total volume to be sampled, until either every respective selected species is detectable according to the then-current sampling plan or an iteration stop limit is reached. The sampling plan(s) and detection prediction(s) are generated using different algorithms.