Oligonucleotide Probes for Cyst Nematode Detection
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Solution Overview
Problem
Current methods for detecting cyst nematodes in agricultural soils are cumbersome, error-prone, and lack regional and temporal stability, making them unsuitable for widespread use and prone to false results due to variations in nematode populations.
Innovation Solution
A method using bidirectional oligonucleotide primers or probes that specifically hybridize to nucleic acid sequences encoding ribosomal RNA molecules of cyst nematodes, allowing for the detection of specific subgenus-clusters of nematodes, providing a stable and accurate detection system across various geographical regions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If morphological methods are used for nematode detection, then detection can be performed with simple equipment, but the method is too cumbersome and error-prone
Solution Approach 1:
The patent replaces mechanical/morphological detection methods with molecular biology methods (PCR amplification and hybridization). Instead of manually examining nematode morphology under microscopes, the invention uses DNA-based detection where primers and probes specifically bind to nematode genetic material, enabling automated and accurate detection without manual intervention.
Solution Approach 2:
The patent introduces nucleic acid primers and probes as intermediary molecules that specifically bind to nematode DNA. These molecular intermediaries serve as mediators between the sample and the detection system, allowing specific identification of nematodes through hybridization signals rather than direct morphological observation.
2Measurement precision
If region-specific detection methods are used, then detection accuracy for local nematode populations improves, but the method lacks temporal stability and requires frequent updates
Solution Approach 1:
The patent designs primers and probes that target highly conserved regions of nematode ribosomal RNA genes. These universal primers can detect multiple nematode species and populations across different geographical regions and time periods, eliminating the need for region-specific methods while maintaining high detection accuracy through conservation of essential genetic sequences.
Solution Approach 2:
The patent targets specific genetic parameters (conserved regions of ribosomal RNA genes) that remain stable over time and across populations. By focusing detection on these invariant genetic parameters rather than variable morphological or region-specific characteristics, the method achieves both high precision and long-term stability.
3Adaptability or versatility
If non-coding DNA regions are used for detection, then detection can distinguish between species, but the method is prone to false results due to high variability
Solution Approach 1:
The patent applies a two-level detection strategy: first using primers targeting conserved regions for reliable amplification, then using probes targeting variable regions for species-specific identification. This local quality differentiation allows the system to use stable regions for reliable detection and variable regions for precise species discrimination, minimizing false results while maintaining versatility.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The method enables robust and consistent detection of cyst nematodes, reducing false positives and negatives, and is applicable to diverse agricultural regions, ensuring reliable results over time.
Implementation Method 1
providing a pair of bidirectional oligonucleotide primers or an oligonucleotide probe that hybridizes specifically, under stringent hybridization conditions, to a nucleic acid sequence encoding a Small Subunit (SSU) or Large Subunit (LSU) ribosomal RNA (rRNA) molecule
Data Source
AI summary
The present invention relates to a method for determining the presence of a cyst nematode in a sample comprising the steps of: providing a pair of bidirectional oligonucleotide primers or an oligonucleotide probe that hybridizes specifically, under stringent hybridization conditions, to a nucleic acid sequence encoding the SSU rRNA or LSU rRNA, or the complement or transcript thereof, of a sub genus-cluster of nematodes, said subgenus-cluster comprising cyst nematodes belonging to at least one species of nematode, and wherein said primers or probe do not hybridize to a nucleic acid sequence encoding the LSU rRNA, or the complement or transcript thereof, of cyst nematodes not part of said subgenus-cluster of cyst nematodes; providing a sample in which the presence of the cyst nematode is to be detected, and performing a nucleic acid detection assay on said sample using said pair of bidirectional oligonucleotide primers or said oligonucleotide probe.