How CRISPR and Biotechnology Can Revolutionize Conservation
Quick Summary
- Contemporary conservation management faces a variety of challenges, one of those challenges being the ability to identify species accurately when visual identification is unreliable.
- The CRISPR based biotechnological platform dubbed SHERLOCK is a field applicable, easy to use, and inexpensive field tool for addressing this very problem.
- SHERLOCK and its successful adaptation in conservation settings is groundbreaking for the field of ecology.
Contemporary conservation management faces a variety of challenges. One of those challenges being the ability to identify species accurately when visual identification is unreliable. Conservation teams generally have two approaches to biomonitoring, visual identification and genetic identification. The former provides a real-time and inexpensive way to classify species, but runs the risk of human error when working with messy ecosystems in the field. Meanwhile, the latter provides a highly accurate classification of species, but is expensive and relies on built up scientific infrastructure outside the field. The CRISPR based biotechnological platform dubbed SHERLOCK is a field applicable, easy to use, and inexpensive field tool for addressing this very problem.
SHERLOCK is a nucleic acid based detection platform that is designed to target a specific RNA sequence. Unlike more well known CRISPR Cas9 platforms that are designed to make precision cuts, SHERLOCK assays operate on a CRISPR Cas13a platform. The Cas13a enzyme gives SHERLOCK a unique ability in which, when the target sequence is detected, it makes collateral cuts that cleave any nearby RNA sequence. This reaction then, in turn, produces a visual fluorescent when the target sequence is detected.
While functioning similarly to other non-CRISPR based genetic identification methods like qPCR or DNA Barcoding, SHERLOCK differs in that it is programmed directly using genetic data of the target species. Non-CRISPR based platforms use genetic samples to amplify and identify sequences as one process, however, SHERLOCK is preprogrammed using said genetic data. Being preamplified and utilizing predesigned RNA allows for it interact with the Cas13a enzyme that enables a way for sequence-specific targeting. This even allows SHERLOCK to operate using non-extraction methods for near real-time field surveys using eDNA or mucus swabs without the need to extract DNA.
This enables SHERLOCK to operate as a field-ready kit that can be used without much training, unlike other non-CRISPR based methods like qPCR and DNA Barcoding, which rely on genetic material being analyzed using lab equipment. This makes them reliant on nearby laboratory infrastructure, is time consuming, requires specialized training, and unsuitable for remote or field conditions that SHERLOCK otherwise can operate in. Such versatility allows SHERLOCK to be used for a multitude of use cases, such as the identification of endangered species and the monitoring of invasive ones.
As SHERLOCK was not originally designed for ecological monitoring, someone had to adapt the technology for conservation uses. This adaptation, development, and refinement of the SHERLOCK technology for conservation has been explored by UC Davis' own Genomic Variation Laboratory, headed by Dr. Andrea Schreier, whose lab and their partners have refined the technology to a portable, battery-powered device, that works with lateral flow strips, over the years. Starting by testing SHERLOCK'S rapid species identification abilities for differentiating Delta Smelt, Longfin Smelt, and Wakasagi, as well as other testing on Chinook Salmon runs. The lab has since explored the technology's explosive versatility, from SHERLOCK assays being used to monitor Vernal Pools throughout the Central Valley, operate as genetic fire alarms for invasive Zebra Mussels, Quagga Mussels, and Nutria in the San Francisco Bay Delta, with plans to even use it as a way detect the Chytrid fungus that ravage amphibian populations.
SHERLOCK and its successful adaptation in conservation settings is groundbreaking for the field of ecology. It's success demonstrates the immense utility of CRISPR based technologies. SHERLOCK proves that advanced biotechnology is not limited to the lab, nor does it need to require specialized gear, rigorous training, and expensive equipment to still be effective. And SHERLOCK research continues to develop, such as searching for ways to create an even more sensitive 2-step amplification process, to make it even more effective in wider settings. Demonstrating that research and development of conservation biotechnology shows no hint at slowing down.
This breakthrough paves the way for future research and development to work to adapt other biotechnologies and develop new ones for even greater field ready conservation use. Contemporary conservation and ecological research sit at the beginning of a revolutionary time. By embracing the development and refinement of future conservation biotechnologies, tools like CRISPR have the ability to transform the way future conservation management takes place, both in aquatic and terrestrial systems. Biotechnology can expand the range, availability, and areas of use of high quality molecular tools to new locations. Enabling for advanced tools to be applied to more systems than previously possible. In a time where genetic and genomic research is accelerating at a breakneck pace, it'll be interesting to see how these technologies can be adapted to continue to protect the planet's ecosystems.
Sources:
https://pmc.ncbi.nlm.nih.gov/articles/PMC7497203/
https://pmc.ncbi.nlm.nih.gov/articles/PMC12142720/