Reflection - Wk9
This week’s class covered emerging e-DNA technologies with a student-led presentation by my group about LAMP (loop-mediated isothermal amplification) with highlights from Williams et al.’s 2019 paper “Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp.”. I am intrigued by LAMP technology, especially for its potential in-the-field, rapid eDNA detection capabilities.
From our research we shared some of the benefits of this technology: No need for an expensive thermocycler because the samples are processed at a constant temperature (63-65C) with a single heat block; no need for special reagents; can use template DNA or RNA; it uses a single-tube technique which makes it faster to process and more cost effective (and less plastic waste downstream!); it is sensitive due to the use of six primers; it is more resistant to inhibitors versus PCR; uses one protocol; and it is most ideal for rapid testing. Some of the downsides are that it is: more difficult to design the primers (need six versus two for PCR); not effective (yet) for metabarcoding applications as it is primarily a single-species detection method; a single protocol is helpful for simplifying the process, but does not allow for as much optimization or customization as in PCR work. Although there are many benefits to LAMP technology, I think it depends on the type of study whether one should rely solely on it. For example, if I conducted a long-term study using eDNA to better understand Eastern brook trout (Salvelinus fontinalis) migration I would approach it with dual methods of LAMP and qPCR. LAMP would be helpful for field detection to quickly identify the presence of brookies, and qPCR would be helpful to verify their presence and also be useful to answer larger ecosystem questions through metabarcoding.
In the Williams et al. article, the researchers used the Gene-Z device for in-the field, rapid detection of Dreissena sp. at two sites, Klinger Lake and Muskegon Lake. The device was developed by Dr. Syed Hashsham’s group at the Environmental Genomics Lab at Michigan State University. I tried to find out more information about it, such as who manufacturers it or how to procure the device, but it seems like the prototype did not become further developed for the market. However, I did find a couple of papers which describe researchers’ recent efforts to develop portable LAMP devices: Priye et al.’s “A smartphone-based diagnostic platform for rapid detection of Zika, chikungunya, and dengue viruses “ and Velders et al.’s “Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection“ .