eDNA
@Roba Olana, last edited by @Yaman Garg
- Environmental DNA is analyzing genetic material from a given species (skin, hair, scales, or waste products shed) for either disease detection or species sampling instead of collecting the sample directly from the animal.
- A helpful introductory document:
- Since 2011, Goldberg and WSU colleagues Alexander Fremier and Katherine Strickler have played an instrumental role in bringing eDNA from a proof of concept to a practical tool for species conservation.
eDNA may offer an early warning signal for deadly frog pathogen
When Colleen Kamoroff and her graduate advisor Caren Goldberg collected water samples to look for the DNA of non-native fish species, they could not have guessed the potential importance of their timing. One month after they sampled water from 13 lakes in California's Sequoia Kings Canyon National Park in 2015, endangered mountain yellow-legged frogs in [...]
https://news.mongabay.com/2018/04/edna-may-offer-an-early-warning-signal-for-deadly-frog-pathogen/
Early warning system for deadly amphibian pathogen
Environmental DNA is a new technology that detects telltale bits of genetic material that living creatures shed into their environment. Scientists demonstrate for the first time that it can be used to detect the presence of a deadly pathogen before it wipes out populations of amphibians.
- This technique can be applied to study the expansion or presence, but not prevalence, of Bsal over larger areas in a reliable, cost‐effective, and efficient way. (Van der Sluijs et al., 2020)
The conventional non-portable protocol for detection of pathogens using eDNA generally uses one of the following methodologies, where eDNA is extracted from fungal zoospores caught on the water filter used:
- Described in (Van der Sluijs et al., 2020) section 2.1 and 2.3, used by (Miaud et al., 2019) and Dufresnes et al., 2019), first mentioned in (Pont et al., 2018) also found here:
- QIAShredder Based protocol described in (Goldberg et al., 2011), recent papers that use it are (Kamoroff and Goldberg, 2017) and (Kolby et al., 2015)
- Described in (Barnes et al., 2014) and used recently in (Barnes et al., 2020)
- Described in (Chestnut et al., 2014)
- Described in (Vilaca et al., 2019) which uses extraction procedure from (Spens et al., 2016)
- Note: The conventional non-portable protocol for swabs is described in (Hyatt et al., 2007)
A portable analyzing protocol for eDNA is given by Biomeme (who also have a similar-ish protocol for swabbing) and using ANDe filtration system:
To briefly summarize: the water is filtered through the filter using the ANDe machine to capture zoospores, the filter is then processed through a sample prep kit similar to Biomeme's M1 Sample Prep (summarized in 🧫Nucleic Acid Extraction), the purified DNA is put in Biomeme's Go Strips (PCR tubes with lyophilized master mix for amplification), which are then transferred to a portable thermocycler for amplification and detection.
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