We are proud to present our most recent publication as a PLOS Biology Community Page entitled:
‘Portable sequencing as a teaching tool in conservation and biodiversity research’
Portable technologies allow for in situ molecular biodiversity monitoring that has been historically out of reach for many researchers in habitat nations. In the realm of education, portable tools such as DNA sequencers facilitate in situ hands-on training in real-time sequencing and interpretation techniques. Here, we provide step-by-step protocols as a blueprint for a terrestrial conservation genetics field training program that uses low-cost, portable devices to conduct genomics-based training directly in biodiverse habitat countries.
The concept to build out a “Green Lab” in the Peruvian Amazon was spearheaded by @surroundscience of @fieldprojectsorg and we (Mrinalini Watsa, Gideon Erkenswick, myself and Stefan Prost) held our first program a couple of summers ago. We wanted to put together this blueprint of what we learned in the process, so that others can apply their own genetics-based programs with portable lab equipment in any environment.
The community page and protocols are open access on PLOS Biology, which you can find here: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000667
Fig 1. Biomonitoring training programs and examples from case studies.
Top: the location and setup of the Green Lab, a molecular genomics field laboratory in southeastern Peru. Middle: portable PCR devices analyzing locally collected specimens, including a bat and its ectoparasite, a saddleback tamarin primate, and a butterfly, which were photographed in the Madre de Dios region of Peru. Bottom: imaging of amplicons during agarose gel electrophoresis using smartphones, loading of a flowcell with a field-prepped library onto ONT’s MinION portable sequencer, and the output from WIMP [13] of the phylogenetic analysis of the fecal microbiome analyzed during a field training program conducted at the Green Lab. Data for Fig 1 are provided in S1 Data. ONT, Oxford Nanopore Technologies; WIMP, What’s in my Pot?. Image Credit: Bat: Ishaan Raghunandan; Tamarin: Timothy Paine; Arthropod ectoparasites, butterfly, and laboratory images: Aaron Pomerantz.
We also made a video sharing our experience from the first course in Peru here:
Please let us know what you think! Many thanks go to the organizations and companies who helped apply portable tools and reagents to these programs, including @oxfordnanopore, @nebiolabs, @zymoresearch, @minipcr, @minionesystems, @promega_corporation