Our partners at IDT (Integrated DNA Technologies) have published an article on the Freedom4 and it's applications in researching the Adélie Penguins in Antarctica. To find the full article click here or else here is a summary of the article.
Developing onsite genotyping of Antarctic penguins
Clade-specific PrimeTime® Custom qPCR Assays
Adélie penguins live on sea ice but breed on ice-free land in Antarctica.
The challenges of developing a conservation program for Adélie penguins
Adélie penguins live only along the coastline of Antarctica and are considered “Near Threatened” , in part, because their sea-ice habitat is vulnerable to changes from global warming. Two genetic variants, or clades, of Adélie penguins have been identified. Understanding population trends across these clades will aid the design of conservation programs for these penguins.
Dr Jonathan Banks, Senior Scientist at the Cawthron Institute (see the Researcher profile), is studying the mating behaviors of Adélie penguins that live around the Ross Sea, approximately 4000 km south of New Zealand. Dr Banks can use DNA samples from feathers to determine whether selected mating pairs of Ross Sea penguins are from one or both Adélie clades. This process is complicated as the mating season is short and usually one of the mating pair feeds at sea while the other incubates the pair’s eggs on land. Having access to onsite molecular testing would simplify sample processing and ultimately increase the number of mating pairs that could be included in this project.
Selecting robust qPCR assays for a mobile PCR thermal cycler
In collaboration with Dr Jo-Ann Stanton (University of Otago; Otago, New Zealand) and Dr Elisabeth Wagner (IDT; Coralville, IA, USA), Dr Banks has validated qPCR assays that distinguish the two Adélie penguin clades. By comparing genetic sequences from the two penguin types, Dr Wagner helped identify potential primer sites targeting the penguin mitochondrial genome. They identified a 138 nucleotide sequence within the d-loop region that varied between the two Adélie penguin groups and designed qPCR primers specific for each clade. Before use in the field, Drs Stanton and Banks validated the rigor of the SYBR® Green–based assays using archived penguin DNA stored under variable conditions. High resolution melt curves distinguished true positive results from amplification of primer-dimers. Clade identification results using the selected PrimeTime qPCR Assays completely corroborated data obtained by DNA sequencing. Full details of the assays are to be published in the New Zealand Journal of Zoology.
As a finalist of the Freedom for You grant sponsored by Ubiquitome, Dr Banks wants to use the Ubiquitome Freedom4 device (see the sidebar, From benchtop to handheld, battery-operated instrument) with the PrimeTime®qPCR Assays to perform onsite molecular genotyping in Antarctica. “Significant time and resources can be saved by eliminating the long, complex transport chain. Helicopters, light aircraft, and intercontinental aircraft are all required just to get samples to the New Zealand laboratory, and then return results to me in Antarctica,” notes Dr Banks.
Field testing around the world
Several researchers around the world wish to incorporate the Freedom4 device into field testing projects. To learn more about Dr Banks’ research and additional field application stories that use the Freedom4 device, visitwww.UbiquitomeBio.com.
To read about the successful use of PrimeTime qPCR Assays with different species, instruments, and probe and intercalating dyes, see the list of peer-reviewed research articles on the PrimeTime citations page. The Related reading section below provides qPCR education and support materials for both novice and experienced qPCR researchers.