About This ProjectThe North American wood frog Rana sylvatica can survive being frozen solid - no heartbeat, no brain activity. This animal survives the winter in a frozen state. In the Spring, the wood frog thaws out and spontaneously reanimates itself. The wood frog holds the key to organ cryopreservation, understanding how we can rapidly chill people in trauma cases while transporting them to hospital, as well as the key to long-term suspended animation.
Ask the ScientistsJoin The Discussion
What is the context of this research?
The North American wood frog is an animal that has adopted a strategy of overwintering by burrowing into the leaf litter and other forest floor material and freezing. The frog can do this by flooding its blood with glucose and urea and other small molecules. The glucose acts in a similar manner to an antifreeze, and the urea helps depress the metabolism and help preserve the cells during the freeze/thaw process. Over the last 20 to 30 years, the wood frog's physiology has been studied by numerous researchers and we have a pretty good idea how it manages to survive the freeze event from a biochemical and whole organism physiological perspective. What we don't have, is the most critical aspect of solving the last aspect of the mystery - we don't have the genome.
What is the significance of this project?
The wood frog is an example of a vertebrate animal who can undergo freezing and survive. One of the biggest problems with human organ transplants are the incompatibility and unavailability of the correct organ to correct recipient within a critical time frame. If we could freeze and/or chill preserve organs, we could save thousands of people every year. We could also save soldiers on the battlefield by stabilizing them, thus permitting them to be medievaced up to an hour later.
The genome of the wood frog contains the instructions on how to survive freezing. More importantly, wood frog in the summer can NOT survive freezing, while winter frogs can. To understand how the wood frog alters its gene expression in a seasonal manner, we need the genome to map these changes.
What are the goals of the project?
I have wood frog tissue and the all the necessary skills and equipment to isolate, sequence, assemble and annotate the wood frog genome. If funded, I will:
(1) Isolate the genomic DNA of the North American wood frog.
(2) Using the TruSeq Synthetic Long-Read DNA Kit (Illumina) I will sequence the genomic DNA.
(3) Assemble the sequenced genomic DNA using the Illumina TruSeq Synthetic Long-Read DNA kit application to assemble the genome.
(4) Annotate the genome using both previously annotated frogs (Xenopus laevis and Xenopus tropicalis), as guides, as well as standard and recommended bioinformatics pipelines. Essentially, we will annotate (find) the wood frog genes by looking for similar genes already identified in other organisms. This strategy has been very successful with other animals.
I need this funding in order to complete the project. I cannot achieve the goals without the Illumina Tru-Seq Synthetic Long-Read DNA Kit, and I do not have a sequencer (HiSeq2000) at my institution. However, many large academic universities have these instruments (HiSeq2000) and routinely perform turn-key sequencing projects.
Without this funding, the sequencing cannot be performed. I do have access to all the required computational and database resources as part of my role as Supervisor of the Center for Bioinformatics and Functional Genomics.
Meet the Team
Team BioBiologist; Interested in adaptation and evolution. My objectives are to understand how changes at the molecular level influence the success of the entire organism. Projects include how higher vertebrates have become freeze tolerant, the stability of globular proteins, functional genomics of seasonal acclimations.
I'm an avid vinyl record collector, backpacker, mountain biker, and have an interest in the outdoors.
This project is special to me ever since I heard of the freezing frogs in a second year biochemistry class. Ever since that time, I became convinced that sequencing the wood frog genome would unlock the key to to understanding this unique organism and enable us to exploit this knowledge for the benefit of humankind.
Press and MediaHere's a link to an Animal Planet segment from Corwin's Quest on the wood frog: http://www.animalplanet.com/tv-shows/other/videos/...
Here's a blog post at Byte Size Biology: http://bytesizebio.net/2014/10/01/sequencing-the-f...
Additional InformationHere is an example of the past work I have done to successfully identify a suite of proteins expressed in wood frog liver: http://www.mdpi.com/1422-0067/12/12/8406
Here is a link to the APS Comparative Approaches to Grand Challenges in Physiology in October 2014, where I will give a talk on the (soon to be published) seasonal differences of the expressed genes in wood frog liver: http://www.the-aps.org/mm/Conferences/APS-Conferen...
Here is a link to the kit I intend to use: http://products.illumina.com/products/truseq-synth...
Cover photo of frozen wood frog by Janet Storey.
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