The Drown Lab has been awarded a two year grant to engage undergraduate researchers using new genomic technology to explore the Alaska soil microbiome. We’ll be traveling across the state and working with undergraduates using the latest Nanopore sequencing devices (MinIONs).
Devin is heading out to the Oxford Nanopore New York Community meeting this week to learn from the community as well as present on the Alaska MinION Hackathons. You can follow along with the action on Twitter below:
Given winter’s rapid approach, the permafrost experimental plots are getting special attention. Preemptive vegetation surveying and soil core collections are propelling the Drown lab into a future greenhouse hibernation…and I am excited about it! Do you know what this means? Vegetation surveying, soil samples and an empty greenhouse? Sounds like a pilot study to me. Maybe come January, this smiling face will be found working alongside the IAB Research Greenhouse coordinator, Mark Wright.
This week I got to check out the US Army Corps of Engineers’ research stomping grounds, also known as the Fairbanks Permafrost Experiment Station (FPES). Accompanied by my proficient permafrost guides, Jackson and Alex, I explored this unique study site. Together we drilled soil cores, slogged through the rain and battled prolific mosquitoes. Fun field days in Fairbanks!
On August 20th, Biology and Wildlife graduate students and researchers traveled to UAF’s Toolik Field Station for an awakening taste of arctic atmosphere. Devin and I used this nine hour road trip north of Fairbanks for investigation…in the 68th degree.
Toolik provided an opportunity to use the MinION sequencing capabilities in the field and sample for microbes on the North Slope.
Soil sampling and DNA sequencing with the MinION was supplemented with an abundance of scarlet alpine bearberry (Arctostaphylos alpina) and characteristically Alaskan Arctic beauty.
Undergraduate research activities at UAF cover a broad spectrum of disciplines, from climate science to life science, engineering to anthropology, and music to theater. This year, Jackson Drew presented his URSA sponsored independent research project on the Alaska Soil Microbiome. The MinION Hackathon crew also presented their work using nanopore sequencing technology. Continue reading URSA Research Day 2016
Undergraduate researcher Maddie McCarthy was recently awarded a BLaST Undergraduate Research Experience. Maddie will have a completely funded summer of research ahead of her. She’ll be digging into the soil microbial communities of the Fairbanks Permafrost Experimental Station. Continue reading Identification antibiotic resistance in the microbial communities of a Fairbanks permafrost gradient
Undergraduate researcher Alex Wynne was recently awarded an URSA Summer Research Project. This includes funds for his project and a stipend for the summer. He’ll use next-generation sequencing to characterize the relative abundances of methanogens and methane oxidizers found within a permafrost thaw gradient. By analyzing the relative amount of methane related microbes associated with each disturbance treatment, he will deduce how the thawing of permafrost may contribute to the net amount of greenhouse gases being released into the atmosphere.
Thanks to the efforts of Ian Herriot who initiated the application to the Oxford Nanopore MinION Access programme (MAP), we have acquired access to a new nanopore sequencer (pictured above). The MinION at just 87 grams and half the size of an iPhone is so portable that it will visit the International Space Station as a proof of concept in remote collection of DNA sequence data. Working in collaboration with the IAB DNA Core Lab, the Drown lab will begin experimenting with this technology in the near future and expand access to potential undergraduate researchers in Spring 2016. This device can provide opportunities for student researchers to generate their own low cost DNA sequence data (as little as $500 / experiment).
The news finally came through this past week that my first Alaska INBRE Pilot grant was awarded. The goal of the proposed research is to develop a general evolutionary theory to understand host-symbiont interactions. This is an important missing component of current investigations of the human microbiome and its interpretation in regard to human health. In terms of human pathogens, we may better understand the conditions for disease emergence as well as those that favor increases and decreases in disease virulence.