Tag Archives: MinION

MinION Meeting

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:


Travel to Toolik (68° 38′ N, 149° 36′ W, AK)

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.

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Some of UAF’s Biology and Wildlife graduate students and scientists pose at the Toolik Field Station welcome sign.

Toolik provided an opportunity to use the MinION sequencing capabilities in the field and sample for microbes on the North Slope.

Materials for soil extraction.
Materials for soil extraction.

Soil sampling and DNA sequencing with the MinION was supplemented with an abundance of scarlet alpine bearberry (Arctostaphylos alpina) and characteristically Alaskan Arctic beauty.

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Hiking along the Atigun river outside of the Arctic National Wildlife Refuge.

University of Alaska Biomedical Research Conference

MaddieAnastasia, and Devin attended the 9th annual University of Alaska Biomedical Research Conference (UA-BRC). For the undergraduates, this was their first research conference and they presented their work using the MinION nanopore sequencer to explore genomics. As you can see below, they drew a crowd to their poster.

UA_BRC_2016

This two-day conference showcased biomedical and One Health related research from graduate students, undergraduate students, researchers, and faculty through-out Alaska in the form of oral presentations and poster sessions. There were two workshops about career issues relevant to undergraduate and graduate student training including internship opportunities, STEM student recruitment, networking, entrepreneurship/innovation, and employer expectations.

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URSA Research Day 2016

URSA Research Day 2016
URSA Research Day 2016

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

Identification antibiotic resistance in the microbial communities of a Fairbanks permafrost gradient

IMG_20160405_190655Undergraduate 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

MinION Hackathon 2016

Interested in Genomics and Technology? Sign up for the first MinION Hackathon at UAF. We’ll explore bleeding edge genomics technology in a two part mini-workshop.

The MinION (Oxford Nanopore) 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. This nanopore based machine demonstrates the future of genomic data acquisition by direct sequencing of single molecules without extra PCR amplification steps. In the near future, the machine will allow for the direct acquisition of data from biological samples (including saliva and blood) without lengthy time consuming steps. There are current applications identifying viral pathogens in near real-time and it was used during the recent Ebola outbreak.

This URSA sponsored, free workshop will take place in two parts: 1) Hands on genomics lab experience where we prepare genetic samples and initiate DNA sequencing. 2) Bioinformatics lab experience where we analyze our new genomic data.  Each part will last around three hours and there will be opportunities for further research if you are interested. This workshop is meant to introduce you to the new technology available at UAF. The workshop will conclude with a poster presentation of our collective results at the 2016 URSA research day (April 26).

Using Nanopore Sequencing to Explore Genomics

I found out today that URSA has generously provided me funds to explore using the MinION nanopore sequencer (Oxford Nanopore Technologies) for undergraduate research. Funds from this proposal will facilitate independent undergraduate genomic research opportunities using bleeding edge technology and a simplified workflow. 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. This device can provide opportunities for student researchers to generate their own low cost DNA sequence data (as little as $500 / experiment). In the near future, the machine will allow for the direct acquisition of data from biological samples (including saliva and blood) without lengthy time consuming steps. There are current applications identifying viral pathogens in near real-time.

In the future, students will design their own independent research projects that integrates this technology. This resource could support projects that propose environmental microbial community profiling and bacterial or even eukaryotic whole genome sequencing to just name a few opportunities. Additionally, the equipment can be integrated into fieldwork (e.g. Toolik) or works at remote campuses. The proposed research presents an opportunity for undergraduates to learn the methods and techniques of collecting and analyzing genomic data using bleeding edge technology. By providing training in the methods of genomic analysis, we are better preparing future Alaskans to generate and interpret data in the genomics era.