NMU tackles Nex-Gen DNA sequencing

Northern Michigan University. NEX-GEN DNA sequencing. Zambia.

You might not think these three things go together all that well, but they do now. Thanks to the Progressive Research, Innovation and Mutual Exploration award, or PRIME—three faculty members and six NMU students spent the last year collaborating with overseas partners to gain samples of wildebeest DNA, analyzing and sequencing the data.

“DNA sequencing is a big topic right now. The idea was to use the PRIME funding to do next generation sequencing to do a much larger data sequencing project than we’ve been able to do in the past,” explained co-investigator Katherine Teeter, Biology professor.

Teeter, Alec Lindsay (Biology) and Jeff Horn (Computer Science) led the project, employing biology and computer science students. The team also partnered with Matt Becker, CEO for the Zambian Carnivore Programme in Zambia, forming the project, “Genetic diversity of blue wildebeest populations in Zambia and Southern Africa.” Teeter said that “just by having this genetic diversity information we can make a lot of inferences about population dynamics, specifically for this subspecies of wildebeest which hasn’t been studied much.”

Specifically, the blue wildebeest is targeted for analysis, also known as Connochaetes aurinus. The main population the team is working on is from the Liuwa Plain-Mussuma Transfrontier Conservation Area, or the Liuwa Plain.

Zambian partners, led by Becker, do radio tracking of populations, darting and taking samples of the wildebeests. Their interest lies in land use changes in Zambia and how those changes are affecting migration patterns and diversity, particularly within this subspecies and similar ones in two other national parks.

“By looking at the genetic diversity we can use those data to estimate if the population is expanding or contracting and see if there have been other changes over the past 50 years,” Teeter explained.

Lindsay added, “This study will establish an important baseline of genetic diversity in blue wildebeest, and provide information about the migration and population history of this species.”

Lindsay and Teeter explained that to perform a genetic analysis of blue wildebeest in Zambia, the team uses cutting-edge massively parallel DNA sequencing techniques, and a method known as Restriction-site Associated DNA sequencing (RADseq). This method will allow sampling thousands of small sections of the genomes of many individual wildebeest, and subsequent sequencing of all of these individuals at once. Because the massively parallel sequencing methods generate very large data files, containing millions of short DNA sequences, it is not possible to analyze these files on standard laptop or desktop computers. For this reason, they will perform data analyses on the Williac cluster, a ten node stack of computers run by NMU’s Math and Computer Science department, which is largely Horn’s contribution. These bioinformatic analyses are a critical component of this work.

“We used to do just little bits of analysis at a time. When you want to get a big picture of what is going on with the genome, this paralleling method is much better, and offers a lot more,” Teeter said.

Four undergraduate students in Biology—Rebecca Nyinawabeze, Ellie Ewald, Natalie Yeck and Eric Krause—spent the year extracting DNA from the samples sent from Zambia and Southern Africa and analyzing them. There were some “troubleshooting” steps required along the way, which Teeter said is all part of the learning process. The students had 90 samples complete by August 2016.

“It’s been a opportunity for them to get involved in research and experience how that’s different than just learning about biology in the lab. One of them said it was really interesting to see in the lab how we make sure everything works like it is supposed to, but with this project sometimes it doesn’t work and you have to do it over again and find out why it’s not working. You have to do this procedure over and over and over.”

Likewise, Computer Science students had the opportunity to conduct real-world work. Students working with co-investigator Jeff Horn helped make the immense data analysis possible. That team, which included undergraduates Charles Mogan, Justin Syria, Daniel Wilbern and Nolan Earl, helped upgraded the cluster, which is used to reassemble the chromosome form all the pieces generated. It is a massive amount of computation, and an upgrade was necessary, as well as acquisition of two new nodes. Horn said expanding from 10 nodes to 12, as well as expanding from 40 physical cores to 50. The team was also able to update solid state drives.

“We had 120 gigabyte drives years ago and now we have terabyte drives. These are big files and the extra speed is vital.”

A reliable operating system, with automatic updates, was time consuming but vital, Horn explained, because the system and data has to be secure. Hacking attempts are constant, he said, from all over the world, and part of his role is to keep the data safe. Given the entire process, and novelty of the DNA analysis, Horn noted that “very few universities of our size are doing this, if any.”

“It’s a great learning experience for the students. It’s very different from core computer science. In the sense that it is applied, its computational science. It is bringing together everything they have learned,” he said. “Students don’t often get the experience of troubleshooting in real-world in this way. Needing to be able to problem solve throughout the process and learn that way, it’s better than the classroom.”

Teeter said students also a sense of what biologists do as a profession as opposed to what is done in class. It was nice to have a group of students working together, so they could answer each other’s questions, and give it a sense of community.

The team plans to publish the data to share with colleagues in the field, and use that for prelim data to do a more extensive project, partnering with the Zambia Carnivore Programme, which is interested in continuing the collaboration.

“One of the things we view as a benefit is strengthening this Zambia connection. The Zambia Carnivore Programme is creating opportunities to discuss faculty exchanges, student exchanges, and international collaborations with other partners. It would be great to strengthen those connections,” Teeter said. “Basically having the funding to make something tangible to come out of this may open doors to continuing research projects, and additional student and faculty exchanges.”