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Student in nature

It's PRIME time: Progressive Research and Innovative Mutual Exploration Fund

A novel internal funding mechanism called the Northern PRIME fund addresses challenges related to current funding trends by offering a) greater seed money for proposed projects with potentially impactful outcomes and high likelihood of success in external competitions and b) extensive opportunity for networking and cross-disciplinary collaboration that can facilitate tackling of substantive concepts.

Informational sessions for PRIME 2019 will be held. Contact Erica Goff for more information.

PRIME at a glance

  • Funding of up $20,000 per team for 1 year projects
  • Intensive hands-on opportunity for students: Projects must include student involvement (minimum of 2) working hands-on in the scholarly activity
  • Multi-disciplinary focus
  • Minimum of 1 quantifiable deliverable (publication or equivalent such as an art display, or substantive preliminary data set)
  • Synopsis of project and achieved outcomes will be published on the PRIME website and other NMU marketing products
  • Participation in the annual symposium
  • Submission of a proposal to an external funding agency within 1 year of PRIME project completion.

View PRIME guidelines here. The required internal cover page can be downloaded here.

Benefits to NMU

  • Additional opportunity for student involvement in scholarship projects, offering intensive, hands-on experience in their chosen discipline and related disciplines.
  • Increased collaboration among faculty/staff, which will facilitate larger-scale projects resulting in greater external funding potential.
  • Production of preliminary data with the potential to lead to substantial external funding and impactful, long-term projects. Extensive opportunity for marketability of NMU’s (1) highly qualified scholars, (2) advanced hands-on experience for students at all levels, and (3) insightfulness in embracing a cutting-edge approach to research in a competitive environment while providing a platform for fundraising and administration of interdisciplinary projects.

Read about funded PRIME projects: SpeedMaker device and Nex-Gen in Zambia.

Modeled after a highly successful effort at the University of Michigan called MCubed, the PRIME fund is an example of cutting-edge efforts to ensure NMU investigators can compete for significant external funds. The key components of PRIME are:

  • up to $20K for each one-year, multi-disciplinary project;
  • Heavy emphasis on student involvement
  • A high-visibility scholarship symposium to celebrate multi-disciplinary projects; and
  • An interactive website managed by the Grants and Contracts Office that publicizes PRIME projects, investigators and students, and facilitates networking and collaboration campus-wide.

Teams of two or three faculty and/or staff, from different disciplines or professional areas, can request funding for up to $20,000. Each project will involve at least two students, result in a minimum of one quantifiable deliverable (publication in a relevant and reputable journal or equivalent per such as an art display, or substantive preliminary dataset), and be used as leverage to develop substantial proposals to external funding agencies.

The evaluation rubric for PRIME applications is available here.

The Grants and Contracts Office will be facilitating the publicity, proposal submission and award management process. A review committee will review all submitted proposals.

See associated Northern PRIME guidelines for information regarding submission.

See FAQs for more information.

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.”

PRIME project offers hope to "walk again"

After falling 12 feet onto her back on bare concrete, while working on her parents’ farm, Emily DeVooght was told she may never walk again. Or run. Or ride her horse. Or work (much) on the farm.  She had crushed her T12 vertebrae, and was, according to her doctors, a paraplegic.

That news didn’t sit with her well. Nor did her physical therapist accept it.

Kim Spranger, a PT with UP Rehab Services in Marquette, was familiar with a product called SpeedMaker TM, used to help injured athletes regain muscle strength and flexibility, or to help train healthy athletes for increased performance. The original device—a harness over the chest and waist with straps that go around the thighs to cultivate resistance — can be modified for use in clinical settings. In this new version, dubbed NewGait TM by its creators, additional bands extend from the straps just below the knees to straps on the feet, which, according to the company, offers “assistance to both hip flexion and dorsiflexion (muscles), allowing for increased stride length and stride frequency.” The important point is that NewGait TM allowed DeVooght to overcome the physical limitations imposed by her injury.

“The first time I put it on I gained so much confidence, like I was in control of my body again… It has helped me tremendously,” she said, a quote captured in a promotional video published by SpeedMaker at speedmakerathletics.com/newgait.

In just four weeks, DeVooght had taken her first steps, with assistance from the device. In time, she is expected to enjoy a full recovery, which means she’ll be back to work on farm, among other things.  

“Even for me, I just knew it was going to make a difference but I had no idea to what level,” Spranger said.

Randall Jensen, professor of Exercise Science at NMU, said traumatic injury is not the only potential circumstance for new therapies to utilize NewGait TM. Working with students and groups of NMU athletes, Jensen conducted a study helping to prove efficacy of the SpeedMaker TM device in athletic therapy in 2015. The project was funded by NMU’s internal PRIME fund (Progressive Research and Innovative mutual Exploration). Now he’s partnering with colleague Sarah Clarke, assistant professor of Exercise Science at NMU, and physical therapists in the Gwinn/Marquette area to gather data on how NewGait TM can help patients experiencing muscle weakness or functionality problems due to diseases such as Multiple Sclerosis.

The collaborative studies will examine the efficacy of this modified device when utilized in clinical applications to improve an individual’s gait, muscle strength and functional capacity. In addition to DeVooght’s promising story, PTs have noted anecdotal evidence of success in clinical settings among MS and other patients. NewGait TM creators claim on the website the device has potential to improve gait, balance and core stabilization, addressing physical challenges related to MS, traumatic brain injuries, amputations, ankle fractures, paralysis, knee replacements, strokes, lower back injuries, hemiplegia, osteoarthritis of the knees and hip replacements. Jensen and his collaborators aim to gather data to support these claims.

Additionally, Jensen and Clarke will extend the impact of this practice by providing in-service education for physical therapists in the Upper Peninsula (UP) region. This in-service education will present data on the efficacy of the device in addition to instruction on fitting and use, particularly for patients with neurological motor deficits. The SpeedMaker TM device has already been tested among athletes, and now investigators will focus on the NewGait TM version.

Spranger of UP Rehab noted the device modifies gait to improve flex movements via motor learning changes. These changes occur when the body moves through a specific movement pattern that may induce muscle memory. Long-term muscle memory happens when a movement is repeated many times, eventually allowing it to occur without conscious effort. Muscle memory may also mean that less volitional muscle force needs to be developed. An acute case study conducted by UP Rehab on an MS patient reported using the NewGaitTM device during a six-week rehabilitation program led to improvements in walking gait technique and performance. These improvements were demonstrated via increases in stride length, decreased time to walk 50 meters and increases in the ability to walk for distance.

Clarke and other team members are seeking funds to continue to gather evidence regarding efficacy of SpeedMaker TM and NewGait TM, which are being used increasingly with success by therapists in the Gwinn/Marquette area. Additionally they hope to continue training therapists in the wider UP region on the use of the device via in-service education. Such training will allow for enhanced delivery of care across the UP region and the potential for improving quality of life of patients with MS and, potentially, other neuromuscular conditions.

 

The next application deadline for the second round of Northern PRIME Fund support is July 20, 2018.