Dr. Kristy Kounovsky-Shafer, associate dean of the College of Arts and Sciences and professor in the department of chemistry at the University of Nebraska at Kearney (UNK), holds a doctorate in analytical chemistry and a bachelor’s degree in both chemistry and mathematics with a minor in biology. She received her doctorate from the University of Wisconsin–Madison, where she went on to work in the development of Nanocoding, a physical mapping platform that utilizes fluorescently stained single DNA molecules elongated in nanoslits and imaged with a fluorescent microscope to create a genetic barcode, determining its location in the genome.
While at UNK, Dr. Kounovsky-Shafer has been a part of the Institutional Development Award Program (IDeA) Networks of Biomedical Research Excellence (INBRE) since 2015, developing devices to elute and concentrate DNA. The devices are 3D printed to allow for rapid prototyping. DNA that is concentrated can be used for other genome analysis systems, such as Nanocoding and Optical Mapping.
Dr. Kounovsky-Shafer has experience in developing systems for genome analysis through the fabrication of devices such as soft lithography, e-beam lithography and 3D printing. She has also worked to test the devices using microscopy or blue light transilluminators and develop new methods to elute and concentrate DNA. She is currently developing a system to keep the DNA intact for sequencing or physical mapping platforms.
Q&A
Why are you interested in supporting national security?
I wanted to do what I could to contribute my services to the military, having a long history of family members serving. My dad was in the Air Force and was stationed in Thailand and the Philippines during the Vietnam War. One grandfather was a Marine in France in WWI, and another was in the Army Air Force, stationed in the Pacific during WWII. Although I did not formally serve in the military, I want to help in any way that I can. My background in developing devices could support national security objectives.
What challenges do you think you could help solve?
National security challenges tied to large DNA molecules are pathogen detection gaps, synthetic biology or bioengineering risks and genomic supply chain integrity, to name a few. With pathogen detection gaps, most sequencing systems use short reads to analyze DNA and struggle to capture large structural variations or engineered insertions and deletions.
Engineered organisms might hold large synthetic sections of DNA that might be missed with small read lengths. Detection of altered DNA that may affect the resilience, yield, or biosecurity of crops requires the use of large DNA molecules to identify these variations. In order to have longer reads, a method is needed to increase the DNA size before it is introduced into the sequencing system.
I was trained as an Analytical Chemist in developing devices for DNA. In graduate school, the team I worked with developed a device to analyze DNA by elongating DNA, which was labeled at sequence-specific locations, in nanoslits. At the University of Nebraska at Kearney, I have been utilizing 3D printing to create devices that protect and concentrate large DNA molecules. I have been developing devices for DNA analysis for almost 20 years and can help work on problems that require these devices to be developed.
Read more about Dr. Kounovsky-Shafer’s research on DNA analysis:
What do you see in the next five to ten years in your space that you think is important for national security leaders to consider?
Developing genome analysis devices with longer DNA would aid in better detection or identification of engineered or naturally emerging pathogens. Additionally, it may help trace pathogens back to their source by identifying unusual sequence patterns or analyzing longer reads to detect unnatural constructs, which can identify DNA synthesized in labs or genome editing that might be missed with short reads. This is difficult, unless you have a method to protect the large DNA molecules, which is where my lab research comes in.
What are you working on now that excites you?
I received a National Institutes of Health grant a year ago to develop a method for eluting and concentrating large DNA molecules for genome analysis. We developed two different devices to help protect large DNA that can be used for sequencing or other platforms that need large DNA molecules. These longer DNA molecules will make assembly of sequencing easier, which will help identify larger variations associated with cancer, new pathogens, genome editing, etc. I am excited to see how my technology might be used in the future. I have been meeting with a company about what we are working on and how their technology and my technology may fit together.
Learn more about Dr. Kounovsky-Shafer via her UNK Bio.
