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Seeking answers in a molecular maze — II

 Image C shows a composite image of each color. This image was obtained using confocal microscopy.

One ongoing project in Dr. Sliwinski’s lab is to continue tracking soil archaea using DNA fingerprinting.

“In addition to my work, other labs around the world have found DNA evidence of archaea in the soil. They are on every continent and in every soil tested,” he says. “Part of what now needs to get done is an accounting of which species of archaea are where, over space and over time.”

He has created a modified version of the DNA fingerprinting technique that he developed in graduate school to separate and differentiate the DNA sequences of different groups of soil archaea.

In testing this new DNA fingerprinting technique with soil samples from an Iowa prairie, one of Dr. Sliwinski’s undergraduate students discovered that a wide range of Thaumarchaeota species inhabit Iowa soil.

For a recent publication in the journal Archaea, Dr. Sliwinski returned to the same temperate forest sites in Wisconsin where he previously studied soil archaea ecology as a graduate student. “I wanted to know whether the community of archaea stays the same or does it change over time,” he explains. “Is it a dynamic community, or is it the same species dominating the area?”

He collected samples in 2001 and 2010–2012 from several plots at two collection sites. In order to compare archaeal communities on a variety of spatial scales, he collected soil samples from spots that were only centimeters apart in the same plots, and collected samples at sites which are kilometers away from each other.  He then isolated DNA from the soil samples and used a molecular biology tool called the polymerase chain reaction (PCR) to make millions of copies of archaeal DNA sequences recovered from the samples.

Dr. Sliwinski then applied his new method of DNA analysis to those sequences. This allowed him to distinguish broad groups of archaea in the soil while simultaneously differentiating similar DNA sequences of more closely related archaea.

With this method he was able to more finely resolve the diversity of archaea soil communities from the Wisconsin study sites over time and on different spatial levels. “What we found was that soil archaea community composition is patchy–the species changed in some patches while in others they remained the same,” Dr. Sliwinski says. “Depending on spatial scale, different species of archaea may be the dominant community members.”

The results also showed that community composition fluctuated over time at each plot.

In the future, Dr. Sliwinski plans to analyze archaeal DNA in soil samples that he has collected from across the country, from Maine to California, and examine whether or not there is a difference in the archaeal communities in soil samples from different states.

“If you just sample enough soil, see what’s there, you might find an outlier — a community where archaea are growing that are different from the archaea that are more cosmopolitan,” he says.

“You might find a little niche of some very interesting species, and those might be the ones that grow easily in the lab. That would be a huge discovery for an undergraduate,” he adds. “If you can get a new species to grow in the lab, you can learn more about them. Then by comparing genomic sequences, you can learn more about the ones that don’t grow in the lab.”

Dr. Sliwinski and his research students have already begun work on culturing soil archaea in the laboratory. This is a project that would typically come first in more traditional microbiology labs. “Historically, new species were discovered by first growing them in the lab, but in the entire history of microbiology, only a tiny fraction of microbes have been successfully cultured,” he says. “Molecular biology has turned it around backwards; you now find environmental DNA that suggests a novel microbe exists in a sample. Then you pick and choose which samples have species you want to study.” 

 Currently, there are only a few types of soil archaea which have been grown successfully in laboratories, says Dr. Sliwinski.

He and his student are currently working to develop an inorganic, silica-based solid matrix with which to fill the petri dishes that they will use in their attempts to cultivate archaea in the lab. This design is distinct from the organic agar gels typically used to grow bacteria and other microorganisms in a laboratory setting.

“Nobody knows why the majority of soil archaea aren’t growing in petri dishes on standard media. One idea is that petri dishes in lab can be a toxic environment. So sugar is great, but if too much sugar is present it might be poisonous to microbes that are adapted to living in a low-sugar environment such as soil,” Dr. Sliwinski explains.

Once the silica matrix petri dishes with growth medium are ready to use, Dr. Sliwinski and his student will then add soil slurries from their samples, allow the microorganisms in the soil slurries to grow on the matrix, and then extract the DNA and test for archaea using PCR. This PCR test will confirm if they are successful in growing soil archaea in the lab.

In addition to his work on archaea and plants, Dr. Sliwinski has found another interesting biological question to investigate using the tools of molecular biology. In the summer of 2016, Dr. Sliwinski and a member of his undergraduate research team joined a project with researchers from the University of Iowa’s Carver College of Medicine which focused on Ebola infections. Infection with Ebola virus causes hemorrhagic fever in humans and has had a high mortality rate during recent epidemics in Africa.

This research was conducted as a part of the FUTURE in Biomedicine Program at UI, which is designed to encourage the growth and success of talented undergraduate researchers and to promote collaborations between faculty at primarily undergraduate colleges and universities in Iowa and researchers at the Carver College of Medicine. The objective of their project was to examine whether the virus could have been transmitted through contact with the skin of infected individuals during the 2013–2015 Ebola epidemic in West Africa.

Dr. Sliwinski and his student approached this question by studying which cells in the skin are actually infected by the virus. In one set of experiments they infected donated human skin samples from surgeries with a genetically-modified vesicular stomatitis virus (foot and mouth disease) and tracked the infection over time. This virus was engineered to express Ebola glycoprotein in order to model with a safer virus to understand how Ebola infects human cells. The glycoprotein is a molecule on the virus which is required for entry into human cells. The modified virus was also designed to express a green fluorescent protein, a molecule used to track the virus during examination of infected skin samples under fluorescent microscopes. These experiments demonstrated that the model virus could infect cells in human skin.

Next, using immunohistochemistry–a method which uses antibodies tagged with fluorescent probes to label specific molecules and cells in tissue samples — and confocal microscopy to examine the samples, Dr. Sliwinski and his student explored further to determine which skin layers and cell types in the samples were actually infected by the modified virus. With these experiments they showed that like Ebola, the model virus expressing Ebola glycoprotein infected both the epidermal and dermal layers of the skin samples. They identified epidermal keratinocytes as one cell type which was infected by the model virus. This work also showed that an important type of immune cell in the skin called Langerhans cells were not infected.

In separate experiments using an in vitro human skin dermis model made from fibroblast cells, keratinocytes, and a dermal equivalent substance, Dr. Sliwinski and his student found that in the dermis only fibroblasts were infected by the model Ebola virus. Together, these findings increase knowledge of which cells in the skin can be infected by Ebola virus and may ultimately help to reveal if Ebola transmission in humans can occur via the skin.

Dr. Sliwinski says some of the interesting questions to ask next include how the virus moves through the cells and layers of the skin. He also says that because his work was done with a model system, further study is necessary to better determine how actual Ebola infection works in the skin of living animals.

Dr. Sliwinski says that what he appreciates most about his position at UNI is this ability to work on the broad range of research questions that he finds interesting. “As a scientist, I’m in a place where I can literally study any molecular biology question,” he adds. “Over my time at UNI, I’ve allowed my research program to expand into three phases: we study archaea, we study plant genes, and we study Ebola.”

Mir Ashfaquzzaman, UNI STEM Graduate Assistant
Posted: 03-09-17

Seeking answers in a molecular maze — I

Dr. Marek K. Sliwinski, Associate Professor, Biology

Dr. Marek K. Sliwinski, an associate professor of biology at the University of Northern Iowa, believes “it is an exciting time to be a molecular biologist.”
“The progress made by the scientific community in only the past few decades has revolutionized biology,” he says.
“Molecular biology provides the most interesting answers to biological questions,” he adds. “So, research students in my lab design experiments at the level of DNA and proteins.”
His parents, immigrants to the United States from Poland, wanted him to pursue higher studies, and then a career, in medicine. In his early years as an undergraduate at the University of California, San Diego, he had psychology as major and was taking biology and chemistry classes, in preparation for medical school, with a career in psychiatry in mind.
His interests began to change after volunteering in a secure psychiatric hospital ward and, for a time, he considered pursuing a more exciting career in psychology as an FBI criminal profiler of serial killers.
However, he changed his mind after an undergraduate research project with Dr. Niko Christenfeld in social psychology. “Dr. Christenfeld left a lasting impression on me. He would chase any topics that he found interesting,” he recounts. “Even today, Dr. Christenfeld describes his research program as ‘comprising multiple, changing, only-partly-overlapping areas’ on his faculty profile (”
“As undergraduates in his Introduction to Social Psychology course, we all wanted to be like him when we grew up; I began exploring a career as a scientist,” he adds.
Eventually, through his other coursework Dr. Sliwinski became interested in the explanatory power of biological research.
“I remember taking a course in molecular biology and being awed by the fact that changes inside cells could be traced directly to changes in phenotypes such as behavior,” he recalls. “In biology–at least at the molecular level–it looked like you could do all the controls necessary to prove something. In a social psychology experiment, it wasn’t always possible to manipulate all the variables.”
“I realized that there was an intense satisfaction in discovering cause and effect,” he adds. “I thought, whatever my job, I would be happy as long as it was possible to get that feeling of satisfaction by discovering something new.”
The best tool for “cracking open causality” in different questions, Dr. Sliwinski felt, was molecular biology. So, he began his research career in biology as an undergraduate researcher with Dr. Milton Saier. He worked on a bioinformatics project analyzing the genomes of microorganisms in order to study transport proteins.
“At the time, the first genome sequences were being published, so the possibilities seemed endless,” he says. “There were so many genes with unknown functions that even after you solved one puzzle by linking a gene to a phenotype, you could do it over and over and over again.”
This work led to his inclusion as an author in multiple publications as an undergraduate.
After graduating from UC, San Diego, Dr. Sliwinski left the West Coast for the Midwest and enrolled in the Ph.D. program in Plant Pathology at the University of Wisconsin – Madison.
“I graduated as a double major in Psychology and Microbiology with a minor in Philosophy, so on paper, my interests were obviously diverse. I wanted a program where my background was an asset,” he says. “I found a discipline that allowed me to work both inside at the lab bench and outside collecting samples in the sunshine. The Plant Pathology program at UW Madison was a perfect fit.”
Though as a Ph.D. student he was in a department which studied plant diseases, Dr. Sliwinski did his research on healthy plants.
“I studied healthy plants in their native environment, which is soil teeming with a healthy community of microbes,” he says. “I was looking for ways to characterize the microbial community living on roots with molecular techniques such as DNA fingerprinting. I was interested in a particular group of microbes called the archaea, which had only recently been discovered in soil.”
Archaea comprise one of three domains in the modern taxonomic ranking of cellular life. A domain is the broadest classification of organisms in this system. These are a group of prokaryotic microorganisms similar in some ways to bacteria in terms of size and structure, but vastly different in many other biochemical, genetic, physiological, and evolutionary aspects.
One of Dr. Sliwinski’s published projects from graduate school described a new way of using DNA fingerprinting to characterize in the rhizosphere a specific group of archaea called Thaumarchaeota.
The rhizosphere is the space around roots in which plants can influence the biochemistry of the soil and where complex interactions take place between plants and the microorganisms living on and around their roots.
This new DNA fingerprinting method allowed him to differentiate types of archaea present in samples from the rhizosphere based on differences in the DNA sequences of an evolutionarily-conserved gene in archaea.
Dr. Sliwinski then published a study in which he used his molecular technique to compare the types of Thaumarchaeota found living in the rhizosphere to those in soil outside of this dynamic zone of plant-microbe interactions.
This work showed that Thaumarchaeota associated with a variety of land plants growing in the temperate habitat of Wisconsin soil. “The archaea were found on every plant sampled, from mosses to grasses and trees,” he says.
He also showed that the composition of the Thaumarchaeota community on plant roots was distinct, and that the rhizosphere was colonized by a greater diversity of Thaumarchaeota than the surrounding bulk soil.
After his Ph.D., Dr. Sliwinski accepted a postdoctoral position in the Department of Botany at Madison. “I was looking for a lab where I could add to what I had learned in graduate school but in a different model system. I wanted to manipulate genes to see how evolution worked at the level of DNA,” he says. “Luckily, I found a number of labs at Madison which were doing just that using organisms such as flies, maize, and mustards.”
Dr. Sliwinski worked with plants in the mustard family, studying how genes control the differences in flower placement between plant species and how these differences reflect the evolutionary relationships between certain plant species. He also published his work on the transport system within plant cells.
“This was a very productive time in my career. As a postdoc, you feel empowered because you’ve been trained as a scientist by completing graduate school, and now you get to just do science without all the other commitments that come with a faculty position,” he recalls. “It’s like burning the candle at both ends. You practically live in the lab, and you generate tons of data.”
Since beginning his research program at UNI in 2008, Dr. Sliwinski has continued working on the questions that interested him as a graduate student and as a postdoc.
“I’ve set up my lab to be able to do molecular techniques–that is where my undergraduates start their research projects,” he says. “If they can master a molecular technique or even develop a new one, then they can apply it to any organism.”
To be continued

Mir Ashfaquzzaman, UNI STEM Graduate Assistant
Posted: 03-06-17

Hoping to make the world a better place

Jake Parks, left, with friends at a UNI Panthers game

Jake Parks enjoys learning how the physical world works; he has perpetually been in awe about the infinitude of the universe and its intricacy. So, the decision to major in physics was not difficult for him to make.

The decision to enroll in the University of Northern Iowa was not difficult, either; he found the sense of community here overwhelming.

“People here, from students to faculty, truly care about you,” Jake says. “It makes the intimidating experiences of college much more manageable.”

In fact, the experience has been awesome for him.

“I have met a lot of really great people, learned some really important things both in and outside the classroom, and made some close friends within a very short time of my stay here,” he says. “I hope to keep doing so.”

The undergraduate coursework has been challenging but fulfilling.

“I has been hard majoring in physics,” Jake admits. “However, when a tough subject finally clicks for me, and I can explain it to others and apply it, it is so fulfilling.”

Modern Physics has been his favorite class so far.

“It is an entirely different way of looking at physics, making me rethink everything that I thought I knew,” he says. “It is difficult but cool.”

Modern Physics has also been part of a unique experience for Jake.

“In one of the Modern Physics labs, we performed a famous experiment where we determined the charge-to-mass ratio of an electron,” he recalls. “It was so cool because the original experiment won its creators the Nobel Prize, and to think that we got to replicate their work in our lab was sweet, in a really nerdy way.”

Jake is a serious student, alright. “I work for the physics department as a tutor for Physics 1 and 2 students,” he says. “It is a great way for me to stay sharp on my basic physics knowledge while making some extra spending/saving money.”

But he is no nerd. “I love to sing, laugh, and perform; so, I am part of the Men’s Glee Club here at UNI,” he says. “I also love to play basketball at the WRC [Wellness and Recreation Center] with friends.”

Jake also volunteers for the Office of Admissions as a Student Admissions Ambassador.

Student Admissions Ambassadors showcase UNI to “prospective and admitted students,” he explains. “We also perform community service events such as volunteering at the food bank and cleaning up highways.”

He has recently signed up as a STEM Ambassador, too.

“The physics department has been very good to me and has given me a lot of opportunities so I thought becoming a STEM ambassador would be a good way to give back,” he says.

After graduating from UNI, Jake plans to get a degree in mechanical engineering from the University of Iowa before starting to work full time.

Jake believes STEM subjects are both “challenging and fulfilling, and can be used to change the world for the better.

“Whether it is an engineer who finds a way to manufacture something more efficiently, or an actuary who saves a family money with an insurance policy, there is always a way that STEM majors are making the world a better place,” he explains.

So, his advice for middle and high school students interested in STEM majors is: “Go for it.”

Mir Ashfaquzzaman, UNI STEM Graduate Assistant
Posted: 02-28-17

MVMs: Magic in math classroom

Dr. Adam Feldhaus, an assistant professor of mathematics at the University of Northern Iowa, has always felt that manipulative technology for mathematics education is currently way too expensive for most elementary schools.
“Classroom sets of physical manipulatives are expensive while most computer-based virtual manipulatives are either non-intuitive or based on dated technology or locked behind publishing deals or some combination thereof,” he says.
These manipulatives are a powerful learning tool for students to learn mathematics, especially at the elementary level, he adds.
The challenge, thus, is to develop a technology that is not just affordable but also engaging and accessible for elementary students.
That is exactly what Dr. Feldhaus and Dr. Sarah Diesburg, an assistant professor of computer science at UNI, have been working on for the past couple of years.
“We wanted to create a modern manipulative platform that relies on inputs that most students are familiar with (i.e. touchscreens), can be widely available, and are cost-effective for schools on a limited budget,” Dr. Feldhaus says.
It all began on the sidelines of a university program, with Dr. Feldhaus sharing his thoughts on manipulative technology for elementary mathematics with Dr. Diesburg.
This initial exchange of ideas led to a series of brainstorming sessions, eventually crystalizing into a grant proposal towards developing Motion Virtual Manipulatives (MVMs). The project was approved in 2015.
Dr. Diesburg and Dr. Feldhaus say that the MVMs will not just be an effective tool for teaching core mathematical concepts in the elementary classroom but also potentially reach students who do not respond to typical mathematics instruction.
The manipulatives will function in an environment built on Ubi Interactive, a hardware plus software solution that turns any surface into a touch screen.
“Our technology can turn any blank wall into a virtual touch screen that functions similarly to the way modern touch screens work (similar to an iPad),” explains Dr. Diesburg. “We have built a suite of mathematics manipulatives into that technology, as well as a method to ‘play back’ specific actions for evaluation.”
“We would like to learn if our platform is comparable to current technology solutions as well as how students use our touch-screen user interface,” she says.
Moreover, a data-collection tool has been built in that will allow the researchers to “improve the software and answer questions about the mathematical thinking of the students,” she adds.
Dr. Feldhaus says the MVMs could be used daily in the elementary school classroom.
“This toolset is highly expandable, and we would like to work to create something that is useful for multiple concepts in the mathematics classroom,” he adds.
Although the project began with the objective of developing an affordable manipulative technology for elementary mathematics classroom, the two UNI professors plan to continually work on the manipulatives, and enhance and expand their utility.
“First, we would like to grow our suite of available manipulatives to be something more complete for use in K-8 classrooms,” says Dr. Feldhaus. “Beyond that, we have been approached by other education researchers who see applications of our software to high school math, and also to other subjects such as literacy, science, and computer programming.”
The involvement of undergraduate students has been an important aspect of the research project.
“It has been great!” Dr. Diesburg says. “Undergraduate researchers built the software for our research and helped us throughout the entire design process.”
On one occasion at least, the help may not have been intended as such.
“We ran into the perfect training tool for our platform by accident,” she recalls. “We were working on developing complex training exercises when one of us put on the game Angry Birds for a break. It turns out this game is a fabulous way to train students how to point, drag and perform other gestures in our environment!”
The experience has also been inspirational for many undergraduate students.
“After working with us, many have decided that they would like to pursue graduate school,” Dr. Feldhaus says. “One specific undergraduate alumni, Cole Boudreau, is now successfully enrolled in graduate school at the University of Toronto.”

Posted: 02-08-17

For the love of physics

When he was a little boy, Byron Fritch would have a lot of questions in his mind about everyday occurrences: How does a bird fly? How does a suspension bridge bear the weight of so many cars? Then, as he grew older, he found out that physics and mathematics had answers to most of these questions and more. He has known since that physics is what he wants to study. So, once he completed high school, the question was not what but where to study.
Byron chose the University of Northern Iowa, among other reasons, for the size of its campus. “The campus is just big enough to meet new people every day, if you so desired, but small enough to get to know your professors,” he says.
Knowing the professors has been a part of his “wonderful experience” at UNI. “The professors here care about you as an individual,” he says. “I can walk into their office and ask questions if I don’t understand something in class.”
That helps because undergraduate coursework is difficult.
“If a non-physics major were to take an upper-level physics class, they would probably say that the coursework is pretty challenging,” he says.
However, difficulty is something Byron looks forward to. “I like being challenged and the physics courses are a perfect combination for me,” he adds.
He singles out Dr. Paul Shand’s Modern Physics class as his most favorite. “Modern Physics essentially covers every major physics discovery in the 20th century,” he says.
“The topics range from Einstein’s Theory of Relativity to the Schrodinger Equation,” he adds. “I find these topics so interesting because it corrects some of the huge failures in Newtonian physics.”
Another high point has been the research with nanocellulose aerogel under the supervision of Dr. Tim Kidd.
“This material is very lightweight with an extremely low density,” Byron explains. “Being composed of nanocellulose allows the material to be relatively non-reactive but safe for humans.”
“We are currently in the process of trying to use this material to break down water into hydrogen and oxygen,” he continues. “If we find that this works, we can then collect hydrogen and use it as a renewable fuel.”
Byron wants to go on and get a Ph.D. in physics. He also wants to raise awareness among the general populace about the need for scientific research.
“We are at a critical point,” he says. “The need for scientific research is being increasingly questioned in society. It is important that people understand the positive impacts scientific research has had on humanity and do not devalue and deny results that have been repeatedly proved.”
Byron has recently taken interest in long-distance running.
“Running is not something that I did in high school,” he admits. “But I have run a half and a full marathon since starting college. I am not signed up for any right now but will surely be finishing more of those in the future.”
Besides being the vice-president of the UNI Physics Club, Byron is also a Student Admissions Ambassador.
“This allows me to connect with high school students interested to enroll in UNI,” he says. “I share with these prospective students the story of my college life and the great things that UNI has to offer.”
To prospective STEM students, his advice is: “Don’t be in it for the job outlook or the possible salary after graduation. Decide to be a STEM major because you enjoy learning about it and how it applies to the world around you.”
“Classes are going to be difficult,” he warns. “Do not be afraid to reach out to classmates and professors for help when you need it.”
“Just because I say it will be difficult does not mean you should shy away from it,” he adds. “The most important thing is to do something that you enjoy.” 

Posted: 01-30-17


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