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Seeking answers in a molecular maze — I

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

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