BTI-NAIST Exchange Marks 15 Years

BTI-NAIST Exchange Marks 15 Years

Tim Montgomery

Following a visit to Minnesota by three Japanese graduate students from the Nara Institute of Science and Technology (NAIST), a group of four Minnesota graduate students from the BioTechnology Institute (BTI) visited Japan in mid-October. Chris Flynn, Grayson Wawrzyn, Jessica Eichmiller and Maria Rebolleda-Gomez were graciously hosted by their NAIST counterparts on a 3-week trip that completed the 15th exchange in a program organized by former BTI Director, Ken Valentas in 1996.

The 15th BTI-NAIST exchange featured a symposium on progress in microbial biotechnology, enzyme engineering and systems biology – and a five-year renewal of the agreement that created the program.

Since its conception, the exchange has successfully connected graduate students from one institution to research groups in the other based on common interests with the intent of learning new skills and techniques. Students from the host laboratory also become cultural mentors for the visitors. Lasting professional and personal bonds are forged in the process, sometimes resulting in collaborative research initiatives.

“I think that my favorite part of Japan,” commented Grayson Wawrzyn, “was learning to be part of a culture so strikingly different from our own.”

Wawrzyn, a graduate student researcher in the lab of Claudia Schmidt-Dannert, was assigned to Takashi Hashimoto’s laboratory and worked with one of his students to help characterize some of the enzymes involved in nicotine biosynthesis in tobacco plants.

Other members of the BTI group participated in equally compelling genomic research projects. Eichmiller studied novel intracellular proline transporters and tested the stress tolerance of mutant yeast strains in the lab of Hiroshi Takagi. Rebolleda-Gomez was introduced to systems biology in the study of bacterial genomics while in the lab of Hirotada Mori. And Flynn learned how cells repair damaged DNA while in the Maki lab.

For Japanese lab members who are required to present their lab work in English each week, working with the exchange group from BTI was an opportunity to practice speaking scientific English.

Living and working together, lab groups also had fun together. Several of the Japanese labs had their own baseball teams, and the last week of the exchange featured ‘lab Olympics day’ where Japanese lab members dressed in super hero outfits competed for fun in a series of relay races.

In addition to experiencing traditional Japanese foods like sushi and okinomiyaki, BTI exchange members also experienced the cultural environment in trips to local shrines around Nara and the old hilltop estates in Arishiyama near Kyoto. The highlight of their cultural experience was a 4-day holiday break that brought most of the group to Tokyo before members went their separate ways. Wawrzyn and Rebolleda-Gomez explored Tokyo further while Eichmiller visited a Japanese friend and Flynn and his wife toured a world heritage shrine and marveled at the beauty of the ponds and cascading waterfalls of Chuzenji in Nikko.

“The hospitality of our hosts was superb,” concluded Flynn. “Everyone was super friendly.”

Added Eichmiller, “an unexpected benefit of the trip to Japan is that I can better relate to my Japanese colleagues at the University.”

A Rewarding Experience in Japan

A Rewarding Experience in Japan

by Tim Montgomery

Janice Frias, Katherine Volzing, Chad Satori and Josh Ochocki visited Japan this past November as part of the BioTechnology Institute’s ongoing exchange program with the Nara Institute of Science and Technology (NAIST). They travelled to Japan with returning exchange students from NAIST whom they had previously hosted at BTI.

Exciting cultural experiences complemented the students’ lab work at NAIST, beginning with an informal welcome party where dried squid “candy” was served. The BTI group stayed on-campus in guest houses, were chaperoned to various tourist and cultural attractions and experienced new food and pastimes – from a hearty noodle meal of hiroshimayaki to a traditional foot bath where fish nibbled the dirt particles off their toes.

Katherine Volzing visited the ginza, a high style shopping district in Tokyo, and was invited to breakfast with a family in the Tsukiji Fish Market where they served her raw tuna on a stick.

“It looked yucky,” she confessed, “but it was the best thing I ever ate.”

Cultural excursions included time spent at the Todai-ji Temple in Nara; the Kiyomizu Temple, Sanjeusangen-do Temple Garden and Ginkaku-ji Gardens in Kyoto; the Floating Torii at Miyajima; Himeji Castle, and aboard the 200 mph Shinkansen or “bullet train” while in transit. But the exchange group from BTI also accomplished quite a bit in their lab work.

“Professor Takagi said we were the best working group ever,” exclaimed Chad Satori proudly. Satori was excited to work with cell transfections and binding assays in the Sato lab in a change of pace from his mostly analytical work under Edgar Arriaga at BTI.

Janice Frias, who has worked to synthesize biohydrocarbons in the Wackett lab at BTI, was assigned to the lab of NAIST exchange coordinator Hiroshi Takagi, Professor of Cell Biotechnology specializing in applied microbiology and protein engineering. Frias assisted in Takagi’s work with stress tolerance in yeast as an element in improving industrial fermentation in the production of bioethanol.

Frias, Satori and the other members of the exchange group from BTI each found their assignments while at NAIST to be rewarding. Distefano lab member Josh Ochocki was introduced to the work of Professor Kinichi Nakashima exploring neuron stem cells and how they develop into different types of brain cells. And Katherine Volzing found her experience in the lab of Ko Kato examining differentiation in gene expression in stem cells extracted from mice to be a change of pace from her statistical and computational modeling in the Kaznessis lab at BTI. All were impressed with the professionalism as well as the aggressive English requirements of their Japanese counterparts.

“They’re required to put together and present their lab work and plate results in English each week,” explained Janice Frias in amazement.

“The labs were impeccably clean,” concluded Chad Satori. “And everyone was very professional and kind.”

Managing Microbes in Brazil’s Agricultural South

BTI Director travels to Brazil to mentor students researching bioremediation of agriculture chemicals.

BY ALLISON KRONBERG

BTI Director Michael Sadowsky understands both French and Spanish, but hardly a word of Portuguese. Yet this summer he launched a two-year collaborative research initiative in Ponta Grossa, Brazil, as part of the Brazilian Government’s Science Without Borders Project.

Sponsored by Brazilian National Council for Scientific and Technological Development (CNPQ), Brazil’s equivalent of the National Science Foundation, the program allows Sadowsky to share his expertise in microbiology and bioremediation with colleagues and students in this Southern Brazilian industrial and agricultural center.

In Brazil, Sadowsky works alongside his long-time colleague Marcos Pileggi, a professor of biology and evolution at the Universidade Estadual de Ponta Grossa. Along with Pileggi’s students, the pair will conduct research on bacterial pesticide degradation that could help protect Brazil’s environment and save money for local farmers and pesticide manufacturers.

According to Sadowsky, Brazilian farmers receive concentrated chemicals from pesticide and herbicide companies, often in five-gallon buckets. Farmers then transfer the liquid to large tanks and add water to dilute the chemicals before spraying.

But not all of the pesticide is used and the toxic residue can’t be thrown away or dumped in the environment. Some manufactures provide a pick-up service for the remaining liquid, and store it in large tanks where it degrades over time. But if the biodegradation is incomplete, they burn it — and burning liquid is very expensive.

With Sadowsky’s help, Pileggi and his lab of 10 undergraduate and graduate students hope to identify bacteria that will naturally and efficiently degrade the concentrated liquid waste. During Sadowsky’s first 10-day trip, the group created a research plan and took initial steps toward isolating bacteria capable of degrading leftover pesticides and herbicides.

“Bacteria are the most versatile tool we have for degrading compounds in the environment,” Sadowsky said. “We are trying to find more environmentally friendly ways of doing things, and very often that involves old-fashioned microbiology.”

The team put the chemicals in a tank and added different types of bacteria to see which microbes would survive and grow using the pesticides and herbicides as a food source. The technique (called enrichment) was developed in the late 1800s and is still considered the most effective way to find bacteria that can breakdown chemical compounds.

Sadowsky, who also serves as co-Director of MnDRIVE’s microbial bioremediation initiative, began international scientific work in the 80s, and he has visited Brazil a few times before, but this is his first fully funded research trip abroad.

“Brazil is a good place to perform the research,” Sadowsky said, “because some of the herbicides and pesticides the lab is now studying have been banned in the United States.”

The seed for the collaboration was planted almost five years ago when Pileggi came to Minnesota to research pesticide degradation with Sadowsky’s lab. Now, upon Pillegi’s request, the two professors have swapped roles.

“This is a great experience for me,” Sadowsky said. “Hopefully we’ll develop some new technologies out of this research. But that’s going to take some time, and we’ll have to see if it really comes to fruition.”

Sadowsky’s trip has a strong educational focus as well, and supports Science Without Border’s goal of increasing the number of Brazilian Ph.D.’s  through international scientific research and collaboration.

“Mike is helping me organize my Environmental Microbiology Laboratory with more focus and efficiency,” Pileggi said. “He pushed us a lot, and we enjoyed it.”

Students from the Universidade Estadual de Ponta Grossa, can continue their training at institutions like the Federal University system, which grants Ph.D.’s.

Sadowsky will travel to Brazil six times over the next two years. Once the project is complete, he hopes to invite some of the Brazilian students to the United States where they can receive advanced training in new and emerging technologies.

Primordial Peptides

UMN researcher Burckhard Seelig wins the prestigious Simons Investigator Award and joins the Collaboration on the Origins of Life

University of Minnesota researcher Burckhard Seelig (BMBB, BTI) has a longstanding interest in how the earliest forms of life may have come into existence. This year, his efforts were rewarded with a 5-year, one million dollar grant from the New York-based Simons Collaboration on the Origins of Life. One of two scientists invited to join the Collaboration in 2015, Seelig is part of a 21-member multi-disciplinary team looking at potential scenarios for how life could have started from non-biological matter, and the planetary conditions that could have supported the origin of life.

The goal of this Simons Collaboration is to fund an interactive community of investigators using systems reaching across disciplines, technologies, and institutions to advance our understanding of the processes which led to the emergence of life.

“This collaboration is a unique opportunity,” said Seelig. “There are a number of physicists, chemists, and biochemists, like me, but there are also planetary scientists and geobiologists. So, based on our knowledge of early planetary conditions, you can ask what kind of chemistry could have existed and talk to the chemist to find out what kind of reactions could have occurred. Then you can talk to the biochemists to see what you could make from those chemicals.”

In a field where much of the work is dominated by hypotheses, Seelig works experimentally to investigate the missing link between early non-biological amino acids, building blocks for complex proteins, and the modern alphabet of 20 amino acids that make up life’s universal genetic code.

“Today’s genetic code uses 20 amino acids. It did not start with all 20 right away, that’s for sure, but which ones exactly and in what order? This subject has been mostly theoretical. In our lab, we can actually make proteins using likely earlier versions of the genetic code and we can test them,” explained Seelig.

Dialing back the clock, his lab will test ever smaller alphabets of amino acids for their ability to produce functional proteins necessary for the survival of protocells at the origin of life. “If you have an alphabet of only early amino acids, can you make proteins as functional as those we have today? Probably not. But you can see what functions they have and ask what minimum alphabet is necessary to make a functional folded protein. So far, we don’t know. That’s what we’re trying to investigate with this project,” said Seelig. “The further you go back in time,” says Seelig, “the noisier the picture gets because we have less and less reliable information. We will never be able to really tell how life began, but what we hope to do is come up with realistic scenarios about how parts of this process could have happened. In our case, it’s about proteins.”

The award will fund two postdoctoral researchers and help support basic research, providing a welcome balance for the lab’s ongoing applied research on the synthesis of designer enzymes for medical applications and use in the pharmaceutical industry.

Dr. Seelig is a faculty member in the College of Biological Sciences Department of Biochemistry, Molecular Biology and Biophysics and a member of the University of Minnesota BioTechnology Institue.

BTI Faculty Members Dan Knights and Kechun Zhang Named 2015-2017 McKnight Land-Grant Professors

Please join us in congratulating Assistant Professors Dan Knights and Kechun Zhang, who were among the eight recipients of the 2015-2017 McKnight Land-Grant Professorship. The award is designed to advance the careers of promising junior faculty members who demonstrate the potential to make significant contributions to their departments and disciplines.

Dan Knights (BTI/Computer Science & Engineering)
Trillions of bacteria live in our guts, protecting us from infection and aiding our digestion. An imbalance of these bacteria, called dysbiosis, may contribute to obesity, diabetes, cancer, Crohn’s, and many other diseases, yet each person’s bacterial diversity is so distinct that we cannot easily identify when a microbiome is “unhealthy.” In his research, Dan combines expertise in data mining and biology to advance detection and treatment of dysbiosis in obesity and autoimmune diseases.

Kechun Zhang (BTI/Chemical Engineering & Materials Science)
Transforming traditional chemical production into a green and sustainable future is a great challenge facing human society. The current biorefinery process utilizes food resources and is limited by the metabolic capability of natural microorganisms. To enhance the viability of biomanufacturing, Kechun is engineering a new metabolic pathway in industrial yeast for more efficient fermentation of value-added chemicals from lignocellulosic feedstocks such as corn stover, sugar beet pulp, and citrus peel.