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.”

Departments

BioTechnology Institute

The BioTechnology Institute is the central University of Minnesota vehicle for coordinated research in the biological, chemical, and engineering aspects of biotechnology. more >>

Department of Bioproducts and Biosystems Engineering

The Department of Bioproducts and Biosystems Engineering was formed on July 1, 2006, from the merger of the former departments of “Bio-based Products” and “Biosystems and Agricultural Engineering.” The department focus is on discovery, development and application of renewable resources and sustainable technologies to meet society’s needs while enhancing the environment in Minnesota and beyond. more >>

Department of Biochemistry, Molecular Biology
and Biophysics – Microbial Biochemistry and Biotechnology Division

The department has equally strong interests in understanding the molecular mechanisms of metabolic diseases and cancer, developing novel strategies in biocatalysis and biotechnology, and advancing knowledge through structural biology and molecular biophysics. more >>

Department of Chemistry

The Department of Chemistry has graduate faculty specializing in interdisciplinary areas of chemical biology that include: bioanalytical and biomaterials chemistry, computational chemistry, design and synthesis, enzyme chemistry, structure and spectroscopy, and nucleic acids. more >>

Department of Chemical Engineering
and Materials Science

The Department of Chemical Engineering and Materials Science has a graduate focus on biotechnology and bioengineering research. more >>

Department of Medicinal Chemistry

The College of Pharmacy has a Medicinal Chemistry department and graduate program that is one of the top-rated in the country. This department consists of a diverse group of faculty members, graduate students and postdoctoral-fellows working at the interface of chemistry and biology and is home to the editorial office of the Journal of Medicinal Chemistry. more >>

Grant Programs

Cyanuric Acid – Melamine Biocatalysis Project:
Fundamental Science and Business Opportunities

PIs: Lawrence Wackett, Michael Sadowsky, Steve Heilmann

Emphasis has evolved from swimming pool clean-up to food safety. Progress includes development of an enzyme-based kit to test foods. more >>

Novel Bioderived Polyesters

PIs: Friedrich Srienc, Romas Kazlauskas

Genetically engineered bacterial polymerases to produce new polymers with a range of properties including molecular weight, conductivity, stability and biodegradability.

Biocatalytic Azide Incorporation
for Proteomics and Protein Labeling

PIs: Mark Distefano, Wei-Shou Hu, Claudia Schmidt-Dannert

Have shown that certain protein substrates can be labeled with azide in vivo using a mutant enzyme. Work continues to broaden the substrate by modifying the enzyme, and a high throughput assay has been developed to test the various substrates and mutant enzymes.

Hydrothermal Carbonization of Algae
and Application of “Synthetic Coal”

PIs: Kenneth Valentas, Marc von Keitz, Fred Schendel, Paul Lefebvre, Steve Heilmann

Treatment of algae at high temperature and pressure to create a synthetic coal-like product and a byproduct with potential for use as a fertilizer. more >>

Cloning and Characterization of an
Oat2 Transporter from Humans

PIs: Robert Brooker

The human Oat 2 gene (organic anion transporter) has been cloned and expressed in yeast.

Engineering Proteins and Cellular Biocatalysts for
Electrode Binding via High Throughput in vitro Selection

PIs: Burckhard Seelig, Jeffrey Gralnick, Daniel Bond

An E. Coli gene permitting E. Coli to bind to gold surfaces has been cloned and will be tested in another bacterium.

Diverting Fatty Acid Metabolism
to Make Liquid Fuels

PIs: Romas Kazlauskas, Lawrence Wackett

Have succeeded in mimicking the production of beta-keto thioesters of CoA by enzymatically producing N-acetyl cysteamine thioester with the goal of finding a late intermediate in the synthesis of long chain fatty acids and converting it to a long chain combustible product.

High Intensity Enzymatic Biocatalysis for
Direct Conversion of Solar Energy into Chemical Fuels

PIs: Ping Wang, William Tze

An explorative study of cofactor regeneration via solar power driven water electrolysis.

Engineered “Platelets” Linking Microbial
Electrochemistry to Redox Enzymes

PIs: Daniel Bond, Stephen Campbell

One enzyme has been purified and tested for binding potential.

Engineering a Designer Cellulolytic
Ethanol-Producing Microorganism

PIs: Wei-Shou Hu, Prodromos Daoutidis, Yiannis Kaznessis

Have discovered an anaerobe that can degrade cellulose and produce ethanol.

The Fight for Safer Food

The Fight for Safer Food

To confront the threat of persistent foodborne pathogens, Steve Bowden turns to novel techniques to understand and take down those threats.

By Kyle Wong

Nearly one in six Americans suffer from foodborne illnesses each year, according to the Centers for Disease Control and Prevention (CDC). Scientists like the University of Minnesota’s Steve Bowden are working to change that.

Standard food-safety processes like pasteurization, freezing, and fermentation kill foodborne pathogenic bacteria, but these pathogens evolve to survive. Through mutation and the acquisition of new genes, pathogens can cause outbreaks from unfamiliar sources such as fresh produce, spices, and peanut butter. Bowden, an assistant professor in the Department of Food Science and Nutrition and a member of the BioTechnology Institute, is developing strategies to eliminate new and persistent pathogens.

One common offender is Salmonella, a bacterial species that infects millions of Americans each year, leading to thousands of hospitalizations and hundreds of deaths. Bowden studies how Salmonella responds to stresses in the food environments where it thrives. He seeks to identify common genetic traits that enable Salmonella to survive and grow under varied conditions. Ultimately, he hopes to develop procedures that eliminate harmful bacteria from the food system. “We want to understand why certain outbreaks occur in specific types of food and if there is a correlation with the genes found in those specific types of bacteria,” says Bowden.

To target specific foodborne pathogens, Bowden’s lab engineers a type of virus called a bacteriophage that infects and then kills bacteria. But identifying phages that work is only half the battle. Because pathogens are so diverse, effective treatment requires the right combination of phages to remove all of the pathogen targets and ensure food safety. To make things more complicated, the food matrix can also affect the phage’s efficacy. One cocktail of phages might succeed on one food but fail to remove the same pathogen in another.

Nonetheless, the Food and Drug Administration (FDA) has approved some phage cocktails. They are entirely harmless to humans and assist in the control of foodborne pathogenic bacteria during food processing. Their potential use as a safe, natural method to improve food safety is garnering interest in the food industry. Still, further research is required to enhance their efficacy and improve manufacturing methods.

Despite these challenges, Bowden’s longstanding fascination with molecular biology and microbiology keeps him motivated: “I was surprised by how many foodborne illnesses there are. I want to make use of genome sequencing to try and control these pathogens. What’s interesting about molecular biology is how we can apply it to make the world safer.”

Bowden’s drive to understand foodborne pathogens couldn’t have come at a better time. Addressing global threats to food safety, such as climate change and antibiotic resistance, requires broad thinking and a flexible approach. Bowden brings a global perspective to his work. After earning his Ph.D. in biochemistry at the University of Cambridge, he worked as a postdoc in the United Kingdom and Japan. “I feel lucky to have been in so many labs and learn different perspectives,” he says. “It’s helped broaden my appreciation for different ways to do research.”

The experience helped prepare Bowden for his research at the University of Minnesota. “The drive to understand a problem and develop techniques to study that problem has kept me in academia,” he says. “I’m excited to see what direction it takes.”

Kyle Wong is a writing intern in the University of Minnesota Science Communications Lab, majoring in Microbiology. He can be reached at wong0511@umn.edu

A Micro Lens on a Macroscopic Question

A Micro Lens on a Macroscopic Question

A Q&A with PhD Candidate Anna Bennett
By Reed Grumann 

Anna Bennett, a PhD candidate working in Trinity Hamilton’s lab, collects and studies photosynthetic bacteria that live in the extreme conditions found in Yellowstone’s hot springs. Bennett characterizes these cyanobacteria and their environment, providing data to inform evolutionary models of photosynthesis on Earth. 

How did you end up at the University of Minnesota?

At the time I began the application process for graduate school, I was working at an Air Force base in Ohio. I was researching synthetic biology with E. coli, and I knew that I wanted to get outside more, which is why I was looking into applying for environmental microbiology labs. I was accepted to study at the University of Cincinnati in the Hamilton Lab when she made the decision to move to the University of Minnesota. I decided to move too. I was really excited about her work with hot springs and extreme microbes, so it was the only lab that I interviewed with.

What stuck out to you about these extremophiles as compared to others?

I think it’s really interesting that these bacteria can perform photosynthesis. A lot of people only consider plants and a few types of algae when they think about photosynthesis, but these bacteria can do it, too. In fact, they were the first in Earth’s history to do it, but we still don’t know much about them.

Our basic question is “What did early organisms that performed photosynthesis look like?” I work to develop a better understanding of the physiology and ecology of their modern relatives to inform those evolutionary questions. 

What are the implications of your research?

The data we collect on the physiology and ecology of these cyanobacteria can be used to inform evolutionary models. To put it into broad terms, my results will help inform questions about the evolution of photosynthesis, and since photosynthesis led to oxygen on Earth, questions about the evolution of Earth as a whole. 

You work on the largest and smallest elements of biology—the environment and microbes. How do they complement each other?

Microbes are very important for large scale environmental cycles and tend to be important at the starting point of those cycles. Many of the microbes that we study fix carbon, which means they take carbon in a typically unusable form and make it usable. Since humans and animals are unable to do this for ourselves, we depend on the carbon that plants (and some microbes) fix. So microbes are critically essential for the rest of the environment. Without them we don’t have plants, we don’t have cows, and we don’t have us.

 

Reed Grumann is a writing intern in the Science Communications Lab, majoring in Microbiology and Political Science. He can be reached at gruma017@umn.edu