Professor Oliver Fiehn Awarded Paul K. and Ruth R. Stumpf Professorship in Plant Biochemistry

The UC Davis College of Biological Sciences has named Oliver Fiehn, professor of molecular and cellular biology, to the Paul K. and Ruth R. Stumpf Professorship in Plant Biochemistry.

An internationally recognized scholar, Fiehn has more than 220 publications to his name. He has driven significant developments in the field of metabolomics, the study of small molecules known as metabolites. Metabolites are the end products of cellular processes and form the chemistry of all life.

The Role of Plant Metabolites

Professor Oliver Fiehn holds joint appointments with the College of Biological Sciences Department of Molecular and Cellular Biology and the UC Davis Genome Center.

Fiehn’s research centers on the systematic analysis of plant metabolites, which provide the essential functions for plant survival. He seeks to understand and categorize plant metabolic profiles to help provide a snapshot of the cellular physiology of different species.

“Metabolism occurs in every living cell and therefore I have complete freedom to study planet Earth and everything that lives on it,” said Fiehn, whose enthusiasm for science is infectious. “The fun part with phytochemistry and plant biology is that everything I find is made by plants.”

Fiehn holds appointments in the Department of Molecular and Cellular Biology as well as the Genome Center, where he serves as the director of the National Institutes of Health West Coast Metabolomics Center. The center aids research and exploration in the role of metabolomics in disease progression.

“The strengths of UC Davis in plant sciences, health and chemistry come together nicely at the Metabolomics Center,” said Fiehn. “As director, I aim to elevate the role of informatics in understanding complex regulation of metabolism, which is influenced by advances in big data and collaboration across UC Davis.”

Fiehn joined UC Davis in 2004 after completing a postdoc and an assistant professorship at the Max Planck Institute for Molecular and Plant Physiology in Potsdam, Germany.

At the Intersection of Plant Metabolism and Big Data

While most people think of metabolism in terms of the food they eat and energy derived from food, plants synthesize hundreds of thousands of other compounds to ensure their survival. This complex machinery allows plants to survive in an array of environments, from rain-starved deserts to lush rainforests. Metabolites protect plants from environmental threats and provide the means for reproduction.

Metabolites vary significantly from species to species. There are close to 400,000 known plant species and each one has its own specific metabolic repertoire, which is tailored to the species’ ecological niche.

These chemical compounds accomplish a variety of tasks. Flowering plants developed vibrant colors and alluring scents to attract pollinating insects, which assist with fertilization. The tobacco plant, for example, produced nicotine as a chemical defense from pests. The scent of a fresh-cut lawn comes from a compound that helps grass cells heal wounds.

Though plants appear silent, their metabolites are constantly sending messages through their environments.  “The communication of plants is a chemical communication,” said Fiehn.

Tasked with identifying a seemingly infinite variety of metabolites is intimidating at best. But through advances in mass spectrometry and big data, Fiehn is developing tools for researchers to categorize and share information about plant compounds. A proponent of open access to scientific data, Fiehn has created the MassBank of North America, a free digital repository of metabolite mass spectra. It works like a digitized field guide, providing researchers with insights into metabolite chemical structures.

“Other people can download the spectra, and next time they see the characteristics that match the profile, they can identify the metabolite,” Fiehn said. “It’s a little bit like a dictionary.”

But the database is just getting started. Since not all chemical compounds are readily available for profiling, Fiehn is exploring new methods to try to virtually predict the mass spectra of plant metabolites.

“Ultimately, we would like to predict the metabolic repertoire of plants just by examining their genome,” he said, noting that it’s an ambitious endeavor.

The tools and databases Fiehn and his colleagues are developing have many potential applications in biomedical and health research. When ingested, plant-produced metabolites pass through and are often stored in the human body, where they can have implications for overall health. Many chemical compounds responsible for the flavors and pigments of plants are known for their disease preventative properties.

“We specifically want to understand the impact of nutrition and disease, including the effects of microbiota changes,” said Fiehn.

Recognizing Excellence in Plant Biochemistry

The resources from the Stumpf Professorship open the possibility of bringing more students interested in phytochemistry to his lab.

“We take our mission of research and education very seriously,” he said. “I usually have four to six undergraduate students working with me, for example, on secondary plant metabolite spectral libraries. We will now push forward with this theme and I would love to enroll students who would like to use informatics tools.”

 “Oliver Fiehn’s work in plant metabolomics is driving a greater understanding of plant traits and how we utilize these characteristics to advance scientific knowledge,” said Mark Winey, dean of the College of Biological Sciences. “His research continues the passion and spirit of scientific inquiry that Paul Stumpf brought to plant biology.”

The Stumpf Professorship is awarded to a senior faculty member in the Departments of Plant Biology and Molecular and Cellular Biology whose distinguished scholarship is nationally recognized. The endowment will help support Fiehn’s research, teaching and service to the UC Davis community for the next five to seven years.

Established in 1999, the endowed professorship was formed by the late Paul K. and Ruth R. Stumpf. Paul Stumpf, a professor and founding father of biochemistry programs at UC Davis, pioneered the study of plant lipids and received many accolades for his contributions to the field. He was a member of the U.S. National Academy of Sciences and the Royal Danish Academy of Sciences, a fellow of the American Association for the Advancement of Science and was twice named as a Guggenheim Foundation Fellow, among many other accomplishments. Stumpf passed away on Feb. 10, 2007.

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Upcoming Talks and Events

Events on January 14, 2019
WCMC: Hands-on LC-MS Data processing and Statistics
Starts: 12:00 am
Ends: January 19, 2019 - 12:00 am
Location: UC Davis Conference Center, 550 Alumni Ln, Davis, CA 95616, USA
Description: Registration: http://ucanr.edu/survey/survey.cfm?surveynumber=15575

This course will feature hands-on training with real-world metabolomics data covering LC/MS compound identification, data processing, statistical analysis, network mapping and data interpretation.

We will instruct using a variety of software, workflows, and algorithms but also give theoretical background information and overviews. We will focus on utilizing open source software and only refer to commercial or vendor software when necessary.

All participants will be trained on laptops that were specifically purchased for course training, with all software already installed and data available to use.

The course will include:

untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
The course fees are $ 2,500 per participant to cover expenses for instructors, organization, materials and meals.

more Info:

Jeannette Martins

email: jmartins@ucdavis.edu

phone: +1-530-754-5357

Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.
Events on May 16, 2019
WCMC: Best practice in operating mass spectrometers in Metabolomics
Starts: 12:00 am
Ends: May 20, 2019 - 12:00 am
Location: Genome and Biomedical Sciences Facility, 451 Health Science Dr, Davis, CA 95616, USA
Description: Registration: https://goo.gl/forms/TGeuALrTMfTpGh0O2

This course will enhance your standing and expertise to prepare and successfully run samples in a metabolomic laboratory. It is designed to provide hands-on practical exercises using gas and liquid chromatography coupled to mass spectrometry (GC-MS & LC-MS). The course will focus on untargeted data acquisition in metabolomics with both nominal mass and accurate mass instruments. You will learn how to operate the instruments, how to collect metabolite profiles on complex samples and how to prepare and derivatize samples, troubleshoot instruments, acquire data and perform data quality control routines (QA/QC). Overall, you will receive comprehensive understanding of the current best practices in the metabolomics laboratory.

The course will include:


1. Fundamentals of mass spectrometry, chromatography, and metabolomics.
2. hands-on exercises on sample preparation, including extraction and derivatization
of complex samples for untargeted metabolomics profiling
3. Hands-on exercises to learn how to operate both gas and liquid chromatography
coupled to mass spectrometry (GC-MS & LC-MS).
4. quality control routines (QA/QC) in order to ensure comparable data, reproducibility, and instrument performance.
Events on August 19, 2019
International Summer Sessions in Metabolomics
Starts: 12:00 am
Ends: August 31, 2019 - 12:00 am
Location: UC Davis Alumni Center
Description: Registration: https://docs.google.com/forms/d/e/1FAIpQLSeVnMXxhkMtlET-RGDgW99jA3lr1wS4hypU0kI6O1yGV0GqBg/viewform?usp=sf_link

Contact: Jeannette Martins jmartins@ucdavis.edu

Please, contact us now if you need letters of support to obtain funding from your home institutions.

The West Coast Metabolomics Center organizes an instructional course for researchers for researcher which need a deeper and broader understanding in the field of Metabolomics. This course will span 12 days from August 19-30, 2019.

In order to serve the group interests best and have interesting open discussions we have a small class of 22 participants. The participants come always from all over the world and have a very diverse research background.

The course will include:

study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
sample preparation and quality control
in-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
exercises on flux analysis in cancer cells by isotope tracer analysis
untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
Past course participation:
2018 course: 25 researchers from USA, Brazil, China, Japan, Korea, Taiwan, Russia, Norway, Germany, Poland, Canada
2017 course: 24 researchers from USA, Saudi-Arabia, China, , Korea, Italy, Denmark, Iran, United Kingdom
2016 course: 23 researchers from USA, Saudi-Arabia, China, Thailand, Japan, Italy, Brazil, Chile, Korea, and Canada.
2015 course: 21 researchers from USA, China, Germany, Brazil, Switzerland, Denmark, Canada, Korea, Malaysia, and Netherlands.
2014 course: 20 researchers from USA, New Zealand, Italy, Denmark, China, Canada, Turkey and Switzerland
2013 course: 20 researchers from USA, New Zealand, Costa Rica, Denmark, Luxembourg, Brazil, Columbia, Japan, Korea and Taiwan.
For questions, please contact our program representative Jeannette Martins (jmartins@ucdavis.edu).

Visiting Scientists
Participation in this course is mandatory for visiting international researchers who want to engage in collaborative research projects.
The minimum time span for such collaborative visits is 3 months, preferred is 12 months.
An additional payment of $500 for the visa has to be paid prior to arrival at UC Davis.

Each year, up to five international researchers have started such research visits, funded by agencies in their home countries.
Please contact us at least 6 months in advance to help you with letters of support, booking your course, and obtaining a visa for you.
Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.

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