ETH facilities @ Bioscience, Wageningen BU Bioscience, Wageningen - - PowerPoint PPT Presentation

ETH facilities @ Bioscience, Wageningen

Ric de Vos, 27th May 2019

BU Bioscience, Wageningen Plant Research, WUR

ric.devos@wur.nl

Hotels at Bioscience–WPR

• Wageningen AgroGenomics Centre
• Elio Schijlen, Sara Diaz-Trivino
• Proteomics Facility
• Twan America, Ingrid van der Meer
• Plant Metabolomics Facility
• Ric de Vos, Roland Mumm, Robert Hall
• Etho-Analysis: HT-screening insect behaviour
• Maarten Jongsma
• In-house data processing workflows
• pre-processing, bioinformatics, statistics, interpretation

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WUR building ‘Radix’

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• 10X Genomics Chromium
• Illumina (MiSeq, HiSeq2500, NovaSeq)
• Pacbio Sequel
• Bionano Genomics Saphyr
• ONT Minion/GridION
• Bioinformatics

AgroGenomics Hotel

Proteomics Hotel

• 1D or 2D nanoLC-HR MS/MS
• identify ten thousands peptides
• identify a few thousand proteins
• Comparison of multiple samples (large numbers)
• select and identify differential peptides  markers
• Untargeted: open window, holistic view
• Targeted: specific, fast, sensitive: 10-100 proteins, 15 min/run

nanoLC-QEx Orbitrap FTMS UPLC-triplequad MS

Many applications

Not restricted to plants!

• Characterise protein extracts:
• identification of proteins
• resolve protein isoforms - conjugations
• find low abundant proteins / unwanted impurities
• Differences in composition related to, for instance,
• (a)biotic stress, disease resistance
• batch production effects due to variation source material
• food processing: fermentations, storage, etc.
• protein allergies

Etho-Analysis Hotel: plant-insect interactions

• High-throughput screening system
• Video-tracking of (pest) insect

movements in leaf arenas for 1-8h

• Moving behaviour depends on the leaf

quality as sensed by the insect

• In-house developed software to extract

data: EthoAnalysis

• Insect behaviour can be related to e.g.

in vivo traits, plant/insect genetics, proteins, metabolites, ....

Metabolomics: GCMS and LCMS platforms

Targeted and comprehensive analyses including data processing; statistics if needed

... next to HPLC’s with various other detectors

• identifying metabolites that are key to plant/product traits
• (a)biotic stress resistance, flavour, colour, shelf-life, .....
• understanding the biosynthesis of these quality-related metabolites
• genetics: natural variation, molecular markers for key metabolites
• determining pre- and post-harvest effects:
• environment, development, ripening, processing, seed storage, .......
• biobased & circular economy: sustainable production, waste usage, ......
• essentially any plant species, tissue or products derived thereof
• tomato, cabbages, potato, strawberry, apple, lettuce, melon, coffee, rice, ......
• leaves, stems, roots, flowers, fruits, seeds, seedlings, trichomes, ......
• algae, seaweed, microbes, mushrooms, human fluids, .....

A myriad of metabolomics projects and topics

Example of an ETH-Metabolomics project

”Healthier lettuce for healthier food”

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30k euro grant for guest Centre Genetic Resources (NWO-ZonMW ETH call 2016)

• Breeding towards more healthy and sustainable, ‘Green’ lettuce varieties
• Deep-phytochemical profiling of leaves of 150 Lactuca genotypes, grown by CGN
• biodiversity in both vitamin C and 2028 other known and (yet) unknown metabolites
• All metabolites were statistically coupled to plant resistance traits
• novel marker compounds for disease resistance identified
• Output: all phytochemical data available in CGN’s open database; scientific paper

Van Treuren et al 2018, Metabolomics 14

Hotel project – unfolding a project together

• Consulting phase: HUGELY IMPORTANT
• goal, interests and expectations from both sides
• Write project proposal together:
• Meeting evaluation criteria
• Hotel boundaries
• Budget constraints
• Timeline
• Risk Assessment (feasibility)
• Communication and reporting
• Collaborative scientific paper(s)

What is of interest to Hotel?

• Scientific challenge:
• novel topic, application or innovative technique
• Prospects:
• ability to expand on our know-how and portfolio for

acquiring new research projects

• high-quality scientific papers
• possibilities for future, larger collaborative projects
• Feasibility:
• technological and budget boundaries
• delivering good quality samples in time

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Happy guest Neutral guest Unhappy guest

Only a good collaboration makes both guest and Hotel happy

Questions?