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?