ETH facilities @ Bioscience, Wageningen BU Bioscience, Wageningen Plant Research, WUR Ric de Vos, 27 th May 2019 ric.devos@wur.nl
Hotels at Bioscience – WPR WUR building ‘Radix’ 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 2
AgroGenomics Hotel • 10X Genomics Chromium • Illumina (MiSeq, HiSeq2500, NovaSeq) • Pacbio Sequel • Bionano Genomics Saphyr • ONT Minion/GridION • Bioinformatics 3
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 ... n ext to HPLC’s with various other detectors
A myriad of metabolomics projects and topics • 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, .....
Example of an ETH-Metabolomics project ” Healthier lettuce for healthier food ” 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 10
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 12
Questions? Only a good collaboration makes both guest and Hotel happy Happy guest Neutral guest Unhappy guest
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