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

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