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X-WR-CALDESC:Events for Graduate School EPS
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DTSTART;TZID=Europe/Amsterdam:20260415T160000
DTEND;TZID=Europe/Amsterdam:20260415T170000
DTSTAMP:20260709T220917
CREATED:20260407T074717Z
LAST-MODIFIED:20260413T091719Z
UID:5520-1776268800-1776272400@graduateschool-eps.info
SUMMARY:Understanding the genetic mechanism of Brassica napus resistance against cabbage stem flea beetle
DESCRIPTION:Understanding the genetic mechanism of Brassica napus resistance against cabbage stem flea beetle\nRachel Wells\, Department of Crop Genetics\, John Innes Centre \nWednesday April 15th; time 16.00; location Wageningen\, Radix W01\nContact: Guusje Bonnema\, Plant Breeding\, WUR \nRachel’s research involves the identification of genetic resistance to Brassica pests and disease\, with a strong focus on cabbage stem flea beetle (CSFB). Her research group uses captive colonies\, to study CFSB development and genetics\, and controlled and field plant variety screens for both adult and larval CSFB damage in Brassica napus and related species\, such as Sinapis alba. These experiments can be used to look at plant-pest interaction and ultimately determine the genes and mechanisms associated with pest resistance. This work is complemented by collaboration with the University of Hertfordshire on light leaf spot\, focussing on mutation breeding and genome editing to target disease susceptibility.
URL:https://graduateschool-eps.info/event/understanding-the-genetic-mechanism-of-brassica-napus-resistance-against-cabbage-stem-flea-beetle/
CATEGORIES:EPS courses,Seminars
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Amsterdam:20260420T140000
DTEND;TZID=Europe/Amsterdam:20260420T170000
DTSTAMP:20260709T220917
CREATED:20251222T105451Z
LAST-MODIFIED:20260604T232319Z
UID:5262-1776693600-1776704400@graduateschool-eps.info
SUMMARY:Workshop: Biosynthesis of Natural Products – From Genes to Molecules to Data
DESCRIPTION:Date: 20 April 2026 (14:00–17:00 + borrel afterwards)\nLocation: Room B9210+B9211\,  Aurora building nr. 127\, Wageningen Campus\nInstructors:  Joelle Mergola Greef (LU) · Barbara Terlouw (WUR) · Esteban Charria Girón (WUR)\nAudience: Wageningen University & Research / Affiliated institutes (max. 50 participants)\nRegistration: open (deadline 13 April)\nContact: Esteban Charria Girón (esteban.charriagiron@wur.nl) \nLearning goals\nBy the end of the workshop\, participants will: \n\nRecognize the core logic of assembly-line biosynthesis for polyketide\, nonribosomal peptide\, RiPP\, terpene\, and hybrids.\nInterpret basic biosynthetic gene cluster (BGC) architectures and infer likely building blocks and tailoring steps.\nFormulate simple experimental set ups to test biosynthetic hypotheses.\nIdentify bioinformatics tools for natural products discovery available at BIF (e.g. genome mining\, biosynthesis-informed fingerprints\, knowledge graphs).\n\nProgram (14:00–17:00)\n14:00–14:10 – Welcome & framing: “From genes to molecules to data”: Short welcome\, practical information\, and introductions of the three instructors. Brief audience poll (wet-lab vs computational vs both)\, workshop expectations\, and an overview of the storyline: from biosynthetic gene clusters to molecules\, data & AI\, and back. \n14:10–14:30 – Lightning pitches: Selected lightning talks from participants (5 talks x 4 min each). Each pitch briefly answers: \n\nWhat are you working on?\nHow does natural products biosynthesis play a role in your work?\nOne concrete question or challenge you have (one slide).\n\n14:30–15:30 – Three perspectives\, one pipeline \n1) Chemical logic of biosynthesis: Going over the building blocks and substrates employed in different pathways (acetyl/malonyl units\, amino acids\, isoprene units\, shikimate-derived intermediates\, etc.). Typical reactions in natural product biosynthesis: C–C and C–N bond formation\, redox chemistry\, and tailoring reactions. Also explain how the “same” chemistry is wired differently in Bacteria\, fungi\, and plants. \n2) Experimental hooks & what we actually see: How can we translate biosynthetic insights into real experiments: \n\nScreening and untargeted metabolomics (What is there?).\nWhat you expect to see in LC-MS/MS experiments for a PKS vs NRPS product.\nTypical follow-up experiments: feeding experiments\, co-culture\, mutants\, overexpression.\nHeterologous expression of target BGCs and what can go wrong (e.g. shunt products or side pathways in host).\n\n3) Anecdotes of NP discoveries – From bioinformatics to experimental data and back: How genome mining tools identify signatures of the chemistry just discussed (domain architectures\, motifs\, “biosynthetic fingerprints”) and how ML/fingerprints/knowledge graphs\, together with core reference databases (e.g. MIBiG\, MITE\, NPAtlas\, and others)\, can support discovery – illustrated via concrete stories: \n\nHow genome mining + pathway logic guided biosynthetic pathway elucidation for tridecaptin and marushamycin.\nCollaborative biosynthesis / oligomerization\, showing how BGC predictions\, MS/MS data and context-dependent expression come together.\nNocardichelin biosynthesis and lipopeptide discovery guided by Harvest.\n\n15:20–15:35 – Mini panel Q&A: Joint Q&A with all three instructors \n15:35–15:45 – Coffee / tea break \n15:45–16:45 – Rotating mini-workshops (3 stations): Participants are divided into three groups (A\, B\, C). Each group visits all three stations in rotation (~20 minutes per station\, plus short changeovers). \nStation 1 — Reading BGCs like a map: Participants work with printed BGC cartoons (PKS\, NRPS\, hybrid) and: \n\nIdentify the biosynthetic class and building blocks.\nDiscuss the roles of key tailoring enzymes.\n\nStation 2 — From phenotype to molecules: Using a case study (e.g. antibiotic discovery)\, groups see figures (inhibition data or FERMO output) and: \n\nPropose what biosynthetic class might be involved (based on MS/MS and BGC results).\nSuggest follow-up experiments to test their hypotheses.\n\nStation 3 — Tools & AI: Demo or screenshots of BGC-to-compound prediction (RetroMol and Harvest)\, biosynthesis-informed fingerprints and knowledge graph concepts. Short exercise in which participants discuss how two example molecules might be represented and connected in such a system. \n16:45–17:00 – Wrap-up: Final recap of key messages and practical information about slides/materials\, tools\, and any mailing list or follow-up activities. \nBorrel & networking (from 17:00)\nInformal borrel after the workshop\, offering time for networking and follow-up discussions. Participants are encouraged to connect across groups and disciplines\, and to explore potential collaborations within the WUR and friends ecosystem. \nFee\nThe fee for this workshop for all participants is € 50\,- \nCancellation\nYou may cancel free of charge up to two weeks before the start of the course. After this date you will be charged the participation fee. In case of a no-show you will be charged the participation fee with an added € 50\,- cancellation fee. \nRegistration
URL:https://graduateschool-eps.info/event/workshop-biosynthesis-of-natural-products-from-genes-to-molecules-to-data/
LOCATION:Aurora building\, Wageningen Campus\, Vijfde Polder 1\, Wageningen\, 6708 WC
CATEGORIES:EPS courses,Recurring events incidental
ORGANIZER;CN="WUR Bioinformatics":MAILTO:esteban.charriagiron@wur.nl
END:VEVENT
BEGIN:VEVENT
DTSTART;VALUE=DATE:20260421
DTEND;VALUE=DATE:20260423
DTSTAMP:20260709T220917
CREATED:20250925T132602Z
LAST-MODIFIED:20260604T232241Z
UID:4865-1776729600-1776902399@graduateschool-eps.info
SUMMARY:EPS Bioinformatics course - Module 2 “Comparative genomics & Phylogeny and Transcriptomics ”
DESCRIPTION:Date: 21 and 22 of April 2026\nTarget group: PhD candidates\, postdocs and interested persons (max 40)\nLocation: Campus Wageningen University & Research\, Forum building\, room B0432\nRegistration: closed \nDay 1 – 21 April 2026 “ Comparative genomics & Phylogeny ” \nJoin the course module and learn about the evolutionary relationships between species and uncover the genetic basis of biological diversity. \n\nPrinciples of comparative genomics and genome evolution\nMethods to identify orthologs\, paralogs\, and gene families\nTools and techniques for building phylogenetic trees\nUnderstanding genome conservation and divergence across species\n\nTrainers: Michael Seidl (UU) & Eric Schranz (WUR) \nDay 2 – 22 April 2026 “ Transcriptomics”  \nDuring the course module your get insight into the RNA landscape\, helping you understand how genes are expressed\, regulated\, and interpreted in various biological contexts – from development to disease. \n\nFoundations of transcription and RNA biology\nHigh-throughput technologies: Microarrays & RNA-Seq\nRNA extraction\, library preparation\, and sequencing pipelines\nData analysis: Mapping\, quantification\, and differential expression\nIntroduction to single-cell transcriptomics and emerging trends\n\nTrainers: Tijs Bliek (UvA) & Misha Paauw (UvA) \n\n\nCourse fees\n\n\n\nCategories\nFee\n\n\n\n\nEPS PhD candidates with approved TSP & WUR PhD candidates with approved TSP\n€215\n\n\nOther PhD candidates\n€325\n\n\nEPS or WUR postdocs\n€325\n\n\nAcademic staff\n€430\n\n\nIndustry\n€1000\n\n\n\n\nCancellation \nYou may cancel free of charge up to 1 month before the start of the course. After this date you will be charged the lowest fee (EPS/WUR PhD candidates with an approved TSP). \nIf you can find someone to replace you in the course and supply the course coordinator with the name and contact information of your replacement\, you will only be charged a € 50\,- cancellation fee.
URL:https://graduateschool-eps.info/event/eps-bioinformatics-course-module-2-comparative-genomics-phylogeny-and-transcriptomics/
LOCATION:Wageningen Campus\, Droevendaalsesteeg 4\, Wageningen\, Gelderland\, 6708 PB\, Netherlands
CATEGORIES:EPS courses,Recurring events annual
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Amsterdam:20260428T143000
DTEND;TZID=Europe/Amsterdam:20260428T160000
DTSTAMP:20260709T220917
CREATED:20260413T092125Z
LAST-MODIFIED:20260413T092125Z
UID:5536-1777386600-1777392000@graduateschool-eps.info
SUMMARY:BIC Seminar: Prof. Rainer Hedrich
DESCRIPTION:BIC Seminar: Prof. Rainer Hedrich \nProbing plant signalling via Channelrhodopsin optogenetics \nDate: 28 April 2026 \nTime: 14:50 \nLocation: C0333\, Orion\, Wageningen Campus \nAbstract: \nMembrane electrical excitation\, often associated with the transient rise in cytosolic Ca2+ and H+ concentration\, represent universal signalling elements that couple a wide range of stimuli to their characteristic responses\, including in plants. Despite decades of intensive research\, many of the signal transduction elements involved in Ca2+ and pH signalling are yet to be elucidated. Progress has been hampered due to our inability to trigger defined changes in cytosolic Ca2+ concentration\, without provoking changes in plasma membrane electrical properties. Over the past 5 years\, new game-changing ion channel optogenetic tools have been introduced into plants to answer long-standing questions in plant biology. \nIn this presentation I will describe how we have engineered the light-gated ChannelRhodopsins CHRs selective for anions (ACR1)\, H+ (KCR2) or Ca2+ (XXM2.0) and to obtain stable expression in Arabidopsis and tobacco plants. These tools provide us with the unique opportunity to non-invasively induce voltage\, Ca2+ and H+ signals in guard cells as well as any plant cell/tissue/organ type of interest. Furthermore\, I will describe how CHRs provide a valuable tool to non-invasively excite the plasma membrane\, trigger H+ or Ca2+ influx\, and provoke H+ or Ca2+ induced Ca2+ release. This allows to study the interrelation between plant pH and Ca2+ signalling on one side\, and electrical excitation on the other. Depending on the CHR and stimulation features (pulse number\, length\, and frequency) one can remote control single cell action\, long-distance transport as well as growth and shape or plant organs. Our findings challenge established paradigms relating to the way proton\, calcium\, and voltage signalling are interconnected in plants and rethink of mechanisms involved.
URL:https://graduateschool-eps.info/event/bic-seminar-prof-rainer-hedrich/
LOCATION:Wageningen Campus\, Droevendaalsesteeg 4\, Wageningen\, Gelderland\, 6708 PB\, Netherlands
CATEGORIES:EPS courses,Seminars
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