Max Planck Institute of Molecular Plant Physiology View Institution's Website 9 articles published in JoVE Biochemistry Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization Mustafa Bulut1, Alisdair R. Fernie1,2, Saleh Alseekh1,2 1Max-Planck-Institute of Molecular Plant Physiology, 2Center of Plant Systems Biology and Biotechnology In this protocol, we present an optimized workflow, which combines an efficient and fast sample preparation of many samples. In addition, we provide a step-by-step guide to reduce analytical variations for high-throughput evaluation of metabolic GWAS studies. Developmental Biology Live Cell Imaging of Microtubule Cytoskeleton and Micromechanical Manipulation of the Arabidopsis Shoot Apical Meristem Yang Wang1, Arun Sampathkumar1 1Max Planck Institute of Molecular Plant Physiology Here we describe a protocol for live cell imaging of the cortical microtubule cytoskeleton at the shoot apical meristem and monitoring its response to changes in physical forces. Genetics Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis Eleftheria Saplaoura*1, Valentina Perrera*2, Vincent Colot3, Friedrich Kragler1 1Max Planck Institute of Molecular Plant Physiology, 2Department of Molecular Medicine, Medical School, University of Padua, 3 The methylated RNA immunoprecipitation assay is an antibody-based method used to enrich for methylated RNA fragments. Coupled with deep sequencing, it leads to the identification of transcripts carrying the m5C modification. Developmental Biology A Multi-Omics Extraction Method for the In-Depth Analysis of Synchronized Cultures of the Green Alga Chlamydomonas reinhardtii Umarah Mubeen1, Lais Albuquerque Giraldi1, Jessica Jüppner1, Patrick Giavalisco1,2 1Max Planck Institute of Molecular Plant Physiology, 2Max Planck Institute of Biology of Ageing System-wide analysis of multiple biomolecules is crucial to gain functional and mechanistic insights into biological processes. Hereby, an extensive protocol is described for high throughput extraction of lipids, metabolites, proteins and starch from a single sample harvested from synchronized Chlamydomonas culture. Biochemistry 2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes Marcin Luzarowski*1, Izabela Wojciechowska*1, Aleksandra Skirycz1 1Max Planck Institute of Molecular Plant Physiology Protein-protein and protein-metabolite interactions are crucial for all cellular functions. Herein, we describe a protocol that allows parallel analysis of these interactions with a protein of choice. Our protocol was optimized for plant cell cultures and combines affinity purification with mass spectrometry-based protein and metabolite detection. Biochemistry A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample Mohamed Salem1,2, Michal Bernach1, Krzysztof Bajdzienko1, Patrick Giavalisco1 1Max Planck Institute of Molecular Plant Physiology, Golm, Germany, 2Department of Pharmacognosy, Faculty of Pharmacy, Cairo University A protocol for comprehensive extraction of lipids, metabolites and proteins from biological tissues using one sample is presented. Biochemistry High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE Toshio Moriya1, Michael Saur1, Markus Stabrin1, Felipe Merino1, Horatiu Voicu2, Zhong Huang2, Pawel A. Penczek2, Stefan Raunser1, Christos Gatsogiannis1 1Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 2Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston This paper presents a protocol for processing cryo-EM images using the software suite SPHIRE. The present protocol can be applied for nearly all single particle EM projects that target near-atomic resolution. Environment Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry Colin Ruprecht1, Takayuki Tohge1, Alisdair Fernie1, Cara L. Mortimer2, Amanda Kozlo2, Paul D. Fraser2, Norma Funke1, Igor Cesarino3,4, Ruben Vanholme3,4, Wout Boerjan3,4, Kris Morreel3,4, Ingo Burgert5,6, Notburga Gierlinger5,6, Vincent Bulone7, Vera Schneider8, Andrea Stockero8, Juan Navarro-Aviñó9, Frank Pudel10, Bart Tambuyser11, James Hygate12, Jon Bumstead13, Louis Notley13, Staffan Persson1,14 1Max Planck Institute for Molecular Plant Physiology, 2School of Biological Sciences, Plant Molecular Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, 3Department of Plant Systems Biology, VIB, 4Department of Plant Biotechnology and Bioinformatics, UGhent, 5Institute for Building Materials, ETH Zurich, 6Applied Wood Materials, EMPA, 7Division of Glycoscience, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), 8European Research and Project Office GmbH, 9ABBA Gaia S.L., 10Pflanzenöltechnologie, 11Capax Environmental Services, 12Green Fuels, 13Neutral Consulting Ltd, 14Plant Cell Biology Research Centre, School of Botany, University of Melbourne Plant biomass offers a renewable resource for multiple products, including fuel, feed, food, and a variety of materials. In this paper we investigate the properties of tobacco tree (Nicotiana glauca) and poplar as suitable sources for a biorefinery pipeline. Biology A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation Stefan Schmollinger1,2, Daniela Strenkert1,2, Vittoria Offeddu1,2, André Nordhues1,2, Frederik Sommer1,2, Michael Schroda1,2 1Max Planck Institute of Molecular Plant Physiology, 2University of Kaiserslautern We present a variation of the QUICK (QUantitative Immunoprecipitation Combined with Knockdown) approach that was introduced previously to distinguish between true and false protein-protein interactions. Our approach is based on 15N metabolic labeling, the modulation of affinities of protein-protein interactions by the presence/absence of ATP, immunoprecipitation, and quantitative mass spectrometry.
