6 articles published in JoVE

• 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 Giavalisco^{1,2 1}Max 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 Skirycz^{1 1}Max 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 Salem^1,2, Michal Bernach¹, Krzysztof Bajdzienko¹, Patrick Giavalisco^{1 1}Max 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 Gatsogiannis^{1 1}Department 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 Cesarino^3,4, Ruben Vanholme^3,4, Wout Boerjan^3,4, Kris Morreel^3,4, Ingo Burgert^5,6, Notburga Gierlinger^5,6, Vincent Bulone⁷, Vera Schneider⁸, Andrea Stockero⁸, Juan Navarro-Aviñó⁹, Frank Pudel¹⁰, Bart Tambuyser¹¹, James Hygate¹², Jon Bumstead¹³, Louis Notley¹³, Staffan Persson^{1,14 1}Max 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 Schmollinger^1,2, Daniela Strenkert^1,2, Vittoria Offeddu^1,2, André Nordhues^1,2, Frederik Sommer^1,2, Michael Schroda^{1,2 1}Max 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.