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  1. Methodology

    UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts

    The complexity of RNA regulation is one of the current frontiers in animal and plant molecular biology research. RNA-binding proteins (RBPs) are characteristically involved in post-transcriptional gene regulat...

    Zhicheng Zhang, Kurt Boonen, Piero Ferrari, Liliane Schoofs, Ewald Janssens, Vera van Noort, Filip Rolland and Koen Geuten

    Plant Methods 2016 12:42

    Published on: 3 November 2016

  2. Research

    Infiltration-RNAseq: transcriptome profiling of Agrobacterium-mediated infiltration of transcription factors to discover gene function and expression networks in plants

    Transcription factors (TFs) coordinate precise gene expression patterns that give rise to distinct phenotypic outputs. The identification of genes and transcriptional networks regulated by a TF often requires ...

    Donna M. Bond, Nick W. Albert, Robyn H. Lee, Gareth B. Gillard, Chris M. Brown, Roger P. Hellens and Richard C. Macknight

    Plant Methods 2016 12:41

    Published on: 19 October 2016

  3. Research

    RADIX: rhizoslide platform allowing high throughput digital image analysis of root system expansion

    Phenotyping of genotype-by-environment interactions in the root-zone is of major importance for crop improvement as the spatial distribution of a plant’s root system is crucial for a plant to access water and ...

    Chantal Le Marié, Norbert Kirchgessner, Patrick Flütsch, Johannes Pfeifer, Achim Walter and Andreas Hund

    Plant Methods 2016 12:40

    Published on: 5 September 2016

  4. Methodology

    A method for detecting single mRNA molecules in Arabidopsis thaliana

    Despite advances in other model organisms, there are currently no techniques to explore cell-to-cell variation and sub-cellular localization of RNA molecules at the single-cell level in plants.

    Susan Duncan, Tjelvar S. G. Olsson, Matthew Hartley, Caroline Dean and Stefanie Rosa

    Plant Methods 2016 12:13

    Published on: 5 August 2016

  5. Methodology

    Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants

    The double digest restriction-site associated DNA sequencing technology (ddRAD-seq) is a reduced representation sequencing technology by sampling genome-wide enzyme loci developed on the basis of next-generati...

    Guo-Qian Yang, Yun-Mei Chen, Jin-Peng Wang, Cen Guo, Lei Zhao, Xiao-Yan Wang, Ying Guo, Li Li, De-Zhu Li and Zhen-Hua Guo

    Plant Methods 2016 12:39

    Published on: 4 August 2016

  6. Methodology

    Detecting N-myristoylation and S-acylation of host and pathogen proteins in plants using click chemistry

    The plant plasma membrane is a key battleground in the war between plants and their pathogens. Plants detect the presence of pathogens at the plasma membrane using sensor proteins, many of which are targeted t...

    Patrick C. Boyle, Simon Schwizer, Sarah R. Hind, Christine M. Kraus, Susana De la Torre Diaz, Bin He and Gregory B. Martin

    Plant Methods 2016 12:38

    Published on: 3 August 2016

  7. Methodology

    Application of unmanned aerial systems for high throughput phenotyping of large wheat breeding nurseries

    Low cost unmanned aerial systems (UAS) have great potential for rapid proximal measurements of plants in agriculture. In the context of plant breeding and genetics, current approaches for phenotyping a large n...

    Atena Haghighattalab, Lorena González Pérez, Suchismita Mondal, Daljit Singh, Dale Schinstock, Jessica Rutkoski, Ivan Ortiz-Monasterio, Ravi Prakash Singh, Douglas Goodin and Jesse Poland

    Plant Methods 2016 12:35

    Published on: 24 June 2016

  8. Methodology

    High-throughput phenotyping of lateral expansion and regrowth of spaced Lolium perenne plants using on-field image analysis

    Genetic studies and breeding of agricultural crops frequently involve phenotypic characterization of large collections of genotypes grown in field conditions. These evaluations are typically based on visual ob...

    Peter Lootens, Tom Ruttink, Antje Rohde, Didier Combes, Philippe Barre and Isabel Roldán-Ruiz

    Plant Methods 2016 12:32

    Published on: 10 June 2016

  9. Methodology

    RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation

    In order to maintain high yields while saving water and preserving non-renewable resources and thus limiting the use of chemical fertilizer, it is crucial to select plants with more efficient root systems. Thi...

    Christian Jeudy, Marielle Adrian, Christophe Baussard, Céline Bernard, Eric Bernaud, Virginie Bourion, Hughes Busset, Llorenç Cabrera-Bosquet, Frédéric Cointault, Simeng Han, Mickael Lamboeuf, Delphine Moreau, Barbara Pivato, Marion Prudent, Sophie Trouvelot, Hoai Nam Truong…

    Plant Methods 2016 12:31

    Published on: 7 June 2016

  10. Methodology

    High-throughput quantification of more than 100 primary- and secondary-metabolites, and phytohormones by a single solid-phase extraction based sample preparation with analysis by UHPLC–HESI–MS/MS

    Plant metabolites are commonly functionally classified, as defense- or growth-related phytohormones, primary and specialized metabolites, and so forth. Analytical procedures for the quantifications of these me...

    Martin Schäfer, Christoph Brütting, Ian T. Baldwin and Mario Kallenbach

    Plant Methods 2016 12:30

    Published on: 26 May 2016

  11. Methodology

    A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly

    Nicotiana benthamiana has been widely used in laboratories around the world for studying plant-pathogen interactions and posttranscriptional gene expression silencing. Yet the explorat...

    Michal Goralski, Paula Sobieszczanska, Aleksandra Obrepalska-Steplowska, Aleksandra Swiercz, Agnieszka Zmienko and Marek Figlerowicz

    Plant Methods 2016 12:28

    Published on: 20 May 2016

  12. Research

    Solanum venturii, a suitable model system for virus-induced gene silencing studies in potato reveals StMKK6 as an important player in plant immunity

    Virus-induced gene silencing (VIGS) is an optimal tool for functional analysis of genes in plants, as the viral vector spreads throughout the plant and causes reduced expression of selected gene over the whole...

    David Dobnik, Ana Lazar, Tjaša Stare, Kristina Gruden, Vivianne G. A. A. Vleeshouwers and Jana Žel

    Plant Methods 2016 12:29

    Published on: 20 May 2016

  13. Methodology

    Protocol: a method to study the direct reprogramming of lateral root primordia to fertile shoots

    Plants have the remarkable property to elaborate entire body plan from any tissue part. The conversion of lateral root primordium (LRP) to shoot is an ideal method for plant propagation and for plant researche...

    Abdul Kareem, Dhanya Radhakrishnan, Xin Wang, Subhikshaa Bagavathiappan, Zankhana B. Trivedi, Kaoru Sugimoto, Jian Xu, Ari Pekka Mähönen and Kalika Prasad

    Plant Methods 2016 12:27

    Published on: 12 May 2016

  14. Software

    ExactSearch: a web-based plant motif search tool

    Plant biologists frequently need to examine if a sequence motif bound by a specific transcription or translation factor is present in the proximal promoters or 3′ untranslated regions (3′ UTR) of a set of pla...

    Chathura Gunasekara, Avinash Subramanian, Janaki Venkata Ram Kumar Avvari, Bin Li, Su Chen and Hairong Wei

    Plant Methods 2016 12:26

    Published on: 28 April 2016

  15. Methodology

    An improved procedure for isolation of high-quality RNA from nematode-infected Arabidopsis roots through laser capture microdissection

    Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profo...

    Muhammad Shahzad Anjam, Yvonne Ludwig, Frank Hochholdinger, Chisato Miyaura, Masaki Inada, Shahid Siddique and Florian M. W. Grundler

    Plant Methods 2016 12:25

    Published on: 26 April 2016

  16. Methodology

    The utility of flow sorting to identify chromosomes carrying a single copy transgene in wheat

    Identification of transgene insertion sites in plant genomes has practical implications for crop breeding and is a stepping stone to analyze transgene function. However, single copy sequences are not always ea...

    Petr Cápal, Takashi R. Endo, Jan Vrána, Marie Kubaláková, Miroslava Karafiátová, Eva Komínková, Isabel Mora-Ramírez, Winfriede Weschke and Jaroslav Doležel

    Plant Methods 2016 12:24

    Published on: 25 April 2016

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