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  1. Content type: Software

    Research in plant science laboratories often involves usage of many different species, cultivars, ecotypes, mutants, alleles or transgenic lines. This creates a great challenge to keep track of the identity of...

    Authors: Vivien Exner, Matthias Hirsch-Hoffmann, Wilhelm Gruissem and Lars Hennig

    Citation: Plant Methods 2008 4:1

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  2. Content type: Methodology

    MicroRNAs (miRNAs) are a class of small non-coding RNAs with a critical role in development and environmental responses. Efficient and reliable detection of miRNAs is an essential step towards understanding th...

    Authors: Erika Varkonyi-Gasic, Rongmei Wu, Marion Wood, Eric F Walton and Roger P Hellens

    Citation: Plant Methods 2007 3:12

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  3. Content type: Methodology

    Chromatin remodeling, histone modifications and other chromatin-related processes play a crucial role in gene regulation. A very useful technique to study these processes is chromatin immunoprecipitation (ChIP...

    Authors: Max Haring, Sascha Offermann, Tanja Danker, Ina Horst, Christoph Peterhansel and Maike Stam

    Citation: Plant Methods 2007 3:11

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  4. Content type: Research

    The results of transcriptome microarray analysis are usually presented as a list of differentially expressed genes. As these lists can be long, it is hard to interpret the desired experimental treatment effect...

    Authors: Ana Rotter, Björn Usadel, Špela Baebler, Mark Stitt and Kristina Gruden

    Citation: Plant Methods 2007 3:10

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  5. Content type: Methodology

    Quantitative reverse transcription – polymerase chain reaction (qRT-PCR) has been demonstrated to be particularly suitable for the analysis of weakly expressed genes, such as those encoding transcription facto...

    Authors: Camila Caldana, Wolf-Rüdiger Scheible, Bernd Mueller-Roeber and Slobodan Ruzicic

    Citation: Plant Methods 2007 3:7

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  6. Content type: Methodology

    The diploid, Solanum caripense, a wild relative of potato and tomato, possesses valuable resistance to potato late blight and we are interested in the genetic base of this resistance. Due to extremely low levels ...

    Authors: Joy Nakitandwe, Friederike Trognitz and Bodo Trognitz

    Citation: Plant Methods 2007 3:2

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  7. Content type: Methodology

    There is considerable interest in rapid assays or screening systems for assigning gene function. However, analysis of gene function in the flowers of some species is restricted due to the difficulty of produci...

    Authors: Yongjin Shang, Kathy E Schwinn, Michael J Bennett, Donald A Hunter, Toni L Waugh, Nilangani N Pathirana, David A Brummell, Paula E Jameson and Kevin M Davies

    Citation: Plant Methods 2007 3:1

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  8. Content type: Research

    Genome analysis of soybean (Glycine max L.) has been complicated by its paleo-autopolyploid nature and conserved homeologous regions. Landmarks of expressed sequence tags (ESTs) located within a minimum tile path...

    Authors: Kay L Shopinski, Muhammad J Iqbal, Jeffry L Shultz, Dheepakkumaran Jayaraman and David A Lightfoot

    Citation: Plant Methods 2006 2:20

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  9. Content type: Methodology

    The floral dip method of transformation by immersion of inflorescences in a suspension of Agrobacterium is the method of choice for Arabidopsis transformation. The presence of a marker, usually antibiotic- or her...

    Authors: Samuel J Harrison, Ellie K Mott, Kate Parsley, Sue Aspinall, John C Gray and Amanda Cottage

    Citation: Plant Methods 2006 2:19

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  10. Content type: Review

    Genetic engineering of commercially important crops has become routine in many laboratories. However, the inability to predict where a transgene will integrate and to efficiently select plants with stable leve...

    Authors: Ana Paula Santos, Eva Wegel, George C Allen, William F Thompson, Eva Stoger, Peter Shaw and Rita Abranches

    Citation: Plant Methods 2006 2:18

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  11. Content type: Methodology

    We have developed a functional genomics approach based on expression cloning in Xenopus oocytes to identify plant transporter function. We utilized the full-length cDNA databases to generate a normalized library ...

    Authors: Hussam H Nour-Eldin, Morten HH Nørholm and Barbara A Halkier

    Citation: Plant Methods 2006 2:17

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  12. Content type: Methodology

    The Agrobacterium vacuum (Bechtold et al 1993) and floral-dip (Clough and Bent 1998) are very efficient methods for generating transgenic Arabidopsis plants. These methods allow plant transformation without the n...

    Authors: Elke Logemann, Rainer P Birkenbihl, Bekir Ülker and Imre E Somssich

    Citation: Plant Methods 2006 2:16

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  13. Content type: Methodology

    Mg chelatase is a multi-subunit enzyme that catalyses the first committed step of chlorophyll biosynthesis. Studies in higher plants and algae indicate that the Mg chelatase reaction product, Mg-protoporphyrin...

    Authors: Ruairidh JH Sawers, Phyllis R Farmer, Peter Moffett and Thomas P Brutnell

    Citation: Plant Methods 2006 2:15

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  14. Content type: Methodology

    Strategies for robust quantitative comparison between different biological samples are of high importance in experiments that address biological questions beyond the establishment of protein lists. Here, we pr...

    Authors: Wolfgang R Engelsberger, Alexander Erban, Joachim Kopka and Waltraud X Schulze

    Citation: Plant Methods 2006 2:14

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  15. Content type: Methodology

    Transient assays using protoplasts are ideal for processing large quantities of genetic data coming out of hi-throughput assays. Previously, protoplasts have routinely been prepared from dicot tissue or cell s...

    Authors: Rebecca Bart, Mawsheng Chern, Chang-Jin Park, Laura Bartley and Pamela C Ronald

    Citation: Plant Methods 2006 2:13

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  16. Content type: Methodology

    The ultimate goal of proteomic analysis of a cell compartment should be the exhaustive identification of resident proteins; excluding proteins from other cell compartments. Reaching such a goal closely depends...

    Authors: Leila Feiz, Muhammad Irshad, Rafael F Pont-Lezica, Hervé Canut and Elisabeth Jamet

    Citation: Plant Methods 2006 2:10

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  17. Content type: Methodology

    The creation of minimally redundant tile paths (hereafter MTP) from contiguous sets of overlapping clones (hereafter contigs) in physical maps is a critical step for structural and functional genomics. Build 4...

    Authors: JL Shultz, C Yesudas, S Yaegashi, AJ Afzal, S Kazi and DA Lightfoot

    Citation: Plant Methods 2006 2:9

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  18. Content type: Methodology

    Uncovering the key sequence elements in gene promoters that regulate the expression of plant genomes is a huge task that will require a series of complementary methods for prediction, substantial innovations i...

    Authors: Kathryn E Holt, A Harvey Millar and James Whelan

    Citation: Plant Methods 2006 2:8

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  19. Content type: Methodology

    The pH is an important parameter controlling many metabolic and signalling pathways in living cells. Recombinant fluorescent pH indicators (pHluorins) have come into vogue for monitoring cellular pH. They are ...

    Authors: Alexander Schulte, Inken Lorenzen, Markus Böttcher and Christoph Plieth

    Citation: Plant Methods 2006 2:7

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  20. Content type: Editorial

    As an Open Access journal dedicated to promoting technological innovation in plant biology, Plant Methods occupies a unique niche amongst plant journals. To fund its open access policy, and to enable it to contin...

    Authors: Brian G Forde and Michael R Roberts

    Citation: Plant Methods 2006 2:6

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  21. Content type: Methodology

    In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic k...

    Authors: Yoshikazu Hasegawa, Motoaki Seki, Yoshiki Mochizuki, Naohiko Heida, Katsura Hirosawa, Naoki Okamoto, Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Kisik Lee, Shigehiko Kanaya, Taku Demura, Kazuo Shinozaki, Akihiko Konagaya and Tetsuro Toyoda

    Citation: Plant Methods 2006 2:5

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  22. Content type: Methodology

    The preparation of expressional cDNA libraries for use in the yeast two-hybrid system is quick and efficient when using the dedicated Clontech™ product, the MATCHMAKER Library Construction and Screening Kit 3....

    Authors: Sergiy Lopato, Natalia Bazanova, Sarah Morran, Andrew S Milligan, Neil Shirley and Peter Langridge

    Citation: Plant Methods 2006 2:3

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  23. Content type: Methodology

    Abscission is the regulated dropping of plant organs, such as leaves or flower petals. This process involves a break down of the cell wall between layers of cells in the abscission zone, causing the organ to b...

    Authors: Kevin A Lease, Sung Ki Cho and John C Walker

    Citation: Plant Methods 2006 2:2

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  24. Content type: Commentary

    Appropriate biological interpretation of microarray data calls for relevant experimental annotation. The widely accepted MIAME guidelines provide a generic, organism-independant standard for minimal informatio...

    Authors: Philip Zimmermann, Beatrice Schildknecht, David Craigon, Margarita Garcia-Hernandez, Wilhelm Gruissem, Sean May, Gaurab Mukherjee, Helen Parkinson, Seung Rhee, Ulrich Wagner and Lars Hennig

    Citation: Plant Methods 2006 2:1

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  25. Content type: Methodology

    In silico analyses based on sequence similarities with animal channels have identified a large number of plant genes likely to encode ion channels. The attempts made to characterise such putative plant channel...

    Authors: E Hosy, G Duby, A-A Véry, A Costa, H Sentenac and J-B Thibaud

    Citation: Plant Methods 2005 1:14

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  26. Content type: Research

    We describe novel plasmid vectors for transient gene expression using Agrobacterium, infiltrated into Nicotiana benthamiana leaves. We have generated a series of pGreenII cloning vectors that are ideally suited t...

    Authors: Roger P Hellens, Andrew C Allan, Ellen N Friel, Karen Bolitho, Karryn Grafton, Matthew D Templeton, Sakuntala Karunairetnam, Andrew P Gleave and William A Laing

    Citation: Plant Methods 2005 1:13

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  27. Content type: Methodology

    High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available f...

    Authors: John P Hammond, Martin R Broadley, David J Craigon, Janet Higgins, Zoe F Emmerson, Henrik J Townsend, Philip J White and Sean T May

    Citation: Plant Methods 2005 1:10

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  28. Content type: Methodology

    Protein phosphorylation is accepted as a major regulatory pathway in plants. More than 1000 protein kinases are predicted in the Arabidopsis proteome, however, only a few studies look systematically for in vivo p...

    Authors: Florian Wolschin and Wolfram Weckwerth

    Citation: Plant Methods 2005 1:9

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  29. Content type: Methodology

    In situ hybridisation can provide cellular, and in some cases sub-cellular, resolution of mRNA levels within multicellular organisms and is widely used to provide spatial and temporal information on gene expressi...

    Authors: Sinéad Drea, Julia Corsar, Brian Crawford, Peter Shaw, Liam Dolan and John H Doonan

    Citation: Plant Methods 2005 1:8

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  30. Content type: Methodology

    Eukaryotic organisms are defined by the presence of a nucleus, which encloses the chromosomal DNA, and is characterized by its DNA content (C-value). Complex eukaryotic organisms contain organs and tissues tha...

    Authors: Changqing Zhang, Fang Cheng Gong, Georgina M Lambert and David W Galbraith

    Citation: Plant Methods 2005 1:7

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  31. Content type: Methodology

    Plant genome sequence data now provide opportunities to conduct molecular genetic studies at the level of the whole gene locus and above. Such studies will be greatly facilitated by adopting and developing fur...

    Authors: Laura C Roden, Berthold Göttgens and Effie S Mutasa-Göttgens

    Citation: Plant Methods 2005 1:6

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  32. Content type: Methodology

    Many established PCR-based approaches in plant molecular biology rely on lengthy and expensive methods for isolation of nucleic acids. Although several rapid DNA isolation protocols are available, they have no...

    Authors: Kenneth Berendzen, Iain Searle, Dean Ravenscroft, Csaba Koncz, Alfred Batschauer, George Coupland, Imre E Somssich and Bekir Ülker

    Citation: Plant Methods 2005 1:4

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