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  1. In vivo detection of protein-bound genomic regions can be achieved by combining chromatin-immunoprecipitation with next-generation sequencing technology (ChIP-seq). The large amount of sequence data produced by t...

    Authors: Jose M Muiño, Kerstin Kaufmann, Roeland CHJ van Ham, Gerco C Angenent and Pawel Krajewski

    Citation: Plant Methods 2011 7:11

    Content type: Software

    Published on:

  2. Artificial chromosomes (ACs) are a promising next-generation vector for genetic engineering. The most common methods for developing AC constructs are to clone and combine centromeric DNA and telomeric DNA frag...

    Authors: Li Lin, Dal-Hoe Koo, Wenli Zhang, Joseph St Peter and Jiming Jiang

    Citation: Plant Methods 2011 7:10

    Content type: Methodology

    Published on:

  3. There is an increasing demand for renewable resources to replace fossil fuels. However, different applications such as the production of secondary biofuels or combustion for energy production require different...

    Authors: Guanwu Zhou, Gail Taylor and Andrea Polle

    Citation: Plant Methods 2011 7:9

    Content type: Research

    Published on:

  4. In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queri...

    Authors: Sandra Dèrozier, Franck Samson, Jean-Philippe Tamby, Cécile Guichard, Véronique Brunaud, Philippe Grevet, Séverine Gagnot, Philippe Label, Jean-Charles Leplé, Alain Lecharny and Sébastien Aubourg

    Citation: Plant Methods 2011 7:8

    Content type: Database

    Published on:

  5. Plant viruses are useful expression vectors because they can mount systemic infections allowing large amounts of recombinant protein to be produced rapidly in differentiated plant tissues. Pepino mosaic virus ...

    Authors: Raquel N Sempere, Pedro Gómez, Verónica Truniger and Miguel A Aranda

    Citation: Plant Methods 2011 7:6

    Content type: Methodology

    Published on:

  6. Small RNAs emerged over the last decade as key regulators in diverse biological processes in eukaryotic organisms. To identify and study small RNAs, good and efficient protocols are necessary to isolate them, ...

    Authors: FlordeFátima Rosas-Cárdenas, Noé Durán-Figueroa, Jean-Philippe Vielle-Calzada, Andrés Cruz-Hernández, Nayelli Marsch-Martínez and Stefan de Folter

    Citation: Plant Methods 2011 7:4

    Content type: Methodology

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  7. With the establishment of advanced technology facilities for high throughput plant phenotyping, the problem of estimating plant biomass of individual plants from their two dimensional images is becoming increa...

    Authors: Mahmood R Golzarian, Ross A Frick, Karthika Rajendran, Bettina Berger, Stuart Roy, Mark Tester and Desmond S Lun

    Citation: Plant Methods 2011 7:2

    Content type: Methodology

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  8. Inkjet micropatterning is a versatile deposition technique with broad applications in numerous fields. However, its application in plant science is largely unexplored. Leaf expansion is one of the most importa...

    Authors: Lisheng Wang, Simon T Beyer, Quentin CB Cronk and Konrad Walus

    Citation: Plant Methods 2011 7:1

    Content type: Methodology

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  9. Quantification of transcripts, proteins, or metabolites is straightforward when the factor used to normalize these values remains constant between samples. However, normalization factors often vary among sampl...

    Authors: Hiroshi Shimada, Takeshi Obayashi, Naoki Takahashi, Minami Matsui and Atsushi Sakamoto

    Citation: Plant Methods 2010 6:29

    Content type: Methodology

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  10. Virus-induced gene silencing (VIGS) is an alternative reverse genetics tool for silencing of genes in some plants, which are difficult to transform. The pea early-browning virus (PEBV) has been developed as a ...

    Authors: Mette Grønlund, Anne Olsen, Elisabeth I Johansen and Iver Jakobsen

    Citation: Plant Methods 2010 6:28

    Content type: Methodology

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  11. Programmed cell death (PCD) is an essential process for the life cycle of all multicellular organisms. In higher plants however, relatively little is known about the cascade of genes and signalling molecules r...

    Authors: Bennett Young, Raymond Wightman, Robert Blanvillain, Sydney B Purcel and Patrick Gallois

    Citation: Plant Methods 2010 6:27

    Content type: Methodology

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  12. Gene silencing vectors based on Barley stripe mosaic virus (BSMV) are used extensively in cereals to study gene function, but nearly all studies have been limited to genes expressed in leaves of barley and wheat....

    Authors: Andrzej Pacak, Katrin Geisler, Bodil Jørgensen, Maria Barciszewska-Pacak, Lena Nilsson, Tom Hamborg Nielsen, Elisabeth Johansen, Mette Grønlund, Iver Jakobsen and Merete Albrechtsen

    Citation: Plant Methods 2010 6:26

    Content type: Methodology

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  13. About 10% of all genes in eukaryote genomes are predicted to encode transcription factors. The specific binding of transcription factors to short DNA-motifs influences the expression of neighbouring genes. How...

    Authors: Luise H Brand, Tobias Kirchler, Sabine Hummel, Christina Chaban and Dierk Wanke

    Citation: Plant Methods 2010 6:25

    Content type: Methodology

    Published on:

  14. Some plants inhabiting saline environment remove salts via the salt glands embedded in the epidermal tissues. Cytological studies of salt glands will provide valuable information to our understanding of the se...

    Authors: Wee-Kee Tan, Tit-Meng Lim and Chiang-Shiong Loh

    Citation: Plant Methods 2010 6:24

    Content type: Methodology

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  15. The cultivar Micro-Tom (MT) is regarded as a model system for tomato genetics due to its short life cycle and miniature size. However, efforts to improve tomato genetic transformation have led to protocols dep...

    Authors: Lilian E Pino, Simone Lombardi-Crestana, Mariana S Azevedo, Danielle C Scotton, Lucélia Borgo, Vera Quecini, Antonio Figueira and Lázaro EP Peres

    Citation: Plant Methods 2010 6:23

    Content type: Methodology

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  16. Complete chloroplast genome sequences provide a valuable source of molecular markers for studies in molecular ecology and evolution of plants. To obtain complete genome sequences, recent studies have made use ...

    Authors: Robin A Atherton, Bennet J McComish, Lara D Shepherd, Lorraine A Berry, Nick W Albert and Peter J Lockhart

    Citation: Plant Methods 2010 6:22

    Content type: Methodology

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  17. Salicylic acid (SA) is a key defense signal molecule against biotrophic pathogens in plants. Quantification of SA levels in plants is critical for dissecting the SA-mediated immune response. Although HPLC and ...

    Authors: George Marek, Ryan Carver, Yezhang Ding, Deepak Sathyanarayan, Xudong Zhang and Zhonglin Mou

    Citation: Plant Methods 2010 6:21

    Content type: Methodology

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  18. The biosynthesis of plant natural products in sub-dermal secretory cavities is poorly understood at the molecular level, largely due to the difficulty of physically isolating these structures for study. Our ai...

    Authors: Jason QD Goodger, Allison M Heskes, Madeline C Mitchell, Drew J King, Elizabeth H Neilson and Ian E Woodrow

    Citation: Plant Methods 2010 6:20

    Content type: Methodology

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  19. The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DN...

    Authors: Daniel J Marshall, Alice Hayward, Dominic Eales, Michael Imelfort, Jiri Stiller, Paul J Berkman, Terry Clark, Megan McKenzie, Kaitao Lai, Chris Duran, Jacqueline Batley and David Edwards

    Citation: Plant Methods 2010 6:19

    Content type: Database

    Published on:

  20. Although the complete genome sequence and annotation of Arabidopsis were released at the end of year 2000, it is still a great challenge to understand the function of each gene in the Arabidopsis genome. One w...

    Authors: Yong-Li Xiao, Julia C Redman, Erin L Monaghan, Jun Zhuang, Beverly A Underwood, William A Moskal, Wei Wang, Hank C Wu and Christopher D Town

    Citation: Plant Methods 2010 6:18

    Content type: Methodology

    Published on:

  21. Despite the wide spread application of confocal and multiphoton laser scanning microscopy in plant biology, leaf phenotype assessment still relies on two-dimensional imaging with a limited appreciation of the ...

    Authors: Nathalie Wuyts, Jean-Christophe Palauqui, Geneviève Conejero, Jean-Luc Verdeil, Christine Granier and Catherine Massonnet

    Citation: Plant Methods 2010 6:17

    Content type: Methodology

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  22. A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of Eucalyptus, a genus that includes over 700 species, some of which are used worldwide...

    Authors: Carolina P Sansaloni, César D Petroli, Jason Carling, Corey J Hudson, Dorothy A Steane, Alexander A Myburg, Dario Grattapaglia, René E Vaillancourt and Andrzej Kilian

    Citation: Plant Methods 2010 6:16

    Content type: Methodology

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  23. Cloning of gene casettes and other DNA sequences into the conventional vectors for biolistic or Agrobacterium-mediated transformation is hampered by a limited amount of unique restriction sites and by the difficu...

    Authors: Kim H Hebelstrup, Michael W Christiansen, Massimiliano Carciofi, Birgitte Tauris, Henrik Brinch-Pedersen and Preben B Holm

    Citation: Plant Methods 2010 6:15

    Content type: Methodology

    Published on:

  24. Successful defence of tobacco plants against attack from the oomycete Phytophthora nicotianae includes a type of local programmed cell death called the hypersensitive response. Complex and not completely understo...

    Authors: Alfredo J Ibáñez, Judith Scharte, Philipp Bones, Alexander Pirkl, Stefan Meldau, Ian T Baldwin, Franz Hillenkamp, Engelbert Weis and Klaus Dreisewerd

    Citation: Plant Methods 2010 6:14

    Content type: Methodology

    Published on:

  25. Functional mapping is a powerful approach for mapping quantitative trait loci (QTLs) that control biological processes. Functional mapping incorporates mathematical aspects of growth and development into a gen...

    Authors: Qin Li, Zhongwen Huang, Meng Xu, Chenguang Wang, Junyi Gai, Youjun Huang, Xiaoming Pang and Rongling Wu

    Citation: Plant Methods 2010 6:13

    Content type: Methodology

    Published on:

  26. Genotype analysis using multiple single nucleotide polymorphisms (SNPs) is a useful but labor-intensive or high-cost procedure in plant research. Here we describe an alternative genotyping method that is suite...

    Authors: Naoki Hirotsu, Naomi Murakami, Takayuki Kashiwagi, Kazuhiro Ujiie and Ken Ishimaru

    Citation: Plant Methods 2010 6:12

    Content type: Methodology

    Published on:

  27. Suppression subtractive hybridization is a popular technique for gene discovery from non-model organisms without an annotated genome sequence, such as cowpea (Vigna unguiculata (L.) Walp). We aimed to use this me...

    Authors: Nanette Coetzer, Inge Gazendam, Dean Oelofse and Dave K Berger

    Citation: Plant Methods 2010 6:10

    Content type: Methodology

    Published on:

  28. Microarrays are a powerful tool used for the determination of global RNA expression. There is an increasing requirement to focus on profiling gene expression in tissues where it is difficult to obtain large qu...

    Authors: Tara J Holman, Michael H Wilson, Kim Kenobi, Ian L Dryden, T Charlie Hodgman, Andrew TA Wood and Michael J Holdsworth

    Citation: Plant Methods 2010 6:9

    Content type: Methodology

    Published on:

  29. Metabolic engineering of seed biosynthetic pathways to diversify and improve crop product quality is a highly active research area. The validation of genes driven by seed-specific promoters is time-consuming s...

    Authors: James R Petrie, Pushkar Shrestha, Qing Liu, Maged P Mansour, Craig C Wood, Xue-Rong Zhou, Peter D Nichols, Allan G Green and Surinder P Singh

    Citation: Plant Methods 2010 6:8

    Content type: Methodology

    Published on:

  30. In situ hybridization is a general molecular method typically used for the localization of mRNA transcripts in plants. The method provides a valuable tool to unravel the connection between gene expression and ana...

    Authors: Jaana Vuosku, Suvi Sutela, Mira Sääskilahti, Johanna Kestilä, Anne Jokela, Tytti Sarjala and Hely Häggman

    Citation: Plant Methods 2010 6:7

    Content type: Methodology

    Published on:

  31. Progress in plant cell cycle research is highly dependent on reliable methods for detection of cells replicating DNA. Frequency of S-phase cells (cells in DNA synthesis phase) is a basic parameter in studies o...

    Authors: Edit Kotogány, Dénes Dudits, Gábor V Horváth and Ferhan Ayaydin

    Citation: Plant Methods 2010 6:5

    Content type: Methodology

    Published on:

  32. TILLING (Targeting Induced Local Lesions in Genomes) is a reverse genetics procedure for identifying point mutations in selected gene(s) amplified from a mutagenized population using high-throughput detection ...

    Authors: Yellamaraju Sreelakshmi, Soni Gupta, Reddaiah Bodanapu, Vineeta Singh Chauhan, Mickey Hanjabam, Sherinmol Thomas, Vijee Mohan, Sulabha Sharma, Rajeswari Srinivasan and Rameshwar Sharma

    Citation: Plant Methods 2010 6:3

    Content type: Methodology

    Published on:

  33. Interphase chromosome organization and dynamics can be studied in living cells using fluorescent tagging techniques that exploit bacterial operator/repressor systems and auto-fluorescent proteins. A nuclear-lo...

    Authors: Antonius JM Matzke, Koichi Watanabe, Johannes van der Winden, Ulf Naumann and Marjori Matzke

    Citation: Plant Methods 2010 6:2

    Content type: Methodology

    Published on:

  34. The β-glucuronidase (GUS) gene reporter system is one of the most effective and employed techniques in the study of gene regulation in plant molecular biology. Improving protocols for GUS assays have rendered ...

    Authors: Simone Fior and Paolo D Gerola

    Citation: Plant Methods 2009 5:19

    Content type: Methodology

    Published on:

  35. The data generated during a course of a biological experiment/study can be sometimes be massive and its management becomes quite critical for the success of the investigation undertaken. The accumulation and a...

    Authors: Raju Naik Vankadavath, Appibhai Jakir Hussain, Reddaiah Bodanapu, Eros Kharshiing, Pinjari Osman Basha, Soni Gupta, Yellamaraju Sreelakshmi and Rameshwar Sharma

    Citation: Plant Methods 2009 5:18

    Content type: Software

    Published on:

  36. Aliphatic molecules containing free carboxyl groups are important intermediates in many metabolic and signalling reactions, however, they accumulate to low levels in tissues and are not efficiently ionized by ...

    Authors: Mario Kallenbach, Ian T Baldwin and Gustavo Bonaventure

    Citation: Plant Methods 2009 5:17

    Content type: Methodology

    Published on:

  37. Protoplasts isolated from leaves are useful materials in plant research. One application, the transient expression of recombinant genes using Arabidopsis mesophyll protoplasts (TEAMP), is currently commonly used ...

    Authors: Fu-Hui Wu, Shu-Chen Shen, Lan-Ying Lee, Shu-Hong Lee, Ming-Tsar Chan and Choun-Sea Lin

    Citation: Plant Methods 2009 5:16

    Content type: Methodology

    Published on:

  38. The diploid woodland strawberry (Fragaria vesca) is an attractive system for functional genomics studies. Its small stature, fast regeneration time, efficient transformability and small genome size, together with...

    Authors: Janet P Slovin, Kyle Schmitt and Kevin M Folta

    Citation: Plant Methods 2009 5:15

    Content type: Methodology

    Published on:

  39. The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. Th...

    Authors: Ivan I Atanassov, Ilian I Atanassov, JPeter Etchells and Simon R Turner

    Citation: Plant Methods 2009 5:14

    Content type: Methodology

    Published on:

  40. The establishment of mutant populations together with the strategies for targeted mutation detection has been applied successfully to a large number of organisms including many species in the plant kingdom. Co...

    Authors: Antoine LF Gady, Freddy WK Hermans, Marion HBJ Van de Wal, Eibertus N van Loo, Richard GF Visser and Christian WB Bachem

    Citation: Plant Methods 2009 5:13

    Content type: Methodology

    Published on:

  41. Quantitative multi-elemental analysis by inductively coupled plasma (ICP) spectrometry depends on a complete digestion of solid samples. However, fast and thorough sample digestion is a challenging analytical ...

    Authors: Thomas H Hansen, Kristian H Laursen, Daniel P Persson, Pai Pedas, Søren Husted and Jan K Schjoerring

    Citation: Plant Methods 2009 5:12

    Content type: Methodology

    Published on:

  42. Fluorescent hybridization techniques are widely used to study the functional organization of different compartments within the mammalian nucleus. However, few examples of such studies are known in the plant ki...

    Authors: Leïla Tirichine, Philippe Andrey, Eric Biot, Yves Maurin and Valérie Gaudin

    Citation: Plant Methods 2009 5:11

    Content type: Methodology

    Published on:

  43. Dense genetic maps, together with the efficiency and accuracy of their construction, are integral to genetic studies and marker assisted selection for plant breeding. High-throughput multiplex markers that are...

    Authors: Maggie Knox, Carol Moreau, James Lipscombe, David Baker and Noel Ellis

    Citation: Plant Methods 2009 5:10

    Content type: Methodology

    Published on:

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