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		Methodology An efficient flat-surface collar-free grafting method for Arabidopsis thaliana seedlings Nayelli Marsch Martínez, John Franken, Karla L Gonzalez-Aguilera, Stefan de Folter, Gerco Angenent, Elena R Alvarez-Buylla Plant Methods 2013, 9:14 (4 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Grafting is an extremely important technique for the study of long distance signalling in plants. The authors describe substantial improvements to existing methodologies that both increase the success rate and the throughput of hypocotyl grafting in Arabidopsis.
		Methodology A selective pretreatment method for determination of endogenous active brassinosteroids in plant tissues: double layered solid phase extraction combined with boronate affinity polymer monolith microextraction Jun Ding, Li-Jing Mao, Bi-Feng Yuan, Yu-Qi Feng Plant Methods 2013, 9:13 (18 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary Measurement of brassinosteroids, an important class of phytohormone, typically requires large amounts of tissue and laborious extraction and sample preparation. Here, a new method based on double layered solid phase extraction combined with boronate affinity polymer monolith microextraction is described which permits accurate determination of several biologically-active brassinosteroid from relatively small tissue samples.
		Software Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites Parsa Hosseini, Ivan Ovcharenko, Benjamin F Matthews Plant Methods 2013, 9:12 (11 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary This article describes a software tool that can identify transcription factor binding sites from amongst large collections of promoter sequences by integrating a number of different approaches. The method is able to identify more over-represented binding site sequences than other common approaches.
		Methodology Visualizing water-filled versus embolized status of xylem conduits by desktop x-ray microtomography Jussi-Petteri Suuronen, Marko Peura, Kurt Fagerstedt, Ritva Serimaa Plant Methods 2013, 9:11 (8 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The hydraulic conductivity of the stem is a major factor determining the capability of trees to transport water from the soil to transpiring leaves. During drought conditions, the conducting capacity of the xylem can be reduced by some conduits being filled with gas, i.e. embolized. In this paper the authors show that desktop x-ray microtomography is an effective method for evaluating the water-filled versus embolized status of the stem xylem in a small living sapling. Due to its non-destructive nature, the risk of inducing embolisms during sampling is greatly reduced and compared with synchrotron imaging beamlines, the methodology is more accessible yet still provides sufficient resolution to visualize the water contents of individual cells.
		Methodology Emission spectra profiling of fluorescent proteins in living plant cells Evelien Mylle, Mirela-Corina Codreanu, Joanna Boruc, Eugenia Russinova Plant Methods 2013, 9:10 (3 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary Fluorescent proteins are an important tool for a wide variety of in vivo applications in plant biology. The authors confirm here for nine different fluorescent proteins that their in vivo emission spectra are similar to those determined in vitro and so are not influenced by the cellular environment. This information is critical for those interested in simultaneous recording of multiple fluorophores in living cells (e.g. during time-lapse experiments). They show that the collected emission spectra can be used successfully to distinguish the multiple fluorophores in vivo using a computational analysis called 'linear unmixing'. Finally, in the course of this work, they generated a collection of 20 Gateway entry clones carrying the different fluorescent protein genes which will be a valuable resource for the plant science community.
		Methodology Rapid separation of developing Arabidopsis seeds from siliques for RNA or metabolite analysis Philip David Bates, Jeremy Burke Jewell, John Browse Plant Methods 2013, 9:9 (26 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary This simple method greatly speeds up the process of harvesting developing seeds from their siliques while preserving their contents in liquid nitrogen. It should be a boon for anyone who uses Arabidopsis as a model system for studying seed development.
		Software Recovering complete plant root system architectures from soil via X-ray μ-Computed Tomography Stefan Mairhofer, Susan Zappala, Saoirse Tracy, Craig Sturrock, Malcolm John Bennett, Sacha Jon Mooney, Tony Paul Pridmore Plant Methods 2013, 9:8 (20 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology A novel system for in situ determination of heat tolerance of plants: first results on alpine dwarf shrubs Othmar Buchner, Matthias Karadar, Ines Bauer, Gilbert Neuner Plant Methods 2013, 9:7 (14 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary With increasing global temperatures, understanding how plants respond to heat stress in their natural habitat has become more and more important. The authors describe a system that can be used in the field to apply controlled heat treatments either in natural sunlight or in the dark and without having to remove plant parts. Because the plants remain in situ, their ability to recover from the heat stress can also be monitored.
		Review Advances in plant gene-targeted and functional markers: a review Péter Poczai, Ildikó Varga, Maarja Laos, András Cseh, Neil Bell, Jari PT Valkonen, Jaakko Hyvönen Plant Methods 2013, 9:6 (13 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The authors provide a comprehensive review of advances in PCR-based multi-locus techniques for DNA fingerprinting using both gene-targeted and functional markers.
		Methodology Accounting for variation in designing greenhouse experiments with special reference to greenhouses containing plants on conveyor systems Chris J Brien, Bettina Berger, Huwaida Rabie, Mark Tester Plant Methods 2013, 9:5 (8 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary The authors have tackled the problem of how best to design greenhouse experiments and the approaches that should be taken for statistical analysis of the data. For example, is it better to move plants around the greenhouse during an experiment or to leave them in the same place and account for the environmental gradients in the final statistical analysis?
		Methodology Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants Simon J Conn, Bradleigh Hocking, Maclin Dayod, Bo Xu, Asmini Athman, Sam Henderson, Lucy Aukett, Vanessa Conn, Monique K Shearer, Sigfredo Fuentes, Stephen D Tyerman, Matthew Gilliham Plant Methods 2013, 9:4 (5 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| 1 comment \| Editor’s summary Hydroponics is an extremely useful technique for growing plants under controlled nutrient conditions, particularly where clean roots are needed for physiological or microscopic analysis or for RNA extraction. The detailed protocol set out here should make it straightforward for other laboratories to rapidly and successfully adopt the technique. A video is also available at http://t.co/WoAYgYy84C.
		Methodology Rhizo-lysimetry: facilities for the simultaneous study of root behaviour and resource use by agricultural crop and pasture systems Philip L Eberbach, Jeffrey Hoffmann, Sergio J Moroni, Leonard J Wade, Leslie A Weston Plant Methods 2013, 9:3 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new crop research facility is described that allows both root growth and changes in soil water content to be monitored under field conditions. The facility is of particular relevance given problems with long-term drought in southern Australia and global concerns about climate change and limiting water supplies.
		Methodology Synchronous high-resolution phenotyping of leaf and root growth in Nicotiana tabacum over 24-h periods with GROWMAP-plant Tom Ruts, Shizue Matsubara, Achim Walter Plant Methods 2013, 9:2 (23 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary GROWMAP-plant is an elegant new method that allows growth processes to be monitored simultaneously in the above and below-ground parts of the plant over 24 h periods. The method is validated by using it to demonstrate the differences between roots and leaves in the sensitivity of their growth patterns to environmental perturbation.
		Methodology Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems Guillaume Lobet, Xavier Draye Plant Methods 2013, 9:1 (4 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Improved methods for analysing root architecture are always being sought, This paper makes a significant cntribution to progress in this field by developing a novel procedure for analysing roots grown in rhizotrons. The method combines the strengths of two classical methods: in situ recording of root placement (by tracing on acetate sheets) and high resolution scanning of root system fragments after removal from the rhizotron.
		Methodology Inflorescence stem grafting made easy in Arabidopsis Nazia Nisar, Shelley Verma, Barry J Pogson, Christopher I Cazzonelli Plant Methods 2012, 8:50 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Most micrografting experiments in Arabidopsis use hypocotyl grafts. To enable detailed studies of long distance signals that promote reproduction, the authors have developed improved techniques for inflorescence grafting in Arabidopsis.
		Methodology CalloseMeasurer: a novel software solution to measure callose deposition and recognise spreading callose patterns Ji Zhou, Thomas Spallek, Christine Faulkner, Silke Robatzek Plant Methods 2012, 8:49 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The authors present a detailed series of image analysis tools for the detection and measurement in plant tissues of callose deposition, an important defence against fungal pathogens. The software should be very useful for researchers interested in quantifying callose-mediated defences against plant pathogens. In addition, automated analysis of the progress of callose development over time can be used to track fungal development within the leaf.
		Methodology Protocol: Chromatin immunoprecipitation (ChIP) methodology to investigate histone modifications in two model diatom species Xin Lin, Leïla Tirichine, Chris Bowler Plant Methods 2012, 8:48 (7 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A detailed protocol for performing chromatin immunoprecipitation experiments with two model diatoms is described. The authors report that the method can be easily adapted to other diatoms and eukaryotic phytoplankton species.
		Methodology An UPLC-MS/MS method for highly sensitive high-throughput analysis of phytohormones in plant tissues Gerd Ulrich Balcke, Vinzenz Handrick, Nick Bergau, Mandy Fichtner, Anja Henning, Hagen Stellmach, Alain Tissier, Bettina Hause, Andrej Frolov Plant Methods 2012, 8:47 (22 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this paper, the authors present a UPLC-based protocol for rapid, high sensitivity analysis of phytohormones from relatively small samples of plant tissue. In particular, improvements in detection limits following testing of different solid phase extraction techniques and different buffers are a useful extension of current knowledge. The protocol is fully validated and applied here to measure hormone changes following mechanical wounding in tomato.
		Methodology Plant lighting system with five wavelength-band light-emitting diodes providing photon flux density and mixing ratio control Akira Yano, Kazuhiro Fujiwara Plant Methods 2012, 8:46 (22 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Light emitting diodes (LEDs) are a rapidly developing alternative to conventional lighting for plant growth facilities. This paper provides methodology to exploit one of the biggest potential advantages of LEDs viz the ability to exercise much greater control over photon flux densities and the mixtures of wavelengths. This will be of particular interest to those with research interests in photobiology or in the applied potential of using light spectra to control plant development.
		Methodology PhenoPhyte: a flexible affordable method to quantify 2D phenotypes from imagery Jason M Green, Heidi Appel, Erin MacNeal Rehrig, Jaturon Harnsomburana, Jia-Fu Chang, Peter Balint-Kurti, Chi-Ren Shyu Plant Methods 2012, 8:45 (6 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The analysis of digital images for plant phenotyping is an increasingly important issue in plant science. This paper provides a versatile, web-based method for semi-automated quantification of two-dimensional traits from digital images. The method is validated by using it to analyse a variety of traits in multiple plant species.
		Methodology FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei Filipe Borges, Rui Gardner, Telma Lopes, Joseph P Calarco, Leonor C Boavida, R Slotkin, Robert A Martienssen, Jörg D Becker Plant Methods 2012, 8:44 (17 October 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary The paper provides simple and efficient FACS-based purification protocols for Arabidopsis microspores, vegetative nuclei and sperm cells.
		Software Phytotracker, an information management system for easy recording and tracking of plants, seeds and plasmids Jeroen Nieuwland, Emily Sornay, Angela Marchbank, Barend HJ de Graaf, James AH Murray Plant Methods 2012, 8:43 (13 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 'Phytotracker' is a database utility for managing DNA, plants and seed stocks in a typical plant science research laboratory. The system is a relatively simple, user-friendly database application based on the commercial Filemaker software platform. It provides a simple mechanism for recording the generation, use and storage of DNA, plants and seeds, and can print labels for use in experiments or for storage of stocks.
		Methodology Concurrent profiling of indole-3-acetic acid, abscisic acid, and cytokinins and structurally related purines by high-performance-liquid-chromatography tandem electrospray mass spectrometry Scott C Farrow, RJ Neil Emery Plant Methods 2012, 8:42 (12 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method is described for the concurrent extraction, purification and analysis of diverse plant hormones from 100 mg quantities of Arabidopsis thaliana leaf tissue.
		Methodology A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters Yun-Ru Chen, Yi Zheng, Bao Liu, Silin Zhong, Jim Giovannoni, Zhangjun Fei Plant Methods 2012, 8:41 (20 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An efficient, low-cost method for the preparation of libraries for small RNA sequencing based on the production of customized pre-adenylated adapters using T4 RNA ligase.
		Methodology A novel xylogenic suspension culture model for exploring lignification in Phyllostachys bamboo Shinjiro Ogita, Taiji Nomura, Takao Kishimoto, Yasuo Kato Plant Methods 2012, 8:40 (14 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Bamboo is a remarkable plant but one that is difficult to study. The authors describe a model suspension culture system that will be invaluable for investigating the process of lignification in living bamboo cells.

	All
		Methodology An efficient flat-surface collar-free grafting method for Arabidopsis thaliana seedlings Nayelli Marsch Martínez, John Franken, Karla L Gonzalez-Aguilera, Stefan de Folter, Gerco Angenent, Elena R Alvarez-Buylla Plant Methods 2013, 9:14 (4 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Grafting is an extremely important technique for the study of long distance signalling in plants. The authors describe substantial improvements to existing methodologies that both increase the success rate and the throughput of hypocotyl grafting in Arabidopsis.
		Methodology A selective pretreatment method for determination of endogenous active brassinosteroids in plant tissues: double layered solid phase extraction combined with boronate affinity polymer monolith microextraction Jun Ding, Li-Jing Mao, Bi-Feng Yuan, Yu-Qi Feng Plant Methods 2013, 9:13 (18 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary Measurement of brassinosteroids, an important class of phytohormone, typically requires large amounts of tissue and laborious extraction and sample preparation. Here, a new method based on double layered solid phase extraction combined with boronate affinity polymer monolith microextraction is described which permits accurate determination of several biologically-active brassinosteroid from relatively small tissue samples.
		Software Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites Parsa Hosseini, Ivan Ovcharenko, Benjamin F Matthews Plant Methods 2013, 9:12 (11 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary This article describes a software tool that can identify transcription factor binding sites from amongst large collections of promoter sequences by integrating a number of different approaches. The method is able to identify more over-represented binding site sequences than other common approaches.
		Methodology Visualizing water-filled versus embolized status of xylem conduits by desktop x-ray microtomography Jussi-Petteri Suuronen, Marko Peura, Kurt Fagerstedt, Ritva Serimaa Plant Methods 2013, 9:11 (8 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The hydraulic conductivity of the stem is a major factor determining the capability of trees to transport water from the soil to transpiring leaves. During drought conditions, the conducting capacity of the xylem can be reduced by some conduits being filled with gas, i.e. embolized. In this paper the authors show that desktop x-ray microtomography is an effective method for evaluating the water-filled versus embolized status of the stem xylem in a small living sapling. Due to its non-destructive nature, the risk of inducing embolisms during sampling is greatly reduced and compared with synchrotron imaging beamlines, the methodology is more accessible yet still provides sufficient resolution to visualize the water contents of individual cells.
		Methodology Emission spectra profiling of fluorescent proteins in living plant cells Evelien Mylle, Mirela-Corina Codreanu, Joanna Boruc, Eugenia Russinova Plant Methods 2013, 9:10 (3 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary Fluorescent proteins are an important tool for a wide variety of in vivo applications in plant biology. The authors confirm here for nine different fluorescent proteins that their in vivo emission spectra are similar to those determined in vitro and so are not influenced by the cellular environment. This information is critical for those interested in simultaneous recording of multiple fluorophores in living cells (e.g. during time-lapse experiments). They show that the collected emission spectra can be used successfully to distinguish the multiple fluorophores in vivo using a computational analysis called 'linear unmixing'. Finally, in the course of this work, they generated a collection of 20 Gateway entry clones carrying the different fluorescent protein genes which will be a valuable resource for the plant science community.
		Methodology Rapid separation of developing Arabidopsis seeds from siliques for RNA or metabolite analysis Philip David Bates, Jeremy Burke Jewell, John Browse Plant Methods 2013, 9:9 (26 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary This simple method greatly speeds up the process of harvesting developing seeds from their siliques while preserving their contents in liquid nitrogen. It should be a boon for anyone who uses Arabidopsis as a model system for studying seed development.
		Software Recovering complete plant root system architectures from soil via X-ray μ-Computed Tomography Stefan Mairhofer, Susan Zappala, Saoirse Tracy, Craig Sturrock, Malcolm John Bennett, Sacha Jon Mooney, Tony Paul Pridmore Plant Methods 2013, 9:8 (20 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Methodology A novel system for in situ determination of heat tolerance of plants: first results on alpine dwarf shrubs Othmar Buchner, Matthias Karadar, Ines Bauer, Gilbert Neuner Plant Methods 2013, 9:7 (14 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary With increasing global temperatures, understanding how plants respond to heat stress in their natural habitat has become more and more important. The authors describe a system that can be used in the field to apply controlled heat treatments either in natural sunlight or in the dark and without having to remove plant parts. Because the plants remain in situ, their ability to recover from the heat stress can also be monitored.
		Review Advances in plant gene-targeted and functional markers: a review Péter Poczai, Ildikó Varga, Maarja Laos, András Cseh, Neil Bell, Jari PT Valkonen, Jaakko Hyvönen Plant Methods 2013, 9:6 (13 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The authors provide a comprehensive review of advances in PCR-based multi-locus techniques for DNA fingerprinting using both gene-targeted and functional markers.
		Methodology Accounting for variation in designing greenhouse experiments with special reference to greenhouses containing plants on conveyor systems Chris J Brien, Bettina Berger, Huwaida Rabie, Mark Tester Plant Methods 2013, 9:5 (8 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary The authors have tackled the problem of how best to design greenhouse experiments and the approaches that should be taken for statistical analysis of the data. For example, is it better to move plants around the greenhouse during an experiment or to leave them in the same place and account for the environmental gradients in the final statistical analysis?
		Methodology Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants Simon J Conn, Bradleigh Hocking, Maclin Dayod, Bo Xu, Asmini Athman, Sam Henderson, Lucy Aukett, Vanessa Conn, Monique K Shearer, Sigfredo Fuentes, Stephen D Tyerman, Matthew Gilliham Plant Methods 2013, 9:4 (5 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| 1 comment \| Editor’s summary Hydroponics is an extremely useful technique for growing plants under controlled nutrient conditions, particularly where clean roots are needed for physiological or microscopic analysis or for RNA extraction. The detailed protocol set out here should make it straightforward for other laboratories to rapidly and successfully adopt the technique. A video is also available at http://t.co/WoAYgYy84C.
		Methodology Rhizo-lysimetry: facilities for the simultaneous study of root behaviour and resource use by agricultural crop and pasture systems Philip L Eberbach, Jeffrey Hoffmann, Sergio J Moroni, Leonard J Wade, Leslie A Weston Plant Methods 2013, 9:3 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new crop research facility is described that allows both root growth and changes in soil water content to be monitored under field conditions. The facility is of particular relevance given problems with long-term drought in southern Australia and global concerns about climate change and limiting water supplies.
		Methodology Synchronous high-resolution phenotyping of leaf and root growth in Nicotiana tabacum over 24-h periods with GROWMAP-plant Tom Ruts, Shizue Matsubara, Achim Walter Plant Methods 2013, 9:2 (23 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary GROWMAP-plant is an elegant new method that allows growth processes to be monitored simultaneously in the above and below-ground parts of the plant over 24 h periods. The method is validated by using it to demonstrate the differences between roots and leaves in the sensitivity of their growth patterns to environmental perturbation.
		Methodology Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems Guillaume Lobet, Xavier Draye Plant Methods 2013, 9:1 (4 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Improved methods for analysing root architecture are always being sought, This paper makes a significant cntribution to progress in this field by developing a novel procedure for analysing roots grown in rhizotrons. The method combines the strengths of two classical methods: in situ recording of root placement (by tracing on acetate sheets) and high resolution scanning of root system fragments after removal from the rhizotron.
		Methodology Inflorescence stem grafting made easy in Arabidopsis Nazia Nisar, Shelley Verma, Barry J Pogson, Christopher I Cazzonelli Plant Methods 2012, 8:50 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Most micrografting experiments in Arabidopsis use hypocotyl grafts. To enable detailed studies of long distance signals that promote reproduction, the authors have developed improved techniques for inflorescence grafting in Arabidopsis.
		Methodology CalloseMeasurer: a novel software solution to measure callose deposition and recognise spreading callose patterns Ji Zhou, Thomas Spallek, Christine Faulkner, Silke Robatzek Plant Methods 2012, 8:49 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The authors present a detailed series of image analysis tools for the detection and measurement in plant tissues of callose deposition, an important defence against fungal pathogens. The software should be very useful for researchers interested in quantifying callose-mediated defences against plant pathogens. In addition, automated analysis of the progress of callose development over time can be used to track fungal development within the leaf.
		Methodology Protocol: Chromatin immunoprecipitation (ChIP) methodology to investigate histone modifications in two model diatom species Xin Lin, Leïla Tirichine, Chris Bowler Plant Methods 2012, 8:48 (7 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A detailed protocol for performing chromatin immunoprecipitation experiments with two model diatoms is described. The authors report that the method can be easily adapted to other diatoms and eukaryotic phytoplankton species.
		Methodology An UPLC-MS/MS method for highly sensitive high-throughput analysis of phytohormones in plant tissues Gerd Ulrich Balcke, Vinzenz Handrick, Nick Bergau, Mandy Fichtner, Anja Henning, Hagen Stellmach, Alain Tissier, Bettina Hause, Andrej Frolov Plant Methods 2012, 8:47 (22 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this paper, the authors present a UPLC-based protocol for rapid, high sensitivity analysis of phytohormones from relatively small samples of plant tissue. In particular, improvements in detection limits following testing of different solid phase extraction techniques and different buffers are a useful extension of current knowledge. The protocol is fully validated and applied here to measure hormone changes following mechanical wounding in tomato.
		Methodology Plant lighting system with five wavelength-band light-emitting diodes providing photon flux density and mixing ratio control Akira Yano, Kazuhiro Fujiwara Plant Methods 2012, 8:46 (22 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Light emitting diodes (LEDs) are a rapidly developing alternative to conventional lighting for plant growth facilities. This paper provides methodology to exploit one of the biggest potential advantages of LEDs viz the ability to exercise much greater control over photon flux densities and the mixtures of wavelengths. This will be of particular interest to those with research interests in photobiology or in the applied potential of using light spectra to control plant development.
		Methodology PhenoPhyte: a flexible affordable method to quantify 2D phenotypes from imagery Jason M Green, Heidi Appel, Erin MacNeal Rehrig, Jaturon Harnsomburana, Jia-Fu Chang, Peter Balint-Kurti, Chi-Ren Shyu Plant Methods 2012, 8:45 (6 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The analysis of digital images for plant phenotyping is an increasingly important issue in plant science. This paper provides a versatile, web-based method for semi-automated quantification of two-dimensional traits from digital images. The method is validated by using it to analyse a variety of traits in multiple plant species.
		Methodology FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei Filipe Borges, Rui Gardner, Telma Lopes, Joseph P Calarco, Leonor C Boavida, R Slotkin, Robert A Martienssen, Jörg D Becker Plant Methods 2012, 8:44 (17 October 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary The paper provides simple and efficient FACS-based purification protocols for Arabidopsis microspores, vegetative nuclei and sperm cells.
		Software Phytotracker, an information management system for easy recording and tracking of plants, seeds and plasmids Jeroen Nieuwland, Emily Sornay, Angela Marchbank, Barend HJ de Graaf, James AH Murray Plant Methods 2012, 8:43 (13 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 'Phytotracker' is a database utility for managing DNA, plants and seed stocks in a typical plant science research laboratory. The system is a relatively simple, user-friendly database application based on the commercial Filemaker software platform. It provides a simple mechanism for recording the generation, use and storage of DNA, plants and seeds, and can print labels for use in experiments or for storage of stocks.
		Methodology Concurrent profiling of indole-3-acetic acid, abscisic acid, and cytokinins and structurally related purines by high-performance-liquid-chromatography tandem electrospray mass spectrometry Scott C Farrow, RJ Neil Emery Plant Methods 2012, 8:42 (12 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method is described for the concurrent extraction, purification and analysis of diverse plant hormones from 100 mg quantities of Arabidopsis thaliana leaf tissue.
		Methodology A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters Yun-Ru Chen, Yi Zheng, Bao Liu, Silin Zhong, Jim Giovannoni, Zhangjun Fei Plant Methods 2012, 8:41 (20 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An efficient, low-cost method for the preparation of libraries for small RNA sequencing based on the production of customized pre-adenylated adapters using T4 RNA ligase.
		Methodology A novel xylogenic suspension culture model for exploring lignification in Phyllostachys bamboo Shinjiro Ogita, Taiji Nomura, Takao Kishimoto, Yasuo Kato Plant Methods 2012, 8:40 (14 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Bamboo is a remarkable plant but one that is difficult to study. The authors describe a model suspension culture system that will be invaluable for investigating the process of lignification in living bamboo cells.