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Plant Methods

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https://www.readbyqxmd.com/read/28163771/a-high-throughput-stereo-imaging-system-for-quantifying-rape-leaf-traits-during-the-seedling-stage
#1
Xiong Xiong, Lejun Yu, Wanneng Yang, Meng Liu, Ni Jiang, Di Wu, Guoxing Chen, Lizhong Xiong, Kede Liu, Qian Liu
BACKGROUND: The fitness of the rape leaf is closely related to its biomass and photosynthesis. The study of leaf traits is significant for improving rape leaf production and optimizing crop management. Canopy structure and individual leaf traits are the major indicators of quality during the rape seedling stage. Differences in canopy structure reflect the influence of environmental factors such as water, sunlight and nutrient supply. The traits of individual rape leaves traits indicate the growth period of the rape as well as its canopy shape...
2017: Plant Methods
https://www.readbyqxmd.com/read/28115979/application-of-3d-printing-to-prototype-and-develop-novel-plant-tissue-culture-systems
#2
Mukund R Shukla, Amritpal S Singh, Kevin Piunno, Praveen K Saxena, A Maxwell P Jones
BACKGROUND: Due to the complex process of designing and manufacturing new plant tissue culture vessels through conventional means there have been limited efforts to innovate improved designs. Further, development and availability of low cost, energy efficient LEDs of various spectra has made it a promising light source for plant growth in controlled environments. However, direct replacement of conventional lighting sources with LEDs does not address problems with uniformity, spectral control, or the challenges in conducting statistically valid experiments to assess the effects of light...
2017: Plant Methods
https://www.readbyqxmd.com/read/28077951/spatially-localized-bench-top-x-ray-scattering-reveals-tissue-specific-microfibril-orientation-in-moso-bamboo
#3
Patrik Ahvenainen, Patrick G Dixon, Aki Kallonen, Heikki Suhonen, Lorna J Gibson, Kirsi Svedström
BACKGROUND: Biological materials have a complex, hierarchical structure, with vital structural features present at all size scales, from the nanoscale to the macroscale. A method that can connect information at multiple length scales has great potential to reveal novel information. This article presents one such method with an application to the bamboo culm wall. Moso (Phyllostachys edulis) bamboo is a commercially important bamboo species. At the cellular level, bamboo culm wall consists of vascular bundles embedded in a parenchyma cell tissue matrix...
2017: Plant Methods
https://www.readbyqxmd.com/read/28053649/predicting-grain-yield-using-canopy-hyperspectral-reflectance-in-wheat-breeding-data
#4
Osval A Montesinos-López, Abelardo Montesinos-López, José Crossa, Gustavo de Los Campos, Gregorio Alvarado, Mondal Suchismita, Jessica Rutkoski, Lorena González-Pérez, Juan Burgueño
BACKGROUND: Modern agriculture uses hyperspectral cameras to obtain hundreds of reflectance data measured at discrete narrow bands to cover the whole visible light spectrum and part of the infrared and ultraviolet light spectra, depending on the camera. This information is used to construct vegetation indices (VI) (e.g., green normalized difference vegetation index or GNDVI, simple ratio or SRa, etc.) which are used for the prediction of primary traits (e.g., biomass). However, these indices only use some bands and are cultivar-specific; therefore they lose considerable information and are not robust for all cultivars...
2017: Plant Methods
https://www.readbyqxmd.com/read/28053648/harnessing-anthocyanin-rich-fruit-a-visible-reporter-for-tracing-virus-induced-gene-silencing-in-pepper-fruit
#5
Jihyun Kim, Minkyu Park, Eun Soo Jeong, Je Min Lee, Doil Choi
BACKGROUND: Virus-induced gene silencing (VIGS) has become a powerful tool for post-genomic technology in plant species. This is important, especially in select plants, such as the pepper plant, that are recalcitrant to Agrobacterium-mediated transformation. Although VIGS in plants has been widely employed as a powerful tool for functional genomics, scattering phenotypic effects by uneven gene silencing has been implemented in order to overcome challenges in experiments with fruit tissues...
2017: Plant Methods
https://www.readbyqxmd.com/read/28053647/the-plant-leaf-movement-analyzer-palma-a-simple-tool-for-the-analysis-of-periodic-cotyledon-and-leaf-movement-in-arabidopsis-thaliana
#6
Lucas Wagner, Christoph Schmal, Dorothee Staiger, Selahattin Danisman
BACKGROUND: The analysis of circadian leaf movement rhythms is a simple yet effective method to study effects of treatments or gene mutations on the circadian clock of plants. Currently, leaf movements are analysed using time lapse photography and subsequent bioinformatics analyses of leaf movements. Programs that are used for this purpose either are able to perform one function (i.e. leaf tip detection or rhythm analysis) or their function is limited to specific computational environments...
2017: Plant Methods
https://www.readbyqxmd.com/read/28053646/comparison-of-three-genomic-dna-extraction-methods-to-obtain-high-dna-quality-from-maize
#7
Amani Abdel-Latif, Gamal Osman
BACKGROUND: The world's top three cereals, based on their monetary value, are rice, wheat, and corn. In cereal crops, DNA extraction is difficult owing to rigid non-cellulose components in the cell wall of leaves and high starch and protein content in grains. The advanced techniques in molecular biology require pure and quick extraction of DNA. The majority of existing DNA extraction methods rely on long incubation and multiple precipitations or commercially available kits to produce contaminant-free high molecular weight DNA...
2017: Plant Methods
https://www.readbyqxmd.com/read/28035231/a-method-for-detecting-single-mrna-molecules-in-arabidopsis-thaliana
#8
Susan Duncan, Tjelvar S G Olsson, Matthew Hartley, Caroline Dean, Stefanie Rosa
BACKGROUND: 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. RESULTS: Here we describe a method for imaging individual mRNA molecules in Arabidopsis thaliana root cells using multiple singly labeled oligonucleotide probes. We demonstrate detection of both mRNA and nascent transcripts of the housekeeping gene Protein Phosphatase 2A...
2016: Plant Methods
https://www.readbyqxmd.com/read/27933095/direct-derivation-of-maize-plant-and-crop-height-from-low-cost-time-of-flight-camera-measurements
#9
Martin Hämmerle, Bernhard Höfle
BACKGROUND: In agriculture, information about the spatial distribution of crop height is valuable for applications such as biomass and yield estimation, or increasing field work efficiency in terms of fertilizing, applying pesticides, irrigation, etc. Established methods for capturing crop height often comprise restrictions in terms of cost and time efficiency, flexibility, and temporal and spatial resolution of measurements. Furthermore, crop height is mostly derived from a measurement of the bare terrain prior to plant growth and measurements of the crop surface when plants are growing, resulting in the need of multiple field campaigns...
2016: Plant Methods
https://www.readbyqxmd.com/read/27904648/editing-of-the-urease-gene-by-crispr-cas-in-the-diatom-thalassiosira-pseudonana
#10
Amanda Hopes, Vladimir Nekrasov, Sophien Kamoun, Thomas Mock
BACKGROUND: CRISPR-Cas is a recent and powerful addition to the molecular toolbox which allows programmable genome editing. It has been used to modify genes in a wide variety of organisms, but only two alga to date. Here we present a methodology to edit the genome of Thalassiosira pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas. RESULTS: A single construct was assembled using Golden Gate cloning...
2016: Plant Methods
https://www.readbyqxmd.com/read/27895701/a-dna-based-real-time-pcr-assay-for-robust-growth-quantification-of-the-bacterial-pathogen-pseudomonas-syringae-on-arabidopsis-thaliana
#11
Annegret Ross, Imre E Somssich
BACKGROUND: The interaction of Pseudomonas syringae with Arabidopsis is one of the most commonly used systems to study various bacterial-host interrelationships. Currently, most studies are based on the growth quantification of the pathogen to characterize resistance or virulence targets. However, the standard available method for determining bacterial proliferation in planta is laborious and has several limitations. RESULTS: Here we present an alternative robust approach, which is based on the quantification of bacterial DNA by real-time PCR...
2016: Plant Methods
https://www.readbyqxmd.com/read/27891171/a-rapid-approach-to-investigate-spatiotemporal-distribution-of-phytohormones-in-rice
#12
Wen-Jing Cai, Tian-Tian Ye, Qing Wang, Bao-Dong Cai, Yu-Qi Feng
BACKGROUND: Phytohormones play crucial roles in almost all stages of plant growth and development. Accurate and simultaneous determination of multiple phytohormones enabled us to better understand the physiological functions and the regulatory networks of phytohormones. However, simultaneous determination of multiple phytohormones in plant is still a challenge due to their low concentrations, structural and chemical diversity, and complex matrix of plant tissues. Therefore, development of a simple and selective method for the simultaneous determination of multiple phytohormones is highly needed...
2016: Plant Methods
https://www.readbyqxmd.com/read/27872654/chlorophyll-a-fluorescence-under-half-of-the-adaptive-growth-irradiance-for-high-throughput-sensing-of-leaf-water-deficit-in-arabidopsis-thaliana-accessions
#13
Kumud B Mishra, Anamika Mishra, Kateřina Novotná, Barbora Rapantová, Petra Hodaňová, Otmar Urban, Karel Klem
BACKGROUND: Non-invasive and high-throughput monitoring of drought in plants from its initiation to visible symptoms is essential to quest drought tolerant varieties. Among the existing methods, chlorophyll a fluorescence (ChlF) imaging has the potential to probe systematic changes in photosynthetic reactions; however, prerequisite of dark-adaptation limits its use for high-throughput screening. RESULTS: To improve the throughput monitoring of plants, we have exploited their light-adaptive strategy, and investigated possibilities of measuring ChlF transients under low ambient irradiance...
2016: Plant Methods
https://www.readbyqxmd.com/read/27843484/measures-for-interoperability-of-phenotypic-data-minimum-information-requirements-and-formatting
#14
Hanna Ćwiek-Kupczyńska, Thomas Altmann, Daniel Arend, Elizabeth Arnaud, Dijun Chen, Guillaume Cornut, Fabio Fiorani, Wojciech Frohmberg, Astrid Junker, Christian Klukas, Matthias Lange, Cezary Mazurek, Anahita Nafissi, Pascal Neveu, Jan van Oeveren, Cyril Pommier, Hendrik Poorter, Philippe Rocca-Serra, Susanna-Assunta Sansone, Uwe Scholz, Marco van Schriek, Ümit Seren, Björn Usadel, Stephan Weise, Paul Kersey, Paweł Krajewski
BACKGROUND: Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time-consuming experiments, the findings can be fostered by reusing and combining existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata...
2016: Plant Methods
https://www.readbyqxmd.com/read/27833650/protocol-a-fast-comprehensive-and-reproducible-one-step-extraction-method-for-the-rapid-preparation-of-polar-and-semi-polar-metabolites-lipids-proteins-starch-and-cell-wall-polymers-from-a-single-sample
#15
Mohamed A Salem, Jessica Jüppner, Krzysztof Bajdzienko, Patrick Giavalisco
BACKGROUND: The elucidation of complex biological systems requires integration of multiple molecular parameters. Accordingly, high throughput methods like transcriptomics, proteomics, metabolomics and lipidomics have emerged to provide the tools for successful system-wide investigations. Unfortunately, optimized analysis of different compounds requires specific extraction procedures in combination with specific analytical instrumentation. However, the most efficient extraction protocols often only cover a restricted number of compounds due to the different physico-chemical properties of these biological compounds...
2016: Plant Methods
https://www.readbyqxmd.com/read/27822293/a-rapid-and-cost-effective-fluorescence-detection-in-tube-fdit-method-to-analyze-protein-phosphorylation
#16
Xiao Jin, Jin-Ying Gou
BACKGROUND: Protein phosphorylation is one of the most important post-translational modifications catalyzed by protein kinases in living organisms. The advance of genome sequencing provided the information of protein kinase families in many organisms, including both model and non-model plants. The development of proteomics technologies also enabled scientists to efficiently reveal a large number of protein phosphorylations of an organism. However, kinases and phosphorylation targets are still to be connected to illustrate the complicated network in life...
2016: Plant Methods
https://www.readbyqxmd.com/read/27822292/uv-crosslinked-mrna-binding-proteins-captured-from-leaf-mesophyll-protoplasts
#17
Zhicheng Zhang, Kurt Boonen, Piero Ferrari, Liliane Schoofs, Ewald Janssens, Vera van Noort, Filip Rolland, Koen Geuten
BACKGROUND: 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 regulation through interaction with RNA. Recently, the mRNA-bound proteome of mammalian cell lines has been successfully cataloged using a new method called interactome capture. This method relies on UV crosslinking of proteins to RNA, purifying the mRNA using complementary oligo-dT beads and identifying the crosslinked proteins using mass spectrometry...
2016: Plant Methods
https://www.readbyqxmd.com/read/27777610/infiltration-rnaseq-transcriptome-profiling-of-agrobacterium-mediated-infiltration-of-transcription-factors-to-discover-gene-function-and-expression-networks-in-plants
#18
Donna M Bond, Nick W Albert, Robyn H Lee, Gareth B Gillard, Chris M Brown, Roger P Hellens, Richard C Macknight
BACKGROUND: 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 stable transformation and expression changes in plant cells. However, the production of stable transformants can be slow and laborious with no guarantee of success. Furthermore, transgenic plants overexpressing a TF of interest can present pleiotropic phenotypes and/or result in a high number of indirect gene expression changes...
2016: Plant Methods
https://www.readbyqxmd.com/read/27602051/radix-rhizoslide-platform-allowing-high-throughput-digital-image-analysis-of-root-system-expansion
#19
Chantal Le Marié, Norbert Kirchgessner, Patrick Flütsch, Johannes Pfeifer, Achim Walter, Andreas Hund
BACKGROUND: 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 nutrient resources of the soil. However, so far it is unclear to what extent genetic variations in root system responses to spatially varying soil resources can be utilized for breeding applications. Among others, one limiting factor is the absence of phenotyping platforms allowing the analysis of such interactions...
2016: Plant Methods
https://www.readbyqxmd.com/read/27493679/development-of-a-universal-and-simplified-ddrad-library-preparation-approach-for-snp-discovery-and-genotyping-in-angiosperm-plants
#20
Guo-Qian Yang, Yun-Mei Chen, Jin-Peng Wang, Cen Guo, Lei Zhao, Xiao-Yan Wang, Ying Guo, Li Li, De-Zhu Li, Zhen-Hua Guo
BACKGROUND: 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-generation sequencing. ddRAD-seq has been widely applied to SNP marker development and genotyping on animals, especially on marine animals as the original ddRAD protocol is mainly built and trained based on animal data. However, wide application of ddRAD-seq technology in plant species has not been achieved so far...
2016: Plant Methods
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