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Plant Methods

Piyush Priya, Archana Yadav, Jyoti Chand, Gitanjali Yadav
Background: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data...
2018: Plant Methods
Javier Tello, María Ignacia Montemayor, Astrid Forneck, Javier Ibáñez
Background: Low pollen viability may limit grapevine yield under certain conditions, causing relevant economic losses to grape-growers. It is usually evaluated by the quantification of the number of viable and non-viable pollen grains that are present in a sample after an adequate pollen grain staining procedure. Although the manual counting of both types of grains is the simplest and most sensitive approach, it is a laborious and time-demanding process. In this regard, novel image-based approaches can assist in the objective, accurate and cost-effective phenotyping of this trait...
2018: Plant Methods
Amit Levy, Choaa El-Mochtar, Chunxia Wang, Michael Goodin, Vladimir Orbovic
Background: Transient gene expression is a powerful tool to study gene function in plants. In citrus, Agrobacterium transformation is the method of choice for transient expression studies, but this method does not work efficiently with many gene constructs, and there is a need for a more robust transient expression system in citrus leaves. Biolistic particle delivery is an alternative to Agrobacterium transformation, and in some plants, such as Arabidopsis, gives higher transformation rates in leaf tissues than Agrobacterium...
2018: Plant Methods
Mohammed Albaqami, Anireddy S N Reddy
Background: Pre-mRNA splicing is an essential post-transcriptional process in all eukaryotes. In vitro splicing systems using nuclear or cytoplasmic extracts from mammalian cells, yeast, and Drosophila have provided a wealth of mechanistic insights into assembly and composition of the spliceosome, splicing regulatory proteins and mechanisms of pre-mRNA splicing in non-plant systems. The lack of an in vitro splicing system prepared from plant cells has been a major limitation in splicing research in plants...
2018: Plant Methods
Ji Zhou, Christopher Applegate, Albor Dobon Alonso, Daniel Reynolds, Simon Orford, Michal Mackiewicz, Simon Griffiths, Steven Penfield, Nick Pullen
Background: Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic...
2017: Plant Methods
Jun Lu, Mengjuan Bai, Haoran Ren, Jinyi Liu, Changquan Wang
Background: Roses are widely used as garden ornamental plants and cut flowers. Rosa chinensis cv 'Old Blush' has been used as a model genotype in rose studies due to its contribution to recurrent flowering and tea scent traits of modern roses. The deficiency of efficient genetic transformation systems is a handicap limiting functional genetics studies of roses. Agrobacterium-mediated transient transformation offers a powerful tool for the characterization of gene function in plants. Results: A convenient and highly efficient Agrobacterium mediated genetic transformation protocol using R...
2017: Plant Methods
Milan Šulc, Jiří Matas
Background: Fine-grained recognition of plants from images is a challenging computer vision task, due to the diverse appearance and complex structure of plants, high intra-class variability and small inter-class differences. We review the state-of-the-art and discuss plant recognition tasks, from identification of plants from specific plant organs to general plant recognition "in the wild". Results: We propose texture analysis and deep learning methods for different plant recognition tasks...
2017: Plant Methods
Annamária Kiss, Typhaine Moreau, Vincent Mirabet, Cerasela Iliana Calugaru, Arezki Boudaoud, Pradeep Das
Background: Developmental biology has made great strides in recent years towards the quantification of cellular properties during development. This requires tissues to be imaged and segmented to generate computerised versions that can be easily analysed. In this context, one of the principal technical challenges remains the faithful detection of cellular contours, principally due to variations in image intensity throughout the tissue. Watershed segmentation methods are especially vulnerable to these variations, generating multiple errors due notably to the incorrect detection of the outer surface of the tissue...
2017: Plant Methods
Chien-Yuan Lin, Bryon S Donohoe, Neha Ahuja, Deborah M Garrity, Rongda Qu, Melvin P Tucker, Michael E Himmel, Hui Wei
Background: Switchgrass (Panicum virgatum), a robust perennial C4-type grass, has been evaluated and designated as a model bioenergy crop by the U.S. DOE and USDA. Conventional breeding of switchgrass biomass is difficult because it displays self-incompatible hindrance. Therefore, direct genetic modifications of switchgrass have been considered the more effective approach to tailor switchgrass with traits of interest. Successful transformations have demonstrated increased biomass yields, reduction in the recalcitrance of cell walls and enhanced saccharification efficiency...
2017: Plant Methods
Muhammad Waqar Hameed, Ilona Juszczak, Ralph Bock, Joost Thomas van Dongen
Background: To investigate translational regulation of gene expression in plant mitochondria, a mitochondrial polysome isolation protocol was established for tobacco to investigate polysomal mRNA loading as a proxy for translational activity. Furthermore, we developed an oligonucleotide based microarray platform to determine the level of Nicotiana tabacum and Arabidopsis thaliana mitochondrial mRNA. Results: Microarray analysis of free and polysomal mRNAs was used to characterize differences in the levels of free transcripts and ribosome-bound mRNAs in various organs of tobacco plants...
2017: Plant Methods
Konstantinos N Blazakis, Maria Kosma, George Kostelenos, Luciana Baldoni, Marina Bufacchi, Panagiotis Kalaitzis
Background: The morphological analysis of olive leaves, fruits and endocarps may represent an efficient tool for the characterization and discrimination of cultivars and the establishment of relationships among them. In recent years, much attention has been focused on the application of molecular markers, due to their high diagnostic efficiency and independence from environmental and phenological variables. Results: In this study, we present a semi-automatic methodology of detecting various morphological parameters...
2017: Plant Methods
Krzysztof Kucypera, Marcin Lipowczan, Anna Piekarska-Stachowiak, Jerzy Nakielski
Background: The development of cell pattern in the surface cell layer of the shoot apex can be investigated in vivo by use of a time-lapse confocal images, showing naked meristem in 3D in successive times. However, how this layer is originated from apical initials and develops as a result of growth and divisions of their descendants, remains unknown. This is an open area for computer modelling. A method to generate the surface cell layer is presented on the example of the 3D paraboloidal shoot apical dome...
2017: Plant Methods
Srinivas Belide, Thomas Vanhercke, James Robertson Petrie, Surinder Pal Singh
Background: Sorghum (Sorghum bicolor L.) is one of the world's most important cereal crops grown for multiple applications and has been identified as a potential biofuel crop. Despite several decades of study, sorghum has been widely considered as a recalcitrant major crop for transformation due to accumulation of phenolic compounds, lack of model genotypes, low regeneration frequency and loss of regeneration potential through sub-cultures. Among different explants used for genetic transformation of sorghum, immature embryos are ideal over other explants...
2017: Plant Methods
Ye Ji Park, Si Hyun Seong, Min Sun Kim, Sang Wan Seo, Mee Ree Kim, Hyun Sik Kim
Background: Plant extracts contain a huge variety of pharmacologically active substances. Conventionally, various chromatographic methods must be applied several times to purify functional compounds to measure their functional activity. However, conventional purification methods are time-consuming and expensive due to the laborious purification process. Recently, a high-throughput discovery method that replaces such time-consuming purification processes was introduced; this method uses 15 T ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry (15 T FT-ICR MS) and a high-throughput screening method...
2017: Plant Methods
Emi Tanaka, Jean-Phillippe F Ral, Sean Li, Raj Gaire, Colin R Cavanagh, Brian R Cullis, Alex Whan
Background: The proportion of granule types in wheat starch is an important characteristic that can affect its functionality. It is widely accepted that granule types are either large, disc-shaped A-type granules or small, spherical B-type granules. Additionally, there are some reports of the tiny C-type granules. The differences between these granule types are due to its carbohydrate composition and crystallinity which is highly, but not perfectly, correlated with the granule size. A majority of the studies that have considered granule types analyse them based on a size threshold rather than chemical composition...
2017: Plant Methods
Kelvin T Chiong, Mona B Damaj, Carmen S Padilla, Carlos A Avila, Shankar R Pant, Kranthi K Mandadi, Ninfa R Ramos, Denise V Carvalho, T Erik Mirkov
Background: Several high-throughput molecular genetic analyses rely on high-quality genomic DNA. Copurification of other molecules can negatively impact the functionality of plant DNA preparations employed in these procedures. Isolating DNA from agronomically important crops, such as sugarcane, rice, citrus, potato and tomato is a challenge due to the presence of high fiber, polysaccharides, or secondary metabolites. We present a simplified, rapid and reproducible SDS-based method that provides high-quality and -quantity of DNA from small amounts of leaf tissue, as required by the emerging biotechnology and molecular genetic applications...
2017: Plant Methods
Zi Wang, Pieter Verboven, Bart Nicolai
Background: X-ray micro-CT has increasingly been used for 3D imaging of plant structures. At the micrometer resolution however, limitations in X-ray contrast often lead to datasets with poor qualitative and quantitative measures, especially within dense cell clusters of plant tissue specimens. The current study developed protocols for delivering a cesium based contrast enhancing solution to varying plant tissue specimens for the purpose of improving 3D tissue structure characterization within plant specimens, accompanied by new image processing workflows to extract the additional data generated by the contrast enhanced scans...
2017: Plant Methods
Xiong Xiong, Lingfeng Duan, Lingbo Liu, Haifu Tu, Peng Yang, Dan Wu, Guoxing Chen, Lizhong Xiong, Wanneng Yang, Qian Liu
Background: Rice panicle phenotyping is important in rice breeding, and rice panicle segmentation is the first and key step for image-based panicle phenotyping. Because of the challenge of illumination differentials, panicle shape deformations, rice accession variations, different reproductive stages and the field's complex background, rice panicle segmentation in the field is a very large challenge. Results: In this paper, we propose a rice panicle segmentation algorithm called Panicle-SEG, which is based on simple linear iterative clustering superpixel regions generation, convolutional neural network classification and entropy rate superpixel optimization...
2017: Plant Methods
Pouria Sadeghi-Tehran, Nicolas Virlet, Kasra Sabermanesh, Malcolm J Hawkesford
Background: Accurately segmenting vegetation from the background within digital images is both a fundamental and a challenging task in phenotyping. The performance of traditional methods is satisfactory in homogeneous environments, however, performance decreases when applied to images acquired in dynamic field environments. Results: In this paper, a multi-feature learning method is proposed to quantify vegetation growth in outdoor field conditions. The introduced technique is compared with the state-of the-art and other learning methods on digital images...
2017: Plant Methods
Daniel Pflugfelder, Ralf Metzner, Dagmar van Dusschoten, Rüdiger Reichel, Siegfried Jahnke, Robert Koller
Background: Root systems are highly plastic and adapt according to their soil environment. Studying the particular influence of soils on root development necessitates the adaptation and evaluation of imaging methods for multiple substrates. Non-invasive 3D root images in soil can be obtained using magnetic resonance imaging (MRI). Not all substrates, however, are suitable for MRI. Using barley as a model plant we investigated the achievable image quality and the suitability for root phenotyping of six commercially available natural soil substrates of commonly occurring soil textures...
2017: Plant Methods
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