MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Plant Methods' source. Mon, 06 Feb 2012 14:26:19 +0100 http://www.medworm.com/index.php?rid=5656304&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F8%2F1%2F5 PhosphoRice is a web-based tool specifically designed to predict phosphorylation sites in rice. It can be accessed at http://bioinformatics.fafu.edu.cn/PhosphoRice. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5656304 Fri, 03 Feb 2012 05:00:00 +0100 5656304 http://www.medworm.com/index.php?rid=5643749&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F8%2F1%2F4 The authors describe a very convenient way to preserve plant cell cultures that doesn't require any specialised equipment and avoids the use of freezing. A combination of low temperature (5oC) and a phosphate-free medium allows the cells to remain viable for 6 months and, importantly to resume active growth without a lag when they are returned to standard culture conditions. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5643749 Mon, 30 Jan 2012 05:00:00 +0100 5643749 http://www.medworm.com/index.php?rid=5624610&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F8%2F1%2F3 Hyperspectral imaging (HSI) offers high potential as a non-invasive diagnostic tool for disease detection. In this paper leaf characteristics and spectral reflectance of sugar beet leaves diseased with Cercospora leaf spot, powdery mildew and leaf rust at different development stages were connected. Light microscopy was used to describe the morphological changes in the host tissue due to pathogen colonisation. Under controlled conditions a hyperspectral imaging line scanning spectrometer (ImSpector V10E) with a spectral resolution of 2.8 nm from 400 to 1000 nm and a spatial resolution of 0.19 mm was used for continuous screening and monitoring of disease symptoms during pathogenesis. A pixel-wise mapping of spectral reflectance in the visible and near-infrared range enabled the detection a... Plant Methods journals http://www.medworm.com/rss/comments.php?id=5624610 Tue, 24 Jan 2012 05:00:00 +0100 5624610 http://www.medworm.com/index.php?rid=5603832&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F8%2F1%2F2 Conclusion: This UFLC-ESI-MS method is convenient, sensitive, reliable, and inexpensive for quantification of multiple phytohormones and metabolites compared to current methods. The results obtained by application of this method in studying rice-bacterial interaction provide a basis for understanding the molecular mechanisms of rice defense responses. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5603832 Sun, 15 Jan 2012 05:00:00 +0100 5603832 http://www.medworm.com/index.php?rid=5592854&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F8%2F1%2F1 Conclusions: We have set up a method for high yield purification of intact tomato fruit chromoplasts suitable for precursor uptake assays and metabolic analyses. Using targeted radiolabeled precursors we have been able to unravel novel biochemical and metabolic aspects related with carotenoid and lipid biosynthesis in tomato fruit chromoplasts. The reported chromoplast system could represent a valuable platform to address the validation and characterization of functional processes predicted from recent transcriptomic and proteomic data. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5592854 Fri, 13 Jan 2012 05:00:00 +0100 5592854 http://www.medworm.com/index.php?rid=5556712&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F49 Conclusions: This speedy, yet less labor-intensive, protocol overcomes major limitations associated with genetic manipulation in rice. Moreover, our protocol uses mature seeds as the explant, which can easily be obtained in quantity throughout the year and kept viable for a long time. Such an easy, efficient and generalized protocol has the potential to be a major tool for crop improvement and gene-function studies on the model monocot plant rice. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5556712 Fri, 30 Dec 2011 05:00:00 +0100 5556712 http://www.medworm.com/index.php?rid=5533157&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F48 Proteins in the plant apoplast are essential for many physiological processes. We have analysed and compared six different infiltration solutions for proteins contained in the apoplast to recognize the most suitable method for leaves and to establish proteome maps for each extraction. The efficiency of protocols was evaluated by comparing the protein patterns resolved by 1-DE and 2-DE, and revealed distinct characteristics for each infiltration solution. Nano-LC-ESI-Q-TOF MS analysis of all fractions was applied to cover all proteins differentially extracted by infiltration solutions and led to the identification of 328 proteins in total in apoplast preparations. The predicted subcellular protein localisation distinguished the examined infiltration solutions in those with high or low amoun... Plant Methods journals http://www.medworm.com/rss/comments.php?id=5533157 Thu, 22 Dec 2011 05:00:00 +0100 5533157 http://www.medworm.com/index.php?rid=5533158&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F47 Transcriptional activity of entire genes in chloroplasts is usually assayed by run-on analyses. To determine not only the overall intensity of transcription of a gene, but also the rate of transcription from a particular promoter, we created the Reverse RNase Protection Assay (RePro): in-organello run-on transcription coupled to RNase protection to define distinct transcript ends during transcription. We demonstrate successful application of RePro in plastid promoter analysis and transcript 3' end processing. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5533158 Tue, 20 Dec 2011 05:00:00 +0100 5533158 http://www.medworm.com/index.php?rid=5512266&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F46 The authors describe a set of tools that should greatly facilitate investigations of both the mycorrhizal and rhizobial symbioses with pea. The tools include an improved transformation method and techniques for targeted inoculation of roots with the symbiont to enable the processes involved in establishing the symbiosis to be studied in more detail. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5512266 Thu, 15 Dec 2011 05:00:00 +0100 5512266 http://www.medworm.com/index.php?rid=5500990&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F45 In Arabidopsis thaliana we demonstrate that dying root hairs provide an easy and rapid in vivo model for the morphological identification of apoptotic-like programmed cell death (AL-PCD) in plants. The model described here is transferable between species, can be used to investigate rates of AL-PCD in response to various treatments and to identify modulation of AL-PCD rates in mutant/transgenic plant lines facilitating rapid screening of mutant populations in order to identify genes involved in AL-PCD regulation. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5500990 Tue, 13 Dec 2011 05:00:00 +0100 5500990 http://www.medworm.com/index.php?rid=5500991&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F44 The authors describe an automated facility that can enable the high-throughput evaluation of yield-related traits in rice. The facility could greatly facilitate the phenotyping process in breeding, genetics and functional genomics. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5500991 Mon, 12 Dec 2011 05:00:00 +0100 5500991 http://www.medworm.com/index.php?rid=5492476&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F43 The authors demonstrate how high resolution melt analysis can be a useful tool to characterise allelic series of EMS-induced mutations, as generated for example in TILLING populations. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5492476 Thu, 08 Dec 2011 05:00:00 +0100 5492476 http://www.medworm.com/index.php?rid=5482928&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F42 Conclusion: Our results demonstrate that the new pEG101-SacB/R destination vector can be used for Gateway(R) cloning in Agrobacterium tumefaciens. pEG101-SacB/R will be a valuable tool for high-throughput functional analysis of genes in planta. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5482928 Wed, 07 Dec 2011 05:00:00 +0100 5482928 http://www.medworm.com/index.php?rid=5482929&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F41 To simulate expected future global warming, hexagonal arrays of infrared heaters have previously been used to warm open-field canopies of upland crops such as wheat. Through the use of concrete-anchored posts, improved software, overhead wires, extensive grounding, and monitoring with a thermal camera, the technology was safely and reliably extended to paddy rice fields. The system maintained canopy temperature increases within 0.5degreesC of daytime and nighttime set-point differences of 1.3 and 2.7degreesC 67% of the time. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5482929 Tue, 06 Dec 2011 05:00:00 +0100 5482929 http://www.medworm.com/index.php?rid=5473507&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F40 We present optimised manual and automated protocols for the extraction of total RNA from 9-day-old Arabidopsis seedlings in a 96 well plate format using silica membrane-based methodology. Consistent and reproducible yields of high quality RNA are isolated averaging 8.9 ug total RNA per sample (~20 mg plant tissue). The purified RNA is suitable for subsequent qPCR analysis of the expression of over 500 genes in triplicate from each sample. Using the automated procedure, 192 samples (2x 96 well plates) can easily be fully processed (samples homogenised, RNA purified and quantified) in less than half a day. Additionally we demonstrate that plant samples can be stored in RNAlater at -20 degrees C (but not 4 degrees C) for 10 months prior to extraction with no significant effect on RNA yield or... Plant Methods journals http://www.medworm.com/rss/comments.php?id=5473507 Fri, 02 Dec 2011 05:00:00 +0100 5473507 http://www.medworm.com/index.php?rid=5465083&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F39 Accurate analysis of DNA methylation by bisulphite sequencing depends on the complete conversion of all cytosines into uracil. Until now there has been no standard or universal gene identified as an endogenous control to monitor the conversion frequency in plants. Here, we report the development of PCR based assays for one nuclear gene IND (INDEHISCENT) and two mitochondrial genes, NAD (NICOTINAMIDE ADENINE DINUCLEOTIDE) and ATP1 (ATPase SUBUNIT 1). We demonstrated their efficacy as bisulphite conversion controls in Brassica and other plant taxa. The target regions amplified by four primer pairs were found to be consistently free from DNA methylation. Primer pairs for IND.a and NAD were effective within Brassica species, whereas two primer pairs for ATP1 provided reliable controls across a... Plant Methods journals http://www.medworm.com/rss/comments.php?id=5465083 Fri, 02 Dec 2011 05:00:00 +0100 5465083 http://www.medworm.com/index.php?rid=5465084&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F38 The authors describe an improved method for sequencing and assembly of organellar genomes using the Roche 454 GS FLX platform. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5465084 Tue, 29 Nov 2011 05:00:00 +0100 5465084 http://www.medworm.com/index.php?rid=5427886&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F37 Conclusions: This new method is applicable to the analysis of dynamic changes in endogenous concentrations of hormones to study plant developmental processes or plant responses to biotic and abiotic stresses in complex tissues. An example is shown in which a hormone profiling is obtained from leaves of plants exposed to salt stress in the aromatic plant, Rosmarinus officinalis. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5427886 Fri, 18 Nov 2011 05:00:00 +0100 5427886 http://www.medworm.com/index.php?rid=5396665&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F36 Conclusions: This work constitutes a breakthrough in holoparasitic plant research methods. The method described here is a robust system for transformation and regeneration of a holoparasitic plant and will facilitate research on unique parasitic plant capabilities such as host plant recognition, haustorial formation, penetration and vascular connection. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5396665 Tue, 08 Nov 2011 05:00:00 +0100 5396665 http://www.medworm.com/index.php?rid=5375009&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F35 The authors have investigated the most critical parameters for succesful application of the ChIP technique to Chlamydmonas, an important model organsism for plant research, and they provide a step-by-step protocol. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5375009 Thu, 03 Nov 2011 04:00:00 +0100 5375009 http://www.medworm.com/index.php?rid=5343444&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F34 An efficient micrografting method has been developed for the wild tobacco species, Nicotiana attenuata. This will allow important questions about long distance signals and their adaptive functions to be addressed in an ecological context. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5343444 Thu, 20 Oct 2011 04:00:00 +0100 5343444 http://www.medworm.com/index.php?rid=5310619&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F33 The new vectors described here should greatly facilitate the process of constructs BAC genomic libraries and transferring selected fragments to binary BAC (BIBAC) vectors. This will be of particular interest to those doing positional cloning and wanting to perform complementation tests by reintroducing genomic fragments via Agrobacterium transformation. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5310619 Tue, 11 Oct 2011 04:00:00 +0100 5310619 http://www.medworm.com/index.php?rid=5292742&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F32 Conclusions: The Arabidopsis seedling flood-inoculation assay provides a rapid, efficient and economical method for studying Arabidopsis-Pseudomonas interactions with minimal growth chamber space and time. This assay could also provide an excellent system for investigating the virulence mechanisms of P. syringae. Using this method, we demonstrated that FLS2 plays a critical role in conferring NHR against nonhost pathovars of P. syringae, but not to Xanthomonas campestris pv. vesicatoria. This method is potentially ideal for high-throughput screening of both Arabidopsis and pathogen mutants. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5292742 Thu, 06 Oct 2011 04:00:00 +0100 5292742 http://www.medworm.com/index.php?rid=5281321&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F31 Conclusions: The Maize Microarray Annotation Database will assist users of the Agilent-016047 maize microarray in (i) refining gene lists for global expression analysis, and (ii) confirming the annotation of candidate genes before functional studies. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5281321 Sat, 01 Oct 2011 04:00:00 +0100 5281321 http://www.medworm.com/index.php?rid=5268486&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F30 Conclusions: We show here a simplified and highly efficient transient gene expression system using photosynthetically active rice green tissue protoplasts and its broad applications in protein immunoblot, localization and protein-protein interaction assays. These rice green tissue protoplasts will be particularly useful in studies of light/chloroplast-related processes. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5268486 Fri, 30 Sep 2011 04:00:00 +0100 5268486 http://www.medworm.com/index.php?rid=5268487&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F29 Plastids are small organelles equipped with their own genomes (plastomes). Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray) consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol fo... Plant Methods journals http://www.medworm.com/rss/comments.php?id=5268487 Wed, 28 Sep 2011 04:00:00 +0100 5268487 http://www.medworm.com/index.php?rid=5257178&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F27 Conclusions: These findings demonstrate that variable-angle TIRFM is appropriate for quantitative live imaging of cells in intact tissues of Arabidopsis thaliana. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5257178 Sat, 24 Sep 2011 04:00:00 +0100 5257178 http://www.medworm.com/index.php?rid=5257177&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F28 Wheat is one of the most important crops in Australia, and the identification of young plants is an important step towards developing an automated system for monitoring crop establishment and also for differentiating crop from weeds. In this paper, a framework to differentiate early narrow-leaf wheat from two common weeds from their digital images is developed. A combination of colour, texture and shape features is used. These features are reduced to three descriptors using Principal Component Analysis. The three components provide an effective and significant means for distinguishing the three grasses. Further analysis enables threshold levels to be set for the discrimination of the plant species. The PCA model was evaluated on an independent data set of plants and the results show accura... Plant Methods journals http://www.medworm.com/rss/comments.php?id=5257177 Sat, 24 Sep 2011 04:00:00 +0100 5257177 http://www.medworm.com/index.php?rid=5155507&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F26 We outline a high throughput procedure that improves outlier detection in cell wall screens using FT-NIR spectroscopy of plant leaves. The improvement relies on generating a calibration set from a subset of a mutant population by taking advantage of the Mahalanobis distance outlier scheme to construct a monosaccharide range predictive model using PLS regression. This model was then used to identify specific monosaccharide outliers from the mutant population. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5155507 Wed, 17 Aug 2011 23:00:00 +0100 5155507 http://www.medworm.com/index.php?rid=5094191&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F25 ${item.shortDescription} (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5094191 Tue, 02 Aug 2011 23:00:00 +0100 5094191 http://www.medworm.com/index.php?rid=5068490&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F24 ${item.shortDescription} (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5068490 Tue, 26 Jul 2011 23:00:00 +0100 5068490 http://www.medworm.com/index.php?rid=5048205&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F23 Prenylquinones are mainly located in biological membranes where they function as electron and proton carriers in the photosynthetic and respiratory electron transport chains. The authors describe a rapid method for the simultaneous profiling of eleven prenylquinones in plant tissues, including alpha-tocopherol, phylloquinone, plastochromanol-8 and plastoquinone-9. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5048205 Wed, 20 Jul 2011 23:00:00 +0100 5048205 http://www.medworm.com/index.php?rid=5035362&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F22 Conclusions: Our method is rapid and economical, and allows many samples to be prepared simultaneously for protein analysis. Our method is useful not only for Arabidopsis research but also research on certain other species. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5035362 Thu, 14 Jul 2011 23:00:00 +0100 5035362 http://www.medworm.com/index.php?rid=5006240&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F21 Matrix-Assisted Laser Desorption/Ionisation (MALDI) mass spectrometry imaging (MSI) uses the power of high resolution time of flight mass spectrometry coupled to the raster of laser shots across the cut surface of tissues to provide new insights into the spatial distribution of biomolecules within biological tissues. We consider the history of this technique in animals and plants and discuss the potential for analysis of proteins by this technique in plants. We discuss the bottleneck of protein biomarker identification from MALDI-MSI and alternative approaches to address this problem. We review the technical considerations needed for such analysis and present these alongside examples from our own work and a protocol for MALDI-MSI of proteins in plant samples. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=5006240 Mon, 04 Jul 2011 23:00:00 +0100 5006240 http://www.medworm.com/index.php?rid=4991702&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F19 Conclusion: The described methodology allows for the rapid, combined analysis of metabolic intermediates, major storage products and transcripts in a tissue-specific manner. The protocols are robust for oilseed rape, and should be readily adjustable for other crop species. The suite of methods applied to LM tissues represents an important step in the context of both the systems biology and the biotechnology of oilseeds. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4991702 Wed, 29 Jun 2011 23:00:00 +0100 4991702 http://www.medworm.com/index.php?rid=4991701&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F20 Conclusion: A first TILLING population for a high throughput identification of EMS-induced point mutations in sunflower genome has been successfully obtained. This represents a powerful tool to a better understanding of gene function in sunflower. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4991701 Wed, 29 Jun 2011 23:00:00 +0100 4991701 http://www.medworm.com/index.php?rid=4983181&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F18 Conclusions: The community resource presented here is a useful toolkit for plant research, particularly for future studies in plant development, which will require the simultaneous observation of the effect of various hormones, signaling pathways and crosstalk. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4983181 Tue, 28 Jun 2011 23:00:00 +0100 4983181 http://www.medworm.com/index.php?rid=4967516&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F17 Conclusions: This work collates an integrated set of detailed protocols for the measurement of components of the ethylene biosynthetic pathway, starting from well-established methods. These protocols have been optimised for smaller sample volumes, increased efficiency, repeatability and accuracy. The detailed protocol allows other scientists to rapidly implement these methods in their own laboratories in a consistent and efficient way. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4967516 Wed, 22 Jun 2011 23:00:00 +0100 4967516 http://www.medworm.com/index.php?rid=4919938&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F14 Conclusion: The described DART-MS combined by multivariate analysis allows for rapid screening and metabolic characterization of lots of Arabidopsis mutant seeds without complex metabolic preparation steps. Moreover, potential novel metabolic markers can be detected and used to clarify the genetic relationship between Arabidopsis cultivars. Furthermore this technique can be applied to predict the novel gene function of metabolic mutants regardless of morphological phenotypes. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4919938 Thu, 09 Jun 2011 23:00:00 +0100 4919938 http://www.medworm.com/index.php?rid=4919937&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F15 Conclusions: The ALSV-based VIGS system developed have provides a valuable new addition to the tool box for functional genomics in apple, pear, and Japanese pear. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4919937 Thu, 09 Jun 2011 23:00:00 +0100 4919937 http://www.medworm.com/index.php?rid=4847192&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F12 Conclusions: This protocol demonstrates significant improvements in both the efficiency and ease of use over existing safflower transformation protocols. This is the first complete method of genetic transformation of safflower that generates stably-transformed plants and progeny, allowing this crop to benefit from modern molecular applications. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4847192 Thu, 19 May 2011 23:00:00 +0100 4847192 http://www.medworm.com/index.php?rid=4847191&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F13 Conclusions: This paper presents a simple, high-resolution method for analysis of proanthocyanidin accumulation in organs, tissues and cells of two plant species with different patterns of proanthocyanidin accumulation, namely Lotus corniculatus and Trifolium repens (white clover). This technique was used to characterize cell type-specific patterns of proanthocyanidin accumulation in white clover flowers at different stages of development. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4847191 Thu, 19 May 2011 23:00:00 +0100 4847191 http://www.medworm.com/index.php?rid=4801573&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F11 Conclusions: The software ChIP-seq Analysis in R (CSAR) enables fast and accurate detection of protein-bound genomic regions through the analysis of ChIP-seq experiments. Compared to existing methods, we found that our package shows greater robustness against PCR-artefacts and better control of the error rate. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4801573 Sun, 08 May 2011 23:00:00 +0100 4801573 http://www.medworm.com/index.php?rid=4718897&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F10 Conclusions: We successfully developed a procedure that circumvents the problem of cloning and maintaining long arrays of telomeric DNA sequences that are not stable in E. coli. Our procedure allows development of AC constructs in different eukaryotic species that are capped with long and designed sizes of telomeric DNA fragments. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4718897 Thu, 14 Apr 2011 23:00:00 +0100 4718897 http://www.medworm.com/index.php?rid=4703479&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F9 Conclusions: These results show that FTIR-ATR spectroscopy is suitable as a high-throughput method for lignin and energy estimations in large data sets. Our study revealed that the intra-specific variations in lignin and energy contents were unrelated to each other and that the lignin content, therefore, was no predictor of the energy content. Employing principle component analyses we showed that factor loadings for the energy content were mainly associated with carbohydrate ring vibrations, whereas those for lignin were mainly related to aromatic compounds. Therefore, our analysis suggests that it may be possible to optimize the energy content of trees without concomitant increase in lignin. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4703479 Sat, 09 Apr 2011 23:00:00 +0100 4703479 http://www.medworm.com/index.php?rid=4651942&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F8 Conclusion: Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4651942 Mon, 28 Mar 2011 23:00:00 +0100 4651942 http://www.medworm.com/index.php?rid=4574624&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F6 Conclusions: A stable PepMV vector was generated by expressing the transgene as a CP fusion using the sequence encoding the foot-and-mouth disease virus (FMDV) 2A catalytic peptide to separate them. We have generated a novel tool for the expression of recombinant proteins in plants and for the functional analysis of virus and plant genes. Our experiments have also highlighted virus requirements for replication in single cells as well as intercellular and long-distance movement. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4574624 Fri, 11 Mar 2011 00:00:00 +0100 4574624 http://www.medworm.com/index.php?rid=4570011&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F5 Conclusions: A root-herbivore system consisting of Arabidopsis thaliana and larvae of the opportunistic herbivore Bradysia spp. has been established that mimics herbivory in the rhizosphere. Bradysia infestation of Arabidopsis grown in this culture system significantly affects plant performance. The culture method will allow simple profiling and in vivo functional analysis of root defenses such as chemical defense metabolites that are released in response to belowground insect attack. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4570011 Thu, 10 Mar 2011 00:00:00 +0100 4570011 http://www.medworm.com/index.php?rid=4449687&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F7%2F1%2F3 Conclusions: This study describes a sensitive, high-throughput approach for measuring seed size and seed size distribution. The method provides a low cost and robust solution that can be easily implemented into the workflow of studies relating to various aspects of seed development. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4449687 Tue, 08 Feb 2011 00:00:00 +0100 4449687 http://www.medworm.com/index.php?rid=4298293&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F29 Conclusion: Genomic DNA copy number and ploidy are useful as general normalization factors, providing an easy method for determining the number of transcripts, proteins, and metabolites in a cell. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4298293 Wed, 29 Dec 2010 00:00:00 +0100 4298293 http://www.medworm.com/index.php?rid=4257901&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F28 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 VIGS vector and used in pea for functional analysis of several genes. However, the available PEBV-VIGS protocols are inadequate for studying genes involved in the symbiosis with arbuscular mycorrhizal fungi (AMF).Here we describe a PEBV-VIGS protocol suitable for reverse genetics studies in pea of genes involved in the symbiosis with AMF and show its effectiveness in silencing genes involved in the early and late stages of AMF symbiosis. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4257901 Tue, 14 Dec 2010 00:00:00 +0100 4257901 http://www.medworm.com/index.php?rid=4212728&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F27 Conclusions: The observation that YFP fluorescence is lost during the plant PCD process provides a new tool to study the genetic regulation and cell biology of the process. In addition, plant cell biologists should make a note of this effect of PCD on YFP fluorescence to avoid misinterpretation of their data and to select a pH insensitive reporter if appropriate. This method represents an efficient and streamlined tool expected to bring insights on the process leading to the pH shift occurring during PCD. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4212728 Tue, 30 Nov 2010 00:00:00 +0100 4212728 http://www.medworm.com/index.php?rid=4202634&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F25 Conclusions: We successfully applied our DPI-ELISA protocol to investigate the DNA-binding specificities of three different classes of transcription factors from Arabidopsis thaliana. However, the analysis of the binding affinity of any DNA-binding protein to any given DNA sequence can be performed via this method. The DPI-ELISA is cost efficient, less time-consuming than other methods and provides a qualitative and quantitative readout. The presented DPI-ELISA protocol is accompanied by advice on trouble-shooting, which will enable scientists to rapidly establish this versatile and easy to use method in their laboratories. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4202634 Thu, 25 Nov 2010 00:00:00 +0100 4202634 http://www.medworm.com/index.php?rid=4081280&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F24 Conclusions: The study of salt glands directly at the glandular level are made possible with the successful isolation of these specialized structures. Preparation of materials for subsequent microscopic observations of salt glands could be achieved within a day. Potential applications of confocal fluorescence microscopic techniques could also be performed using these isolated glands. Experiments designed and targeted directly at the salt glands were explored and cytological information obtained herein could be further incorporated towards the understanding of the mechanism underlying secretion in plant salt glands. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4081280 Mon, 18 Oct 2010 23:00:00 +0100 4081280 http://www.medworm.com/index.php?rid=4011454&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F22 Conclusions: We report successful whole genome sequencing of chloroplast DNA from karaka, obtained efficiently and with high fidelity. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=4011454 Mon, 27 Sep 2010 23:00:00 +0100 4011454 http://www.medworm.com/index.php?rid=3997858&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F21 Conclusions: The rapid SA extraction method by direct boiling of leaf discs further reduced the cost and time required for the biosensor Acinetobacter sp. ADPWH_lux-based SA estimation, and allowed the screening for npr1 suppressors that accumulated less SA than npr1 after pathogen infection in a high-throughput manner. The highly efficacious SA estimation protocol can be applied in genetic screen for SA metabolic mutants and characterization of enzymes involved in SA metabolism. The mutants isolated in this study may help identify new components in the SA-related signaling pathways. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3997858 Wed, 22 Sep 2010 23:00:00 +0100 3997858 http://www.medworm.com/index.php?rid=3888582&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F19 Conclusions: The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3888582 Thu, 19 Aug 2010 23:00:00 +0100 3888582 http://www.medworm.com/index.php?rid=3721382&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F17 Conclusions: The pipeline for the three-dimensional imaging and analysis of plant leaves provides the means to include variables on internal tissues in leaf growth studies and the assessment of leaf phenotypes. It also allows the visualisation and quantification of alterations in leaf structure alongside changes in leaf functioning observed under environmental constraints. Data obtained using this procedure can further be integrated in leaf development and functioning models. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3721382 Thu, 01 Jul 2010 23:00:00 +0100 3721382 http://www.medworm.com/index.php?rid=3647873&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F15 Conclusions: The USER TM technology is very well suited for generating a toolbox of vectors for transformation and it opens an opportunity to engineer complex vectors, where several genetic elements of different origin are combined in a single cloning reaction. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3647873 Wed, 09 Jun 2010 23:00:00 +0100 3647873 http://www.medworm.com/index.php?rid=3647874&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F14 Conclusion: The described methodology allows for rapid assessment of infection-specific changes in the plant metabolism, in particular of phenolics, alkaloids, oxylipins and carbohydrates. Moreover, potential novel biomarkers can be detected and used to predict the quality of plant infections. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3647874 Tue, 08 Jun 2010 23:00:00 +0100 3647874 http://www.medworm.com/index.php?rid=3620966&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F13 Conclusions: The model provides a basis for deciphering the genetic architecture of trait expression adjusted to different biotic and abiotic environments for any organism. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3620966 Tue, 01 Jun 2010 23:00:00 +0100 3620966 http://www.medworm.com/index.php?rid=3490031&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F12 Conclusion: Our ASP methodology allows characterization of SNPs genotypes without electrophoresis, expensive probes or specialized equipment, and is highly versatile due to the flexibility in the design of primers. The method could be established easily in any molecular biology laboratory, and is applicable to diverse organisms. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3490031 Tue, 20 Apr 2010 23:00:00 +0100 3490031 http://www.medworm.com/index.php?rid=3456346&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F11 Conclusion: Here we provide a chromatin immunoprecipitation procedure for tomato leaves that could be combined with high-throughput sequencing to generate a detailed map of epigenetic modifications or genome-wide nucleosome positioning data. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3456346 Thu, 08 Apr 2010 23:00:00 +0100 3456346 http://www.medworm.com/index.php?rid=3428399&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F10 Conclusions: We developed the SSHscreen-SSHdb software pipeline, which greatly facilitates gene discovery using suppression subtractive hybridization by improving the selection of clones for sequencing after screening the library on a small number of microarrays. Annotation of the sequence information and collaboration was further enhanced through a web-based SSHdb database, and we illustrated this through identification of drought responsive genes from cowpea, which can now be investigated in gene function studies. SSH is a popular and powerful gene discovery tool, and therefore this pipeline will have application for gene discovery in any biological system, particularly non-model organisms. SSHscreen 2.0.1 and a link to SSHdb are available from http://microarray.up.ac.za/SSHscreen. (Sour... Plant Methods journals http://www.medworm.com/rss/comments.php?id=3428399 Wed, 31 Mar 2010 23:00:00 +0100 3428399 http://www.medworm.com/index.php?rid=3358312&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F8 Conclusions: The LEC2-extended N. benthamiana assay allows the transient activation of seed-specific promoters in leaf tissue. In this study we have used the assay as a rapid preliminary screen of a complex seed-specific transgenic construct prior to stable transformation, a feature that will become increasingly useful as genetic engineering moves from the manipulation of single genes to the engineering of complex pathways. We propose that the assay will prove useful for other applications wherein rapid expression of transgenes driven by seed-specific constructs in leaf tissue are sought. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3358312 Thu, 11 Mar 2010 00:00:00 +0100 3358312 http://www.medworm.com/index.php?rid=3243137&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F7 Conclusions: In plants, cell death is an integral part of both development and defence, and hence it is a common phenomenon in all stages of the life cycle. Our results suggest that extensive nucleic acid fragmentation during cell death processes can be a considerable source of non-specific signals in traditional in situ mRNA hybridization. Thus, the visualization of potential nucleic acid fragmentation simultaneously with the in situ mRNA hybridization assay may be necessary to ensure the correct interpretation of the signals in the case of non-specific hybridization of probes in plant tissues. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3243137 Fri, 05 Feb 2010 00:00:00 +0100 3243137 http://www.medworm.com/index.php?rid=3219876&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F6 Conclusions: The proposed extraction protocol leads to highly reproducible metabolic fingerprints and allows optimal handling of field-collected plant material and further processing in the laboratory, which is demonstrated for an exemplary field data-set. Calculation of Xi values is a useful tool to judge similarities between chromatograms. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3219876 Fri, 29 Jan 2010 00:00:00 +0100 3219876 http://www.medworm.com/index.php?rid=3215814&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F4 Conclusion: The system has been evolved and tested over several years in a transformation service unit, where it increased efficiency. Additionally, the system provided rapid access to data for quality control and decision making. The system can be easily modified for the use in other research environments. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3215814 Wed, 27 Jan 2010 00:00:00 +0100 3215814 http://www.medworm.com/index.php?rid=3207824&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F3 Conclusion: NEATTILL is a convenient procedure that can be applied to all organisms, the genomes of which have been mutagenized and are being scanned for multiple alleles of various genes by TILLING for understanding gene-to-phenotype relationships. It is a time-saving, less labour intensive and reasonably cost-effective method. Tissue arraying can cut costs byup to 90% and minimizes the risk of exposing the DNA to nucleases. Before arraying, different tissues should be evaluated for DNA quality, as the case study in tomato showed that cotyledons rather than leaves are better suited for DNA isolation. The protocol described here for nucleic acid isolation can be generally adapted for large-scale projects such as insertional mutagenesis, transgenic confirmation, mapping and fingerprinting w... Plant Methods journals http://www.medworm.com/rss/comments.php?id=3207824 Tue, 26 Jan 2010 00:00:00 +0100 3207824 http://www.medworm.com/index.php?rid=3184900&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F2 Conclusions: The results illustrate the propensity of operator repeat arrays to form heterochromatin that can silence the neighbouring gene encoding the RP-FP fusion protein. Supplying the RP-FP fusion protein in trans from a second T-DNA largely alleviates this problem. Depending on the promoter used to drive expression of the RP-FP fusion protein gene, the fluorescent tagged sites can be visualized at high frequency in different cell types. The ability to observe fluorescent dots on both interphase and mitotic chromosomes allows tagged sites to be tracked throughout the cell cycle. These improvements enhance the versatility of the fluorescent tagging technique for future studies of chromosome arrangement and dynamics in living plants. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3184900 Tue, 19 Jan 2010 00:00:00 +0100 3184900 http://www.medworm.com/index.php?rid=3175226&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F6%2F1%2F1 Research in plant molecular biology involves DNA purification on a daily basis. Although different commercial kits enable convenient extraction of high-quality DNA from E. coli cells, PCR and agarose gel samples as well as plant tissues, each kit is designed for a particular type of DNA extraction work, and the cost of purchasing these kits over a long run can be considerable. Furthermore, a simple method for the isolation of binary plasmid from Agrobacterium tumefaciens cells with satisfactory yield is lacking. Here we describe an easy protocol using homemade silicon dioxide matrix and seven simple solutions for DNA extraction from E. coli and A. tumefaciens cells, PCR and restriction digests, agarose gel slices, and plant tissues. Compared with the commercial kits, this protocol allows r... Plant Methods journals http://www.medworm.com/rss/comments.php?id=3175226 Thu, 14 Jan 2010 00:00:00 +0100 3175226 http://www.medworm.com/index.php?rid=3074834&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F18 Conclusions: The phenotyping of large population of plants both in the laboratory and in the field is very efficiently managed using PDA. The data is transferred to a specialized database(s) where it can be further analyzed and catalogued. The "PHENOME" aids collection and analysis of data obtained in large-scale mutagenesis, assessing quantitative trait loci (QTLs), raising mapping population, sampling of several individuals in one or more ecological niches etc. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3074834 Thu, 10 Dec 2009 00:00:00 +0100 3074834 http://www.medworm.com/index.php?rid=3026094&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F17 Conclusions: The method presented was used to detect 16 compounds in leaf extracts of N. attenuata plants. Importantly, the method can be adapted based on the specific analytes of interest with the only consideration that the molecules must contain at least one free carboxyl group. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=3026094 Wed, 25 Nov 2009 00:00:00 +0100 3026094 http://www.medworm.com/index.php?rid=2946543&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F15 Conclusions: The development of the documented YW5AF7 line provides an important tool for Rosaceae functional genomic analyses. These day-neutral plants have a small genome, a seed to seed cycle of 3.0 - 3.5 months, and produce fruit in 7.5 cm pots in a growth chamber. YW5AF7 is runnerless and therefore easy to maintain in the greenhouse, forms abundant branch crowns for vegetative propagation, and produces highly aromatic yellow fruit throughout the year in the greenhouse. F. vesca can be transformed with Agrobacterium tumefaciens, making these plants suitable for insertional mutagenesis, RNAi and overexpression studies that can be compared against a stable baseline of phenotypic descriptors and can be readily genetically substantiated. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2946543 Sat, 31 Oct 2009 00:00:00 +0100 2946543 http://www.medworm.com/index.php?rid=2934128&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F14 Conclusions: The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Our method allows for efficient utilization of the growing sequence and expression data for gene families through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2934128 Wed, 28 Oct 2009 00:00:00 +0100 2934128 http://www.medworm.com/index.php?rid=2868497&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F13 Conclusion: These results demonstrate that CSCE and HRM are fast, affordable and sensitive techniques for mutation detection in DNA pools and therefore allow the rapid identification of new allelic variants in a mutant population. Results from the first screens indicate that the mutagen treatment has been effective with an average mutation detection rate per diploid genome of 1.36 mutation/kb/1000lines. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2868497 Tue, 06 Oct 2009 23:00:00 +0100 2868497 http://www.medworm.com/index.php?rid=2666861&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F11 Conclusion: Our work describes a 3D-FISH protocol that preserves the 3D structure of Arabidopsis interphase nuclei. Moreover, we report for the first time FISH using cryosections of Arabidopsis leaves. This protocol is a valuable tool to investigate nuclear architecture and chromatin organization. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2666861 Sun, 02 Aug 2009 23:00:00 +0100 2666861 http://www.medworm.com/index.php?rid=2648530&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F10 Conclusion: As well as developing a rapid, and high-throughput marker method for genetic studies, the fluorescent SSAP system improved the accuracy of amplicon scoring, increased the available marker number, improved allele discrimination, and was sensitive enough to identify heterozygous loci in F1 and F2 progeny, indicating the potential to develop high-throughput codominant SSAPs. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2648530 Mon, 27 Jul 2009 23:00:00 +0100 2648530 http://www.medworm.com/index.php?rid=2569301&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F9 Conclusion: The unique properties of the pWSRi vector, the ability to silence genes in meristem tissue, the separation of virus and silencing phenotypes, and the broad natural host range of BCTV, suggest that it will have wide utility. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2569301 Wed, 01 Jul 2009 23:00:00 +0100 2569301 http://www.medworm.com/index.php?rid=2503854&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F8 Conclusion: The DAWGPAWS genome annotation pipeline fills an important need in the annotation of plant genomes by generating computational evidences in a high throughput manner, translating these results to a common file format, and facilitating the human curation of these computational results. We have verified the value of DAWGPAWS by using this pipeline to annotate the genes and transposable elements in 220 BAC insertions from the hexaploid wheat genome (Triticum aestivum L.). DAWGPAWS can be applied to annotation efforts in other plant genomes with minor modifications of program-specific configuration files, and the modular design of the workflow facilitates integration into existing pipelines (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2503854 Thu, 18 Jun 2009 23:00:00 +0100 2503854 http://www.medworm.com/index.php?rid=2503855&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F7 Conclusion: The described infrared heating system meets the utilitarian requirements of a heating system for plant physiology studies in that the elevated temperature can be accurately, precisely, and reliably controlled with minimal perturbation of other environmental factors. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2503855 Wed, 10 Jun 2009 23:00:00 +0100 2503855 http://www.medworm.com/index.php?rid=2090537&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F5%2F1%2F1 Conclusions: SAP offers an excellent alternative to existing SNP-discrimination methods such as Cleaved Amplified Polymorphic Sequence (CAPS), or derived CAPS (dCAPS) method. It can also be adapted for high throughput SNP analyses by incorporating fluorophore-labeled primers. SAP is reliable, cost-effective, fast, and simple, and can be applied to all organisms not limited to Arabidopsis thaliana. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2090537 Thu, 08 Jan 2009 05:00:00 +0100 2090537 http://www.medworm.com/index.php?rid=2076076&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F28 Conclusions: The ability of Acinetobacter sp. ADPWH_lux to detect SA in a complex mixture, combined with the enzymatic hydrolysis of SAG in crude extract, allowed the development of a simple, rapid, and inexpensive method to simultaneously measure free and glucose-conjugated SA. This approach is amenable to a high-throughput format, which would further reduce the cost and time required for biosensor-based SA quantification. Possible applications of this approach include characterization of enzymes involved in SA metabolism, analysis of temporal changes in SA levels, and isolation of mutants with aberrant SA accumulation. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=2076076 Wed, 31 Dec 2008 05:00:00 +0100 2076076 http://www.medworm.com/index.php?rid=1948154&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F27 Conclusions: The method presented here allows the acquisition of quantitative numerical estimates of Arabidopsis drought survival times that are amenable to statistical analysis. Furthermore, the required measurements can be obtained quickly and non-invasively using inexpensive equipment and with minimal expertise in chlorophyll fluorometry. This technique enables the rapid assessment and comparison of the relative viability of germplasm during drought, and may complement detailed physiological and water relations studies. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=1948154 Tue, 11 Nov 2008 05:00:00 +0100 1948154 http://www.medworm.com/index.php?rid=1912217&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F26 The gluten analysis of foods has long had limitations, which have precluded food standards authorities from issuing standards for gluten-free foods based on final gluten content. The Codex Alimentarius and the Food and Drug Administration have recently taken steps towards such standards in which they favour the R5-enzyme-linked immunosorbent assay for gluten analysis. If this method is to be widely employed, its limitations should be recognised. Above all, it should be noted the ability of the R5-enzyme-linked immunosorbent assay, and other methods, to measure gluten's toxicity toward celiac disease patients is not validated clinically. Gluten is a complex mixture of proteins and its toxicity is not fully understood. Analytical methods are a valuable tool in the definition of gluten-free f... Plant Methods journals http://www.medworm.com/rss/comments.php?id=1912217 Tue, 28 Oct 2008 04:00:00 +0100 1912217 http://www.medworm.com/index.php?rid=1876965&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F24 Conclusion: Multi-color BiFC is a useful technique to determine interactions simultaneously between a given" bait" protein and multiple "prey" proteins in living plant cells. The vectors we have constructed and tested will facilitate the study of protein-protein interactions in many different plant systems. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=1876965 Wed, 15 Oct 2008 04:00:00 +0100 1876965 http://www.medworm.com/index.php?rid=1838259&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F23 Renilla luciferase (RLUC) is a popular reporter enzyme for gene expression and biosensor applications, but it is an unstable enzyme whose catalytic mechanism remains to be elucidated. We titrated that one RLUC molecule can turn over about one hundred molecules of coelenterazine substrate. Mutagenesis of active site residue Pro220 extended the half-life of photon emission, yielding brighter luminescence in E. coli. Random mutagenesis uncovered two new mutations that stabilized and increased photon emission in vivo and in vitro, while ameliorating substrate inhibition. Further amended with a previously identified mutation, a new triple mutant showed a threefold improved kcat , as well as elevated luminescence in Arabidopsis. This advances the utility of RLUC as a reporter protein, biosensor,... Plant Methods journals http://www.medworm.com/rss/comments.php?id=1838259 Tue, 30 Sep 2008 04:00:00 +0100 1838259 http://www.medworm.com/index.php?rid=1806941&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F21 Conclusions: The mEosFP::FABD-mTn probe retains all the imaging qualities associated with the well tested GFP::mTn probe while allowing for non-invasive, regional photo-conversion that allows colour based discrimination within a living cell. Whereas a number of precautions should be exercised in dealing with photo-convertible probes, mEosFP::FABD-mTn is a versatile live imaging tool for dissecting the organization and activity of the actin cytoskeleton in plants. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=1806941 Fri, 19 Sep 2008 04:00:00 +0100 1806941 http://www.medworm.com/index.php?rid=1672316&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F20 Conclusions: A high-throughput system for DNA extraction from conifer needles and seeds has been developed and validated. The quality of the isolated DNA was comparable with that obtained from two commonly used methods: the silica-spin column and the classic CTAB protocol. Our protocol provides a fully automatable and cost effective solution for processing large numbers of conifer samples. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=1672316 Fri, 01 Aug 2008 04:00:00 +0100 1672316 http://www.medworm.com/index.php?rid=1556931&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F14 Conclusion: Due to the highly conserved chloroplast genome in plant families it is possible to utilize primer pairs designed against one genomic sequence to detect the presence and abundance of plastid genes or transcripts from genomes that have yet to be sequenced. Analysis of steady state transcription of vital system genes is a necessary requirement to comprehensively elucidate gene expression in any organism. The primer pairs reported in this paper were designed for q2(RT)PCR of maize chloroplast genes but should be useful for other members of the Poaceae family. Both in silico and in vitro data are presented to support this assumption. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=1556931 Mon, 02 Jun 2008 04:00:00 +0100 1556931 http://www.medworm.com/index.php?rid=1556932&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F13 Conclusion: We anticipate this microarray-based genotyping platform, based on its low cost-per-sample, to be particularly useful in applications requiring whole-genome molecular marker coverage across large numbers of individuals. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=1556932 Thu, 29 May 2008 04:00:00 +0100 1556932 http://www.medworm.com/index.php?rid=1556933&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F11 Conclusion: The Golm Plant Database system, which is based on a relational database, collects the genetic and environmental information on plant material during its production or experimental use at the Max-Planck-Institute of Molecular Plant Physiology. It thus provides information according to the MIAME standard for the component 'Sample' in a highly standardised format. The Plant Database system thus facilitates collaborative work and allows efficient queries in data analysis for systems biology research. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=1556933 Wed, 21 May 2008 04:00:00 +0100 1556933 http://www.medworm.com/index.php?rid=1556934&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F9 Conclusion: We developed a tool and associated methods for analyzing the complex dynamic of organelle-organelle interactions in real time in planta. Homozygous transgenic Arabidopsis (Kaleidocell) is available through Arabidopsis Biological Resource Center. (Source: Plant Methods) Plant Methods journals http://www.medworm.com/rss/comments.php?id=1556934 Mon, 19 May 2008 04:00:00 +0100 1556934 http://www.medworm.com/index.php?rid=1556935&cid=s_37185_62_f&fid=37185&url=http%3A%2F%2Fwww.plantmethods.com%2Fcontent%2F4%2F1%2F7 The green eukaryote alga Chlamydomonas reinhardtii is a unicellular model to study control of metabolism in a photosynthetic organism. We here present method improvements for metabolite profiling based on GC-TOF mass spectrometry focusing on three parameters: quenching and cell disruption, extract solvent composition and metabolite annotation. These improvements facilitate using smaller cell numbers and hence, smaller culture volumes which enable faster and more precise sampling techniques that eventually lead to a higher number of samples that can be processed, e.g. for time course experiments. Quenching of metabolism was achieved by mixing 1 ml of culture to 1 ml of -70°C cold 70% methanol. After centrifugation, cells were lyophilized and disrupted by milling using 2-6E6 lyophilized cel... Plant Methods journals http://www.medworm.com/rss/comments.php?id=1556935 Mon, 28 Apr 2008 04:00:00 +0100 1556935