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An inbred line of the diploid strawberry Fragaria vesca f. semperflorens for genomic and molecular genetic studies in the RosaceaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 t...
Source: Plant Methods - October 31, 2009 Category: Biology Authors: Janet SlovinKyle SchmittKevin Folta Source Type: journals

A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swapsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - October 28, 2009 Category: Biology Authors: Ivan AtanassovIlian AtanassovJ Peter EtchellsSimon Turner Source Type: journals

Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - October 6, 2009 Category: Biology Authors: Antoine GadyFreddy HermansMarion Van de WalEibertus van LooRichard VisserChristian Bachem Source Type: journals

3D fluorescent in situ hybridization using Arabidopsis leaf cryosections and isolated nucleiEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - August 2, 2009 Category: Biology Authors: Leila TirichinePhilippe AndreyEric BiotYves MaurinValerie Gaudin Source Type: journals

High-throughput retrotransposon-based fluorescent markers: improved information content and allele discriminationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - July 27, 2009 Category: Biology Authors: Maggie KnoxCarol MoreauJames LipscombeDavid BakerNoel Ellis Source Type: journals

Development of a gene silencing DNA vector derived from a broad host range geminivirusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - July 1, 2009 Category: Biology Authors: Edward GolenbergD SatherLeandria HancockKenneth BuckleyNatalie VillafrancoDavid Bisaro Source Type: journals

The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 mo...
Source: Plant Methods - June 18, 2009 Category: Biology Authors: James EstillJeffrey Bennetzen Source Type: journals

Instrumentation enabling study of plant physiological response to elevated nighttime temperatureEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - June 10, 2009 Category: Biology Authors: Abdul MohammedLee Tarpley Source Type: journals

Simple allele-discriminating PCR for cost-effective and rapid genotyping and mappingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - January 8, 2009 Category: Biology Authors: Minh Bui and Zhongchi Liu Source Type: journals

A rapid biosensor-based method for quantification of free and glucose-conjugated salicylic acidEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 - December 31, 2008 Category: Biology Authors: Christopher T DeFraia, Eric A Schmelz and Zhonglin Mou Source Type: journals

A rapid, non-invasive procedure for quantitative assessment of drought survival using chlorophyll fluorescenceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - November 11, 2008 Category: Biology Authors: Nick S Woo, Murray R Badger and Barry J Pogson Source Type: journals

Gluten measurement and its relationship to food toxicity for celiac disease patientsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 validat...
Source: Plant Methods - October 28, 2008 Category: Biology Authors: Diane R Lester Source Type: journals

Vectors for multi-color bimolecular fluorescence complementation to investigate protein-protein interactions in living plant cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - October 15, 2008 Category: Biology Authors: Lan-Ying Lee, Mei-Jane Fang, Lin-Yun Kuang and Stanton Gelvin Source Type: journals

Mutational optimization of the coelenterazine-dependent luciferase from RenillaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Plant Methods - September 30, 2008 Category: Biology Authors: Jongchan Woo and Albrecht G von Arnim Source Type: journals

Visualizing the actin cytoskeleton in living plant cells using a photo-convertible mEos::FABD-mTn fluorescent fusion proteinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - September 19, 2008 Category: Biology Authors: Mike Schenkel, Alison M Sinclair, Daniel Johnstone, J DEREK Bewley and Jaideep Mathur Source Type: journals

Protocol: A high-throughput DNA extraction system suitable for conifersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - August 1, 2008 Category: Biology Authors: Stanislav Bashalkhanov and Om P Rajora Source Type: journals

A plastome primer set for comprehensive quantitative real time RT-PCR analysis of Zea mays: a starter primer set for other Poaceae speciesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 suppor...
Source: Plant Methods - June 2, 2008 Category: Biology Authors: Richard M Sharpe, Sade N Dunn and A. Bruce Cahoon Source Type: journals

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in riceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - May 29, 2008 Category: Biology Authors: Jeremy D Edwards, Jaroslav Janda, Megan T Sweeney, Ambika B Gaikwad, Bin Liu, Hei Leung and David W Galbraith Source Type: journals

A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics researchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - May 21, 2008 Category: Biology Authors: Karin I Köhl, Georg Basler, Alexander Lüdemann, Joachim Selbig and Dirk Walther Source Type: journals

Multidimensional fluorescence microscopy of multiple organelles in Arabidopsis seedlingsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Plant Methods - May 19, 2008 Category: Biology Authors: Naohiro Kato, Dexter Reynolds, Matthew L Brown, Marietta Boisdore, Yukichi Fujikawa, Andrea Morales and Lee A Meisel Source Type: journals

High quality metabolomic data for Chlamydomonas reinhardtiiEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Plant Methods - April 28, 2008 Category: Biology Authors: Do Yup Lee and Oliver Fiehn Source Type: journals