PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories-2

<p><b>Copyright information:</b></p><p>Taken from "PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories"</p><p>http://www.biomedcentral.com/1471-2199/8/77</p><p>BMC Molecular Biology 2007;8():77-77.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2075515.</p><p></p>inding sites in an orientation favorable for a PCR. B) PCR window, selecting Plasmid X as the template, and the two primers. The resulting fragment can be added to the project to be further analyzed and manipulated

PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories-0

<p><b>Copyright information:</b></p><p>Taken from "PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories"</p><p>http://www.biomedcentral.com/1471-2199/8/77</p><p>BMC Molecular Biology 2007;8():77-77.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2075515.</p><p></p>window selecting NotI as an enzyme. C) After adding both digestion products to the project, the project contains three fragments, including the original plasmid. Each of the new fragments can then be further analyzed and manipulated. The fragments can be visualized together and to scale, as shown, or one by one for greater resolution

Development, Optimization, and Single Laboratory Validation of an Event-Specific Real-Time PCR Method for the Detection and Quantification of Golden Rice 2 Using a Novel Taxon-Specific Assay

In this study, we developed, optimized, and in-house validated a real-time PCR method for the event-specific detection and quantification of Golden Rice 2, a genetically modified rice with provitamin A in the grain. We optimized and evaluated the performance of the taxon (targeting rice Phospholipase D α2 gene)- and event (targeting the 3′ insert-to-plant DNA junction)-specific assays that compose the method as independent modules, using haploid genome equivalents as unit of measurement. We verified the specificity of the two real-time PCR assays and determined their dynamic range, limit of quantification, limit of detection, and robustness. We also confirmed that the taxon-specific DNA sequence is present in single copy in the rice genome and verified its stability of amplification across 132 rice varieties. A relative quantification experiment evidenced the correct performance of the two assays when used in combination

Towards Plant Species Identification in Complex Samples: A Bioinformatics Pipeline for the Identification of Novel Nuclear Barcode Candidates

<div><p>Monitoring of the food chain to fight fraud and protect consumer health relies on the availability of methods to correctly identify the species present in samples, for which DNA barcoding is a promising candidate. The nuclear genome is a rich potential source of barcode targets, but has been relatively unexploited until now. Here, we show the development and use of a bioinformatics pipeline that processes available genome sequences to automatically screen large numbers of input candidates, identifies novel nuclear barcode targets and designs associated primer pairs, according to a specific set of requirements. We applied this pipeline to identify novel barcodes for plant species, a kingdom for which the currently available solutions are known to be insufficient. We tested one of the identified primer pairs and show its capability to correctly identify the plant species in simple and complex samples, validating the output of our approach.</p></div

Species detection in various samples using the 23579-aaa barcoding primers.

<p>The tested samples were (A) Purchased maize (<i>Zea mays</i>) DNA. (B) Purchased soya (<i>Glycine max</i>) DNA. (C) A leaf from a rice (<i>Oryza sativa</i>) plant. (D) Fresh strawberries from the supermarket (<i>Fragaria x ananassa</i>). (E) A commercial pack of fruit and cereal muesli. The results are shown on a simplified taxonomy line, with the number of NGS reads assigned to that specific location as a blue circle whose area is proportional to the numerical value. The values in parenthesis represent the (number of clusters:total number of reads).</p

Bioinformatics pipeline for the identification of DNA barcodes in the nuclear genome.

<p>Scheme representing the flow of the different steps in the bioinformatics pipeline designed to process input sequences (top left) in order to output potential primer pairs amplifying novel DNA barcoding targets (bottom right). See text and Supporting Information for details.</p