Detection of food-borne pathogens with DNA arrays on disk

Abstract

ElsevierElena Fito, SF.; Carrera, J.; Rodrigo, J. (2011). A systems biology approach to the evolution of plant-virus interactions. Current Opinion in Plant Biology. 14(4):372-377. doi:10.1016/j.pbi.2011.03.013. Omic approaches to the analysis of plant-virus interactions are becoming increasingly popular. These types of data, in combination with models of interaction networks, will aid in revealing not only host components that are important for the virus life cycle, but also general patterns about the way in which different viruses manipulate host regulation of gene expression for their own benefit and possible mechanisms by which viruses evade host defenses. Here, we review studies identifying host genes regulated by viruses and discuss how these genes integrate in host regulatory and interaction networks, with a particular focus on the physical properties of these networks. A systems biology approach to the evolution of plant-virus interactions The systems biology approachGenomic tools have allowed assessment of gene expression at a genome-wide scale, providing unprecedented views of the host-virus interaction. To make use of all of the information contained in these large data sets, however, it is necessary to use computational and mathematical tools to disentangle the interactions between the molecular components of both biological entities and to identify how these interactions determine the outcome of the infection [1,2••], which is known as the field of genomic systems biology (GSB). GSB is a top-down approach that takes advantage of the recent development of high-throughput experimental techniques for obtaining omic data, and constitutes the antithesis of the reductionist paradigm (with a bottom-up perspective) that has been dominating molecular biology. The GSB approach consists of cycling between the generation of experimental data and modeling by means of reverse-engineering techniques to propose testable hypotheses about biological systems, experimental validation of these hypotheses and quantification of the relevant model parameters, and then using the newly acquired quantitative description to refine the computational model and finally make predictions of the system behavior [3,4•].To complete its infectious cycle, a few components of a virus, including its nucleic acids and encoded proteins, must establish multiple and complex interactions not only among themselves [5,6•,7,8] but also with a myriad of components of the host cell [9,10•,11]. The outcome of all these interactions is that the plant controls the spread of viral infection or, alternatively, the virus overcomes the host defenses and establishes a productive infection that may or may not be associated with the development of symptoms. While the GSB approach is being extensively used in the analysis of animal virus interactions (e.g. hepatitis C, human immunodeficiency, yellow fever, influenza A and herpesviruses), plant virologyhas not yet benefitted to the same extent, and the most relevant studies in the field generally apply some tr...

Arrays on disc for screening and quantification of pollutants

“…For these experiments, four volumes (6,12,18, and 20 L) were compared in terms of signal intensity and reproducibility. For the blanks (absence of analyte), signals were significantly similar for all the tested volumes, varying from 10,870 to 11,950 (arbitrary units), for 6 and 20 L, respectively.…”

“…In this line, arrays on compact disks have shown great potential when they are applied in the areas of food safety and environmental analysis [18,19]. Arrays on disc show high working capacity and present the additional advantage of being scanned by disc drives.…”

Array-on-a-disk? How Blu-ray technology can be applied to molecular diagnostics

“…Indeed, the potential of optical disc drive as the signal-transducing element has been demonstrated for quantitative analysis using regular CDs and DVDs [3][4][5]. Discs have been used as analytical platforms to immobilize probes (proteins and nucleic acids) directly by passive adsorption [6,7], indirectly by means of affinity bioreagents [8] (streptavidin, protein A, concanavalin A, antibodies, etc. ), covalently by previous chemical functionalization of the original disc polymer (polycarbonate) [9] or by spin coating a supplementary film such as polystyrene [10], SU-8 [11], gold, aluminum oxide or graphite [12].…”

Screening methodologies for the determination of water contaminant residues by compact disk technology

“…The strategy is based on hydrophobic interactions between probes and polycarbonate, showing high immobilization yields. 186 Following this research line, Li et al 187 developed bioassays performed directly on a CD in a line array format. The aim was to detect different types of biochemical recognition reactions (biotin-streptavidin binding, DNA hybridization and protein-protein interactions) with standard optical drives.…”

“…in powder infant milk after PCR amplification as a double checking sensor system was also developed. 186 Also, multiplex DNA detection of food three allergens (hazelnut, peanut and soybean) on a DVD has been described. 193 In another work, two approaches under isothermal conditions: recombinase polymerase amplification (RPA) and multiple displacement amplification (MDA) were applied to a duplex assay specific for Salmonella spp.…”