Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ

Optimization of Graphene Oxide-based Quencher-free Molecular Beacon for Meat Product Authentication

BACKGROUND AND OBJECTIVE

Sensitivity is very important in DNA detection. Various attempts have been made to increase detection sensitivity, including increasing the detection capabilities of devices and using DNA probes. This study was aimed to develop a DNA detection method using a quencher-free molecular beacon (QFMB) probe with the help of graphene oxide (GO) as a quencher.

MATERIALS AND METHODS

The GO has the specific ability to adsorb DNA in the form of a single strand but not in a double strand. The optimum interaction between the MB probe and the target DNA (pig DNA) could produce a double-stranded DNA (dsDNA) so that it is detached from the GO surface. The dsDNA that escapes from the surface of the GO can be detected using a spectrofluorometric technique at an excitation wavelength of 482 nm and an emission of 519 nm, with an intensity comparable to its concentration.

RESULTS

The optimum condition that can be used is a GO concentration of 5 μg mL-1, a reaction temperature of 65°C, an incubation time of 6 min, a reaction pH of 7.5 and cation levels of 40 nM. Analysis of the target pork meatball DNA carried out at a concentration interval of 0-500 pg mL-1.

CONCLUSION

So it was concluded that the DNA detection system uses a combination of a quencher-free molecular beacon and graphene oxide, providing a good prospect to be developed into a new method in the halal authentication of meat products using the spectrofluorometric method.

Multiplex and quantitative PCR targeting SCAR markers for strain-level detection and quantification of biofertilizers

Biofertilizers are the eco-friendly bio-input being used to sustain the agriculture by reducing the chemical inputs and improving the soil health. Quality is the major concern of biofertilizer technology which often leads to poor performance in the field and thereby loses the farmers' faith. To authenticate the strain as well as its presumed cell load of a commercial product, sequence characterized amplified region (SCAR) markers were developed for three biofertilizer strains viz., Azospirillum brasilense (Sp7), Bacillus megaterium (Pb1) and Azotobacter chroococcum (Ac1). We evaluated the feasibility of multiplex-PCR and quantitative real-time PCR for SCAR marker-based quality assessment of the product as well as the persistence of the strains during crop growth. We showed that multiplex PCR can concurrently discriminate the strains based on the amplicons' size and detects up to 10⁴ cells per g or per ml of carrier-based or liquid formulation of biofertilizer, respectively. The detection limit of quantitative PCR targeting SCAR markers is 10³  cells per g or ml of biofertilizer. Both the PCR methods detected and quantified them in the maize rhizosphere. Hence SCAR marker-based quality assessment would be a sensitive tool to monitor the biofertilizer production as well as its persistence in the inoculated crop rhizosphere.

Case Investigation and Forensic Evidence for a New Plant Disease: The Case of Lettuce Corky Root

The process of disease diagnosis reminds of the process of solving a crime. This starts with a so-called 'crime scene investigation' (CSI) carried out in a highly systematic manner. The CSI is followed by 'forensic investigation' in specialized laboratories. The final step in solving a crime is the 'crime scene reconstruction' process, which involves systematic elimination of unlikely scenarios and comparison of results from the analysis of physical evidence with eye witness accounts. If more evidence becomes available, an 'old case may be reactivated'. In this review, the same sequence of activities is followed to solve a plant disease problem using a case study of a disease that was difficult to diagnose, namely the 'case' of corky root of lettuce.

Practical benefits of knowing the enemy: modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria

Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California's Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and bacterial taxonomy. Whole-genome sequence analysis needs to become adequately accessible, automated, and affordable in order to be used routinely for identification and epidemiology. The power of molecular tools in accurately identifying bacterial pathogenesis is therefore of value to the farmer, diagnostician, phytobacteriologist, and taxonomist.