Comprehensive assessment of 12 commercial DNA-binding dyes as alternatives to ethidium bromide for agarose gel electrophoresis.

Staining and visualization of the nucleic acid bands on agarose gels using ethidium bromide (EB) has been a widely used technique in molecular biology. Although it is an efficient dye for this purpose, EB is known to be mutagenic and genotoxic in humans. This led to the emergence of various alternative dyes, which were claimed to be safer and more efficient than EB. However, these dyes portray varied sensitivity and interference with the electrophoretic mobility of nucleic acids. This work aimed at assessing ten nucleic acid-binding dyes and two prestained dyes for these properties by three staining techniques, such as precasting, preloading, and poststaining. Of these, preloading was not suitable for any of the dye while poststaining worked optimal for most of them. Precasting was suitable for only four dyes viz. DNA Stain G, SYBR™ safe, EZ-Vision® in-gel, and LabSafe™. Poststaining was, in general, a costlier method than precasting. The work gives a comprehensive understanding of the performance of nucleic acid-binding dyes for routine molecular biology experiments.

Comprehensive in situ and ex situ ß-glucosidase-assisted assessment reveals Indian mangoes as reservoirs of glycosidic aroma precursors.

Mango, a valued commercial fruit in India is popular mostly because of its attractive flavour. Glycosidically bound volatiles (GBV), an underrepresented warehouse of aroma, remain completely unexplored in Indian mangoes. In this study, GBV were profiled in pulps and peels of 10 Indian mango cultivars, leading to detection of 66 GBV which were dominated by monoterpenoids and phenolics. Peels were quantitatively and qualitatively richer in GBV than pulps. Hierarchical clustering and principal component analysis indicated higher contribution of peel GBV to the distinctness of cultivars. Linalool, geraniol, and eugenol were the significant contributors based on the odour units. Direct ß-glucosidase treatment to the juice resulted in the release of lesser number of volatiles than those released from the purified GBV extracts. Apart from providing a comprehensive catalogue of GBV in mangoes, our data suggests the need of critical assessment of the usefulness of ß-glucosidases in aroma improvement of fruit juices.

Non-redundant nature of Lactiplantibacillus plantarum plasmidome revealed by comparative genomic analysis of 105 strains.

Lactiplantibacillus plantarum is a homofermentative lactic acid bacterium (LAB) most often found in fermented foods with many strains displaying probiotic properties. Strains belonging to L. plantarum are more stress tolerant and metabolically flexible than other lactobacilli and display larger genomes and higher plasmid abundance. This study aimed at understanding whether plasmids play a particular role in L. plantarum as compared to chromosomes by comparative genomic analysis. Assessment of chromosomes and 395 plasmids of 105 strains with publicly available complete genome sequences revealed that the majority of the plasmids encoded protein families (PFs) (57.6%) were not encoded by the chromosomes. The most abundant PFs unique to plasmids contained hypothetical proteins while others were involved in exopolysaccharides biosynthesis, biofilm formation, stress tolerance, and carbohydrate metabolism. The sequences of common plasmid-encoded and chromosome-encoded PFs differed from each other, suggesting that they might exhibit different biochemical properties. Common PF genes were predominantly present on larger plasmids pointing to another possible way to reduce redundancy by encoding shared PFs by low copy number plasmids. Overall, this study demonstrates the unique contributions of the plasmids to the versatility, survival, and evolutionary success of L. plantarum while also highlighting a need to functionally characterize hypothetical proteins encoded by them.

Unconventional ß-Glucosidases: A Promising Biocatalyst for Industrial Biotechnology.

ß-Glucosidases primarily catalyze removal of terminal glucosyl residues from a variety of glucoconjugates and also perform transglycosylation and reverse hydrolysis. These catalytic properties can be readily exploited for degradation of lignocellulosic biomass as well as for pharmaceutical, food and flavor industries. ß-Glucosidases have been either isolated in the native form from the producer organism or recombinantly expressed and gaged for their biochemical properties and substrate specificities. Although almond and Aspergillus niger have been instantly recognizable sources of ß-glucosidases utilized for various applications, an intricate pool of novel ß-glucosidases from different sources can provide their potent replacements. Moreover, one can envisage the better efficacy of these novel candidates in biofuel and biorefinery industries facilitating efficient degradation of biomass. This article reviews properties of the novel ß-glucosidases such as glucose tolerance and activation, substrate specificity, and thermostability which can be useful for their applications in lignocellulose degradation, food industry, and pharmaceutical industry in comparison with the ß-glucosidases from the conventional sources. Such ß-glucosidases have potential for encouraging white biotechnology.