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McDonald, D. J.

Publications and source records attributed to McDonald, D. J..

2 recordsLinked to original sources

Exploration of the antimicrobial synergy between selected natural substances on Streptococcus mutans to identify candidates for the control of dental caries

Dental caries is caused by dental plaque, a community of micro-organisms embedded in an extracellular polymer matrix as a biofilm on the tooth surface. Natural products that are widely available could be used as an alternative or adjunctive anti-caries therapy. Sometimes, when two products are used together, they yield a more powerful antimicrobial effect than the anticipated additive effect. These synergistic combinations are often better treatment options because individual agents may not have sufficient antimicrobial action to be effective when used alone. Cranberries contain phenolic compounds like proanthocyanidins (PAC) that disrupt biofilm formation. Manuka honey has high concentrations of the agent methylglyoxal, which is cariostatic. Because these agents have varied modes of antimicrobial action, they show potential for possible synergistic effects when paired. Various cranberry extracts were tested pairwise with manuka honey or methylglyoxal by well-diffusion assays and 96-well checkerboard assays in the presence of Streptococcus mutans to test for synergy. Synergy was demonstrated in two of the cranberry extracts paired with manuka honey. The synergistic combinations found in this research thus can be considered as candidates for the formulation of a dentifrice that could be used to inhibit the formation of dental plaque and thereby avoid the development of caries. Significance and ImpactThe emergence of bacteria resistant to antimicrobial agents has led to a shortage of options when choosing effective treatment agents. Further, some antibiotics used at therapeutic doses can produce undesired side effects. However, by utilizing synergistic combinations of antimicrobial agents, the desired antimicrobial effects can often be produced without subjecting the patient to toxic or irritating doses of individual agents. Streptococcus mutans growth and biofilm formation is a major contributor towards dental caries. In this study, a synergistic combination of Manuka honey and cranberry extracts gives evidence that it can be used as an alternative or adjunctive anti-caries therapy.

microbiology↗

Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR

Heterogeneity in transcription initiation has important consequences for transcript stability and translation, and shifts in transcription start site (TSS) usage are prevalent in various disease and developmental contexts. Accordingly, numerous methods for global TSS profiling have been developed, including our recently published Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a method to profile transcription start sites (TSSs) on a genome-wide scale with minimal cost and time. In parallel to our development of STRIPE-seq, we built TSRexploreR, an R package for end-to-end analysis of TSS mapping data. TSRexploreR provides functions for TSS and TSR detection, normalization, correlation, visualization, and differential TSS/TSR analysis. TSRexploreR is highly interoperable, accepting the data structures of TSS and TSR sets generated by several existing tools for processing and alignment of TSS mapping data, such as CAGEr for Cap Analysis of Gene Expression (CAGE) data. Lastly, TSRexploreR implements a novel approach for the detection of shifts in TSS distribution.

bioinformatics↗