Nephele: genotyping via complete composition vectors and MapReduce

<p>Abstract</p> <p>Background</p> <p>Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences.</p> <p>Results</p> <p>Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on traditional hardware. Nephele can use the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. We were able to generate a neighbour-joined tree of over 10,000 16S samples in less than 2 hours.</p> <p>Conclusions</p> <p>We conclude that using Nephele can substantially decrease the processing time required for generating genotype trees of tens to hundreds of organisms at genome scale sequence coverage.</p

Influence of method and period of storage on the microtensile bond strength of indirect composite resin restorations to dentine

This study evaluated the influence of the method and period of storage on the adhesive bond strength of indirect composite resin to bovine dentin. Ninety bovine incisors were stored in three different solutions: 0.2% thymol, 10% formalin, and 0.2% sodium azide, during 3 periods of storage: 7 days, 30 days and 6 months, resulting in 9 groups (n = 10). The roots were cut off and the buccal surface was ground with #600-grit silicon carbide paper. The surface was conditioned with 37% phosphoric acid for 15 s and a composite resin restoration (TPH Spectrum) was fixed using a one-bottle adhesive system (Adper Single Bond) and a dual-cured resinous cement (Rely X ARC) under a load of 500 g for 5 minutes. The samples were serially cut perpendicular to the bonded interface to obtain slices of 1.2 mm in thickness. Each slab was trimmed with a cylindrical diamond bur resulting in an hourglass shape with a cross-sectional area of approximately 1 mm². The microtensile bond strength (&#956;TBS) testing was performed in a testing machine (EMIC 2000 DL) at a 0.5 mm/minute crosshead-speed until failure. After fracture, the specimens were examined under SEM to analyze the mode of fracture. &#956;TBS Means were expressed in MPa and the data were analyzed by two-way ANOVA (3X3) and the Tukey test (&#945; = 0.05). The storage times of 7 and 30 days produced no significant difference irrespective of the solution type. The formalin and thymol solutions, however, did have a negative influence on bond strength when the teeth were stored for 6 months