3,134 publications from this institution
Abstract Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal reproduction. Dozens of such tests have been described, but many are hampered by long running times, confounding of selection and recombination, and/or inability to isolate the mosaic-producing event. We introduce a test that is exact, nonparametric, rapidly computable, free of the infinite-sites assumption, able to distinguish between recombination and variation in mutation/fixation rates, and able to identify the breakpoints and sequences involved in the mosaic-producing event. Our test considers three sequences at a time: two parent sequences that may have recombined, with one or two breakpoints, to form the third sequence (the child sequence). Excess similarity of the child sequence to a candidate recombinant of the parents is a sign of recombination; we take the maximum value of this excess similarity as our test statistic Δm,n,b. We present a method for rapidly calculating the distribution of Δm,n,b and demonstrate that it has comparable power to and a much improved running time over previous methods, especially in detecting recombination in large data sets.
The availability of biomarkers that allow the estimation of the intake of specific foods and dietary components, as an alternative or addition to self-reported dietary questionnaires, could greatly enhance the effectiveness of nutritional research. The aim of the present study was to assess tartaric acid, one of the major components of red and white wines, as a potential biomarker of wine consumption. A total of twenty-one healthy men participated in a randomised cross-over feeding trial. They consumed a single dose of 100, 200 or 300 ml wine at dinner. Before each intervention, the participants followed a 7 d washout period during which they avoided consuming wine or grape-based products. Morning urine was collected and analysed by liquid chromatography coupled to electrospray ionisation tandem MS. A strong significant correlation was found between wine intake and urinary tartaric acid ( r s = 0·9220; P < 0·001). Using a cut-off value of 8·84 μg/mg creatinine, tartaric acid allowed wine consumers to be differentiated from non-wine consumers. The results suggest that urinary tartaric acid may be a sensitive and specific dietary biomarker of wine consumption.
Abstract SUMMARY: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
Hermida, R. C.; Calvo, C.; Ayala, D. E.; Dominguez, M. J.; Covelo, M.; Mojon, A.; Fernandez, J. R.; Lopez, J. E. Author Information
The aim of this review is to discuss and compare the current trends in liquid–liquid and solid–liquid extraction procedures applied to the analysis of cosmetics. Although classical sample preparation procedures are mostly used in labs, the new trends in sample preparation that provide more effective analyte extractions from these complex matrices are gradually being introduced. Drawbacks inherent to conventional or classical extraction procedures in cosmetic samples are also considered. A detailed revision in the period January 1992 to March 2012 about current sample preparation techniques such as liquid-phase microextraction (LPME), microwave-assisted extraction (MAE), ultrasound-assisted extraction (UAE), accelerated solvent extraction (ASE) and supercritical fluid extraction (SFE) applied to cosmetics is given. In general, these procedures have given rise to faster, greener and more effective extraction techniques for cosmetic analysis with regard to conventional procedures.
The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent. This article is part of the themed issue ‘From DNA barcodes to biomes’.