Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper

Across the life sciences, processing next generation sequencing data commonly relies upon a computationally expensive process where reads are mapped onto a reference sequence. Prior to such processing, however, there is a vast amount of information that can be ascertained from the reads, potentially obviating the need for processing, or allowing optimized mapping approaches to be deployed. Here, we present a method termed FlexTyper which facilitates a “reverse mapping” approach in which high throughput sequence queries, in the form of k-mer searches, are run against indexed short-read datasets in order to extract useful information. This reverse mapping approach enables the rapid counting of target sequences of interest. We demonstrate FlexTyper’s utility for recovering depth of coverage, and accurate genotyping of SNP sites across the human genome. We show that genotyping unmapped reads can correctly inform a sample’s population, sex, and relatedness in a family setting. Detection of pathogen sequences within RNA-seq data was sensitive and accurate, performing comparably to existing methods, but with increased flexibility. We present two examples of ways in which this flexibility allows the analysis of genome features not well-represented in a linear reference. First, we analyze contigs from African genome sequencing studies, showing how they distribute across families from three distinct populations. Second, we show how gene-marking k-mers for the killer immune receptor locus allow allele detection in a region that is challenging for standard read mapping pipelines. The future adoption of the reverse mapping approach represented by FlexTyper will be enabled by more efficient methods for FM-index generation and biology-informed collections of reference queries. In the long-term, selection of population-specific references or weighting of edges in pan-population reference genome graphs will be possible using the FlexTyper approach. FlexTyper is available at https://github.com/wassermanlab/OpenFlexTyper.     

Superoxide-dependent formation of hydroxyl radicals: Detection of hydroxyl radicals by the hydroxylation of aromatic compounds

A mixture of xanthine or hypoxanthine and xanthine oxidase generates the superoxide radical, O₂^$\text{?}$, and H₂O₂. In the presence of iron salts, O₂^$\text{?}$ and H₂O₂ can interact to produce the hydroxyl radical, OH·. Superoxide-dependent formation of OH· can be measured by its ability to hydroxylate salicylate as followed by an improved colorimetric assay described in this paper. A more accurate analysis of OH· can be obtained using its ability to hydroxylate phenol, the hydroxylated products being separated and measured after derivatization using gas-liquid chromatography and electron-capture detection. The derivatization and separation techniques are described.     

The effects of concanavalin A, cerulenin, hydroxyurea and tunicamycin on the incorporation of amino acids and glucosamine in Tetrahymena pyriformis.

1. Pulse labelling of conjugating Tetrahymena pyriformis with glycine and glucosamine gave results consistent with a requirement for de novo synthesis of a lipid-like component which is involved in the addition of sugar to cell glycoprotein. 2. Conjugation of complementary strains of Tetrahymena can be inhibited without gross morphologic and metabolic changes in the cells. The observed inhibition of conjugation is reversible. 3. Concanavalin A stopped conjugation and stimulated both glycine and glucosamine incorporation. 4. Tunicamycin inhibited conjugation but had little influence on total glucosamine incorporation. Amino acid incorporation was slightly enhanced. 5. Hydroxyurea blocked conjugation, inhibited the incorporation of glucosamine and seemed to induce a transient increase in glycine incorporation. 6. Cerulenin inhibited conjugation but had little effect on the incorporation of glycine and glucosamine into the cell.     

Viewpoints: Diet and dietary adaptations in early hominins: The hard food perspective

Recent biomechanical analyses examining the feeding adaptations of early hominins have yielded results consistent with the hypothesis that hard foods exerted a selection pressure that influenced the evolution of australopith morphology. However, this hypothesis appears inconsistent with recent reconstructions of early hominin diet based on dental microwear and stable isotopes. Thus, it is likely that either the diets of some australopiths included a high proportion of foods these taxa were poorly adapted to consume (i.e., foods that they would not have processed efficiently), or that aspects of what we thought we knew about the functional morphology of teeth must be wrong. Evaluation of these possibilities requires a recognition that analyses based on microwear, isotopes, finite element modeling, and enamel chips and cracks each test different types of hypotheses and allow different types of inferences. Microwear and isotopic analyses are best suited to reconstructing broad dietary patterns, but are limited in their ability to falsify specific hypotheses about morphological adaptation. Conversely, finite element analysis is a tool for evaluating the mechanical basis of form‐function relationships, but says little about the frequency with which specific behaviors were performed or the particular types of food that were consumed. Enamel chip and crack analyses are means of both reconstructing diet and examining biomechanics. We suggest that current evidence is consistent with the hypothesis that certain derived australopith traits are adaptations for consuming hard foods, but that australopiths had generalized diets that could include high proportions of foods that were both compliant and tough. Am J Phys Anthropol 151:339–355, 2013.© 2013 Wiley Periodicals, Inc.     

Can biology make ethics objective?

A familiar position regarding the evolution of ethics is that biology can explain the origin of morals but that in doing so it removes the possibility of their having objective justification. This position is set fourth in detail in the writings of Michael Ruse (1986, 1987, 1989, 1990a, 1990b) but it is also taken by many others, notably, Jeffrie Murphy (1982), Andrew Oldenquist (1990), and Allan Gibbard (1990), I argue the contrary view that biology provides a justification of the existence of morals which is objective in the sense of being independent of people's moral views and their particular desires and preferences. Ironically, my argument builds on the very premises which are supposed to undermine the objectivity of morals. But my argument stops short of claiming that biology can give us a basis for justifying some particular system of morals. Drawing on an analogy with social contract theory, I offer a general reason why this more ambitious project cannot be expected to succeed if the argument is pursued along the same lines. Finally, I give reasons why the possibility of objective justification for a particular morality cannot be ruled out in general on evolutionary grounds.     

Prevalence of patent Baylisascaris procyonis infection in raccoons (Procyon lotor) in Ithaca, New York

The prevalence of patent Baylisascaris procyonis infection in raccoons was determined by examining fecal samples collected between July 1986 and May 1987 in Ithaca, New York. September, October, and November had the highest prevalence of infection (35-48%). Significant differences (P less than 0.001) were found when months were grouped by season to test the hypothesis that a fecal sample's probability of being positive does not vary from month to month. Fall was the season contributing most to the overall chi-square statistic. Host sex/age class and prevalence of patent infection were investigated. The raccoons were aged as either juveniles or adults. A significantly higher prevalence of patent infection (P less than 0.001) was found in juveniles when compared to adults. No statistically significant difference was found in other comparisons of host sex and age. Contingency analysis tested the independence of sex/age class/season and presence of eggs. The results of the test were significant (P less than 0.001).