Hidden breakpoints in genome alignments

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in addition to other types of rearrangement, breakpoints of rearrangement can exist that are only detectable by comparison of three or more genomes. An arbitrarily large number of these "hidden" breakpoints can exist among genomes that exhibit no rearrangements in pairwise comparisons. We present an extension of the multichromosomal breakpoint median problem to genomes that have undergone gene gain and loss. We then demonstrate that the median distance among three genomes can be used to calculate a lower bound on the number of hidden breakpoints present. We provide an implementation of this calculation including the median distance, along with some practical improvements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints in simulated data sets under a wide range of evolutionary scenarios. We demonstrate that in simulations the hidden breakpoint counts depend strongly on relative rates of inversion and gene gain/loss. Finally we apply current multiple genome aligners to the simulated genomes, and show that all aligners introduce a high degree of error in hidden breakpoint counts, and that this error grows with evolutionary distance in the simulation. Our results suggest that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure

Observations on the relation of light to the dropping of the tick, Ixodes texallus Banks

Six ferrets were infested with large numbers of nymphs or larvae of the tick Ixodes texallus Banks. The animals were caged separately and subjected to various regimes of continuous light and darkness, from 9 days to 5, 4, and 2 days, and normal photoperiods. Nearly all the engorged ticks dropped from the hosts in the dark

PhyloSift: Phylogenetic analysis of genomes and metagenomes

Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454). © 2014 Darling et al

Are Protein Domains Modules of Lateral Genetic Transfer?

Background: In prokaryotes and some eukaryotes, genetic material can be transferred laterally among unrelated lineages and recombined into new host genomes, providing metabolic and physiological novelty. Although the process is usually framed in terms of gene sharing (e. g. lateral gene transfer, LGT), there is little reason to imagine that the units of transfer and recombination correspond to entire, intact genes. Proteins often consist of one or more spatially compact structural regions (domains) which may fold autonomously and which, singly or in combination, confer the protein's specific functions. As LGT is frequent in strongly selective environments and natural selection is based on function, we hypothesized that domains might also serve as modules of genetic transfer, i.e. that regions of DNA that are transferred and recombined between lineages might encode intact structural domains of proteins

New limits for neutrinoless tau decays

Neutrinoless 3-prong tau lepton decays into a charged lepton and either two charged particles or one neutral meson have been searched for using 4.79fb^(-1) of data collected with the CLEO II detector at Cornell Electron Storage Ring. This analysis represents an update of a previous study and the addition of six decay channels. In all channels the numbers of events found are compatible with background estimates and branching fraction upper limits are set for 28 different decay modes. These limits are either more stringent than those set previously or represent the first attempt to find these decays

genoPlotR: comparative gene and genome visualization in R

Summary: The amount of gene and genome data obtained by next-generation sequencing technologies generates a need for comparative visualization tools. Complementing existing software for comparison and exploration of genomics data, genoPlotR automatically creates publication-grade linear maps of gene and genomes, in a highly automatic, flexible and reproducible way

Volume contraction at the Jahn-Teller transition of LaMnO3_3

We have studied the volume collapse of LaMnO$_3$ at the Jahn- Teller (JT) transition temperature T$_{JT}$=750 K which has recently been found in high temperature powder x- ray and neutron diffraction experiments. We construct a model Hamiltonian involving the pseudospin of Mn$^{3+}$ e$_g$ states, the staggered JT distortion and the volume strain coordinate. We show that the anharmonic coupling between these primary and secondary order parameters leads to the first order JT phase transition associated with a comparatively large reduction of the unit cell volume of $\Delta$V/V$\simeq$ 10$^{-2}$. We explain the temperature dependence of JT distortions and volume strain and discuss the volume change as function of the anharmonic coupling constant. A continuous change to a second order transition as function of model parameters is obtained. This behaviour is also observed under Ba doping.Comment: 5 pages, 4 figure

Random division of an interval

The well-known relation between random division of an interval and the Poisson process is interpreted as a Laplace transformation. With the use of this interpretation a number of (in part known) results is derived very easily