Progressive Mauve: Multiple alignment of genomes with gene flux and rearrangement

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a method to align two or more genomes that have undergone large-scale recombination, particularly genomes that have undergone substantial amounts of gene gain and loss (gene flux). The method utilizes a novel alignment objective score, referred to as a sum-of-pairs breakpoint score. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying genome alignment accuracy which measure the quality of rearrangement breakpoint predictions and indel predictions. The progressive genome alignment algorithm demonstrates markedly improved accuracy over previous approaches in situations where genomes have undergone realistic amounts of genome rearrangement, gene gain, loss, and duplication. We apply the progressive genome alignment algorithm to a set of 23 completely sequenced genomes from the genera Escherichia, Shigella, and Salmonella. The 23 enterobacteria have an estimated 2.46Mbp of genomic content conserved among all taxa and total unique content of 15.2Mbp. We document substantial population-level variability among these organisms driven by homologous recombination, gene gain, and gene loss. Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve .Comment: Revision dated June 19, 200

A stochastic epidemiological model and a deterministic limit for BitTorrent-like peer-to-peer file-sharing networks

In this paper, we propose a stochastic model for a file-sharing peer-to-peer network which resembles the popular BitTorrent system: large files are split into chunks and a peer can download or swap from another peer only one chunk at a time. We prove that the fluid limits of a scaled Markov model of this system are of the coagulation form, special cases of which are well-known epidemiological (SIR) models. In addition, Lyapunov stability and settling-time results are explored. We derive conditions under which the BitTorrent incentives under consideration result in shorter mean file-acquisition times for peers compared to client-server (single chunk) systems. Finally, a diffusion approximation is given and some open questions are discussed.Comment: 25 pages, 6 figure

The Pathologic Affinities of Beriberi and Scurvy

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Calcium isotopic composition of high-latitude proxy carrier Neogloboquadrina pachyderma (sin.)

The accurate reconstruction of sea surface temperature (SST) history in climate-sensitive regions (e.g. tropical and polar oceans) became a challenging task in palaeoceanographic research. Biogenic shell carbonate SST proxies successfully developed for tropical regions often fail in cool water environments. Their major regional shortcomings and the cryptic diversity now found within the major high latitude proxy carrier Neogloboquadrina pachyderma (sin.) highlight an urgent need to explore complementary SST proxies for these cool-water regions. Here we incorporate the genetic component into a calibration study of a new SST proxy for the high latitudes. We found that the calcium isotopic composition (δ44/40Ca) of calcite from genotyped net catches and core-top samples of the planktonic foraminifera Neogloboquadrina pachyderma (sin.) is related to temperature and unaffected by genetic variations. The temperature sensitivity has been found to be 0.17 (±0.02)‰ per 1°C, highlighting its potential for downcore applications in open marine cool-water environments. Our results further indicate that in extreme polar environments, below a critical threshold temperature of 2.0 (±0.5)°C associated with salinities below 33.0 (±0.5)‰, a prominent shift in biomineralization affects the δ44/40Ca of genotyped and core-top N. pachyderma (sin.), becoming insensitive to temperature. These findings highlight the need of more systematic calibration studies on single planktonic foraminiferal species in order to unravel species-specific factors influencing the temperature sensitivity of Ca isotope fractionation and to validate the proxies' applicability

Invisible Active Galactic Nuclei. II Radio Morphologies & Five New HI 21 cm Absorption Line Detections

We have selected a sample of 80 candidates for obscured radio-loud active galactic nuclei and presented their basic optical/near-infrared (NIR) properties in Paper 1. In this paper, we present both high-resolution radio continuum images for all of these sources and HI 21cm absorption spectroscopy for a few selected sources in this sample. A-configuration 4.9 and 8.5 GHz VLA continuum observations find that 52 sources are compact or have substantial compact components with size 0.1 Jy at 4.9 GHz. The most compact 36 sources were then observed with the VLBA at 1.4 GHz. One definite and 10 candidate Compact Symmetric Objects (CSOs) are newly identified, a detection rate of CSOs ~3 times higher than the detection rate previously found in purely flux-limited samples. Based on possessing compact components with high flux densities, 60 of these sources are good candidates for absorption-line searches. Twenty seven sources were observed for HI 21cm absorption at their photometric or spectroscopic redshifts with only 6 detections made (one detection is tentative). However, five of these were from a small subset of six CSOs with pure galaxy optical/NIR spectra and for which accurate spectroscopic redshifts place the redshifted 21cm line in a RFI-free spectral window. It is likely that the presence of ubiquitous RFI and the absence of accurate spectroscopic redshifts preclude HI detections in similar sources (only one detection out of the remaining 22 sources observed, 14 of which have only photometric redshifts). Future searches for highly-redshifted HI and molecular absorption can easily find more distant CSOs among bright, blank field' radio sources but will be severely hampered by an inability to determine accurate spectroscopic redshifts for them due to their lack of rest-frame UV continuum.Comment: AJ accepte

Two Cases of Anaphylactic Serum Disease Over Six Years After the Primary Injection of Horse-Serum (Yersin's Antipest Serum)

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