A Computational Method for the Rate Estimation of Evolutionary Transpositions

Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as transpositions, they are rarely observed and believed to constitute only a small fraction of genome rearrangements happening in the course of evolution. The analysis of transpositions is further obfuscated by intractability of the underlying computational problems. We propose a computational method for estimating the rate of transpositions in evolutionary scenarios between genomes. We applied our method to a set of mammalian genomes and estimated the transpositions rate in mammalian evolution to be around 0.26.Comment: Proceedings of the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), 2015. (to appear

Predictability of repeating earthquakes near Parkfield, California

We analyse sequences of repeating microearthquakes that were identified by applying waveform coherency methods to data from the Parkfield High-Resolution Seismic Network. Because by definition all events in a sequence have similar magnitudes and locations, the temporal behaviour of these sequences is naturally isolated, which, coupled with the high occurrence rates of small events, makes these data ideal for studying interevent time distributions. To characterize the temporal predictability of these sequences, we perform retrospective forecast experiments using hundreds of earthquakes. We apply three variants of a simple algorithm that produces sequence-specific, time-varying hazard functions, and we find that the sequences are predictable. We discuss limitations of these data and, more generally, challenges in identifying repeating events, and we outline the potential implications of our results for understanding the occurrence of large earthquake

Single Leptoquark Production at e+e−e^+e^- and γγ\gamma\gamma Colliders

We consider single production of leptoquarks (LQ's) at $e^+e^-$ and $\gamma\gamma$ colliders, for two values of the centre-of-mass energy, $\sqrt{s}=500$ GeV and 1 TeV. We find that LQ's which couple within the first generation are observable for LQ masses almost up to the kinematic limit, both at $e^+e^-$ and $\gamma\gamma$ colliders, for the LQ coupling strength equal to $\alpha_{em}$. The cross sections for single production of $2^{nd}$- and $3^{rd}$-generation LQ's at $e^+e^-$ colliders are too small to be observable. In $\gamma\gamma$ collisions, on the other hand, $2^{nd}$-generation LQ's with masses much larger than $\sqrt{s}/2$ can be detected. However, $3^{rd}$-generation LQ's can be seen at $\gamma\gamma$ colliders only for masses at most $\sim\sqrt{s}/2$, making their observation more probable via the pair production mechanism.Comment: plain TeX, 14 pages, 6 figures (not included but available on request), some minor changes to the text, one reference added, figures and conclusions unchanged, UdeM-LPN-TH-93-152, McGill-93/2

Discovery of the brightest T dwarf in the northern hemisphere

We report the discovery of a bright (H=12.77) brown dwarf designated SIMP J013656.5+093347. The discovery was made as part of a near-infrared proper motion survey, SIMP (Sondage Infrarouge de Mouvement Propre), which uses proper motion and near-infrared/optical photometry to identify brown dwarf candidates. A low resolution (lambda/dlambda~40) spectrum of this brown dwarf covering the 0.88-2.35 microns wavelength interval is presented. Analysis of the spectrum indicates a spectral type of T2.5+/-0.5. A photometric distance of 6.4+/-0.3 pc is estimated assuming it is a single object. Current observations rule out a binary of mass ratio ~1 and separation >5 AU. SIMP 0136 is the brightest T dwarf in the northern hemisphere and is surpassed only by Eps Indi Bab over the whole sky. It is thus an excellent candidate for detailed studies and should become a benchmark object for the early-T spectral class.Comment: 4 pages, 3 figures, To be published in November 1, 2006 issue of ApJL. Following IAU recommendation, the survey acronym (IBIS) was changed to SIM

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice

Understanding the origins of gut microbial community structure is critical for the identification and interpretation of potential fitnessrelated traits for the host. The presence of community clusters characterized by differences in the abundance of signature taxa, referred to as enterotypes, is a debated concept first reported in humans and later extended to other mammalian hosts. In this study, we provide a thorough assessment of their existence in wild house mice using a panel of evaluation criteria.We identify support for two clusters that are compositionally similar to clusters identified in humans, chimpanzees, and laboratory mice, characterized by differences in Bacteroides, Robinsoniella, and unclassified genera belonging to the family Lachnospiraceae. To further evaluate these clusters, we (i) monitored community changes associated with moving mice from the natural to a laboratory environment, (ii) performed functional metagenomic sequencing, and (iii) subjected wild-caught samples to stable isotope analysis to reconstruct dietary patterns. This process reveals differences in the proportions of genes involved in carbohydrate versus protein metabolism in the functional metagenome, as well as differences in plant- versus meat-derived food sources between clusters. In conjunction with wild-caught mice quickly changing their enterotype classification upon transfer to a standard laboratory chow diet, these results provide strong evidence that dietary history contributes to the presence of enterotype-like clustering in wild mice

Passive monitoring of anisotropy change associated with the Parkfield 2004 earthquake

International audienceWe investigate temporal variations in the polarization of surface waves determined using ambient seismic noise cross-correlations between station pairs at the time of the Mw 6.0 Parkfield earthquake of September 28, 2004. We use data recorded by the High Resolution Seismic Network's 3-component seismometers located along the San Andreas Fault. Our results show strong variations in azimuthal surface wave polarizations, Psi, for the paths containing station VARB, one of the closest stations to the San Andreas Fault, synchronous with the Parkfield earthquake. Concerning the other station pair, only smooth temporal variations of Y are observed. Two principal contributions to these changes in Y are identified and separated. They are: (1) slow and weak variations due to seasonal changes in the incident direction of seismic noise; and (2) strong and rapid rotations synchronous with the Parkfield earthquake for paths containing station VARB. Strong shifts in Y are interpreted in terms of changes in crack-induced anisotropy due to the co-seismic rotation of the stress field. Because these changes are only observed on paths containing station VARB, the anisotropic layer responsible for the changes is most likely localized around VARB in the shallow crust. These results suggest that the polarization of surface waves may be very sensitive to changes in the orientations of distributed cracks and that implementation of our technique on a routine basis may prove useful for monitoring stress changes deep within seismogenic zones. Citation: Durand, S., J. P. Montagner, P. Roux, F. Brenguier, R. M. Nadeau, and Y. Ricard (2011), Passive monitoring of anisotropy change associated with the Parkfield 2004 earthquake, Geophys. Res. Lett., 38, L13303, doi: 10.1029/2011GL047875