Duplicate retention in signalling proteins and constraints from network dynamics

Both single-gene and whole-genome duplications (WGD) are well documented in various organisms (Brenner et al., 1995; Zhang, 2003; Vogel & Chothia, 2006), and it is estimated that single-gene duplication

Clann: investigating phylogenetic information through supertree analyses

Summary: Clann has been developed in order to provide methods of investigating phylogenetic information through the application of supertrees. Availability: Clann has been precompiled for Linux, Apple Macintosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. Supplementary information: Clann has been written in the C programming language. Source code is available on request

Spherical:an iterative workflow for assembling metagenomic datasets

BACKGROUND: The consensus emerging from the study of microbiomes is that they are far more complex than previously thought, requiring better assemblies and increasingly deeper sequencing. However, current metagenomic assembly techniques regularly fail to incorporate all, or even the majority in some cases, of the sequence information generated for many microbiomes, negating this effort. This can especially bias the information gathered and the perceived importance of the minor taxa in a microbiome. RESULTS: We propose a simple but effective approach, implemented in Python, to address this problem. Based on an iterative methodology, our workflow (called Spherical) carries out successive rounds of assemblies with the sequencing reads not yet utilised. This approach also allows the user to reduce the resources required for very large datasets, by assembling random subsets of the whole in a "divide and conquer" manner. CONCLUSIONS: We demonstrate the accuracy of Spherical using simulated data based on completely sequenced genomes and the effectiveness of the workflow at retrieving lost information for taxa in three published metagenomics studies of varying sizes. Our results show that Spherical increased the amount of reads utilized in the assembly by up to 109% compared to the base assembly. The additional contigs assembled by the Spherical workflow resulted in a significant (P?<?0.05) changes in the predicted taxonomic profile of all datasets analysed. Spherical is implemented in Python 2.7 and freely available for use under the MIT license. Source code and documentation is hosted publically at: https://github.com/thh32/Spherical .publishersversionPeer reviewe

Determining the culturability of the rumen bacterial microbiome

The goal of the Hungate1000 project is to generate a reference set of rumen microbial genome sequences. Toward this goal we have carried out a meta-analysis using information from culture collections, scientific literature, and the NCBI and RDP databases and linked this with a comparative study of several rumen 16S rRNA gene-based surveys. In this way we have attempted to capture a snapshot of rumen bacterial diversity to examine the culturable fraction of the rumen bacterial microbiome. Our analyses have revealed that for cultured rumen bacteria, there are many genera without a reference genome sequence. Our examination of culture-independent studies highlights that there are few novel but many uncultured taxa within the rumen bacterial microbiome. Taken together these results have allowed us to compile a list of cultured rumen isolates that are representative of abundant, novel and core bacterial species in the rumen. In addition, we have identified taxa, particularly within the phylum Bacteroidetes, where further cultivation efforts are clearly required. This information is being used to guide the isolation efforts and selection of bacteria from the rumen microbiota for sequencing through the Hungate1000

Preparing the COROT space mission: new variable stars in the galactic Anticenter direction

The activities related to the preparation of the asteroseismic, photometric space mission COROT are described. Photoelectric observations, wide--field CCD photometry, uvbyB calibrations and further time--series have been obtained at different observatories and telescopes. They have been planned to complete the COROT programme in the direction of the galactic Anticenter. In addition to suitable asteroseismic targets covering the different evolutionary stages between ZAMS and TAMS, we discovered several other variable stars, both pulsating and geometrical. We compared results on the incidence of variability in the galactic Center and Anticenter directions. Physical parameters have been obtained and evolutionary tracks fitting them have been calculated. The peculiarities of some individual stars alre pointed out. Paper based on observations collected at the San Pedro Martir, Sierra Nevada, Teide, La Silla, Haute-Provence and Roque de Los Muchachos (Telescopio Nazionale Galileo and Mercator telescopes) observatories.Comment: 13 pages, 9 figures. Accepted for The Astronomical Journal (2005 May volume

Using the forces of hydrodynamic countercurrent chromatography for the study of bacteriophages

Bacteriophages (phages) are viruses that target bacteria, with the ability to lyse and kill host bacterial cells. Due to this, they have been of some interest as a therapeutic since their discovery in the early 1900s, but with the recent increase in antibiotic resistance, phages have seen a resurgence in attention. Current methods of isolation and purification of phages can be long and tedious, with caesium chloride concentration gradients the gold standard for purifying a phage fraction. Isolation of novel phages requires centrifugation and ultrafiltration of mixed samples, such as water sources, effluent or faecal samples etc, to prepare phage filtrates for further testing. We propose countercurrent chromatography as a novel and alternative approach to use when studying phages, as a scalable and high-yield method for obtaining phage fractions. However, the full extent of the usefulness and resolution of separation with this technique has not been researched; it requires optimization and ample testing before this can be revealed. Here we present an initial study to determine survivability of two phages, T4 and ϕX174, using only water as a mobile phase in a Spectrum Series 20 HPCCC. Both phages were found to remain active once eluted from the column. Phages do not fully elute from the column and sodium hydroxide is necessary to flush the column between runs to deactivate remaining phages