Assessment of the bimodality in the distribution of bacterial genome sizes

Bacterial genome sizes have previously been shown to exhibit a bimodal distribution. This phenomenon has prompted discussion regarding evolutionary forces driving genome size in bacteria and its ecological significance. We investigated the level of inherent redundancy in the public database and the effect it has on the shape of the apparent bimodal distribution. Our study reveals that there is a significant bias in the genome sequencing efforts towards a certain group of species, and that correcting the bias using species nomenclature and clustering of the 16S rRNA gene, results in a unimodal rather than the previously published bimodal distribution. The true genome size distribution and its wider ecological implications will soon emerge as we are currently witnessing rapid growth in the number of sequenced genomes from diverse environmental niches across a range of habitats at an unprecedented rate

Dark matter annihilation and decay in dwarf spheroidal galaxies: The classical and ultrafaint dSphs

Dwarf spheroidal (dSph) galaxies are prime targets for present and future gamma-ray telescopes hunting for indirect signals of particle dark matter. The interpretation of the data requires careful assessment of their dark matter content in order to derive robust constraints on candidate relic particles. Here, we use an optimised spherical Jeans analysis to reconstruct the `astrophysical factor' for both annihilating and decaying dark matter in 21 known dSphs. Improvements with respect to previous works are: (i) the use of more flexible luminosity and anisotropy profiles to minimise biases, (ii) the use of weak priors tailored on extensive sets of contamination-free mock data to improve the confidence intervals, (iii) systematic cross-checks of binned and unbinned analyses on mock and real data, and (iv) the use of mock data including stellar contamination to test the impact on reconstructed signals. Our analysis provides updated values for the dark matter content of 8 `classical' and 13 `ultrafaint' dSphs, with the quoted uncertainties directly linked to the sample size; the more flexible parametrisation we use results in changes compared to previous calculations. This translates into our ranking of potentially-brightest and most robust targets---viz., Ursa Minor, Draco, Sculptor---, and of the more promising, but uncertain targets---viz., Ursa Major 2, Coma---for annihilating dark matter. Our analysis of Segue 1 is extremely sensitive to whether we include or exclude a few marginal member stars, making this target one of the most uncertain. Our analysis illustrates challenges that will need to be addressed when inferring the dark matter content of new `ultrafaint' satellites that are beginning to be discovered in southern sky surveys.Comment: 19 pages, 14 figures, submitted to MNRAS. Supplementary material available on reques

Presence and abundance of microplastics in the Thames River Basin, UK

The global increase in plastic production has led to growing concern about the environmental impacts of plastics and their degradation products. Microplastics have been extensively observed and studied in the marine environment but little is known about their presence and abundance in freshwater environments. Although rivers are recognised as a significant source of microplastics to the oceans, they are seldom considered in studies of the environmental presence of microplastics and there are no data reported to date on microplastics in UK rivers (or indeed any freshwater bodies). This study aimed to identify and quantify the abundance and types of plastics in the Thames Basin where population densities and sewage inputs are well described. Ten sampling sites on the River Thames and its tributaries were selected, ranging from densely populated, urban areas to sparsely populated, rural areas. Sites are all downstream of sewage treatment works (STWs) serving known populations, allowing correlation between population density with plastic types and abundances found. In addition samples were collected from sites at known distances downstream of STW outfalls, as well as the effluent itself, to try and establish the proportion of plastics directly entering from STWs, and its fate and transport pathways. River sediment and water samples were collected at all sites. Sediment samples were initially searched by eye, followed by flotation and overflowing using ZnCl2 solution. Plastics collected from the sediments were subsequently identified by Raman spectroscopy. Initial observations indicate that coloured and manmade particles are obviously visible in sediments from sites with high population densities compared to few evident manmade particles in sediments from areas with low population densities. Further analysis will allow for correlation of the plastic types and abundance with population density and sewage inputs to understand the distribution of plastics in river systems

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform

1. Studying fungal biodiversit y using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to generating identified operational taxonomic unit (OTU) abundance tables. 2. Here, we introduce PIPITS, an o pen-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS e xploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables. 3. We pro vide detailed descriptions of the pipeline and show its utility in the analysis of 9 396 092 sequences generated on the MiSeq platform from Illumina MiSeq. 4. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curatedUNITE fungal data set

Dark matter profiles and annihilation in dwarf spheroidal galaxies: prospectives for present and future γ-ray observatories - I. The classical dwarf spheroidal galaxies

Due to their large dynamical mass-to-light ratios, dwarf spheroidal galaxies (dSphs) are promising targets for the indirect detection of dark matter (DM) in γ-rays. We examine their detectability by present and future γ-ray observatories. The key innovative features of our analysis are as follows: (i) we take into account the angular size of the dSphs; while nearby objects have higher γ-ray flux, their larger angular extent can make them less attractive targets for background-dominated instruments; (ii) we derive DM profiles and the astrophysical J-factor (which parametrizes the expected γ-ray flux, independently of the choice of DM particle model) for the classical dSphs directly from photometric and kinematic data. We assume very little about the DM profile, modelling this as a smooth split-power-law distribution, with and without subclumps; (iii) we use a Markov chain Monte Carlo technique to marginalize over unknown parameters and determine the sensitivity of our derived J-factors to both model and measurement uncertainties; and (iv) we use simulated DM profiles to demonstrate that our J-factor determinations recover the correct solution within our quoted uncertainties. Our key findings are as follows: (i) subclumps in the dSphs do not usefully boost the signal; (ii) the sensitivity of atmospheric Cherenkov telescopes to dSphs within ∼20 kpc with cored haloes can be up to ∼50 times worse than when estimated assuming them to be point-like. Even for the satellite-borne Fermi-Large Area Telescope (Fermi-LAT), the sensitivity is significantly degraded on the relevant angular scales for long exposures; hence, it is vital to consider the angular extent of the dSphs when selecting targets; (iii) no DM profile has been ruled out by current data, but using a prior on the inner DM cusp slope 0 ≤γprior≤ 1 provides J-factor estimates accurate to a factor of a few if an appropriate angular scale is chosen; (iv) the J-factor is best constrained at a critical integration angle αc= 2rh/d (where rh is the half-light radius and d is the distance from the dwarf) and we estimate the corresponding sensitivity of γ-ray observatories; (v) the ‘classical' dSphs can be grouped into three categories: well constrained and promising (Ursa Minor, Sculptor and Draco), well constrained but less promising (Carina, Fornax and Leo I), and poorly constrained (Sextans and Leo II); and (vi) observations of classical dSphs with the Fermi-LAT integrated over the mission lifetime are more promising than observations with the planned Cherenkov Telescope Array for DM particle mass ≲ 700 GeV. However, even the Fermi-LAT will not have sufficient integrated signal from the classical dwarfs to detect DM in the ‘vanilla' Minimal Supersymmetric Standard Model. Both the Galactic Centre and the ‘ultrafaint' dwarfs are likely to be better targets and will be considered in future wor

Dielectric properties of liquid crystalline dimer mixtures exhibiting the nematic and twist-bend nematic phases

A detailed investigation of the thermal and dielectric properties of a series of binary mixtures exhibiting the nematic ( N ) and twist-bend nematic ( N TB ) liquid crystal phases is presented. The mixtures consist of an achiral, dimeric liquid crystal CB7CB, which forms the nematic and twist-bend nematic phases, and a calamitic liquid crystal 5CB, which shows the nematic phase. As the concentration of the calamitic liquid crystal is increased, the transition temperatures decrease linearly, and the width of the nematic phase increases. The enthalpies of phase transitions obtained from DSC measurements show that on increasing the concentration of 5CB in the binary mixtures, the enthalpy associated with the N − N TB phase transitions reduces considerably compared to a clear first-order N − N TB transition in pure CB7CB. The real and imaginary parts of the dielectric permittivity are measured as a function of frequency from 100 Hz to 2 MHz in the nematic and twist-bend nematic phases in planar and homeotropic devices. A significant decrease in the average dielectric permittivity as a function of temperature for mixtures forming the N TB phase is observed. Measurements of the imaginary part of the dielectric permittivity show a relaxation peak in the measured frequency window for all of the mixtures exhibiting the N TB phase. The activation energy associated with this relaxation process is calculated and is shown to remain constant irrespective of the composition of the mixtures

Catchment-scale biogeography of riverine bacterioplankton

Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physiochemical status of the river

Does presence of a mid-ocean ridge enhance biomass and biodiversity?

In contrast to generally sparse biological communities in open-ocean settings, seamounts and ridges are perceived as areas of elevated productivity and biodiversity capable of supporting commercial fisheries. We investigated the origin of this apparent biological enhancement over a segment of the North Mid-Atlantic Ridge (MAR) using sonar, corers, trawls, traps, and a remotely operated vehicle to survey habitat, biomass, and biodiversity. Satellite remote sensing provided information on flow patterns, thermal fronts, and primary production, while sediment traps measured export flux during 2007-2010. The MAR, 3,704,404 km 2 in area, accounts for 44.7% lower bathyal habitat (800-3500 m depth) in the North Atlantic and is dominated by fine soft sediment substrate (95% of area) on a series of flat terraces with intervening slopes either side of the ridge axis contributing to habitat heterogeneity. The MAR fauna comprises mainly species known from continental margins with no evidence of greater biodiversity. Primary production and export flux over the MAR were not enhanced compared with a nearby reference station over the Porcupine Abyssal Plain. Biomasses of benthic macrofauna and megafauna were similar to global averages at the same depths totalling an estimated 258.9 kt C over the entire lower bathyal north MAR. A hypothetical flat plain at 3500 m depth in place of the MAR would contain 85.6 kt C, implying an increase of 173.3 kt C attributable to the presence of the Ridge. This is approximately equal to 167 kt C of estimated pelagic biomass displaced by the volume of the MAR. There is no enhancement of biological productivity over the MAR; oceanic bathypelagic species are replaced by benthic fauna otherwise unable to survive in the mid ocean. We propose that globally sea floor elevation has no effect on deep sea biomass; pelagic plus benthic biomass is constant within a given surface productivity regime.Peer reviewe

Theory of the Quantum Hall Smectic Phase II: Microscopic Theory

We present a microscopic derivation of the hydrodynamic theory of the Quantum Hall smectic or stripe phase of a two-dimensional electron gas in a large magnetic field. The effective action of the low energy is derived here from a microscopic picture by integrating out high energy excitations with a scale of the order the cyclotron energy.The remaining low-energy theory can be expressed in terms of two canonically conjugate sets of degrees of freedom: the displacement field, that describes the fluctuations of the shapes of the stripes, and the local charge fluctuations on each stripe.Comment: 20 pages, RevTex, 3 figures, second part of cond-mat/0105448 New and improved Introduction. Final version as it will appear in Physical Review

AdS_3/LCFT_2 - Correlators in Cosmological Topologically Massive Gravity

For cosmological topologically massive gravity at the chiral point we calculate momentum space 2- and 3-point correlators of operators in the postulated dual CFT on the cylinder. These operators are sourced by the bulk and boundary gravitons. Our correlators are fully consistent with the proposal that cosmological topologically massive gravity at the chiral point is dual to a logarithmic CFT. In the process we give a complete classification of normalizable and non-normalizeable left, right and logarithmic solutions to the linearized equations of motion in global AdS_3.Comment: 39 pages + appendices, 1 eps figure, v2: minor changes in text in 4.1.2, corrected typo in (2.31