Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia

The current classification of the rhizobia (root-nodule symbionts) assigns them to six genera. It is strongly influenced by the small subunit (16S, SSU) rRNA molecular phylogeny, but such single-gene phylogenies may not reflect the evolution of the genome as a whole. To test this, parts of the atpD and recA genes have been sequenced for 25 type strains within the alpha -Proteobacteria, representing species in Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium, Agrobacterium, Phyllobacterium, Mycoplana and Brevundimonas. The current genera Sinorhizobium and Mesorhizobium are well supported by these genes, each forming a distinct phylogenetic clade with unequivocal bootstrap support. There is good support for a Rhizobium clade that includes Agrobacterium tumefaciens, and the very close relationship between Agrobacterium rhizogenes and Rhizobium tropici is confirmed. There is evidence for recombination within the genera Mesorhizobium and Sinorhizobium, but the congruence of the phylogenies at higher levels indicates that the genera are genetically isolated. rRNA provides a reliable distinction between genera, but genetic relationships within a genus may be disturbed by recombination

The PL calibration for Milky Way Cepheids and its implications for the distance scale

The rationale behind recent calibrations of the Cepheid PL relation using the Wesenheit formulation is reviewed and reanalyzed, and it is shown that recent conclusions regarding a possible change in slope of the PL relation for short-period and long-period Cepheids are tied to a pathological distribution of HST calibrators within the instability strip. A recalibration of the period-luminosity relation is obtained using Galactic Cepheids in open clusters and groups, the resulting relationship, described by log L/L_sun = 2.415(+-0.035) + 1.148(+-0.044)log P, exhibiting only the moderate scatter expected from color spread within the instability strip. The relationship is confirmed by Cepheids with HST parallaxes, although without the need for Lutz-Kelker corrections, and in general by Cepheids with revised Hipparcos parallaxes, albeit with concerns about the cited precisions of the latter. A Wesenheit formulation of Wv = -2.259(+-0.083) - 4.185(+-0.103)log P for Galactic Cepheids is tested successfully using Cepheids in the inner regions of the galaxy NGC 4258, confirming the independent geometrical distance established for the galaxy from OH masers. Differences between the extinction properties of interstellar and extragalactic dust may yet play an important role in the further calibration of the Cepheid PL relation and its application to the extragalactic distance scale.Comment: Accepted for Publication (Astrophysics & Space Science

Analyses of amplified fragment length polymorphisms (AFLP) indicate rapid radiation of Diospyros species (Ebenaceae) endemic to New Caledonia

Background : Radiation in some plant groups has occurred on islands and due to the characteristic rapid pace of phenotypic evolution, standard molecular markers often provide insufficient variation for phylogenetic reconstruction. To resolve relationships within a clade of 21 closely related New Caledonian Diospyros species and evaluate species boundaries we analysed genome-wide DNA variation via amplified fragment length polymorphisms (AFLP). Results : A neighbour-joining (NJ) dendrogram based on Dice distances shows all species except D. minimifolia,D. parviflora and D. vieillardii to form unique clusters of genetically similar accessions. However, there was little variation between these species clusters, resulting in unresolved species relationships and a star-like general NJ topology. Correspondingly, analyses of molecular variance showed more variation within species than between them. A Bayesian analysis with BEAST produced a similar result. Another Bayesian method, this time a clustering method, STRUCTURE, demonstrated the presence of two groups, highly congruent with those observed in a principal coordinate analysis (PCO). Molecular divergence between the two groups is low and does not correspond to any hypothesised taxonomic, ecological or geographical patterns. Conclusions : We hypothesise that such a pattern could have been produced by rapid and complex evolution involving a widespread progenitor for which an initial split into two groups was followed by subsequent fragmentation into many diverging populations, which was followed by range expansion of then divergent entities. Overall, this process resulted in an opportunistic pattern of phenotypic diversification. The time since divergence was probably insufficient for some species to become genetically well-differentiated, resulting in progenitor/derivative relationships being exhibited in a few cases. In other cases, our analyses may have revealed evidence for the existence of cryptic species, for which more study of morphology and ecology are now required

Chromatin regulation and the histone code in HIV latency

The formation of a latent reservoir of Human Immunodeficiency Virus (HIV†) infection hidden from immune clearance remains a significant obstacle to approaches to eradicate HIV infection. Towards an understanding of the mechanisms of HIV persistence, there is a growing body of work implicating epigenetic regulation of chromatin in establishment and maintenance of this latent reservoir. Here we discuss recent advances in the field of chromatin regulation, specifically in our understanding of the histone code, and how these discoveries relate to our current knowledge of the chromatin mechanisms linked to HIV transcriptional repression and the reversal of latency. We also examine mechanisms unexplored in the context of HIV latency and briefly discuss current therapies aimed at the induction of proviral expression within latently infected cells. We aim to emphasize that a greater understanding of the epigenetic mechanisms which govern HIV latency could lead to new therapeutic targets for latency reversal and clearance cure strategies

Evaluation of pyrolysis chars derived from marine macroalgae silage as soil amendments

Sections PDFPDF Tools Share Abstract Pyrolysis char residues from ensiled macroalgae were examined to determine their potential as growth promoters on germinating and transplanted seedlings. Macroalgae was harvested in May, July and August from beach collections, containing predominantly Laminaria digitata and Laminaria hyperborea ; naturally seeded mussel lines dominated by Saccharina latissima ; and lines seeded with cultivated L. digitata . Material was ensiled, pressed to pellets and underwent pyrolysis using a thermo‐catalytic reforming (TCR) process, with and without additional steam. The chars generated were then assessed through proximate and ultimate analysis. Seasonal changes had the prevalent impact on char composition, though using mixed beach‐harvested material gave a greater variability in elements than when using the offshore collections. Applying the char at 5% (v/v)/2% (w/w) into germination or seedling soils was universally negative for the plants, inhibiting or delaying all parameters assessed with no clear advantage in harvesting date, species or TCR processing methodology. In germinating lettuce seeds, soil containing the pyrolysis chars caused a longer germination time, poorer germination, fewer true leaves to be produced, a lower average plant health score and a lower final biomass yield. For transplanted ryegrass seedlings, there were lower plant survival rates, with surviving plants producing fewer leaves and tillers, lower biomass yields when cut and less regrowth after cutting. As water from the char‐contained plant pots inhibited the lettuce char control, one further observation was that run‐off water from the pyrolysis char released compounds which detrimentally affected cultivated plant growth. This study clearly shows that pyrolysed macroalgae char does not fit the standard assumption that chars can be used as soil amendments at 2% (w/w) addition levels. As the bioeconomy expands in the future, the end use of residues and wastes from bioprocessing will become a genuine global issue, requiring consideration and demonstration rather than hypothesized use

The Large Magellanic Cloud and the Distance Scale

The Magellanic Clouds, especially the Large Magellanic Cloud, are places where multiple distance indicators can be compared with each other in a straight-forward manner at considerable precision. We here review the distances derived from Cepheids, Red Variables, RR Lyraes, Red Clump Stars and Eclipsing Binaries, and show that the results from these distance indicators generally agree to within their errors, and the distance modulus to the Large Magellanic Cloud appears to be defined to 3% with a mean value of 18.48 mag, corresponding to 49.7 Kpc. The utility of the Magellanic Clouds in constructing and testing the distance scale will remain as we move into the era of Gaia.Comment: 23 pages, accepted for publication in Astrophysics and Space Science. From a presentation at the conference The Fundamental Cosmic Distance Scale: State of the Art and the Gaia Perspective, Naples, May 201

Bio-processing of macroalgae Palmaria palmata: metabolite fractionation from pressed fresh material and ensiling considerations for long-term storage

Red algae, belonging to the phylum Rhodophyta, contain an abundance of useful chemicals including bioactive molecules and present opportunities for the production of different products through biorefinery cascades. The rhodophyte Palmaria palmata, commonly termed dulse or dillisk, grows predominantly on the northern coasts of the Atlantic and Pacific Oceans and is a well-known snack food. Due to its abundance, availability and cultivation capacity, P. palmata was selected for study as a potential candidate for a biorefinery process. In addition to studying juice and solid fractions of freshly harvested P. palmata, we have investigated the novel possibility of preserving algal biomass by ensilaging protocols similar to those employed for terrestrial forage crops. In the metabolite partitioning within the solid and liquid fractions following screw-pressing, the majority of the metabolites screened for—water soluble carbohydrates, proteins and amino acids, lipids, pigments, phenolics and antioxidant activity—remained in the solid fraction, though at differing proportions depending on the metabolite, from 70.8% soluble amino acids to 98.2% chlorophyll a and 98.1% total carotenoids. For the ensiling study, screw-pressed P. palmata, with comparative wilted and chopped, and chopped only samples, were ensiled at scale with and without Safesil silage additive. All samples were successfully ensiled after 90 days, with screw-pressing giving lower or equal pH before and after ensiling compared with the other preparations. Of particular note was the effluent volumes generated during ensiling: 26–49% of the fresh weight, containing 16–34% of the silage dry matter. This may be of advantage depending on the final use of the biomass

Solar Wakes of Dark Matter Flows

We analyze the effect of the Sun's gravitational field on a flow of cold dark matter (CDM) through the solar system in the limit where the velocity dispersion of the flow vanishes. The exact density and velocity distributions are derived in the case where the Sun is a point mass. The results are extended to the more realistic case where the Sun has a finite size spherically symmetric mass distribution. We find that regions of infinite density, called caustics, appear. One such region is a line caustic on the axis of symmetry, downstream from the Sun, where the flow trajectories cross. Another is a cone-shaped caustic surface near the trajectories of maximum scattering angle. The trajectories forming the conical caustic pass through the Sun's interior and probe the solar mass distribution, raising the possibility that the solar mass distribution may some day be measured by a dark matter detector on Earth. We generalize our results to the case of flows with continuous velocity distributions, such as that predicted by the isothermal model of the Milky Way halo.Comment: 30 pages, 8 figure

Crossing borders: new teachers co-constructing professional identity in performative times

This paper draws on a range of theoretical perspectives on the construction of new teachers’ professional identity. It focuses particularly on the impact of the development in many national education systems of a performative culture of the management and regulation of teachers’ work. Whilst the role of interactions with professional colleagues and school managers in the performative school has been extensively researched, less attention has been paid to new teachers’ interactions with students. This paper highlights the need for further research focusing on the process of identity co-construction with students. A key theoretical concept employed is that of liminality, the space within which identities are in transition as teachers adjust to the culture of a new professional workplace, and the nature of the engagement of new teachers, or teachers who change schools, with students. The authors argue that an investigation into the processes of this co-construction of identity offers scope for new insights into the extent to which teachers might construct either a teacher identity at odds with their personal and professional values, or a more ‘authentic’ identity that counters performative discourses. These insights will in turn add to our understanding of the complex range of factors impacting on teacher resilience and motivation

The modulation effect for supersymmetric dark matter detection with asymmetric velocity dispersion

The detection of the theoretically expected dark matter is central to particle physics cosmology. Current fashionable supersymmetric models provide a natural dark matter candidate which is the lightest supersymmetric particle (LSP). Such models combined with fairly well understood physics like the quark substructure of the nucleon and the nuclear form factor and the spin response function of the nucleus, permit the evaluation of the event rate for LSP-nucleus elastic scattering. The thus obtained event rates are, however, very low or even undetectable. So it is imperative to exploit the modulation effect, i.e. the dependence of the event rate on the earth's annual motion. In this review we study such a modulation effect in directional and undirectional experiments. We calculate both the differential and the total rates using symmetric as well as asymmetric velocity distributions. We find that in the symmetric case the modulation amplitude is small, less than 0.07. There exist, however, regions of the phase space and experimental conditions such that the effect can become larger. The inclusion of asymmetry, with a realistic enhanced velocity dispersion in the galactocentric direction, yields the bonus of an enhanced modulation effect, with an amplitude which for certain parameters can become as large as 0.46.Comment: 35 LATEX pages, 7 Tables, 8 PostScript Figures include