Extending Seqenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients

Palaeoenvironmental signatures revealed from rare earth element (REE) compositions of vertebrate microremains of the Vesiku Bone Bed (Homerian, Wenlock), Saaremaa Island, Estonia

The Estonian Journal of Earth Sciences is an open access journal and applies the Creative Commons Attribution 4.0 International License CC BY to all its papers (http://creativecommons.org/licenses/by/4.0/). The attached file is the published version of the article

Rare earth elements (REEs) in vertebrate microremains from the upper Pridoli Ohesaare beds of Saaremaa Island, Estonia: geochemical clues to palaeoenvironment c

This is an open access article, available to all readers online, licensed under the Creative Commons Attribution 4.0 International License (CC BY; http://creativecommons.org/licenses/by/4.0/). The attached file is the published version of the article

X-Ray Emission from Central Binary Systems of Planetary Nebulae

We study the conditions under which a main sequence binary companion to the central ionizing star of a planetary nebula (PN) might become magnetically active and thereby display strong X-ray luminosity. Since most PNe are older than few billion years, any main sequence companion will rotate too slowly to have magnetic activity and hence bright X-ray emission, unless it is spun-up. We demonstrate that if the orbital separation during the AGB phase of the PN progenitor is less than 30-60 AU, main sequence companions in the spectral type range F7 to M4 will accrete enough angular momentum from the AGB wind to rotate rapidly, become magnetically active, and exhibit strong X-ray luminosities. Lower mass M stars and brown dwarfs can also become magnetically active, but they should have small orbital separations and hence are less likely to survive the AGB phase of the progenitor. We estimate that 20-30 per cent of elliptical PNe and 30-50 per cent of bipolar PN are likely to have magnetically active companions which will reveal themselves in X-ray observations. Re-analysis of Chandra X-ray Observatory spectroscopy of the compact central source of NGC 7293 indicates that the emitting region of this object possesses abundance anomalies similar to those of coronally active main-sequence stars.Comment: 15 pages, Submitted to Ap

High pressure transport studies of the LiFeAs analogues CuFeTe2 and Fe2As

We have synthesized two iron-pnictide/chalcogenide materials, CuFeTe2 and Fe2As, which share crystallographic features with known iron-based superconductors, and carried out high-pressure electrical resistivity measurements on these materials to pressures in excess of 30 GPa. Both compounds crystallize in the Cu2Sb-type crystal structure that is characteristic of LiFeAs (with CuFeTe2 exhibiting a disordered variant). At ambient pressure, CuFeTe2 is a semiconductor and has been suggested to exhibit a spin-density-wave transition, while Fe2As is a metallic antiferromagnet. The electrical resistivity of CuFeTe2, measured at 4 K, decreases by almost two orders of magnitude between ambient pressure and 2.4 GPa. At 34 GPa, the electrical resistivity decreases upon cooling the sample below 150 K, suggesting the proximity of the compound to a metal-insulator transition. Neither CuFeTe2 nor Fe2As superconduct above 1.1 K throughout the measured pressure range.Comment: 6 pages, 7 figure

Activating metaphors:exploring the embodied nature of metaphorical mapping in political discourse

In this unit activity, I explore how students can make use of the principles of embodied cognition and meaning, and specifically the embodied nature of metaphor to explore political discourse and communication. Work in cognitive linguistics has highlighted the fact that humans construct a view of reality that is informed by our species-specific capacities and limitations, and our interaction with the social and physical world (Tyler, 2012). In these terms, language itself can be viewed as derived from conceptualizations that are based on physical and sensory images (Holme, 2012). Together these comprise a theory of embodied cognition that can be utilised in an educational context (Giovanelli 2014)

Nonuniversal mound formation in nonequilibrium surface growth

We demonstrate, using well-established nonequilibrium limited-mobility solid-on-solid growth models, that mound formation in the dynamical surface growth morphology does not necessarily imply the existence of a surface edge diffusion bias (the Schwoebel barrier). We find mounded morphologies in several nonequilibrium growth models which incorporate no Schwoebel barrier. Our numerical results indicate that mounded morphologies in nonequilibrium surface growth may arise from a number of distinct physical mechanisms, with the Schwoebel instability being one of them.Comment: 5 pages, 4 ps figures included, accepted for publication in Surface Science Letter