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

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

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

Mass Transfer by Stellar Wind

I review the process of mass transfer in a binary system through a stellar wind, with an emphasis on systems containing a red giant. I show how wind accretion in a binary system is different from the usually assumed Bondi-Hoyle approximation, first as far as the flow's structure is concerned, but most importantly, also for the mass accretion and specific angular momentum loss. This has important implications on the evolution of the orbital parameters. I also discuss the impact of wind accretion, on the chemical pollution and change in spin of the accreting star. The last section deals with observations and covers systems that most likely went through wind mass transfer: barium and related stars, symbiotic stars and central stars of planetary nebulae (CSPN). The most recent observations of cool CSPN progenitors of barium stars, as well as of carbon-rich post-common envelope systems, are providing unique constraints on the mass transfer processes.Comment: Chapter 7, in Ecology of Blue Straggler Stars, H.M.J. Boffin, G. Carraro & G. Beccari (Eds), Astrophysics and Space Science Library, Springe

Biallelic SQSTM1 mutations in early-onset, variably progressive neurodegeneration.

OBJECTIVE: To characterize clinically and molecularly an early-onset, variably progressive neurodegenerative disorder characterized by a cerebellar syndrome with severe ataxia, gaze palsy, dyskinesia, dystonia, and cognitive decline affecting 11 individuals from 3 consanguineous families. METHODS: We used whole-exome sequencing (WES) (families 1 and 2) and a combined approach based on homozygosity mapping and WES (family 3). We performed in vitro studies to explore the effect of the nontruncating SQSTM1 mutation on protein function and the effect of impaired SQSTM1 function on autophagy. We analyzed the consequences of sqstm1 down-modulation on the structural integrity of the cerebellum in vivo using zebrafish as a model. RESULTS: We identified 3 homozygous inactivating variants, including a splice site substitution (c.301+2T>A) causing aberrant transcript processing and accelerated degradation of a resulting protein lacking exon 2, as well as 2 truncating changes (c.875_876insT and c.934_936delinsTGA). We show that loss of SQSTM1 causes impaired production of ubiquitin-positive protein aggregates in response to misfolded protein stress and decelerated autophagic flux. The consequences of sqstm1 down-modulation on the structural integrity of the cerebellum in zebrafish documented a variable but reproducible phenotype characterized by cerebellum anomalies ranging from depletion of axonal connections to complete atrophy. We provide a detailed clinical characterization of the disorder; the natural history is reported for 2 siblings who have been followed up for >20 years. CONCLUSIONS: This study offers an accurate clinical characterization of this recently recognized neurodegenerative disorder caused by biallelic inactivating mutations in SQSTM1 and links this phenotype to defective selective autophagy

Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships.

A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R2>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models