Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community.

The candidate phyla radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and the inherent fragmented nature of available genomes. Here, we report the first closed, curated genome of a gracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation. The gracilibacterium rose in abundance after the community switched to dominance by Colwellia Notably, we predict that this gracilibacterium completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways. It appears to acquire pyruvate, acetyl coenzyme A (acetyl-CoA), and oxaloacetate via degradation of externally derived citrate, malate, and amino acids and may use compound interconversion and oxidoreductases to generate and recycle reductive power. The initial genome assembly was fragmented in an unusual gene that is hypervariable within a repeat region. Such extreme local variation is rare but characteristic of genes that confer traits under pressure to diversify within a population. Notably, the four major repeated 9-mer nucleotide sequences all generate a proline-threonine-aspartic acid (PTD) repeat. The genome of an abundant Colwellia psychrerythraea population has a large extracellular protein that also contains the repeated PTD motif. Although we do not know the host for the BD1-5 cell, the high relative abundance of the C. psychrerythraea population and the shared surface protein repeat may indicate an association between these bacteria.IMPORTANCE CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. The amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence

The dynamic genetic repertoire of microbial communities

Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus–host dynamics in generating and shaping within-population diversity

Mooring and Foundation Module Framework for DTOcean Tool

PublishedThe Optimal Design Tools for Ocean Energy Arrays project (DTOcean) is developing a system-level tool to assess cost, reliability, and environmental impact for marine renewable energy (MRE) systems. The DTOcean Tool will integrate several modules covering key aspects of MRE systems (i.e., array layout, moorings and foundations, electrical infrastructure, logistics, in addition to operations and maintenance). This report outlines the proposed architecture and main functions of the DTOcean mooring and foundation design module (the Work Package 4 or WP4 module) and its interaction with other elements and modules of the Tool. This document therefore presents the WP4 module framework which will be populated with algorithms and functions as the Tool is further developed. The module will comprise five sub-modules, in which calculations will be performed to determine and/or design the system and environmental loads, the electrical umbilical, mooring, and foundation systems as well as the foundation required for the electrical substation. Calculations performed in the sub-modules will be based on inputs provided by the user, other Tool modules, and data stored within the global Tool database. Criteria for determining design suitability will not be based solely on whether the specified components are suitable for keeping the device in position. The capital cost of each configuration will be estimated within the WP4 module, with reliability and environmental impact assessments also performed within the Tool. The framework of the WP4 module draws upon findings of previous WP4 deliverables, in which applicable mooring and foundation technologies and methods for their analysis have been reported.European Commission’s 7th Framework; Grant agreement number: 60859

Radio Galaxy Zoo: Cosmological Alignment of Radio Sources

We study the mutual alignment of radio sources within two surveys, FIRST and TGSS. This is done by producing two position angle catalogues containing the preferential directions of respectively $30\,059$ and $11\,674$ extended sources distributed over more than $7\,000$ and $17\,000$ square degrees. The identification of the sources in the FIRST sample was performed in advance by volunteers of the Radio Galaxy Zoo project, while for the TGSS sample it is the result of an automated process presented here. After taking into account systematic effects, marginal evidence of a local alignment on scales smaller than $2.5\deg$ is found in the FIRST sample. The probability of this happening by chance is found to be less than $2$ per cent. Further study suggests that on scales up to $1.5\deg$ the alignment is maximal. For one third of the sources, the Radio Galaxy Zoo volunteers identified an optical counterpart. Assuming a flat $\Lambda$CDM cosmology with $\Omega_m = 0.31, \Omega_\Lambda = 0.69$, we convert the maximum angular scale on which alignment is seen into a physical scale in the range $[19, 38]$ Mpc $h_{70}^{-1}$. This result supports recent evidence reported by Taylor and Jagannathan of radio jet alignment in the $1.4$ deg$^2$ ELAIS N1 field observed with the Giant Metrewave Radio Telescope. The TGSS sample is found to be too sparsely populated to manifest a similar signal

Synthesis of nanocrystalline barium-hexaferrite from nanocrystalline goethite using the hydrothermal method: Particle size evolution and magnetic properties

To characterize particle size/magnetic property relationships, 9 to 50 nm in diameter barium hexaferrite, BaFe{sub 12}O{sub 19} (BHF), particles were prepared using a new synthesis route. By replacing the conventional 50 to 100 nm particles of goethite with nanocrystalline goethite produced via the microwave anneal method of Knight and Sylva, nanocrystalline BHF was synthesized using the hydrothermal method. Evolution of particle size and morphology with respect to concentration and heat treatment time is reported. Hysteresis properties, including coercivity (0.2--1.0 kOe), magnetization saturation (0.1--33.4 emu/g), and magnetization remanence (0.004--22.5 emu/g) are discussed as a function of particle size. The magnetization saturation and remanence of the 7 nm particles is nearly zero, suggesting the superparamagnetic threshold size for BHF is around this size. In addition, the equilibrium morphology of BHF crystals was calculated to be truncated hexagonal prisms which was verified by experiment, and the isoelectric point, pH of 4.1, was measured for 18 nm BHF particles

The WiFeS S7 AGN survey: Current status and recent results on NGC 6300

The Siding Spring Southern Seyfert Spectroscopic Snapshot Survey (S7) is a targeted survey probing the narrow-line regions (NLRs) of a representative sample of ~140 nearby (z<0.02) Seyfert galaxies by means of optical integral field spectroscopy. The survey is based on a homogeneous data set observed using the Wide Field Spectrograph WiFeS. The data provide a 25x38 arcsec$^2$ field-of-view around the galaxy centre at typically ~1.5 arcsec spatial resolution and cover a wavelength range between ~3400 - 7100 $\AA$ at spectral resolutions of ~100 km s$^{-1}$ and ~50 km s$^{-1}$ in the blue and red parts, respectively. The survey is primarily designed to study gas excitation and star formation around AGN, with a special focus on the shape of the AGN ionising continuum, the interaction between radio jets and the NLR gas, and the nature of nuclear LINER emission. We provide an overview of the current status of S7-based results and present new results for NGC 6300.Comment: 5 pages, 1 figure, Refereed Proceeding of the "The Universe of Digital Sky Surveys" conference held at the INAF - Observatory of Capodimonte, Naples, on 25th-28th november 2014, to be published on Astrophysics and Space Science Proceedings, edited by Longo, Napolitano, Marconi, Paolillo, Iodic

What a Difference a Dalton Makes: Bacterial Virulence Factors Modulate Eukaryotic Host Cell Signaling Systems via Deamidation

Pathogenic bacteria commonly deploy enzymes to promote virulence. These enzymes can modulate the functions of host cell targets. While the actions of some enzymes can be very obvious (e.g., digesting plant cell walls), others have more subtle activities. Depending on the lifestyle of the bacteria, these subtle modifications can be crucially important for pathogenesis. In particular, if bacteria rely on a living host, subtle mechanisms to alter host cellular function are likely to dominate. Several bacterial virulence factors have evolved to use enzymatic deamidation as a subtle posttranslational mechanism to modify the functions of host protein targets. Deamidation is the irreversible conversion of the amino acids glutamine and asparagine to glutamic acid and aspartic acid, respectively. Interestingly, all currently characterized bacterial deamidases affect the function of the target protein by modifying a single glutamine residue in the sequence. Deamidation of target host proteins can disrupt host signaling and downstream processes by either activating or inactivating the target. Despite the subtlety of this modification, it has been shown to cause dramatic, context-dependent effects on host cells. Several crystal structures of bacterial deamidases have been solved. All are members of the papain-like superfamily and display a cysteine-based catalytic triad. However, these proteins form distinct structural subfamilies and feature combinations of modular domains of various functions. Based on the diverse pathogens that use deamidation as a mechanism to promote virulence and the recent identification of multiple deamidases, it is clear that this enzymatic activity is emerging as an important and widespread feature in bacterial pathogenesis

Dissecting Galaxies: Separating Star Formation, Shock Excitation and AGN Activity in the Central Region of NGC 613

The most rapidly evolving regions of galaxies often display complex optical spectra with emission lines excited by massive stars, shocks and accretion onto supermassive black holes. Standard calibrations (such as for the star formation rate) cannot be applied to such mixed spectra. In this paper we isolate the contributions of star formation, shock excitation and active galactic nucleus (AGN) activity to the emission line luminosities of individual spatially resolved regions across the central 3 $\times$ 3 kpc$^2$ region of the active barred spiral galaxy NGC$\sim$613. The star formation rate and AGN luminosity calculated from the decomposed emission line maps are in close agreement with independent estimates from data at other wavelengths. The star formation component traces the B-band stellar continuum emission, and the AGN component forms an ionization cone which is aligned with the nuclear radio jet. The optical line emission associated with shock excitation is cospatial with strong $H_2$ and [Fe II] emission and with regions of high ionized gas velocity dispersion ($\sigma > 100$ km s$^{-1}$). The shock component also traces the outer boundary of the AGN ionization cone and may therefore be produced by outflowing material interacting with the surrounding interstellar medium. Our decomposition method makes it possible to determine the properties of star formation, shock excitation and AGN activity from optical spectra, without contamination from other ionization mechanisms.Comment: 16 pages, 12 figures. Accepted for publication in MNRA

Pseudomonas syringae type III effector HopAF1 suppresses plant immunity by targeting methionine recycling to block ethylene induction

Pseudomonas syringae is a Gram-negative bacterium that uses a type III secretion system to inject type III effector (T3E) proteins into the host to cause disease in plants. Multiple P. syringae T3Es promote virulence by targeting immune system signaling pathways using diverse biochemical mechanisms. We provide evidence for a molecular function of the P. syringae T3E HopAF1. We demonstrate that the C-terminal region of HopAF1 has structural homology to deamidases. We demonstrate that an enzyme important for production of the gaseous signaling hormone ethylene is a target for HopAF1 and show that HopAF1 targets methylthioadenosine nucleosidase proteins MTN1 and MTN2 to dampen ethylene production during bacterial infection

Global genomic analysis of microbial biotransformation of arsenic highlights the importance of arsenic methylation in environmental and human microbiomes

Arsenic is a ubiquitous toxic element, the global cycle of which is highly affected by microbial redox reactions and assimilation into organoarsenic compounds through sequential methylation reactions. While microbial biotransformation of arsenic has been studied for decades, the past years have seen the discovery of multiple new genes related to arsenic metabolism. Still, most studies focus on a small set of key genes or a small set of cultured microorganisms. Here, we leveraged the recently greatly expanded availability of microbial genomes of diverse organisms from lineages lacking cultivated representatives, including those reconstructed from metagenomes, to investigate genetic repertoires of taxonomic and environmental controls on arsenic metabolic capacities. Based on the collection of arsenic-related genes, we identified thirteen distinct metabolic guilds, four of which combine the aio and ars operons. We found that the best studied phyla have very different combinations of capacities than less well-studied phyla, including phyla lacking isolated representatives. We identified a distinct arsenic gene signature in the microbiomes of humans exposed or likely exposed to drinking water contaminated by arsenic and that arsenic methylation is important in soil and in human microbiomes. Thus, the microbiomes of humans exposed to arsenic have the potential to exacerbate arsenic toxicity. Finally, we show that machine learning can predict bacterial arsenic metabolism capacities based on their taxonomy and the environment from which they were sampled