Guidance on the use of synthetic fibre ropes for marine energy devices

Deliverable 3.5.2 from the MERiFIC Project A report prepared as part of the MERiFIC Project "Marine Energy in Far Peripheral and Island Communities"his report is a deliverable of MERiFIC Work Package 3: ‘Dynamic Behaviour of Marine Energy Devices’ involving the collaboration of IFREMER (Institut français de recherche pour l'exploitation de la mer) in France and the University of Exeter in the United Kingdom. Although synthetic ropes have been used for the station-keeping of offshore structures for the past two decades predominantly by the oil, gas and shipping industries, there is considerable interest in their utilisation for the station-keeping of marine renewable energy (MRE) devices. Differences in application between typically small, highly responsive devices (e.g. Wave Energy Converters or WECs) and large slow-moving platforms necessitate a unique approach to mooring system design and dedicated mooring component test programs, both guided by relevant certification standards. It is the intention of this report to provide an introduction to synthetic mooring ropes in the context of previous usage in the offshore industry and also to highlight factors which should be considered for their use in MRE mooring systems. The document begins by setting the scene to give background on the fundamental differences between previous applications of synthetic mooring ropes and MRE devices. In Section 2 a brief overview of commercially available ropes is then given. The distinct properties of synthetic materials and rope constructions are summarised with emphasis placed on issues which are likely to be relevant for MRE devices. In the absence of specific advice for this emerging industry, conventional approaches to applying safety factors to synthetic ropes are then introduced. Section 3 highlights in-service considerations relevant for the different lifecycle stages of ropes, from installation and operational procedures (such as maintenance and inspection) to decommissioning. Specific modelling approaches for synthetic ropes are then summarised in Section 4, followed by a summary in Section 5. This document is not intended to be an exhaustive account of all aspects of synthetic mooring ropes and in light of this further references are provided for the interested reader.MERiFIC was selected under the European Cross-Border Cooperation Programme INTERREG IV A France (Channel) – England, co-funded by the ERD

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 Investigation of Different Variables in the Assaying of Silver Cyanide Solutions

The cyanide method of extraction of gold and silver from their ores is extensively used in the United States and elsewhere. It is becoming increasingly more important in its use as the mining of lower grade deposits continues

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

Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol.

Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities

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

Structure-function analysis of the <em>Fusarium oxysporum</em> Avr2 effector allows uncoupling of its immune-suppressing activity from recognition

Plant pathogens employ effector proteins to manipulate their hosts. Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato wilt disease, produces effector protein Avr2. Besides being a virulence factor, Avr2 triggers immunity in I-2 carrying tomato (Solanum lycopersicum). Fol strains that evade I-2 recognition carry point mutations in Avr2 (e.g. Avr2R45H), but retain full virulence. Here we investigate the virulence function of Avr2 and determine its crystal structure. Transgenic tomato and Arabidopsis expressing either wild-type ΔspAvr2 (deleted signal-peptide) or the ΔspAvr2R45H variant become hypersusceptible to fungal, and even bacterial infections, suggesting that Avr2 targets a conserved defense mechanism. Indeed, Avr2 transgenic plants are attenuated in immunity-related readouts, including flg22-induced growth inhibition, ROS production and callose deposition. The crystal structure of Avr2 reveals that the protein shares intriguing structural similarity to ToxA from the wheat pathogen Pyrenophora tritici-repentis and to TRAF proteins. The I-2 resistance-breaking Avr2V41M, Avr2R45H and Avr2R46P variants cluster on a surface-presented loop. Structure-guided mutagenesis enabled uncoupling of virulence from I-2-mediated recognition. We conclude that I-2-mediated recognition is not based on monitoring Avr2 virulence activity, which includes suppression of immune responses via an evolutionarily conserved effector target, but by recognition of a distinct epitope

Niche differentiation is spatially and temporally regulated in the rhizosphere.

The rhizosphere is a hotspot for microbial carbon transformations, and is the entry point for root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter (SOM). However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial functions in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Transcripts were binned using a unique reference database generated from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, the succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition genes, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were highest in the combined rhizosphere-detritusphere, suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling