The Lsm Proteins: Ring Architectures for RNA Capture

20 page(s

Measuring electrochemical noise of a single working electrode for assessing corrosion resistance of polymer coated metals

Electrochemical noise measurement (ENM) of the spontaneous perturbation of current and potential of coated samples immersed in electrolyte determines the resistance of the coating system. ENM offers several advantages: the measurement is relatively simple to make, it is completely non-interfering with the natural process occurring on the surface and the data are simple to interpret. The original standard arrangement for ENM using a pair of samples has limitations for practical applications because two separate and nominally identical working electrodes are needed and this requirement is very hard (if not impossible) to fulfil in on-site application. This paper describes an alternative approach for electrochemical noise measurement to measure the noise resistance (R n) of protective coatings based on use of just one working electrode. In this so-called "Single Cell" (SC) arrangement the electrochemical noise current and electrochemical noise potential between the working electrode and a non-noisy reference electrode is measured separately and consecutively. This new approach has been tested for a range of coating resistances. Also, the coating's resistance has been measured using DC resistance and EIS (at low frequency) and the results were compared with the Rn obtained from the single cell (SC) set up. © 2014 Elsevier B.V

Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria.

Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation

Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio

BACKGROUND: Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be). Multiple insertion events can lead to the assembly of large integron-associated cassette arrays. The most striking examples are found in Vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains. RESULTS: The complete Vibrio sp. DAT722 integron cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene cassette encoded genes). It differs extensively in terms of genomic context as well as gene cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene cassette pool suggests frequent transfer of cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene cassettes and others where cassettes have been inserted into chromosomal locations outside integrons. CONCLUSION: Our systematic approach greatly facilitates the isolation and annotation of large integrons gene cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene gain/loss relative to most other loci on vibrio chromosomes. We identify a relationship between the phylogenetic distance separating two species and the rate at which they exchange gene cassettes, interactions between the non-mobile portion of bacterial genomes and the vibrio gene cassette pool as well as intragenomic translocation events of integrons in vibrios

Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites

Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-α, α+β and α/β fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein-protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions.13 page(s

Place-keeping for health? Charting the challenges for urban park management in practice

There is a growing body of evidence that demonstrates the health and well-being benefits of urban green spaces. There is less evidence on the effect of the management of such spaces on our health and well-being. This paper attempts to address this gap in knowledge by calling on empirical evidence collected in the United Kingdom (UK) city of Sheffield. Interviews conducted with professionals and community groups involved in the management of six district parks are analysed using the place-keeping analytical framework. The results highlight the overriding importance of local and national policy regarding how they inform the availability of funding, which is increasingly dependent on partnerships, and governance arrangements to contribute to a park’s maintenance, which is monitored through evaluation. The findings show how policies without funding can jeopardise the effective management of parks and how the concept of making park management a statutory service might have more traction if we consider its contribution to people’s health

Flood magnitude-frequency and lithologic control on bedrock river incision in post-orogenic terrain

Mixed bedrock-alluvial rivers - bedrock channels lined with a discontinuous alluvial cover - are key agents in the shaping of mountain belt topography by bedrock fluvial incision. Whereas much research focuses upon the erosional dynamics of such rivers in the context of rapidly uplifting orogenic landscapes, the present study investigates river incision processes in a post-orogenic (cratonic) landscape undergoing extremely low rates of incision (> 5 m/Ma). River incision processes are examined as a function of substrate lithology and the magnitude and frequency of formative flows along Sandy Creek gorge, a mixed bedrock-alluvial stream in arid SE-central Australia. Incision is focused along a bedrock channel with a partial alluvial cover arranged into riffle-pool macrobedforms that reflect interactions between rock structure and large-flood hydraulics. Variations in channel width and gradient determine longitudinal trends in mean shear stress (τb) and therefore also patterns of sediment transport and deposition. A steep and narrow, non-propagating knickzone (with 5% alluvial cover) coincides with a resistant quartzite unit that subdivides the gorge into three reaches according to different rock erodibility and channel morphology. The three reaches also separate distinct erosional styles: bedrock plucking (i.e. detachment-limited erosion) prevails along the knickzone, whereas along the upper and lower gorge rock incision is dependent upon large formative floods exceeding critical erosion thresholds (τc) for coarse boulder deposits that line 70% of the channel thalweg (i.e. transport-limited erosion). The mobility of coarse bed materials (up to 2 m diameter) during late Holocene palaeofloods of known magnitude and age is evaluated using step-backwater flow modelling in conjunction with two selective entrainment equations. A new approach for quantifying the formative flood magnitude in mixed bedrock-alluvial rivers is described here based on the mobility of a key coarse fraction of the bed materials; in this case the d84 size fraction. A 350 m3/s formative flood fully mobilises the coarse alluvial cover with τb200-300 N/m2 across the upper and lower gorge riffles, peaking over 500 N/m2 in the knickzone. Such floods have an annual exceedance probability much less than 10- 2 and possibly as low as 10- 3. The role of coarse alluvial cover in the gorge is discussed at two scales: (1) modulation of bedrock exposure at the reach-scale, coupled with adjustment to channel width and gradient, accommodates uniform incision across rocks of different erodibility in steady-state fashion; and (2) at the sub-reach scale where coarse boulder deposits (corresponding to <i>τ</i><sub>b</sub> minima) cap topographic convexities in the rock floor, thereby restricting bedrock incision to rare large floods. While recent studies postulate that decreasing uplift rates during post-orogenic topographic decay might drive a shift to transport-limited conditions in river networks, observations here and elsewhere in post-orogenic settings suggest, to the contrary, that extremely low erosion rates are maintained with substantial bedrock channel exposure. Although bed material mobility is known to be rate-limiting for bedrock river incision under low sediment flux conditions, exactly how a partial alluvial cover might be spatially distributed to either optimise or impede the rate of bedrock incision is open to speculation. Observations here suggest that the small volume of very stable bed materials lining Sandy Creek gorge is distributed so as to minimise the rate of bedrock fluvial incision over time

Erosion Surface and Granitic Morphology in the Sierra de Lihuel Calel, Province of La Pampa, Argentina

Fil: Aguilera, Emilia Yolanda. Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Sato, Ana María. Centro de Investigaciones Geológicas (CIG). Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Llambías, Eduardo Jorge. Centro de Investigaciones Geológicas (CIG). Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Tickyj, Hugo. Departamento de Ciencias Naturales. Facultad de Ciencias Exactas y Naturales. Universidad Nacional de La Pampa; Argentin

IV BCG Vaccination and Aerosol BCG Revaccination Induce Mycobacteria-Responsive γδ T Cells Associated with Protective Efficacy against M. tb Challenge.

Intravenously (IV) delivered BCG provides superior tuberculosis (TB) protection compared with the intradermal (ID) route in non-human primates (NHPs). We examined how γδ T cell responses changed in vivo after IV BCG vaccination of NHPs, and whether these correlated with protection against aerosol M. tuberculosis challenge. In the circulation, Vδ2 T cell populations expanded after IV BCG vaccination, from a median of 1.5% (range: 0.8-2.3) of the CD3+ population at baseline, to 5.3% (range: 1.4-29.5) 4 weeks after M. tb, and were associated with TB protection. This protection was related to effector and central memory profiles; homing markers; and production of IFN-γ, TNF-α and granulysin. In comparison, Vδ2 cells did not expand after ID BCG, but underwent phenotypic and functional changes. When Vδ2 responses in bronchoalveolar lavage (BAL) samples were compared between routes, IV BCG vaccination resulted in highly functional mucosal Vδ2 cells, whereas ID BCG did not. We sought to explore whether an aerosol BCG boost following ID BCG vaccination could induce a γδ profile comparable to that induced with IV BCG. We found evidence that the aerosol BCG boost induced significant changes in the Vδ2 phenotype and function in cells isolated from the BAL. These results indicate that Vδ2 population frequency, activation and function are characteristic features of responses induced with IV BCG, and the translation of responses from the circulation to the site of infection could be a limiting factor in the response induced following ID BCG. An aerosol boost was able to localise activated Vδ2 populations at the mucosal surfaces of the lung. This vaccine strategy warrants further investigation to boost the waning human ID BCG response

Stable isotopic composition of fossil mammal teeth and environmental change in southwestern South Africa during the Pliocene and Pleistocene

The past 5 million years mark a global change from the warmer, more stable climate of the Pliocene to the initiation of glacial-interglacial cycles during the Pleistocene. Marine core sediment records located off the coast of southwestern Africa indicate aridification and intensified upwelling in the Benguela Current over the Pliocene and Pleistocene. However, few terrestrial records document environmental change in southwestern Africa over this time interval. Here we synthesize new and published carbon and oxygen isotope data of the teeth from large mammals (>6 kg) at Langebaanweg (~5 million years ago, Ma), Elandsfontein (1.0 – 0.6 Ma), and Hoedjiespunt (0.35 – 0.20 Ma), to evaluate environmental change in southwestern Africa between the Pliocene and Pleistocene. The majority of browsing and grazing herbivores from these sites yield enamel 13 C values within the range expected for animals with a pure C3 diet, however some taxa have enamel 13C values that suggest the presence of small amounts C4 grasses at times during the Pleistocene. Considering that significant amounts of C4 grasses require a warm growing season, these results indicate that the winter rainfall zone, characteristic of the region today, could have been in place for the past 5 million years. The average 18O value of the herbivore teeth increases ~4.4‰ between Langebaanweg and Elandsfontein for all taxa except suids. This increase may solely be a function of a change in hydrology between the fluvial system at Langebaanweg and the spring-fed environments at Elandsfontein, or a combination of factors that include depositional context, regional circulation and global climate. However, an increase in regional aridity or global cooling between the early Pliocene and mid-Pleistocene cannot explain the entire increase in enamel 18O values. Spring-fed environments like those at Elandsfontein may have 75 provided critical resources for mammalian fauna in the mid-Pleistocene within an increasingly arid southwestern Africa ecosystem