Biochemical characterization of arterivirus nonstructural protein 11 reveals the nidovirus-wide conservation of a replicative endoribonuclease

Nidoviruses (arteriviruses, coronaviruses, and roniviruses) are a phylogenetically compact but diverse group of positive-strand RNA viruses that includes important human and animal pathogens. Nidovirus RNA synthesis is mediated by a cytoplasmic membrane-associated replication/transcription complex that includes up to 16 viral nonstructural proteins (nsps), which carry common enzymatic activities, like the viral RNA polymerase, but also unusual and poorly understood RNA-processing functions. Of these, a conserved endoribonuclease (NendoU) is a major genetic marker that is unique to nidoviruses. NendoU activity was previously verified in vitro for the coronavirus nsp15, but not for any of its distantly related orthologs from other nidovirus lineages, like the arterivirus nsp11. Here, we show that the bacterially expressed nsp11 proteins of two arteriviruses, equine arteritis virus and porcine respiratory and reproductive syndrome virus, possess pyrimidine-specific endoribonuclease activity. RNA cleavage was independent of divalent cations in vitro and was greatly reduced by replacement of residues previously implicated in catalysis. Comparative characterization of the NendoU activity in arteriviruses and severe acute respiratory syndrome coronavirus revealed common and distinct features of their substrate requirements and reaction mechanism. Our data provide the first biochemical evidence of endoribonuclease activity associated with arterivirus nsp11 and support the conclusion that this remarkable RNA-processing enzyme, whose substrate in the infected cell remains to be identified, distinguishes nidoviruses from all other RNA viruses.

Modelling the performance of self-compacting SIFCON of cement slurries containing limestone powder using genetic programming technique

The paper explores the potential of applicability of Genetic programming approach (GP), adopted in this investigation, to model the combined effects of five independent variables to predict the mini-slump, the plate cohesion meter, the induced bleeding test, the J-fiber penetration value, and the compressive strength at 7 and 28 days of self-compacting slurry infiltrated fiber concrete (SIFCON). The variables investigated were the proportions of limestone powder (LSP) and sand, the dosage rates of superplasticiser (SP) and viscosity modifying agent (VMA), and water-to-binder ratio (W/B). Twenty eight mixtures were made with 10-50% LSP as replacement of cement, 0.02-0.06% VMA by mass of cement, 0.6-1.2% SP and 50-150% sand (% mass of binder) and 0.42-0.48 W/B. The proposed genetic models of the self-compacting SIFCON offer useful modelling approach regarding the mix optimisation in predicting the fluidity, the cohesion, the bleeding, the penetration, and the compressive strength.

Effect of Mix Proportions on Rheological and Hardened Properties of Composite Cement Pastes

There is an increasing need to identify the effect of mix composition on the rheological properties of composite cement pastes using simple tests to determine the fluidity, the cohesion and other mechanical properties of grouting applications such as compressive strength. This paper reviews statistical models developed using a fractional factorial design which was carried out to model the influence of key parameters on properties affecting the performance of composite cement paste. Such responses of fluidity included mini-slump, flow time using Marsh cone and cohesion measured by Lombardi plate meter and unit weight, and compressive strength at 3 d, 7 d and 28 d. The models are valid for mixes with 0.35 to 0.42 water-to-binder ratio (W/B), 10% to 40% of pulverised fuel ash (PFA) as replacement of cement by mass, 0.02 to 0.06% of viscosity enhancer admixture (VEA), by mass of binder, and 0.3 to 1.2% of superplasticizer (SP), by mass of binder. The derived models that enable the identification of underlying primary factors and their interactions that influence the modelled responses of composite cement paste are presented. Such parameters can be useful to reduce the test protocol needed for proportioning of composite cement paste. This paper attempts also to demonstrate the usefulness of the models to better understand trade-offs between parameters and compare the responses obtained from the various test methods which are highlighted. The multi parametric optimization is used in order to establish isoresponses for a desirability function of cement composite paste. Results indicate that the replacement of cement by PFA is compromising the early compressive strength and up 26%, the desirability function decreased.

Effect of Mixture Composition on Relative Strength of Highly Flowable Underwater Concrete

Concrete used for underwater repair is often proportioned to spread readily into place and self-consolidate, and to develop high resistance to segregation and water dilution. An investigation was carried out to determine the effect of the dosage of antiwashout admixture, water-cementitious materials ratio (w/cm), and binder composition on the relative residual strength of highly flowable underwater concrete. Two types of antiwashout admixtures were used: a powdered welan gum at 0.07 and 0.15% by mass of binder, and a liquid-based cellulosic admixture employed at a high dosage of 1 to 1.65 L/100 kg of cementitious materials. The w/cms were set at 0.41 and 0.47 to secure adequate performance of underwater concrete for construction and repair. Four binder compositions were used: a Canadian Type 10 cement; a cement with 10% silica fume replacement; a cement with 50% replacement of granulated blast-furnace slag; and a ternary binder containing 6% silica fume and 20% Class F fly ash. Test results indicate that for a given washout mass loss and slump flow consistency, greater relative residual strength can be secured when the dosage of antiwashout admixture is increased, the w/cm is reduced, and a binary binder with 10% silica fume substitution or the ternary binder are employed. Such mixtures can develop relative residual compressive strengths of 85 and 80%, compared to mixtures cast in air, when the value of washout loss is limited to 4 and 6% for mixtures with slump flow values of 450 and 550 mm, respectively.

Optimization of Cement Grouts Containing Silica Fume and Viscosity Modifying Admixture

There is an increasing need to identify the effect of mix composition on the rheological properties of cementitious grouts using minislump, Marsh cone, cohesion plate, washout test, and cubes to determine the fluidity, the cohesion, and other mechanical properties of grouting applications. Mixture proportioning involves the tailoring of several parameters to achieve adequate fluidity, cohesion, washout resistance and compressive strength. This paper proposes a statistical design approach using a composite fractional factorial design which was carried out to model the influence of key parameters on the performance of cement grouts. The responses relate to performance included minislump, flow time using Marsh cone, cohesion measured by Lombardi plate meter, washout mass loss and compressive strength at 3, 7, and 28 days. The statistical models are valid for mixtures with water-to-binder ratio of 0.37–0.53, 0.4–1.8% addition of high-range water reducer (HRWR) by mass of binder, 4–12% additive of silica fume as replacement of cement by mass, and 0.02–0.8% addition of viscosity modifying admixture (VMA) by mass of binder. The models enable the identification of underlying factors and interactions that influence the modeled responses of cement grout. The comparison between the predicted and measured responses indicated good accuracy of the established models to describe the effect of the independent variables on the fluidity, cohesion, washout resistance and the compressive strength. This paper demonstrates the usefulness of the models to better understand trade-offs between parameters. The multiparametric optimization is used to establish isoresponses for a desirability function for cement grout. An increase of HRWR led to an increase of fluidity and washout, a reduction in plate cohesion value, and a reduction in the Marsh cone time. An increase of VMA demonstrated a reduction of fluidity and the washout mass loss, and an increase of Marsh cone time and plate cohesion. Results indicate that the use of silica fume increased the cohesion plate and Marsh cone, and reduced the minislump. Additionally, the silica fume improved the compressive strength and the washout resistance.

Temporal changes in the distribution of native and introduced freshwater amphipods in Lough Neagh, Northern Ireland

Studies of invasion scenarios over long time periods are important to refine explanations and predictions of invasion success and impact. We used data from surveys in 1958 and 1999 of the macroinvertebrates of Lough Neagh, Northern Ireland, to assess changes in the distribution of native and introduced amphipods in relation to the wider assemblage. In 1958, the invader G. tigrinus dominated the shoreline fauna, with the native G. d. celticus present in very low numbers, whereas in 1999 the reverse was evident. In both surveys, G. tigrinus was the only amphipod present in the mid-Lough. G. tigrinus thus seems to have become established within L. Neagh, perhaps overshot and then senesced, with the native species re-establishing on the shoreline, with the invader mostly restricted to the deep mid-Lough. The non-amphipod macroinvertebrate assemblage was similar between the two surveys, in terms of Bray-Curtis community similarity, assemblage diversity, dominance and the taxa based ASPT water quality index. However, the mean density of macroinvertebrates (all taxa combined) was lower in 1999 compared to 1958, largely accounted for by a decline in oligochaete numbers. Since Gammarus species may be predators of other macroinvertebrates and influence their distribution and abundance, we investigated this trophic link in staged laboratory encounters. Both G. tigrinus and G. d. celticus preyed on isopods, alderflies, mayflies, chironomids and mysids, however, the native G. d. celticus had a significantly greater predatory impact on isopods and chironomids than did the invader G. tigrinus. While we cannot definitively ascribe cause and effect in the present scenario, we discuss how replacement of one amphipod species by another may have impacts on the wider macroinvertebrate assemblage.

Green photochemistry: photo-Friedel-Crafts acylations of 1,4-naphthoquinone in room temperature ionic liquids

The photo-Friedel-Crafts acylation of 1,4-naphthoquinone with various aldehydes was investigated in a series of room temperature ionic liquids. High conversions and selectivities were achieved in [C(2)mim](+)-based ionic liquids with the highest isolated yields found in [C(2)mim][NTf2]. The developed procedure allowed for a replacement of hazardous solvents such as benzene and acetonitrile which are commonly used for this transformation.

‘Invasional meltdown’: evidence for unexpected consequences and cumulative impacts of multispecies invasions

Empirical support for ‘invasional meltdown’, where the presence of one invading species facilitates another and compounds negative impacts on indigenous species, is equivocal with few convincing studies. In Ireland, the bank vole was introduced 80 years ago and now occupies a third of the island. The greater white-toothed shrew arrived more recently within the invasive range of the bank vole. We surveyed the abundance of both invasive species and two indigenous species, the wood mouse and pygmy shrew, throughout their respective ranges. The negative effects of invasive on indigenous species were strong and cumulative bringing about species replacement. The greater white-toothed shrew, the second invader, had a positive and synergistic effect on the abundance of the bank vole, the first invader, but a negative and compounding effect on the abundance of the wood mouse and occurrence of the pygmy shrew. The gradual replacement of the wood mouse by the bank vole decreased with distance from the point of the bank vole’s introduction whilst no pygmy shrews were captured where both invasive species were present. Such interactions may not be unique to invasions but characteristic of all multispecies communities. Small mammals are central in terrestrial food webs and compositional changes to this community in Ireland are likely to reverberate throughout the ecosystem. Vegetation composition and structure, invertebrate communities and the productivity of avian and mammalian predators are likely to be affected. Control of these invasive species may only be effected through landscape and habitat management.

Structure-activity relationships of FMRFamide-related peptides contracting Schistosoma mansoni muscle

This study reports the potent myoactivity of flatworm FMRFamide-related peptides (FaRPs) on isolated muscle fibers of the human blood fluke, Schistosoma mansoni. The turbellarian peptides YIRFamide (EC50 4 eta M), GYIRFamide (EC50 1 eta M). and RYIRFamide (EC50 7 eta M), all induced muscle contraction more potently than the cestode FaRP GNFFRFamide (EC50 500 eta M). Using a series of synthetic analogs of the flatworm peptides YIRFamide, GYIRFamide and RYIRFamide, the structure-activity relationships of the muscle FaRP receptor were examined. With a few exceptions, each residue in YIRFamide is important in the maintenance of its myoactivity. Alanine scans resulted in peptides that were inactive (Ala(1), Ala(2), Ala(3) and Ala(4) YIRFamide; Ala(4) and Ala(5) RYIRFamide) or had much reduced potencies (Ala(1), Ala(2) and Ala(3) RYIRFamide). Substitution of the N-terminal (Tyr(1)) residue of YIRFamide with the non-aromatic residues Thr or Arg produced analogs with greatly reduced potency. Replacement of the N-terminal Tyr with aromatic amino acids resulted in myoactive peptides (FIRFamide, EC50 100 eta M; WIRFamide, EC50 0.5 eta M). The activity of YIRFamide analogs which possessed a Leu(2), Phe(2) or Met(2) residue (EC50's 10, 1 and 3 eta M, respectively) instead of Ile(2) was not significantly altered, whereas, YVRFamide had a greatly reduced (EC50 200 eta M) activity. Replacement of the Phe(4) with a Tyr(4) (YIRYamide) also greatly lowered potency. Truncated analogs were either inactive (FRFamide, YRFamide, HRFamide, RFamide, Famide) or had very low potency (IRFamide and MRFamide), with the exception of nLRFamide (EC50 20 eta M). YIRF free acid was inactive. In summary, these data show the general structural requirements of this schistosome muscle FaRP receptor to be similar, but not identical, to those of previously characterized molluscan FaRP receptors. (C) 1997 Elsevier Science Inc.

The effect of construction pattern and unit interlock on the structural behaviour of block pavements

The maintenance or even replacement of cracked pavements requires considerable financial resources and puts a large burden on the budgets of local councils. In addition to these costs, local councils also face liability claims arising from uneven or cracked pedestrian pavements. These currently cost the Manchester City Council and Preston City Council around £6 million a year each. Design procedures are empirical. A better understanding of the interaction between paving blocks, bedding sand and subbase was necessary in order to determine the mode of failure of pavements under load. Increasing applied stress was found to mobilise ‘‘rotational interlock’’, providing increased pavement stiffness and thus increased load dissipation resulting in lower transmitted stress on the subgrade. The indications from the literature
review were that pavements are designed to fail by excessive deformation and that paving blocks remained uncracked at failure. This was confirmed with experimental data which was obtained from tests on segments of pavements that were laid/constructed in a purpose built test frame in the laboratory.

Use of recycled demolition aggregate in precast products, phase II: Concrete paving blocks

A study undertaken at the University of Liverpool has investigated the potential for using construction and demolition waste (C&DW) as aggregate in the manufacture of a range of precast concrete products, i.e. building and paving blocks and pavement flags. Phase II, which is reported here, investigated concrete paving blocks. Recycled demolition aggregate can be used to replace newly quarried limestone aggregate, usually used in coarse (6 mm) and fine (4 mm-to-dust) gradings. The first objective, as was the case with concrete building blocks, was to replicate the process used by industry in fabricating concrete paving blocks in the laboratory. The compaction technique used involved vibration and pressure at the same time, i.e. a vibro-compaction technique. An electric hammer used previously for building blocks was not sufficient for adequate compaction of paving blocks. Adequate compaction could only be achieved by using the electric hammer while the specimens were on a vibrating table. The experimental work involved two main series of tests, i.e. paving blocks made with concrete- and masonry-derived aggregate. Variables that were investigated were level of replacement of (a) coarse aggregate only, (b) fine aggregate only, and (c) both coarse and fine aggregate. Investigation of mechanical properties, i.e. compressive and tensile splitting strength, of paving blocks made with recycled demolition aggregate determined levels of replacement which produced similar mechanical properties to paving blocks made with newly quarried aggregates. This had to be achieved without an increase in the cement content. The results from this research programme indicate that recycled demolition aggregate can be used for this new higher value market and therefore may encourage demolition contractors to develop crushing and screening facilities for this. (C) 2011 Published by Elsevier Ltd.

Functional analysis of the C-terminal domain of the WbaP protein that mediates initiation of O antigen synthesis in Salmonella enterica

WbaP catalyzes the transfer of galactose-1-phosphate onto undecaprenyl phosphate (Und-P). The enzyme belongs to a large family of bacterial membrane proteins required for initiation of the synthesis of O antigen lipopolysaccharide and polysaccharide capsules. Previous work in our laboratory demonstrated that the last transmembrane helix and C-terminal tail region of WbaP (WbaP(CT)) are sufficient for enzymatic activity. Here, we demonstrate the cytoplasmic location of the WbaP C-terminal tail and show that WbaPCT domain N-terminally fused to thioredoxin (TrxA-WbaP(CT)) exhibits improved protein folding and enhanced transferase activity. Alanine replacement of highly conserved charged or polar amino acids identified seven critical residues for enzyme activity in vivo and in vitro. Four of these residues are located in regions predicted to be a-helical. These regions and their secondary structure predictions are conserved in distinct WbaP family members, suggesting they may contribute to form a conserved catalytic center.

Conserved amino acid residues found in a predicted cytosolic domain of the lipopolysaccharide biosynthetic protein WecA are implicated in the recognition of UDP-N-acetylglucosamine

WecA, an integral membrane protein that belongs to a family of polyisoprenyl phosphate N-acetylhexosamine-1-phosphate transferases, is required for the biosynthesis of O-specific LPS and enterobacterial common antigen in Escherichia coli and other enteric bacteria. WecA functions as an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate GlcNAc-1-phosphate transferase. A conserved short sequence motif (His-Ile-His-His; HIHH) and a conserved arginine were identified in WecA at positions 279-282 and 265, respectively. This region is located within a predicted cytosolic segment common to all bacterial homologues of WecA. Both HIHH279-282 and the Arg265 are reminiscent of the HIGH motif (His-Ile-Gly-His) and a nearby upstream lysine, which contribute to the three-dimensional architecture of the nucleotide-binding site among various enzymes displaying nucleotidyltransferase activity. Thus, it was hypothesized that these residues may play a role in the interaction of WecA with UDP-GlcNAc. Replacement of the entire HIHH motif by site-directed mutagenesis produced a protein that, when expressed in the E. coli wecA mutant MV501, did not complement the synthesis of O7 LPS. Membrane extracts containing the mutated protein failed to transfer UDP-GlcNAc into a lipid-rich fraction and to bind the UDP-GlcNAc analogue tunicamycin. Similar results were obtained by individually replacing the first histidine (H279) of the HIHH motif as well as the Arg265 residue. The functional importance of these residues is underscored by the high level of conservation of H279 and Arg265 among bacterial WecA homologues that utilize several different UDP-N-acetylhexosamine substrates.

Selective Orthosteric Free Fatty Acid Receptor 2 (FFA2) Agonists IDENTIFICATION OF THE STRUCTURAL AND CHEMICAL REQUIREMENTS FOR SELECTIVE ACTIVATION OF FFA2 VERSUS FFA3

Free fatty acid receptor 2 (FFA2; GPR43) is a G protein-coupled seven-transmembrane receptor for short-chain fatty acids (SCFAs) that is implicated in inflammatory and metabolic disorders. The SCFA propionate has close to optimal ligand efficiency for FFA2 and can hence be considered as highly potent given its size. Propionate, however, does not discriminate between FFA2 and the closely related receptor FFA3 (GPR41). To identify FFA2-selective ligands and understand the molecular basis for FFA2 selectivity, a targeted library of small carboxylic acids was examined using holistic, label-free dynamic mass redistribution technology for primary screening and the receptor-proximal G protein [S-35] guanosine 5'-(3-O-thio) triphosphate activation, inositol phosphate, and cAMP accumulation assays for hit confirmation. Structure-activity relationship analysis allowed formulation of a general rule to predict selectivity for small carboxylic acids at the orthosteric binding site where ligands with substituted sp(3)-hybridized alpha-carbons preferentially activate FFA3, whereas ligands with sp(2)- or sp-hybridized alpha-carbons prefer FFA2. The orthosteric binding mode was verified by site-directed mutagenesis: replacement of orthosteric site arginine residues by alanine in FFA2 prevented ligand binding, and molecular modeling predicted the detailed mode of binding. Based on this, selective mutation of three residues to their non-conserved counterparts in FFA3 was sufficient to transfer FFA3 selectivity to FFA2. Thus, selective activation of FFA2 via the orthosteric site is achievable with rather small ligands, a finding with significant implications for the rational design of therapeutic compounds selectively targeting the SCFA receptors.

Optimisation of rheological parameters and mechanical properties of superplasticised cement grouts containing metakaolin and viscosity modifying admixture

The objective of this research was to optimise the rheological parameters, hardened properties, and setting times of cement grouts containing metakaolin (MTK), viscosity-modifying agent (VMA) and superplasticiser (SP). All mixes were made with water-to-binder ratio (W/B) of 0.40. The replacement of cement by MTK was varied from 6% to 20% (by mass), and dosages of SP and VMA were varied from 0.3% to 1.4%, and 0.01% and 0.06% (by mass of binder), respectively. Increased SP led to an increase in fluidity, reduction in flow time, plate cohesion, rheological parameters, and an increase in the setting times. Increased VMA demonstrated a reduction in fluidity, an increase in Marsh cone time, plate cohesion, yield stress, and plastic viscosity. Results indicate that the use of MTK increased yield stress, plastic viscosity, cohesion plate, and flow time due to the higher surface area associated with an increase in the water demand. MTK reduced mini-slump and setting times, and improved compressive strength.