Proteornics analysis unravels the functional repertoire of coronavirus nonstructural protein 3

Severe acute respiratory syndrome (SARS) coronavirus infection and growth are dependent on initiating signaling and enzyme actions upon viral entry into the host cell. Proteins packaged during virus assembly may subsequently form the first line of attack and host manipulation upon infection. A complete characterization of virion components is therefore important to understanding the dynamics of early stages of infection. Mass spectrometry and kinase profiling techniques identified nearly 200 incorporated host and viral proteins. We used published interaction data to identify hubs of connectivity with potential significance for virion formation. Surprisingly, the hub with the most potential connections was not the viral M protein but the nonstructurall protein 3 (nsp3), which is one of the novel virion components identified by mass spectrometry. Based on new experimental data and a bioinformatics analysis across the Coronaviridae, we propose a higher-resolution functional domain architecture for nsp3 that determines the interaction capacity of this protein. Using recombinant protein domains expressed in Escherichia coli, we identified two additional RNA-binding domains of nsp3. One of these domains is located within the previously described SARS-unique domain, and there is a nucleic acid chaperone-like domain located immediately downstream of the papain-like proteinase domain. We also identified a novel cysteine-coordinated metal ion-binding domain. Analyses of interdomain interactions and provisional functional annotation of the remaining, so-far-uncharacterized domains are presented. Overall, the ensemble of data surveyed here paint a more complete picture of nsp3 as a conserved component of the viral protein processing machinery, which is intimately associated with viral RNA in its role as a virion component.

Mixed culture fermentation studies on the effects of synbiotics on the human intestinal pathogens Campylobacter jejuni and Escherichia coli

Batch and continuous culture anaerobic fermentation systems, inoculated with human faeces, were utilised to investigate the antimicrobial actions of two probiotics, Lactobacillus plantartan 0407, combined with oligofructose and Bifidobacterium bifidum Bb12, combined with a mixture of oligofructose and xylo-oligosaccharides (50:50 w/w) against E coli and Campylobacter jejuni. In batch fermenters, both E coli and C jejuni were inhibited by the synbiotics, even when the culture pH was maintained at around neutral. In continuous culture C jejuni was inhibited but the synbiotic failed to inhibit E coli. Although no definitive answer in addressing the mechanisms underlying antimicrobial activity was derived, results suggested that acetate and lactate directly were conferring antagonistic action, rather than as a result of lowering culture pH. In the course of the study culturing and fluorescent in situ hybridisation (FISH) methodologies for the enumeration of bacterial populations were compared. Bifidobacterial populations were underestimated using plating techniques, suggesting the non-culturability of certain bifidobacterial species. (C) 2003 Elsevier Ltd. All rights reserved.

Testing white line strength in the dairy cow

The tensile strength of 576 pieces of white line horn collected over 6 mo from 14 dairy cows restricted to parity 1 or 2 was tested. None of the cows had ever been lame. Seven cows were randomly assigned to receive 20 mg/d biotin supplementation, and 7 were not supplemented. Hoof horn samples were taken from zones 2 and 3 (the more proximal and distal sites of the abaxial white line) of the medial and lateral claws of both hind feet on d 1 and on 5 further occasions over 6 mo. The samples were analyzed at 100% water saturation. Hoof slivers were notched to ensure that tensile strength was measured specifically across the white line region. The tensile stress at failure was measured in MPa and was adjusted for the cross-sectional area of the notch site. Data were analyzed in a multilevel model, which accounted for the repeated measures within cows. All other variables were entered as fixed effects. In the final model, there was considerable variation in strength over time. Tensile strength was significantly higher in medial compared with lateral claws, and zone 2 was significantly stronger than zone 3. Where the white line was visibly damaged the tensile strength was low. Biotin supplementation did not affect the tensile strength of the white line. Results of this study indicate that damage to the white line impairs its tensile strength and that in horn with no visible abnormality the white line is weaker in the lateral hind claw than the medial and in zone 3 compared with zone 2. The biomechanical strength was lowest at zone 3 of the lateral hind claw, which is the most common site of white line disease lameness in cattle.

Cigarette smokers have decreased lymphocyte and platelet alpha-tocopherol levels and increased excretion of the gamma-tocopherol metabolite gamma-carboxyethyl-hydroxychroman (gamma-CEHC)

Cigarette smoking is associated with increased oxidative stress and increased risk of degenerative disease. As the major lipophilic antioxidant, requirements for vitamin E may be higher in smokers due to increased utilisation. In this observational study we have compared vitamin E status in smokers and non-smokers using a holistic approach by measuring plasma, erythrocyte, lymphocyte and platelet alpha- and gamma-tocopherol, as well as the specific urinary vitamin E metabolites alpha- and gamma-carboxyethylhydroxychroman (CEHC). Fifteen smokers (average age 27 years, smoking time 7.5 years) and non-smokers of comparable age, gender and body mass index (BMI) were recruited. Subjects completed a 7-day food diary and on the final day they provided a 24 h urine collection and a 20 ml blood sample for measurement of urinary vitamin E metabolites and total vitamin E in blood components, respectively. No significant differences were found between plasma and erythrocyte alpha- and gamma-tocopherol in smokers and non-smokers. However, smokers had significantly lower ce-tocopherol (mean +/-SD, 1.34+/-0.31 mumol/g protein compared with 1.94+/-0.54, P = 0.001) and gamma-tocopherol (0.19 +/- 0.04 mumol/g protein compared with 0.26 +/- 0.08, P = 0.026) levels in their lymphocytes, as well as significantly lower (alpha-tocopherol levels in platelets (1.09 +/- 0.49 mumol/g protein compared with 1.60 +/- 0.55, P = 0.014; gamma-tocopherol levels were similar). Interestingly smokers also had significantly higher excretion of the urinary gamma-tocopherol metabolite, gamma-CEHC (0.49 +/- 0.25 mg/g creatinine compared with 0.32 +/- 0.16, P = 0.036) compared to non-smokers, while their (alpha-CEHC (metabolite of a-tocopherol) levels were similar. There was no significant difference between plasma ascorbate, urate and F-2-isoprostane levels. Therefore in this population of cigarette smokers (mean age 27 years, mean smoking duration 7.5 years), alterations to vitamin E status can be observed even without the more characteristic changes to ascorbate and F-2-isoprostanes. We suggest that the measurement of lymphocyte and platelet vitamin E may represent a valuable biomarker of vitamin E status in relation to oxidative stress conditions.

Mixed culture fermentation studies on the effects of synbiotics on the human intestinal pathogens Campylobacter jejuni and Escherichia coli

Batch and continuous culture anaerobic fermentation systems, inoculated with human faeces, were utilised to investigate the antimicrobial actions of two probiotics, Lactobacillus plantartan 0407, combined with oligofructose and Bifidobacterium bifidum Bb12, combined with a mixture of oligofructose and xylo-oligosaccharides (50:50 w/w) against E coli and Campylobacter jejuni. In batch fermenters, both E coli and C jejuni were inhibited by the synbiotics, even when the culture pH was maintained at around neutral. In continuous culture C jejuni was inhibited but the synbiotic failed to inhibit E coli. Although no definitive answer in addressing the mechanisms underlying antimicrobial activity was derived, results suggested that acetate and lactate directly were conferring antagonistic action, rather than as a result of lowering culture pH. In the course of the study culturing and fluorescent in situ hybridisation (FISH) methodologies for the enumeration of bacterial populations were compared. Bifidobacterial populations were underestimated using plating techniques, suggesting the non-culturability of certain bifidobacterial species. (C) 2003 Elsevier Ltd. All rights reserved.

A non-uniform mesh scheme for compressible flow

A non-uniform mesh scheme is presented for the computation of compressible flows governed by the Euler equations of gas dynamics. The scheme is based on flux-difference splitting and represents an extension of a similar scheme designed for uniform meshes. The numerical results demonstrate that little, if any, spurious oscillation occurs as a result of the non-uniformity of the mesh; and importantly, shock speeds are computed correctly.

Crosstalk with insulin and dependence on PI3K/Akt/mTOR rather than MAPK pathways in upregulation of basal growth following long-term oestrogen deprivation in three human breast cancer cell lines

Background: MCF-7, T-47-D, ZR-75-1 human breast cancer cell lines are dependent on oestrogen for growth but can adapt to grow during long-term oestrogen deprivation. This serves as a model for identification of therapeutic targets in endocrine-resistant breast cancer. Methods: An overlooked complication of this model is that it involves more than non-addition of oestrogen, and inadequate attention has been given to separating molecular events associated with each of the culture manipulations. Results: Insulin and oestradiol were shown to protect MCF-7 cells against upregulation of basal growth, demonstrating a crosstalk in the growth adaptation process. Increased phosphorylation of p44/42MAPK and c-Raf reflected removal of insulin from the medium and proliferation of all three cell lines was inhibited to a lesser extent by PD98059 and U0126 following long-term oestrogen/insulin withdrawal, demonstrating a reduced dependence on the MAPK pathway. By contrast, long-term oestrogen/insulin deprivation did not alter levels of phosphorylated Akt and did not alter the dose-response of growth inhibition with LY294002 in any of the three cell lines. The IGF1R inhibitor picropodophyllin inhibited growth of all MCF-7 cells but only in the long-term oestrogen/insulin-deprived cells was this paralleled by reduction in phosphorylated p70S6K, a downstream target of mTOR. Long-term oestrogen/insulin-deprived MCF-7 cells had higher levels of phosphorylated p70S6K and developed increased sensitivity to growth inhibition by rapamycin. Conclusions: The greater sensitivity to growth inhibition by rapamycin in all three cell lines following long-term oestrogen/insulin deprivation suggests rapamycin-based therapies might be more effective in breast cancers with acquired oestrogen resistance. Keywords Akt, breast cancer cells, endocrine resistance, insulin, MAPK, MCF-7 cells, mTOR, oestrogen, oestrogen-deprived, PI3K, picropodophyllin, rapamycin, T-47-D cells, ZR-75-1 cells

Imitation of lateralised body movements: doing it the hard way

Two experiments examined imitation of lateralised body movement sequences presented at six viewing angles (0º, 60º, 120º, 180º, 240º, and 300º rotation relative to the participant’s body). Experiment 1 found that, when participants were instructed simply to ‘‘do what the model does’’, at all viewing angles they produced more actions using the same side of the body as the model (anatomical matches), than actions using the opposite side (anatomical non-matches). In Experiment 2 participants were instructed to produce either anatomical matches or anatomical non-matches of observed actions. When the model was viewed from behind (0º), the anatomically matching group were more accurate than the anatomically non-matching group, but the non-matching group was superior when the model faced the participant (180º and 240º). No reliable differences were observed between groups at 60º, 120º, and 300º. In combination, the results of Experiments 1 and 2 suggest that, when they are confronting a model, people choose to imitate the hard way; they attempt to match observed actions anatomically, in spite of the fact that anatomical matching is more subject to error than anatomical non-matching.

Redefining the outer boundaries of EU Law: the Zambrano, McCarthy and Dereci trilogy

In its three recent rulings in the cases of Zambrano, McCarthy, and Dereci, the Court appears to have been determined to redefine the external boundaries of EU law, in cases involving the family reunification rights of Union citizens.These three judgments can be read as an indication that for Article 20 TFEU to apply, there is no longer a requirement of a cross-border element on the facts of the case, and that it is sufficient if the contested national measure has the effect of ‘depriving citizens of the Union of the genuine enjoyment of the substance’ of their rights (the ‘Zambrano principle’).The cases can, at the same time, also be read as a confirmation that the free movement provisions do – still – require a cross-border element and, in particular, the exercise of inter-State movement, in order to apply. Though the result in these cases has not been entirely unexpected, especially in the aftermath of the Rottmann ruling, it is rather problematic in that, although it is obvious that the Court wishes to redraw the line dividing the national and EU spheres of competence, it does not make it entirely clear where this line now lies and leaves many essential questions unanswered, which will obviously require some time to be resolved. EU lawyers are consequently, once more, left with having to decipher as best as they can the real intentions of the Court in this new line of case-law, which has been further complicated by the fact that what the Court seems to have given with one hand in Zambrano (and before that in Rottmann), has taken it back to a large extent through its rulings in McCarthy and Dereci, which appear to confine the former two cases to their own exceptional facts.6 Moreover, the ‘reverse discrimination Pandora’s box’, the opening of which appears to have been the real target of these references, remains untouched: instead of providing a direct solution to this problem, the Court has chosen to – once again – broaden the scope of the Treaty provisions in order to include within it as many situations as possible and, thus, prevent the emergence of this type of differential treatment on a case-by-case basis.As will be explained, nonetheless, this is by no means an appropriate solution to the reverse discrimination conundrum.

Causal evidence for frontal involvement in memory target maintenance by posterior brain areas during distracter interference of visual working memory

Dorsolateral prefrontal cortex (DLPFC) is recruited during visual working memory (WM) when relevant information must be maintained in the presence of distracting information. The mechanism by which DLPFC might ensure successful maintenance of the contents of WM is, however, unclear; it might enhance neural maintenance of memory targets or suppress processing of distracters. To adjudicate between these possibilities, we applied time-locked transcranial magnetic stimulation (TMS) during functional MRI, an approach that permits causal assessment of a stimulated brain region's influence on connected brain regions, and evaluated how this influence may change under different task conditions. Participants performed a visual WM task requiring retention of visual stimuli (faces or houses) across a delay during which visual distracters could be present or absent. When distracters were present, they were always from the opposite stimulus category, so that targets and distracters were represented in distinct posterior cortical areas. We then measured whether DLPFC-TMS, administered in the delay at the time point when distracters could appear, would modulate posterior regions representing memory targets or distracters. We found that DLPFC-TMS influenced posterior areas only when distracters were present and, critically, that this influence consisted of increased activity in regions representing the current memory targets. DLPFC-TMS did not affect regions representing current distracters. These results provide a new line of causal evidence for a top-down DLPFC-based control mechanism that promotes successful maintenance of relevant information in WM in the presence of distraction.

Characterisation of the intracellular-glutamate decarboxylase system (GAD): analysis of its function, transcription and role in the acid resistance of various strains of Listeria monocytogenes

The glutamate decarboxylase (GAD) system is important for the acid resistance of Listeria monocytogenes. We previously showed that under acidic conditions, glutamate (Glt)/γ-aminobutyrate (GABA) antiport is impaired in minimal media but not in rich ones, like brain heart infusion. Here we demonstrate that this behavior is more complex and it is subject to strain and medium variation. Despite the impaired Glt/GABA antiport, cells accumulate intracellular GABA (GABA(i)) as a standard response against acid in any medium, and this occurs in all strains tested. Since these systems can occur independently of one another, we refer to them as the extracellular (GAD(e)) and intracellular (GAD(i)) systems. We show here that GAD(i) contributes to acid resistance since in a ΔgadD1D2 mutant, reduced GABA(i) accumulation coincided with a 3.2-log-unit reduction in survival at pH 3.0 compared to that of wild-type strain LO28. Among 20 different strains, the GAD(i) system was found to remove 23.11% ± 18.87% of the protons removed by the overall GAD system. Furthermore, the GAD(i) system is activated at milder pH values (4.5 to 5.0) than the GAD(e) system (pH 4.0 to 4.5), suggesting that GAD(i) is the more responsive of the two and the first line of defense against acid. Through functional genomics, we found a major role for GadD2 in the function of GAD(i), while that of GadD1 was minor. Furthermore, the transcription of the gad genes in three common reference strains (10403S, LO28, and EGD-e) during an acid challenge correlated well with their relative acid sensitivity. No transcriptional upregulation of the gadT2D2 operon, which is the most important component of the GAD system, was observed, while gadD3 transcription was the highest among all gad genes in all strains. In this study, we present a revised model for the function of the GAD system and highlight the important role of GAD(i) in the acid resistance of L. monocytogenes.

Could the presumption of innocence protect the guilty?

At criminal trial, we demand that those accused of criminal wrongdoing be presumed innocent until proven guilty beyond any reasonable doubt. What are the moral and/or political grounds of this demand? One popular and natural answer to this question focuses on the moral badness or wrongness of convicting and punishing innocent persons, which I call the direct moral grounding. In this essay, I suggest that this direct moral grounding, if accepted, may well have important ramifications for other areas of the criminal justice process, and in particular those parts in which we (through our legislatures and judges) decide how much punishment to distribute to guilty persons. If, as the direct moral grounding suggests, we should prefer under-punishment to over-punishment under conditions of uncertainty, due to the moral seriousness of errors which inappropriately punish persons, then we should also prefer erring on the side of under-punishment when considering how much to punish those who may justly be punished. Some objections to this line of thinking are considered.

The role of northern Arabian Sea surface temperature biases in CMIP5 model simulations and future projections of Indian summer monsoon rainfall

Many climate models have problems simulating Indian summer monsoon rainfall and its variability, resulting in considerable uncertainty in future projections. Problems may relate to many factors, such as local effects of the formulation of physical parametrisation schemes, while common model biases that develop elsewhere within the climate system may also be important. Here we examine the extent and impact of cold sea surface temperature (SST) biases developing in the northern Arabian Sea in the CMIP5 multi-model ensemble, where such SST biases are shown to be common. Such biases have previously been shown to reduce monsoon rainfall in the Met Office Unified Model (MetUM) by weakening moisture fluxes incident upon India. The Arabian Sea SST biases in CMIP5 models consistently develop in winter, via strengthening of the winter monsoon circulation, and persist into spring and summer. A clear relationship exists between Arabian Sea cold SST bias and weak monsoon rainfall in CMIP5 models, similar to effects in the MetUM. Part of this effect may also relate to other factors, such as forcing of the early monsoon by spring-time excessive equatorial precipitation. Atmosphere-only future time-slice experiments show that Arabian Sea cold SST biases have potential to weaken future monsoon rainfall increases by limiting moisture flux acceleration through non-linearity of the Clausius-Clapeyron relationship. Analysis of CMIP5 model future scenario simulations suggests that, while such effects are likely small compared to other sources of uncertainty, models with large Arabian Sea cold SST biases suppress the range of potential outcomes for changes to future early monsoon rainfall.

Estimation of optimal gravity wave parameters for climate models using data assimilation

There is a current need to constrain the parameters of gravity wave drag (GWD) schemes in climate models using observational information instead of tuning them subjectively. In this work, an inverse technique is developed using data assimilation principles to estimate gravity wave parameters. Because mostGWDschemes assume instantaneous vertical propagation of gravity waves within a column, observations in a single column can be used to formulate a one-dimensional assimilation problem to estimate the unknown parameters. We define a cost function that measures the differences between the unresolved drag inferred from observations (referred to here as the ‘observed’ GWD) and the GWD calculated with a parametrisation scheme. The geometry of the cost function presents some difficulties, including multiple minima and ill-conditioning because of the non-independence of the gravity wave parameters. To overcome these difficulties we propose a genetic algorithm to minimize the cost function, which provides a robust parameter estimation over a broad range of prescribed ‘true’ parameters. When real experiments using an independent estimate of the ‘observed’ GWD are performed, physically unrealistic values of the parameters can result due to the non-independence of the parameters. However, by constraining one of the parameters to lie within a physically realistic range, this degeneracy is broken and the other parameters are also found to lie within physically realistic ranges. This argues for the essential physical self-consistency of the gravity wave scheme. A much better fit to the observed GWD at high latitudes is obtained when the parameters are allowed to vary with latitude. However, a close fit can be obtained either in the upper or the lower part of the profiles, but not in both at the same time. This result is a consequence of assuming an isotropic launch spectrum. The changes of sign in theGWDfound in the tropical lower stratosphere, which are associated with part of the quasi-biennial oscillation forcing, cannot be captured by the parametrisation with optimal parameters.

The place of diversity within history and the challenge of policy and curriculum

This article is a position paper which examines the political and public discourse around the areas of diversity and social cohesion, and history teaching. It examines the nature of these discourses and shows how they are in tension. Although discourse around diversity often has a focus on mutual understanding and finding areas of commonality, the discourse around history often focuses on the need to provide a sense of identity through a national story. By focusing on a discussion about the purposes of history, rather than merely on debates about content, it is suggested that these discourses can be brought more closely into line and produce a more productive line of policy debate.