Enhanced phosphopeptide isolation by Fe(III)-IMAC using 1,1,1,3,3,3-hexafluoroisopropanol

IMAC can be used to selectively enrich phosphopeptides from complex peptide mixtures, but co-retention of acidic peptides together with the failure to retain some phosphopeptides restricts the general utility of the method. In this study Fe(III)-IMAC was qualitatively and quantitatively assessed using a panel of phosphopeptides, both synthetic and derived from proteolysis of known phosphoproteins, to identify the causes of success and failure in the application of this technique. Here we demonstrate that, as expected, peptides with a more acidic amino acid content are generally more efficiently purified and detected by MALDI-MS after Fe(III)-IMAC than those with a more basic content. Modulating the loading buffer used for Fe(III)-IMAC significantly affects phosphopeptide binding and suggests that conformational factors that lead to steric hindrance and reduced accessibility to the phosphate are important. The use of 1,1,1,3,3,3-hexa-fluoroisopropanol is shown here to significantly improve Fe(III)-IMAC enrichment and subsequent detection of phosphopeptides by MALDI-MS.

Description of Enterococcus canis sp nov from dogs and reclassification of Enterococcus porcinus Teixeira et al. 2001 as a junior synonym of Enterococcus villorum Vancanneyt et al. 2001

Strains from anal swabs and chronic otitis externa in dogs were shown to be phylogenetically related to the Enterococcus faecium species group. They shared a number of phenotypic characteristics with these species, but they could be easily differentiated by biochemical reactions. In addition, the canine strains were unusual in their nearly complete failure to grow on sodium azide-containing enterococci-selective media and in their Voges-Proskauer reactions (usually negative). By using 16S rRNA sequencing and DNA-DNA hybridization of representative strains, as well as tDNA interspacer gene PCR and SDS-PAGE of whole-cell proteins, the group of canine strains was shown to constitute a novel enterococcal species. The name Enterococcus canis sp. nov. is proposed for this species, with LMG 12316(T) (= CCUG 46666(T)) as the type strain. Concurrently, the taxonomic situation and nomenclatural position of Enterococcus porcinus were investigated. As no phenotypic or genotypic differences were found between this species and Enterococcus villorum, the name E. porcinus is considered to be a junior synonym of E. villorum.

Deficient acquisition and consolidation: intertrial free recall performance in Alzheimer's disease and mild cognitive impairment

Previous research demonstrates that dementia of the Alzheimer type (DAT) is characterised by deficits of episodic memory, especially in the acquisition of new material. As well as this deficit in acquisition, some researchers have also argued for a deficit in consolidation in DAT. We examined acquisition and consolidation by measuring the intertrial gained and lost access in DAT, Mild Cognitive Impairment (MCI) and controls. We report findings from a study of clinical data based on assessment of patients using three free recall trials of a word list. We found that both DAT and MCI groups showed a deficit in acquisition and consolidation of items between trials relative to controls. Moreover, the DAT group was significantly impaired relative to the MCI group for both acquisition and consolidation. Correlations within each group showed that there were strong relationships between intertrial measures and standard measures of memory function. Importantly in no group was there a significant correlation between our measures of acquisition and consolidation: we argue that these measures reflect different underlying processes, and the failure to consolidate in DAT and MCI is not related to the deficit in acquisition. Finally, we showed strong correlations between our measure and dementia severity, suggesting that acquisition and consolidation both get worse as the dementia progresses.

Pronominal and anaphoric reference in agrammatism

Subjects with Broca's aphasia have been shown to display difficulties in on-line and off-line tasks involving personal pronouns and reflexives. Off-line tasks have indicated more errors with pronouns than with reflexives while the reverse has been found in on-line studies. In the present off-line study, the comprehension of sentences containing personal pronouns and reflexives is examined in a group of 10 agrammatic participants. Results indicate that subjects had difficulties with both pronouns and reflexives, particularly with reflexives in sentences that contained a quantificational antecedent, as well as with pronouns in exceptional case marking constructions. It is argued that the low performance that subjects exhibited as a group in pronouns and reflexives indicates two distinct impairments, one that concerns coreference and one that concerns A-dependencies, the latter being a manifestation of a general processing failure to link positions. Poor performance on exceptional case marking constructions compared to simple transitive sentences is claimed to be interpreted within theories for reference assignment that distinguish between the two sentence types. (c) 2007 Elsevier Ltd. All rights reserved.

A controlled trial of sip-feed supplements in elderly orthopaedic patients

The potential nutritional and clinical benefits of sip-feed supplements were investigated by means of a controlled trial in elderly female patients admitted for orthopaedic surgery. A nutritional risk assessment procedure (Nutritional Risk Questionnaire, NRQ) was used to identify patients who might benefit from supplementation. Patients identified as high risk who did not receive supplements showed significant losses in triceps skinfold thickness (TSF) and mid-upper arm muscle circumference (MUAMC) measurements during hospitalization. Such changes were not observed in high-risk supplemented patients, but significant losses of MUAMC were also recorded in a group of patients who failed to comply with the supplement. No differences in biochemical parameters, muscle function, or clinical outcome were observed between supplemented and unsupplemented and non-compliant patients. The problems of poor compliance to sip-feed supplements and failure to observe clinical benefit in supplemented patients are discussed.

Role of rpoS in the Development of Cell Envelope Resilience and Pressure Resistance in Stationary-Phase Escherichia coli

This work investigated the role of rpoS in the development of increased cell envelope resilience and enhanced pressure resistance in stationary phase cells of Escherichia coli. Loss of both colony-forming ability and membrane integrity, measured as uptake of propidium iodide (PI), occurred at lower pressures in E. coli BW3709 (rpoS) than in the parental strain (BW2952). The rpoS mutant also released much higher concentrations of protein under pressure than the parent. We propose that RpoS-regulated functions are responsible for the increase in membrane resilience as cells enter stationary phase and that this plays a major role in the development of pressure resistance. Strains from the Keio collection with mutations in two RpoS-regulated genes, cfa (cyclopropane fatty acyl phospholipid synthase) and osmB (outer membrane lipoprotein), were significantly more pressure-sensitive and took up more PI than the parent strains with cfa having the greatest effect. Mutations in the bolA morphogene and other RpoS-regulated lipoprotein genes (osmC, osmE, osmY and ybaY) had no effect on pressure resistance. The cytoplasmic membranes of the rpoS mutant failed to reseal after pressure treatment and strains with mutations in osmB and nlpI (new lipoprotein) were also somewhat impaired in the ability to reseal their membranes. The cfa mutant, though pressure-sensitive, was unaffected in membrane resealing implying that the initial transient permeabilization event is critical for loss of viability rather than the failure to reseal. The enhanced pressure sensitivity of polA, recA and xthA mutants suggested that DNA may be a target of oxidative stress in pressure-treated cells.

Entre moralité et politique: l’éducation de Louis XV et la question de l’instruction financière du prince sous l’Ancien Régime

Studies on princely education rarely focus on the training received by future kings to perform one of their key functions – supervising the finances of the monarchy. Failure to address this issue is all the more surprising than one of the major consequences of Louis XIV’s coronation was to grant the king the direction of finances until the French Revolution, thus raising the issue of the financial education of the prince. Based on a largely unpublished body of primary sources, especially several manuscripts specifically written for the financial education of Louis XV and princes in the XVIIIth century, this article explores the teaching approaches and programme of a highly technical nature that the king’s tutors considered essential to the monarch’s duties.

The death of John Stuart Mill

This article surveys the fiercely contested posthumous assessments of John Stuart Mill in the newspaper and periodical press, in the months following his death in May 1873, and elicits the broader intellectual context. Judgements made in the immediate wake of Mill's death influence biographers and historians to this day and provide an illuminating aperture into the politics and shifting ideological forces of the period. The article considers how Mill's failure to control his posthumous reputation demonstrates both the inextricable intertwining of politics and character in the 1870s, and the difficulties his allies faced. In particular, it shows the sharp division between Mill's middle and working class admirers; the use of James Mill's name as a rebuke to his son; the redefinition of Malthusianism in the 1870s; and how publication of Mill's Autobiography damaged his reputation. Finally, the article considers the relative absence of both theological and Darwinian critiques of Mill.

Motivation in second language acquisition in Chinese research students in the UK

The present study sets out to examine motivation to learn English by Chinese research students in an informal setting. Data were collected, using semi-structured interviews, from four research students at two points in time during their first year in the UK. The main findings are: they believed that learning English was important; their main goal orientations were instrumental and extrinsic; they set learning goals and persisted to attain them; they valued their current learning environment in general and saw it as supportive of their goals; they held both positive and negative attitudes towards the British, which had differential effects on their motivation; their self-perceived support seemed to have a positive impact on their motivation and the development of self-confidence; they tended to attribute their success to stable causes such as the environment and failure to unstable but controllable causes such as effort. It is concluded that qualitative data of this kind may complement insights from quantitative research. Implications for target country institutions in the provision of support are discussed.

British railways and the challenge from road haulage: 1919-39

Interwar Britain witnessed the rapid rise of road transport as a serious competitor to the railways. This article examines road–rail competition for freight traffic. It demonstrates that, contrary to previous accounts—which have been highly critical of the railway companies—their failure to prevent rapid loss of traffic to the roads was the inevitable consequence of the regulatory framework under which the railways had been returned to private control in 1921. Given the constraints imposed by this framework, price competition with road hauliers would have further depressed railway company profits. Railway policy thus concentrated on pressing for a revision of the legislative framework governing road–rail competition.

Elevated atmospheric carbon dioxide impairs the performance of root-feeding vine weevils by modifying root growth and secondary metabolites

Predicting how insect crop pests will respond to global climate change is an important part of increasing crop production for future food security, and will increasingly rely on empirically based evidence. The effects of atmospheric composition, especially elevated carbon dioxide (eCO(2)), on insect herbivores have been well studied, but this research has focussed almost exclusively on aboveground insects. However, responses of root-feeding insects to eCO(2) are unlikely to mirror these trends because of fundamental differences between aboveground and belowground habitats. Moreover, changes in secondary metabolites and defensive responses to insect attack under eCO(2) conditions are largely unexplored for root herbivore interactions. This study investigated how eCO(2) (700 mu mol mol-1) affected a root-feeding herbivore via changes to plant growth and concentrations of carbon (C), nitrogen (N) and phenolics. This study used the root-feeding vine weevil, Otiorhynchus sulcatus and the perennial crop, Ribes nigrum. Weevil populations decreased by 33% and body mass decreased by 23% (from 7.2 to 5.4 mg) in eCO(2). Root biomass decreased by 16% in eCO(2), which was strongly correlated with weevil performance. While root N concentrations fell by 8%, there were no significant effects of eCO(2) on root C and N concentrations. Weevils caused a sink in plants, resulting in 8-12% decreases in leaf C concentration following herbivory. There was an interactive effect of CO(2) and root herbivory on root phenolic concentrations, whereby weevils induced an increase at ambient CO(2), suggestive of defensive response, but caused a decrease under eCO(2). Contrary to predictions, there was a positive relationship between root phenolics and weevil performance. We conclude that impaired root-growth underpinned the negative effects of eCO(2) on vine weevils and speculate that the plant's failure to mount a defensive response at eCO(2) may have intensified these negative effects.

The effect of nonlinearity in CO2 heating rates on the attribution of stratospheric ozone and temperature changes

An analysis of the attribution of past and future changes in stratospheric ozone and temperature to anthropogenic forcings is presented. The analysis is an extension of the study of Shepherd and Jonsson (2008) who analyzed chemistry-climate simulations from the Canadian Middle Atmosphere Model (CMAM) and attributed both past and future changes to changes in the external forcings, i.e. the abundances of ozone-depleting substances (ODS) and well-mixed greenhouse gases. The current study is based on a new CMAM dataset and includes two important changes. First, we account for the nonlinear radiative response to changes in CO2. It is shown that over centennial time scales the radiative response in the upper stratosphere to CO2 changes is significantly nonlinear and that failure to account for this effect leads to a significant error in the attribution. To our knowledge this nonlinearity has not been considered before in attribution analysis, including multiple linear regression studies. For the regression analysis presented here the nonlinearity was taken into account by using CO2 heating rate, rather than CO2 abundance, as the explanatory variable. This approach yields considerable corrections to the results of the previous study and can be recommended to other researchers. Second, an error in the way the CO2 forcing changes are implemented in the CMAM was corrected, which significantly affects the results for the recent past. As the radiation scheme, based on Fomichev et al. (1998), is used in several other models we provide some description of the problem and how it was fixed.

Natural disaster accounting bias and its equivalence across genetic resource stocks

Two sources of bias arise in conventional loss predictions in the wake of natural disasters. One source of bias stems from neglect of accounting for animal genetic resource loss. A second source of bias stems from failure to identify, in addition to the direct effects of such loss, the indirect effects arising from implications impacting animal-human interactions. We argue that, in some contexts, the magnitude of bias imputed by neglecting animal genetic resource stocks is substantial. We show, in addition, and contrary to popular belief, that the biases attributable to losses in distinct genetic resource stocks are very likely to be the same. We derive the formal equivalence across the distinct resource stocks by deriving an envelope result in a model that forms the mainstay of enquiry in subsistence farming and we validate the theory, empirically, in a World-Society-for-the-Protection-of-Animals application

Probabilistic physically-based cloud screening of satellite infra-red imagery for operational sea surface temperature retrieval

We propose and demonstrate a fully probabilistic (Bayesian) approach to the detection of cloudy pixels in thermal infrared (TIR) imagery observed from satellite over oceans. Using this approach, we show how to exploit the prior information and the fast forward modelling capability that are typically available in the operational context to obtain improved cloud detection. The probability of clear sky for each pixel is estimated by applying Bayes' theorem, and we describe how to apply Bayes' theorem to this problem in general terms. Joint probability density functions (PDFs) of the observations in the TIR channels are needed; the PDFs for clear conditions are calculable from forward modelling and those for cloudy conditions have been obtained empirically. Using analysis fields from numerical weather prediction as prior information, we apply the approach to imagery representative of imagers on polar-orbiting platforms. In comparison with the established cloud-screening scheme, the new technique decreases both the rate of failure to detect cloud contamination and the false-alarm rate by one quarter. The rate of occurrence of cloud-screening-related errors of >1 K in area-averaged SSTs is reduced by 83%. Copyright © 2005 Royal Meteorological Society.

What should we expect of a liberal explanatory theory?

One of the most problematic aspects of the ‘Harvard School’ of liberal international theory is its failure to fulfil its own methodological ideals. Although Harvard School liberals subscribe to a nomothetic model of explanation, in practice they employ their theories as heuristic resources. Given this practice, we should expect them neither to develop candidate causal generalizations nor to be value-neutral: their explanatory insights are underpinned by value-laden choices about which questions to address and what concepts to employ. A key question for liberal theorists, therefore, is how a theory may be simultaneously explanatory and value-oriented. The difficulties inherent in resolving this problem are manifested in Ikenberry’s writing: whilst his work on constitutionalism in international politics partially fulfils the requirements of a more satisfactory liberal explanatory theory, his recent attempts to develop prescriptions for US foreign policy reproduce, in a new form, key failings of Harvard School realism.