CO migration in native and mutant myoglobin: atomistic simulations for the understanding of protein function

Molecular dynamics simulations of the events after the photodissociation of CO in the myoglobin mutant L29F in which leucine is replaced by phenylalanine are reported. Using both classical and mixed quantum-classical molecular dynamics calculations, we observed the rapid motion of CO away from the distal heme pocket to other regions of the protein, in agreement with recent experimental results. The experimentally observed and calculated infrared spectra of CO after dissociation are also in good agreement. We compared the results with data from simulations of WT myoglobin. As the time resolution of experimental techniques is increased, theoretical methods and models can be validated at the atomic scale by direct comparison with experiment.

The serialization and publication of 'The return of the native': a new Thomas Hardy letter

This article presents and contextualises a newly-discovered letter by Thomas Hardy, housed in the Chatto & Windus archive at the University of Reading. The letter sheds new light on the publishing history of Hardy's novel 'The return of the native'

Evaluating the intonation of non-native speakers of English using a computerised test battery

This study investigates the intonation of Chinese and Arabic learners of English using the computerized test battery Profiling Elements of Prosody for Speech and Communication (PEPS-C). The aims were to ascertain which aspects of intonation are difficult for these learners, and to determine whether PEPS-C can be used to assess the intonation of adult learners. Although some results were significantly different from native-speaker data, raw scores showed that the learner groups performed well in most tasks, which may indicate that the learners' level is too high for the PEPS-C to be useful. However, the PEPS-C did reveal that Arabic learners performed significantly worse at contrastive stress placement, and Chinese learners performed significantly worse assessing likes and dislikes.

A revision of the South American genus Apuleia (Leguminosae, Cassieae)

Apuleia Mart., a genus of the Leguminosae native to South America, is revised. Species limits within the genus were tested using morphometrics and shape analysis of leaflets and fruits. Morphological evidence indicates that although there is great variation in Apuleia, the genus cannot be reliably separated into different species or infraspecific taxa. Apuleia is monospecific, comprising the single species A. leiocarpa (Vogel) J. F. Macbr.

L1 transfer in the acquisition of manner and path in Spanish by native speakers of English

In this article the authors argue that L1 transfer from English is not only important in the early stages of L2 acquisition of Spanish, but remains influential in later stages if there is not enough positive evidence for the learners to progress in their development (Lefebvre, White, & Jourdan, 2006). The findings are based on analyses of path and manner of movement in stories told by British students of Spanish (N = 68) of three different proficiency levels. Verbs that conflate motion and path, on the one hand, are mastered early, possibly because the existence of Latinate path verbs, such as enter and ascend in English, facilitate their early acquisition by British learners of Spanish. Contrary to the findings of Cadierno (2004) and Cadierno and Ruiz (2006), the encoding of manner, in particular in boundary crossing contexts, seems to pose enormous difficulties, even among students who had been abroad on a placement in a Spanish-speaking country prior to the data collection. An analysis of the frequency of manner verbs in Spanish corpora shows that one of the key reasons why students struggle with manner is that manner verbs are so infrequent in Spanish. The authors claim that scarce positive evidence in the language exposed to and little or no negative evidence are responsible for the long-lasting effect of transfer on the expression of manner.

In vitro gas production and nitrogen degradability of tannin-containing tree fruits in response to incremental levels of polyethylene glycol

This study was designed to determine the response of in vitro fermentation parameters to incremental levels of polyethylene glycol (PEG) when tanniniferous tree fruits (Dichrostachys cinerea, Acacia erioloba, A. erubiscens, A. nilotica and Piliostigma thonningii) were fermented using the Reading Pressure Technique. The trivalent ytterbium precipitable phenolics content of fruit substrates ranged from 175 g/kg DM in A. erubiscens to 607 g/kg DM in A. nilotica, while the soluble condensed tannin content ranged from 0.09 AU550nm/40mg in A. erioloba to 0.52 AU550nm/40 mg in D. cinerea. The ADF was highest in P. thonningii fruits (402 g/kg DM) and lowest in A. nilotica fruits (165 g/kg DM). Increasing the level of PEG caused an exponential rise to a maximum (asymptotic) for cumulative gas production, rate of gas production and nitrogen degradability in all substrates except P. thonningii fruits. Dry matter degradability for fruits containing higher levels of soluble condensed tannins (D. cinerea and P. thonningii), showed little response to incremental levels of PEG after incubation for 24 h. The minimum levels of PEG required to maximize in vitro fermentation of tree fruits was found to be 200 mg PEG/g DM of sample for all tree species except A. erubiscens fruits, which required 100 mg PEG/g DM sample. The study provides evidence that PEG levels lower than 1 g/g DM sample can be used for in vitro tannin bioassays to reduce the cost of evaluating non-conventional tanniniferous feedstuffs used in developing countries in the tropics and subtopics. The use of in vitro nitrogen degradability in place of the favoured dry matter degradability improved the accuracy of PEG as a diagnostic tool for tannins in in vitro fermentation systems.

Investigating the phytotoxicity of the graminicide fluazifop-P-butyl against native UK wildflower species

BACKGROUND: The selective graminicide fluazifop-P-butyl is used for the control of grass weeds in dicotyledonous crops, and commonly applied in amenity areas to reduce grass productivity and promote wildflower establishment. However, evidence suggests that fluazifop-P-butylmight also have phytotoxic effects on somenon-target plants. This study investigates the effects of fluazifop-P-butyl on the emergence, phytotoxicity and above-ground biomass of nine perennial wildflower species and two grass species, following pre- and post-emergent applications at half, full and double label rates in a series of glasshouse experiments. RESULTS: While pre- and post-emergent applications of fluazifop-P-butyl caused reductions in seedling emergence and increased phytotoxicity on native wildflower and grass species, these effects were temporary for the majority of wildflower species tested, and generally only occurred at the double application rate. No differences in biomass were observed at any of the rates, suggesting good selectivity and no long-term effects of fluazifop-P-butyl application on the wildflower species from either pre-emergent or post-emergent applications. CONCLUSION: These results have direct relevance to the management of amenity areas for biodiversity, as they confirm the suitability of these wildflower species for inclusion in seed mixtures where fluazifop-P-butyl is to be applied to control grass productivity.

Genetic diversity of red-fleshed apples (Malus)

Anthocyanins are flavonoid pigments imparting red, blue, or purple pigmentation to fruits, flowers and foliage. These compounds are powerful antioxidants in vitro, and are widely believed to contribute to human health. The fruit of the domestic apple (Malus x domestica) is a popular and important source of nutrients, and is considered one of the top ‘functional foods’—those foods that have inherent health-promoting benefits beyond basic nutritional value. The pigmentation of typical red apple fruits results from accumulation of anthocyanin in the skin. However, numerous genotypes of Malus are known that synthesize anthocyanin in additional fruit tissues including the core and cortex (flesh). Red-fleshed apple genotypes are an attractive starting point for development of novel varieties for consumption and nutraceutical use through traditional breeding and biotechnology. However, cultivar development is limited by lack of characterization of the diversity of genetic backgrounds showing this trait. We identified and cataloged red-fleshed apple genotypes from four Malus diversity collections representing over 3,000 accessions including domestic cultivars, wild species, and named hybrids. We found a striking range of flesh color intensity and pattern among accessions, including those carrying the MYB10 R 6 allele conferring ectopic expression of a key transcriptional regulator of anthocyanin biosynthesis. Although MYB10 R 6 was strongly associated with red-fleshed fruit among genotypes, this allele was neither sufficient nor required for this trait in all genotypes. Nearly all red-fleshed accessions tested could be traced back to ‘Niedzwetzkyana’, a presumed natural form of M. sieversii native to central Asia.

Prediction and functional analysis of native disorder in proteins from the Three Kingdoms of Life

An automatic method for recognizing natively disordered regions from amino acid sequence is described and benchmarked against predictors that were assessed at the latest critical assessment of techniques for protein structure prediction (CASP) experiment. The method attains a Wilcoxon score of 90.0, which represents a statistically significant improvement on the methods evaluated on the same targets at CASP. The classifier, DISOPRED2, was used to estimate the frequency of native disorder in several representative genomes from the three kingdoms of life. Putative, long (>30 residue) disordered segments are found to occur in 2.0% of archaean, 4.2% of eubacterial and 33.0% of eukaryotic proteins. The function of proteins with long predicted regions of disorder was investigated using the gene ontology annotations supplied with the Saccharomyces genome database. The analysis of the yeast proteome suggests that proteins containing disorder are often located in the cell nucleus and are involved in the regulation of transcription and cell signalling. The results also indicate that native disorder is associated with the molecular functions of kinase activity and nucleic acid binding.

Is a native rodent competitively dominant over an invasive rodent in lowland agro-forest habitat of the Philippines?

In the lowland agro-forest of the Sierra Madre Biodiversity Corridor (SMBC), it is considered that a native rodent species, Rattus everetti is competitively dominant over an invasive pest species, Rattus tanezumi. The main aim of this study was to assess the response of R. tanezumi following short term removal of R. everetti. We tested this experimentally by trapping and removing R. everetti from two treatment sites in agro-forest habitat on three occasions over three consecutive months. This was followed by three months of non-removal trapping. Two non-treatment sites were trapped for comparison. Following R. everetti removal, R. everetti individuals rapidly immigrated into the treatment sites and a significantly higher proportion of R. tanezumi females were in breeding condition in the treatment sites than in the non-treatment sites. The results from this study provide evidence of competition between native and invasive rodent species in complex agro-ecosystems. We were also able to demonstrate that R. everetti populations are able to recover rapidly from the non-target effects of short-term lethal control in and around agro-forest.

Impact of the quantity and flavonoid content of fruits and vegetables on markers of intake in adults with an increased risk of cardiovascular disease: the FLAVURS Trial

Purpose Limited robust randomised controlled trials investigating fruit and vegetable (F&V) intake in people at risk of cardiovascular disease (CVD) exist. We aimed to design and validate a dietary strategy of increasing flavonoid-rich versus flavonoid-poor F&V consumption on nutrient biomarker profile. Methods A parallel, randomised, controlled, dose–response dietary intervention study. Participants with a CVD relative risk of 1.5 assessed by risk scores were randomly assigned to one of the 3 groups: habitual (control, CT), high-flavonoid (HF) or low-flavonoid (LF) diets. While the CT group (n = 57) consumed their habitual diet throughout, the HF (n = 58) and LF (n = 59) groups sequentially increased their daily F&V intake by an additional 2, 4 and 6 portions for 6-week periods during the 18-week study. Results Compliance to target numbers and types of F&V was broadly met and verified by dietary records, and plasma and urinary biomarkers. Mean (±SEM) number of F&V portions/day consumed by the HF and LF groups at baseline (3.8 ± 0.3 and 3.4 ± 0.3), 6 weeks (6.3 ± 0.4 and 5.8 ± 0.3), 12 weeks (7.0 ± 0.3 and 6.8 ± 0.3) and 18 weeks (7.6 ± 0.4 and 8.1 ± 0.4), respectively, was similar at baseline yet higher than the CT group (3.9 ± 0.3, 4.3 ± 0.3, 4.6 ± 0.4, 4.5 ± 0.3) (P = 0.015). There was a dose-dependent increase in dietary and urinary flavonoids in the HF group, with no change in other groups (P = 0.0001). Significantly higher dietary intakes of folate (P = 0.035), non-starch polysaccharides (P = 0.001), vitamin C (P = 0.0001) and carotenoids (P = 0.0001) were observed in both intervention groups compared with CT, which were broadly supported by nutrient biomarker analysis. Conclusions The success of improving nutrient profile by active encouragement of F&V intake in an intervention study implies the need for a more hands-on public health approach.