Semi-dwarfing (Rht-B1b) improves nitrogen-use efficiency in wheat, but not at economically optimal levels of nitrogen availability

A UK field experiment compared a complete factorial combination of three backgrounds (cvs Mercia, Maris Huntsman and Maris Widgeon), three alleles at the Rht-B1 locus as Near Isogenic Lines (NILs: rht-B1a (tall), Rht-B1b (semi-dwarf), Rht-B1c (severe dwarf)) and four nitrogen (N) fertilizer application rates (0, 100, 200 and 350 kg N/ha). Linear+exponential functions were fitted to grain yield (GY) and nitrogen-use efficiency (NUE; GY/available N) responses to N rate. Averaged over N rate and background Rht-B1b conferred significantly (P<0.05) greater GY, NUE, N uptake efficiency (NUpE; N in above ground crop / available N) and N utilization efficiency (NUtEg; GY / N in above ground crop) compared with rht-B1a and Rht-B1c. However the economically optimal N rate (Nopt) for N:grain price ratios of 3.5:1 to 10:1 were also greater for Rht-B1b, and because NUE, NUpE and NUtE all declined with N rate, Rht-Blb failed to increase NUE or its components at Nopt. The adoption of semi-dwarf lines in temperate and humid regions, and the greater N rates that such adoption justifies economically, greatly increases land-use efficiency, but not necessarily, NUE.

Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

‘Scripture its own interpreter’: Mary Martha Sherwood, the Bible and female autobiography

This is a reading of the work of Mary Martha Sherwood, the Victorian Evangelist and Children’s Author (and pupil at the Abbey School, Reading). Based upon research on Sherwood’s private correspondences and diary conducted at UCLA with the aid of a Mitzi Myers (this before my arrival at Reading), the essay offers a radical reinterpretation of her work. Previously understood in terms of a rigid, if self-contradictory and ‘anxious’, Evangelism, the essay reads the diary through Sherwood’s little known Biblical scholarship. Through this I argue that Sherwood grants her own writing the status of Biblical truth precisely because of its contradictions and ‘anxiety’.

Wind-driven mixing below the oceanic mixed layer

This study describes the turbulent processes in the upper ocean boundary layer forced by a constant surface stress in the absence of the Coriolis force using large-eddy simulation. The boundary layer that develops has a two-layer structure, a well-mixed layer above a stratified shear layer. The depth of the mixed layer is approximately constant, whereas the depth of the shear layer increases with time. The turbulent momentum flux varies approximately linearly from the surface to the base of the shear layer. There is a maximum in the production of turbulence through shear at the base of the mixed layer. The magnitude of the shear production increases with time. The increase is mainly a result of the increase in the turbulent momentum flux at the base of the mixed layer due to the increase in the depth of the boundary layer. The length scale for the shear turbulence is the boundary layer depth. A simple scaling is proposed for the magnitude of the shear production that depends on the surface forcing and the average mixed layer current. The scaling can be interpreted in terms of the divergence of a mean kinetic energy flux. A simple bulk model of the boundary layer is developed to obtain equations describing the variation of the mixed layer and boundary layer depths with time. The model shows that the rate at which the boundary layer deepens does not depend on the stratification of the thermocline. The bulk model shows that the variation in the mixed layer depth is small as long as the surface buoyancy flux is small.

Restoring species-rich grassland: principles and techniques

Grassland restoration is the dominant activity funded by agri-environment schemes (AES). However, the re-instatement of biodiversity and ecosystem services is limited by a number of severe abiotic and biotic constraints resulting from previous agricultural management. These appear to be less severe on ex-arable sites compared with permanent grassland. We report findings of a large research programme into practical solutions to these constraints. The key abiotic constraint was high residual soil fertility, particularly phosphorus. This can most easily be addressed by targeting of sites of low nutrient status. The chief biotic constraints were lack of propagules of desirable species and suitable sites for their establishment. Addition of seed mixtures or green hay to gaps created by either mechanical disturbance or herbicide was the most effective means of overcoming these factors. Finally, manipulation of biotic interactions, including hemiparasitic plants to reduce competition from grasses and control of mollusc herbivory of sown species, significantly improved the effectiveness of these techniques.

Plant-soil interactions and grassland diversity restoration

Restoration schemes aimed at enhancing plant species diversity of improved agricultural grassland have been a key feature of agri-environmental policy since the mid 1980s. Allied to this has been much research aimed at providing policy makers with guidelines on how best to manage grassland to restore botanical diversity. This research includes long-term studies of the consequences for grassland diversity of management techniques such as different hay cut dates, fertiliser additions, seed introductions and grazing regimes. Studies have also explored the role of introductions of Rhinanthus minor into species-poor swards to debilitate competitive grasses. While these studies have been successful in identifying some management features that control plant species diversity in agricultural grassland, they have taken a largely aboveground perspective on plant community dynamics.

Limiting factors in the restoration of grassland insects

Grasslands restoration is a key management tool contributing to the long-term maintenance of insect populations, providing functional connectivity and mitigating against extinction debt across landscapes. As knowledge of grassland insect communities is limited, the lag between the initiation of restoration and the ability of these new habitats to contribute to the successful enhancement of native biodiversity is unclear. Using two long term data sets, we investigate differences in successional trajectories during the establishment of butterfly (11 years) and phytophagous beetle (13 years) communities during the recreation of calcareous grassland. Overall restoration success was higher for the butterflies than the beetles. However, both shared a general pattern of rapidly increasing restoration success over the first five years, awhich approached an asymptote after c. 10 years. The use of pro-active grassland restoration to mitigate against future environmental change therefore needs to account for such time lag if the value of these habitats is to be fully realised.

Dietary, lifestyle and clinico-pathological factors associated with APC mutations and promoter methylation in colorectal cancers from the EPIC-Norfolk Study

The tumour suppressor APC is the most commonly altered gene in colorectal cancer (CRC). Genetic and epigenetic alterations of APC may therefore be associated with dietary and lifestyle risk factors for CRC. Analysis of APC mutations in the extended mutation cluster region (codons 1276-1556) and APC promoter 1A methylation was performed on 185 archival CRC samples collected from participants of the European Prospective Investigation into Cancer (EPIC)-Norfolk Study, with the aim of relating these to high quality seven-day dietary and lifestyle data collected prospectively. Truncating APC mutations (APC+) and promoter 1A methylation (PM+) were identified in 43% and 23% of CRCs analysed, respectively. Distal CRCs were more likely than proximal CRCs to be APC+ or PM+ (P = 0.04). APC+ CRCs were more likely to be moderately/well differentiated and microsatellite stable than APC- CRCs (P = 0.05 and 0.03). APC+ CRC cases consumed more alcohol than their counterparts (P = 0.01) and PM+ CRC cases consumed lower levels of folate and fibre (P = 0.01 and 0.004). APC+ or PM+ CRC cases consumedhigher levels of processed meat and iron from red meat and red meat products (P=0.007 and 0.006). Specifically, CRC cases harbouring GC to AT transition mutations consumed higher levels of processed meat (35 versus 24 g/day, P = 0.04) and iron from red meat and red meat products (0.8 versus 0.6 mg/day, P = 0.05). In a logistic regression model adjusted for age, sex and cigarette smoking status, each 19g/day (1SD) increment increase in processed meat consumption was associated with cases with GC to AT mutations (OR 1.68, 95% CI 1.03-2.75). In conclusion, APC+ and PM+ CRCs may be influenced by diet and GC to AT mutations in APC are associated with processed meat consumption, suggesting a mechanistic link with dietary alkylating agents, such as N-nitroso compounds.

Use of miniaturized protein arrays for Escherichia coli O serotyping

Serological typing of Escherichia coli O antigens is a well-established method used for differentiation and identification of O serotypes commonly associated with disease. In this feasibility study, we have developed a novel somatic antibody-based miniaturized microarray chip, using 17 antisera, which can be used to detect bound whole-cell E. coli antigen with its corresponding immobilized antibody, to assess the feasibility of this approach. The chip was tested using the related 17 control strains, and the O types found by the microarray chip showed 100% correlation with the O types found by conventional typing. A blind trial was performed in which 100 E. coli isolates that had been O serotyped previously by the conventional assay were tested by the array approach. Overall, the O serotypes of 88% of isolates were correctly identified by the microarray method. For several isolates, ambiguity of O-type designation by microarray arose due to increased sensitivity of this method, allowing signal intensities of cross-reactions to be quantified. Investigation of discrepancies between conventional and microarray O serotyping indicated that some isolates upon storage had become untypeable and, therefore, gave poor signal intensity when tested by the microarray or retested by conventional means. For all 20 serotype O26 and O157 isolates, the apparent discrepancy in O serotyping was analyzed further by a third independent test, which confirmed the microarray results. Therefore, the use of miniaturized protein arrays increases the speed and efficiency of O serotyping in a cost-effective manner, and these preliminary findings suggest the microarray approach may have a higher accuracy than those of traditional O-serotyping methods.