DichroMatch: a website for similarity searching of circular dichroism spectra

Circular dichroism (CD) spectroscopy is a widely used method for examining the structure, folding and conformational changes of proteins. A new online CD analysis server (DichroMatch) has been developed for identifying proteins with similar spectral characteristics by detecting possible structurally and functionally related proteins and homologues. DichroMatch includes six different methods for determining the spectral nearest neighbours to a query protein spectrum and provides metrics of how similar these spectra are and, if corresponding crystal structures are available for the closest matched proteins, information on their secondary structures and fold classifications. By default, DichroMatch uses all the entries in the Protein Circular Dichroism Data Bank (PCDDB) for its comparison set, providing the broadest range of publicly available protein spectra to match with the unknown protein. Alternatively, users can download or create their own specialized data sets, thereby enabling comparisons between the structures of related proteins such as wild-type versus mutants or homologues or a series of spectra of the same protein under different conditions. The DichroMatch server is freely available at http://dichromatch.cryst.bbk.ac.uk

The effects of organic farming on the soil physical environment

The aim of this research was to investigate the effects of organic farming practices on the development of soil physical properties, and in particular, soil structure in comparison with conventional agricultural management. The soil structure of organically and conventionally managed soils at one site was compared in a quantitative manner at different scales of observations using image analysis. Key soil physical and chemical properties were measured as well as the pore fractal geometry to characterise pore roughness. Organically managed soils had higher organic matter content and provided a more stable soil structure than conventionally managed soils. The higher porosity (%) at the macroscale in soil under conventional management was due to fewer larger pores while mesoand microscale porosity was found to be greater under organic management. Organically managed soils typically provided spatially well distributed pores of all sizes and of greater roughness compared to those under conventional management. These variations in the soil physical environment are likely to impact significantly on the performance of these soils for a number of key processes such as crop establishment and water availabilit

Optimal control of organic matter applications

Organic matter amendments appear to increase yield, but need to be sustained, as yield decreases when amendments cease. Here we mathematically devise optimal strategies for organic matter applications that take account of how quickly, in years of application, yields build up with amendments and how long these benefits persist. The empirical idea of a nutrient response curve is used and extended to include more than a single nutrient input as well as the effect of yield-enhancing factors such as organic matter that endure for more than one year. Nonlinear regression is used for the selection and the parameter identification for a reciprocal response curve working with a dataset from Rothamsted’s Woburn organic manuring long term experiment. Such a response curve is then treated analytically to develop economically optimum applications over a period of time. A simple static case is developed first and is shown to be equivalent to the well-known break-even ratio (BER) used in nitrogen fertiliser guidance by the Agricultural and Horticultural Development Board in the UK. The mathematical technique of optimal control is then employed to deduce dynamic strategies where the application of an amendment may change from year to year and for different time frames. Because this empirical modelling methodology can appear complex, we infer a rule-of-thumb for an equilibrium level of yield-enhancement rather like the equilibrium level of organic carbon that builds up over several years. This yield-enhancing power of organic matter is somewhat variable and probably does not persist in soil for as long as the organic matter from which it derives. It appears beneficial to apply amendments at a constant rate for much of the time-frame of interest but to begin with a large application to raise the fertility to the yield-enhancement equilibrium. After a transition year with reduced amendments, applications of organic matter are stopped for the final five years with the example amendment studied, farmyard manure. These conclusions depend on the persistence of the yield-enhancing power of organic matter in soil associated with the soil organic carbon kinetics

The Infrared Massive Stellar Content of M83

We present an analysis of archival Spitzer images and new ground-based and Hubble Space Telescope (HST) near-infrared (IR) and optical images of the field of M83 with the goal of identifying rare, dusty, evolved massive stars. We present point source catalogs consisting of 3778 objects from $Spitzer$ Infrared Array Camera (IRAC) Band 1 (3.6 $\mu$m) and Band 2 (4.5 $\mu$m), and 975 objects identified in Magellan 6.5m FourStar near-IR $J$ and $K_{\rm s}$ images. A combined catalog of coordinate matched near- and mid-IR point sources yields 221 objects in the field of M83. Using this photometry we identify 185 massive evolved stellar candidates based on their location in color-magnitude and color-color diagrams. We estimate the background contamination to our stellar candidate lists and further classify candidates based on their appearance in $HST$ Wide Field Camera 3 (WFC3) observations of M83. We find 49 strong candidates for massive stars which are very promising objects for spectroscopic follow-up. Based on their location in a $B-V$ versus $V-I$ diagram, we expect at least 24, or roughly 50%, to be confirmed as red supergiants.Comment: 32 pages, 23 figures, accepted for publication in A&

Is it possible to increase the sustainability of arable and ruminant agriculture by reducing inputs?

Until recently, agricultural production was optimised almost exclusively for profit but now farming is under pressure to meet environmental targets. A method is presented and applied for optimising the sustainability of agricultural production systems in terms of both economics and the environment. Components of the agricultural production chain are analysed using environmental life-cycle assessment (LCA) and a financial value attributed to the resources consumed and burden imposed on the environment by agriculture, as well as to the products. The sum of the outputs is weighed against the inputs and the system considered sustainable if the value of the outputs exceeds those of the inputs. If this ratio is plotted against the sum of inputs for all levels of input, a diminishing returns curve should result and the optimum level of sustainability is located at the maximum of the curve. Data were taken from standard economic almanacs and from published LCA reports on the extent of consumption and environmental burdens resulting from farming in the UK. Land-use is valued using the concept of ecosystem services. Our analysis suggests that agricultural systems are sustainable at rates of production close to current levels practiced in the UK. Extensification of farming, which is thought to favour non-food ecosystem services, requires more land to produce the same amount of food. The loss of ecosystem services hitherto provided by natural land brought into production is greater than that which can be provided by land now under extensive farming. This loss of ecosystem service is large in comparison to the benefit of a reduction in emission of nutrients and pesticides. However, food production is essential, so the coupling of subsidies that represent a relatively large component of the economic output in EU farming, with measures to reduce pollution are well-aimed. Measures to ensure that as little extra land is brought into production as possible or that marginal land is allowed to revert to nature would seem to be equally well-aimed, even if this required more intensive use of productive areas. We conclude that current arable farming in the EU is sustainable with either realistic prices for products or some degree of subsidy and that productivity per unit area of land and greenhouse gas emission (subsuming primary energy consumption) are the most important pressures on the sustainability of farming

Dynamical Evolution of Globular Cluster Systems formed in Galaxy Mergers: Deep HST/ACS Imaging of Old and Intermediate-Age Globular Clusters in NGC 3610

(ABRIDGED) The ACS camera on board the Hubble Space Telescope has been used to obtain deep images of the giant elliptical galaxy NGC 3610, a well-established dissipative galaxy merger remnant. These observations supersede previous WFPC2 images which revealed the presence of a population of metal-rich globular clusters (GCs) of intermediate age (~1.5-4 Gyr). We detect a total of 580 GC candidates, 46% more than from the previous WFPC2 images. The new photometry strengthens the significance of the previously found bimodality of the color distribution of GCs. Peak colors in V-I are 0.93 +/-0.01 and 1.09 +/- 0.01 for the blue and red subpopulations, respectively. The luminosity function (LF) of the inner 50% of the metal-rich (`red') population of GCs differs markedly from that of the outer 50%. In particular, the LF of the inner 50% of the red GCs shows a flattening consistent with a turnover that is about 1.0 mag fainter than the turnover of the blue GC LF. This is consistent with predictions of recent models of GC disruption for the age range mentioned above and for metallicities that are consistent with the peak color of the red GCs as predicted by population synthesis models. We determine the specific frequency of GCs in NGC 3610 and find a present-day value of S_N = 1.4 +/- 0.6. We estimate that this value will increase to S_N = 3.8 +/- 1.7 at an age of 10 Gyr, which is consistent with typical S_N values for `normal' ellipticals. Our findings constitute further evidence in support of the notion that metal-rich GC populations formed during major mergers involving gas-rich galaxies can evolve dynamically (through disruption processes) into the red, metal-rich GC populations that are ubiquitous in `normal' giant ellipticals.Comment: 15 pages, 14 figures, 4 tables. Accepted for publication in The Astronomical Journal. Figure 6 somewhat degraded to adhere to astro-ph rule

Winds from clu\sters with non-uniform stellar distributions

We present analytic and numerical models of the `cluster wind' resulting from the multiple interactions of the winds ejected by the stars of a dense cluster of massive stars. We consider the case in which the distribution of stars (i.e., the number of stars per unit volume) within the cluster is spherically symmetric, has a power-law radial dependence, and drops discontinuously to zero at the outer radius of the cluster. We carry out comparisons between an analytic model (in which the stars are considered in terms of a spatially continuous injection of mass and energy) and 3D gasdynamic simulations (in which we include 100 stars with identical winds, located in 3D space by statistically sampling the stellar distribution function). From the analytic model, we find that for stellar distributions with steep enough radial dependencies the cluster wind flow develops a very high central density and a non-zero central velocity, and for steeper dependencies it becomes fully supersonic throughout the volume of the cluster (these properties are partially reproduced by the 3D numerical simulations). Therefore, the wind solutions obtained for stratified clusters can differ dramatically from the case of a homogeneous stellar distribution (which produces a cluster wind with zero central velocity, and a fully subsonic flow within the cluster radius). Finally, from our numerical simulations we compute predictions of X-ray emission maps and luminosities, which can be directly compared with observations of cluster wind flows.Comment: 10 pages, 11 figures. MNRAS - Accepted 2007 June 29. Received 2007 June 28; in original form 2007 May 2

The Antennae Galaxies (NGC 4038/4039) Revisited: ACS and NICMOS Observations of a Prototypical Merger

The ACS and NICMOS have been used to obtain new HST images of NGC 4038/4039 ("The Antennae"). These new observations allow us to better differentiate compact star clusters from individual stars, based on both size and color. We use this ability to extend the cluster luminosity function by approximately two magnitudes over our previous WFPC2 results, and find that it continues as a single power law, dN/dL propto L^alpha with alpha=-2.13+/-0.07, down to the observational limit of Mv~-7. Similarly, the mass function is a single power law dN/dM propto M^beta with beta=-2.10+/-0.20 for clusters with ages t<3x10^8 yr, corresponding to lower mass limits that range from 10^4 to 10^5 Msun, depending on the age range of the subsample. Hence the power law indices for the luminosity and mass functions are essentially the same. The luminosity function for intermediate-age clusters (i.e., ~100-300 Myr old objects found in the loops, tails, and outer areas) shows no bend or turnover down to Mv~-6, consistent with relaxation-driven cluster disruption models which predict the turnover should not be observed until Mv~-4. An analysis of individual ~0.5-kpc sized areas over diverse environments shows good agreement between values of alpha and beta, similar to the results for the total population of clusters in the system. Several of the areas studied show evidence for age gradients, with somewhat older clusters appearing to have triggered the formation of younger clusters. The area around Knot B is a particularly interesting example, with an ~10-50 Myr old cluster of estimated mass ~10^6 Msun having apparently triggered the formation of several younger, more massive (up to 5x10^6 Msun) clusters along a dust lane.Comment: 84 pages, 9 tables, 31 figures; ApJ accepte

The Globular Cluster Systems of Five Nearby Spiral Galaxies: New Insights from Hubble Space Telescope Imaging

We use available multifilter Hubble Space Telescope (HST) WFPC2 imaging of five (M81, M83, NGC 6946, M101, and M51) low inclination, nearby spiral galaxies to study ancient star cluster populations. M81 globular clusters (GC) have an intrinsic color distribution which is very similar to those in the Milky Way and M31, with ~40% of the clusters having colors expected for a metal-rich population. On the other hand, the GC system in M51 appears almost exclusively blue and metal poor. This lack of metal-rich GCs associated with the M51 bulge indicates that the bulge formation history of this Sbc galaxy may have differed significantly from that of our own. Ancient clusters in M101, and possibly in NGC 6946, appear to have luminosity distributions which continue to rise to our detection limit (M_V ~ -6.0), well beyond the expected turnover (M_V ~ -7.4) in the luminosity function. This is reminiscent of the situation in M33, a Local Group galaxy of similar Hubble type. The faint ancient cluster candidates in M101 and NGC 6946 have colors and radii similar to their more luminous counterparts, and we suggest that these are either intermediate age (3-9 Gyr) disk clusters or the low mass end of the original GC population. If the faint, excess GC candidates are excluded, we find that the specific frequency (S_N) of ancient clusters formed in later-type spirals is roughly constant, with S_N=0.5 +- 0.2. By combining the results of this study with literature values for other systems, we find that the total GC specific frequencies in spirals appear to correlate best with Hubble type and bulge/total ratio, rather than with galaxy luminosity or galaxy mass (abridged).Comment: 31 pages, 11 tables, 10 figure

Local impacts of climate change on winter wheat in Great Britain

Under future CMIP5 climate change scenarios for 2050, an increase in wheat yield of about 10% is predicted in Great Britain (GB) as a result of the combined effect of CO2 fertilization and a shift in phenology. Compared to the present day, crops escape increases in the climate impacts of drought and heat stresses on grain yield by developing before these stresses can occur. In the future, yield losses from water stress over a growing season will remain about the same across Great Britain with losses reaching around 20% of potential yield, while losses from drought around flowering will decrease and account for about 9% of water limited yield. Yield losses from heat stress around flowering will remain negligible in the future. These conclusions are drawn from a modelling study based on the response of the Sirius wheat simulation model to local-scale 2050-climate scenarios derived from 19 Global Climate Models from the CMIP5 ensemble at 25 locations representing current or potential wheat-growing areas in GB. However, depending on susceptibility to water stress, substantial interannual yield variation between locations is predicted, in some cases suggesting low wheat yield stability. For this reason, local-scale studies should be performed to evaluate uncertainties in yield prediction related to future weather patterns