The pgip family in soybean and three other legume species: evidence for a birth-and-death model of evolution

Background Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) plant cell wall glycoproteins involved in plant immunity. They are typically encoded by gene families with a small number of gene copies whose evolutionary origin has been poorly investigated. Here we report the complete characterization of the full complement of the pgip family in soybean (Glycine max [L.] Merr.) and the characterization of the genomic region surrounding the pgip family in four legume species. Results BAC clone and genome sequence analyses showed that the soybean genome contains two pgip loci. Each locus is composed of three clustered genes that are induced following infection with the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, and remnant sequences of pgip genes. The analyzed homeologous soybean genomic regions (about 126 Kb) that include the pgip loci are strongly conserved and this conservation extends also to the genomes of the legume species Phaseolus vulgaris L., Medicago truncatula Gaertn. and Cicer arietinum L., each containing a single pgip locus. Maximum likelihood-based gene trees suggest that the genes within the pgip clusters have independently undergone tandem duplication in each species. Conclusions The paleopolyploid soybean genome contains two pgip loci comprised in large and highly conserved duplicated regions, which are also conserved in bean, M. truncatula and C. arietinum. The genomic features of these legume pgip families suggest that the forces driving the evolution of pgip genes follow the birth-and-death model, similar to that proposed for the evolution of resistance (R) genes of NBS-LRR-type.

Managing artisanal and small-scale mining in forest areas: perspectives from a poststructural political ecology

Artisanal and small-scale mining (ASM) is an activity intimately associated with social deprivation and environmental degradation, including deforestation. This paper examines ASM and deforestation using a broadly poststructural political ecology framework. Hegemonic discourses are shown to consistently influence policy direction, particularly in emerging approaches such as Corporate Social Responsibility and the Forest Stewardship Council. A review of alternative discourses reveals that the poststructural method is useful for critiquing the international policy arena but does not inform new approaches. Synthesis of the analysis leads to conclusions that echo a growing body of literature advocating for policies to become increasingly sensitive to local contexts, synergistic between actors at difference scales, and to be integrated across sectors.

Emulation of chiral hydrogenation catalysts by adsorbtion of small molecules onto Ni surfaces

Adsorption of small molecules on the Ni{111} and NiO{111} surfaces is investigated under UHV and elevated pressures (~10-1 mbar) of hydrogen and water. The molecules considered are chosen for their relevance to understanding the mechanism of enantioselective hydrogenation on Raney Nickel modified by chiral molecules. Adsorption of water onto, and its subsequent reaction with, oxygen-covered Ni{111} is dependent on the initial atomic oxygen coverage. An OH species (O1s binding energy 531.5eV), oriented perpendicular to the surface, forms at atomic oxygen coverages <0.25ML. The reaction does not consume all the adsorbed oxygen for coverages ≥0.12ML. The p(2×2) atomic oxygen uperstructure is unreactive, while an OH species is formed on the p(√3×√3) superstructure at binding energy 530.9eV. L-alanine is adsorbed on Ni{111} as a model chiral modifier molecule. At low coverages, alanine forms a presumed tridentate alaninate species for coverages ≥0.11ML at 250K. A minority, bidentate zwitterionic species forms at coverages >0.11ML, but was not observed at 300K. Saturation occurs at 0.25ML. At high alanine coverages (≥0.19ML) and H2 pressure (≥1×10-2 mbar), the tridentate L-alaninate converts to bidentate zwitterionic L-alanine at 300K. Thermal evolution of L-alanine on Ni{111} under varying hydrogen pressures is examined. Adsorption of L-alanine onto hydroxylated NiO{111} at 300K in UHV, mimicking a catalyst surface under aqueous conditions, yields the tridentate alaninate which is immune to the effects of elevated hydrogen pressure. Exposing the L-alanine/Ni{111} adsorption system to water (≤10-1 mbar) oxidises the surface and recreates the L-alanine/hydroxylated NiO{111} system. Pyruvic acid on Ni{111} is examined as a model for hydrogenation substrate adsorption. Behaviour is coverage dependent and several conformations are possible at low coverages (≤0.1ML). Annealing at coverages <0.2ML causes a condensation reaction, releasing water onto the surface. High coverages do not condense and a saturation coverage of ~0.35ML is found.

Improving the TanDEM-X Digital Elevation Model for flood modelling using flood extents from Synthetic Aperture Radar images

The topography of many floodplains in the developed world has now been surveyed with high resolution sensors such as airborne LiDAR (Light Detection and Ranging), giving accurate Digital Elevation Models (DEMs) that facilitate accurate flood inundation modelling. This is not always the case for remote rivers in developing countries. However, the accuracy of DEMs produced for modelling studies on such rivers should be enhanced in the near future by the high resolution TanDEM-X WorldDEM. In a parallel development, increasing use is now being made of flood extents derived from high resolution Synthetic Aperture Radar (SAR) images for calibrating, validating and assimilating observations into flood inundation models in order to improve these. This paper discusses an additional use of SAR flood extents, namely to improve the accuracy of the TanDEM-X DEM in the floodplain covered by the flood extents, thereby permanently improving this DEM for future flood modelling and other studies. The method is based on the fact that for larger rivers the water elevation generally changes only slowly along a reach, so that the boundary of the flood extent (the waterline) can be regarded locally as a quasi-contour. As a result, heights of adjacent pixels along a small section of waterline can be regarded as samples with a common population mean. The height of the central pixel in the section can be replaced with the average of these heights, leading to a more accurate estimate. While this will result in a reduction in the height errors along a waterline, the waterline is a linear feature in a two-dimensional space. However, improvements to the DEM heights between adjacent pairs of waterlines can also be made, because DEM heights enclosed by the higher waterline of a pair must be at least no higher than the corrected heights along the higher waterline, whereas DEM heights not enclosed by the lower waterline must in general be no lower than the corrected heights along the lower waterline. In addition, DEM heights between the higher and lower waterlines can also be assigned smaller errors because of the reduced errors on the corrected waterline heights. The method was tested on a section of the TanDEM-X Intermediate DEM (IDEM) covering an 11km reach of the Warwickshire Avon, England. Flood extents from four COSMO-SKyMed images were available at various stages of a flood in November 2012, and a LiDAR DEM was available for validation. In the area covered by the flood extents, the original IDEM heights had a mean difference from the corresponding LiDAR heights of 0.5 m with a standard deviation of 2.0 m, while the corrected heights had a mean difference of 0.3 m with standard deviation 1.2 m. These figures show that significant reductions in IDEM height bias and error can be made using the method, with the corrected error being only 60% of the original. Even if only a single SAR image obtained near the peak of the flood was used, the corrected error was only 66% of the original. The method should also be capable of improving the final TanDEM-X DEM and other DEMs, and may also be of use with data from the SWOT (Surface Water and Ocean Topography) satellite.

Adaptive evolution toward larger size in mammals

The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach that allows the rate of body size evolution to vary across a phylogeny, we find a long-term directional bias toward increasing size in the mammals. This pattern holds separately in 10 of 11 orders for which sufficient data are available and arises from a tendency for accelerated rates of evolution to produce increases, but not decreases, in size. On a branch-by-branch basis, increases in body size have been more than twice as likely as decreases, yielding what amounts to millions and millions of years of rapid and repeated increases in size away from the small ancestral mammal. These results are the first evidence, to our knowledge, from extant species that are compatible with Cope’s rule: the pattern of body size increase through time observed in the mammalian fossil record. We show that this pattern is unlikely to be explained by several nonadaptive mechanisms for increasing size and most likely represents repeated responses to new selective circumstances. By demonstrating that it is possible to uncover ancient evolutionary trends from a combination of a phylogeny and appropriate statistical models, we illustrate how data from extant species can complement paleontological accounts of evolutionary history, opening up new avenues of investigation for both.