Automated Masking of AFLP Markers Improves Reliability of Phylogenetic Analyses

The amplified fragment length polymorphisms (AFLP) method has become an attractive tool in phylogenetics due to the ease with which large numbers of characters can be generated. In contrast to sequence-based phylogenetic approaches, AFLP data consist of anonymous multilocus markers. However, potential artificial amplifications or amplification failures of fragments contained in the AFLP data set will reduce AFLP reliability especially in phylogenetic inferences. In the present study, we introduce a new automated scoring approach, called “AMARE” (AFLP MAtrix REduction). The approach is based on replicates and makes marker selection dependent on marker reproducibility to control for scoring errors. To demonstrate the effectiveness of our approach we record error rate estimations, resolution scores, PCoA and stemminess calculations. As in general the true tree (i.e. the species phylogeny) is not known, we tested AMARE with empirical, already published AFLP data sets, and compared tree topologies of different AMARE generated character matrices to existing phylogenetic trees and/or other independent sources such as morphological and geographical data. It turns out that the selection of masked character matrices with highest resolution scores gave similar or even better phylogenetic results than the original AFLP data sets.     

Transgenically enhanced sorbitol synthesis facilitates phloem-boron mobility in rice

The tolerance of crops to a shortage of boron (B) in the soil varies markedly among species. This variation in tolerance is due, in part, to a species ability to form phloem mobile B-sugar-alcohol complexes (such as B-mannitol or B-sorbitol) which enhance the remobilization of B within the plant. Species lacking the capacity to form B-sugar alcohol complexes are intolerant of even short-term deficits in soil B supply. Here we have genetically engineered rice ( Oryza sativa L.) cultivar Taipei 309 (TP309) with the sorbitol-6-phosphate dehydrogenase (S6PDH) gene, a key enzyme for sorbitol production, and determined the effect of this transformation on the physiology of B remobilization. Sorbitol was detected in the S6PDH transgenic plants as well as in vector-transformed plants and wild-type (TP 309) plants, although the concentration of sorbitol in the S6PDH transgenic plants was significantly enhanced. Remobilization of B from mature leaves to flag leaves correlated with increased levels of sorbitol. The presence of sorbitol and detection of B remobilization in the wild-type and vector-transformed plants suggests that rice utilizes an unknown pathway for sorbitol synthesis and may partly explain the relative insensitivity of rice to B deficits when compared to other graminaceous crops.     

The potential of and limitations to marine population prognosis

Following the 19th century recognition and definition of basic ecological entities, functional analysis has been the highlight of this century. The synthesis of these findings enables ecological prognosis. The population as the basic functional unit has been repeatedly treated; in the marine field, fisheries management approaches developed into multi-species population analysis. As in planktology, theoretical ecology, and classic biocoenotic research, the population interactions are of increasing scientific interest. A mathematical model is suggested that combines these extrinsic and intrinsic functional relationships in order to define the fit of the ecological niche to the environment, the decisive measure of the expected population success, and thus of the probable population development needed for prognostic purposes. It is discussed in how far the orientation towards the predictive power or — with respect to the “skill” of meteorological prognoses — the “ecological prognostic skill” improvement may serve as a means to choose the best investigative strategy.     

Quasielastic light scattering from solutions of lollipop-shaped particles

An expression is derived for the field correlation function of the light scattered from a solution of lollipop-shaped particles. Such particles are a tractable model of certain bacteriophages. They are assumed to consist of an ellipsoidal head containing optically anisotropic scattering material and a tail which does not scatter. Because of the tail, Brownian rotational movement occurs around a center of rotational friction which is at a distance r₀ from the center of the head. The dependence of the field correlation function C(τ) on the rotational diffusion coefficient D_R is given by the factor Σ_lB_l exp[?l(l + 1)D_Rτ]. It is shown that the tail causes the coefficients B_l to be different from zero for all values of l. Therefore, C(τ) contains a term proportional to exp(?2D_Rτ), which is not present when r₀ = 0. We give plots of B_l for various combinations of parameters. It turns out that dynamic light scattering may be used to measure r₀.     

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DNA bending by photolyase in specific and non-specific complexes studied by atomic force microscopy.

Specific and non-specific complexes of DNA and photolyase are visualised by atomic force microscopy. As a substrate for photolyase a 1150 bp DNA restriction fragment was UV-irradiated to produce damaged sites at random positions. Comparison with a 735 bp undamaged DNA fragment made it possible to separate populations of specific and non-specific photolyase complexes on the 1150 bp fragment, relieving the need for highly defined substrates. Thus it was possible to compare DNA bending for specific and non-specific interactions. Non-specific complexes show no significant bending but increased rigidity compared to naked DNA, whereas specific complexes show DNA bending of on average 36 degrees and higher flexibility. A model obtained by docking shows that photolyase can accommodate a 36 degrees bent DNA in the vicinity of the active site.     

Environmental factors, regional body size distributions and spatial variation in body size of local avian assemblages

Aim To determine how well variation in median body size of avian assemblages is predicted by (1) the environmental models usually employed in analyses of Bergmann's rule and (2) random sampling from the regional body size frequency distribution. If body size frequency distributions of local assemblages represent a random sample of a regional frequency distribution, then geographical variation in body sizes of assemblages might be a consequence of the determinants of spatial variation in species richness rather than direct influences on body size per se. Location Southern Africa. Methods Median body masses (as a measure of body size) of avian assemblages were calculated for quarter‐degree grid cells across South Africa and Lesotho. The relationship between median body mass and four environmental variables (minimum and maximum monthly temperatures, precipitation and seasonality in the normalized difference vegetation index, as a measure of seasonality in productivity) was examined using general linear models first without taking spatial autocorrelation into account, and then accounting for it by fitting an exponential spatial covariance structure. Model fit was assessed using the Akaike information criterion and Akaike weights. At each species richness value, random assemblages were sampled by either drawing species randomly from the regional body mass frequency distribution, or drawing species from the regional body mass frequency distribution with a probability proportional to their geographical distribution in the area. The ability of randomizations to predict actual body masses was examined using two‐tailed Fisher exact tests. Results Seasonality in productivity was the only environmental variable that remained a significant predictor of body mass variation in spatially explicit models, though the positive relationship was weak. When species richness was included in the models it remained the only significant predictor of size variation. Randomizations predicted median body mass poorly at low species richness, but well at high richness. Main conclusions Environmental models that have previously been proposed explain little of the variation in body mass across avian assemblages in South Africa. However, much of the variation in the median mass of assemblages could be predicted by randomly drawing species from the regional body mass frequency distribution, particularly using randomizations in which all species were drawn from the regional body mass frequency distribution with equal probability and at high species richness values. This outcome emphasizes the need to consider null expectations in investigations of the geographical variation in body size together with the probable environmental mechanisms underlying spatial variation in average size. Moreover, it suggests that in the South African avifauna, spatial variation in the body sizes of assemblages may be determined indirectly by the factors that influence geographical variation in species richness.     

No Peri- and Postnatal Effects on Calves Born After Transfer of in Vitro Produced Embryos Vitrified by the Open Pulled Straw (OPS) Method

The general objective of this study was to perform follow-up studies including selected peri- and postnatal characteristics on calves born after transfer of in vitro produced (IVP) embryos vitrified by the 'Open Pulled Straw' (OPS) method. An overall pregnancy rate of 16% after transfer of the OPS-vitrified IVP embryos was achieved and resulted in birth of 9 calves, with 11 AI calves serving as controls. There were no immediate or long-term effects on these calves with respect to birth weight, gestation length, perinatal mortality, growth rate, disease susceptibility and reproductive performance.     

Digital Mapping of Soil Organic Carbon Contents and Stocks in Denmark

Estimation of carbon contents and stocks are important for carbon sequestration, greenhouse gas emissions and national carbon balance inventories. For Denmark, we modeled the vertical distribution of soil organic carbon (SOC) and bulk density, and mapped its spatial distribution at five standard soil depth intervals (0−5, 5−15, 15−30, 30−60 and 60−100 cm) using 18 environmental variables as predictors. SOC distribution was influenced by precipitation, land use, soil type, wetland, elevation, wetness index, and multi-resolution index of valley bottom flatness. The highest average SOC content of 20 g kg⁻¹ was reported for 0−5 cm soil, whereas there was on average 2.2 g SOC kg⁻¹ at 60−100 cm depth. For SOC and bulk density prediction precision decreased with soil depth, and a standard error of 2.8 g kg⁻¹ was found at 60−100 cm soil depth. Average SOC stock for 0−30 cm was 72 t ha⁻¹ and in the top 1 m there was 120 t SOC ha⁻¹. In total, the soils stored approximately 570 Tg C within the top 1 m. The soils under agriculture had the highest amount of carbon (444 Tg) followed by forest and semi-natural vegetation that contributed 11% of the total SOC stock. More than 60% of the total SOC stock was present in Podzols and Luvisols. Compared to previous estimates, our approach is more reliable as we adopted a robust quantification technique and mapped the spatial distribution of SOC stock and prediction uncertainty. The estimation was validated using common statistical indices and the data and high-resolution maps could be used for future soil carbon assessment and inventories.     

The Intrinsically Disordered Domain of the Antitoxin Phd Chaperones the Toxin Doc against Irreversible Inactivation and Misfolding

The toxin Doc from the phd/doc toxin-antitoxin module targets the cellular translation machinery and is inhibited by its antitoxin partner Phd. Here we show that Phd also functions as a chaperone, keeping Doc in an active, correctly folded conformation. In the absence of Phd, Doc exists in a relatively expanded state that is prone to dimerization through domain swapping with its active site loop acting as hinge region. The domain-swapped dimer is not capable of arresting protein synthesis in vitro, whereas the Doc monomer is. Upon binding to Phd, Doc becomes more compact and is secured in its monomeric state with a neutralized active site.