Do large‐seeded herbs have a small range size? The seed mass–distribution range trade‐off hypothesis

We aimed to introduce and test the “seed mass–distribution range trade‐off” hypothesis, that is, that range size is negatively related to seed mass due to the generally better dispersal ability of smaller seeds. Studying the effects of environmental factors on the seed mass and range size of species, we also aimed to identify habitats where species may be at risk and need extra conservation effort to avoid local extinctions. We collected data for seed mass, global range size, and indicators for environmental factors of the habitat for 1,600 species of the Pannonian Ecoregion (Central Europe) from the literature. We tested the relationship between species’ seed mass, range size, and indicator values for soil moisture, light intensity, and nutrient supply. We found that seed mass is negatively correlated with range size; thus, a seed mass–distribution range trade‐off was validated based on the studied large species pool. We found increasing seed mass with decreasing light intensity and increasing nutrient availability, but decreasing seed mass with increasing soil moisture. Range size increased with increasing soil moisture and nutrient supply, but decreased with increasing light intensity. Our results supported the hypothesis that there is a trade‐off between seed mass and distribution range. We found that species of habitats characterized by low soil moisture and nutrient values but high light intensity values have small range size. This emphasizes that species of dry, infertile habitats, such as dry grasslands, could be more vulnerable to habitat fragmentation or degradation than species of wet and fertile habitats. The remarkably high number of species and the use of global distribution range in our study support our understanding of global biogeographic processes and patterns that are essential in defining conservation priorities.     

Loss of Kindlin-1 Causes Skin Atrophy and Lethal Neonatal Intestinal Epithelial Dysfunction

Kindler Syndrome (KS), characterized by transient skin blistering followed by abnormal pigmentation, skin atrophy, and skin cancer, is caused by mutations in the FERMT1 gene. Although a few KS patients have been reported to also develop ulcerative colitis (UC), a causal link to the FERMT1 gene mutation is unknown. The FERMT1 gene product belongs to a family of focal adhesion proteins (Kindlin-1, -2, -3) that bind several β integrin cytoplasmic domains. Here, we show that deleting Kindlin-1 in mice gives rise to skin atrophy and an intestinal epithelial dysfunction with similarities to human UC. This intestinal dysfunction results in perinatal lethality and is triggered by defective intestinal epithelial cell integrin activation, leading to detachment of this barrier followed by a destructive inflammatory response.     

Optimal moult strategies in migratory birds

Avian migration, which involves billions of birds flying vast distances, is known to influence all aspects of avian life. Here we investigate how birds fit moult into an annual cycle determined by the need to migrate. Large variation exists in moulting patterns in relation to migration: for instance, moult can occur after breeding in the summer or after arrival in the wintering quarters. Here we use an optimal annual routine model to investigate why this variation exists. The modelled bird's decisions depend on the time of year, its energy reserves, breeding status, experience, flight feather quality and location. Our results suggest that the temporal and spatial variations in food are an important influence on a migratory bird's annual cycle. Summer moult occurs when food has a high peak on the breeding site in the summer, but it is less seasonal elsewhere. Winter moult occurs if there is a short period of high food availability in summer and a strong winter peak at different locations (i.e. the food is very seasonal but in opposite phase on these areas). This finding might explain why only long-distance migrants have a winter moult.     

Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site

dUTP pyrophosphatase, a preventive DNA repair enzyme, contributes to maintain the appropriate cellular dUTP/dTTP ratio by catalyzing dUTP hydrolysis. dUTPase is essential for viability in bacteria and eukaryotes alike. Identification of species-specific antagonists of bacterial dUTPases is expected to contribute to the development of novel antimicrobial agents. As a first general step, design of dUTPase inhibitors should be based on modifications of the substrate dUTP phosphate chain, as modifications in either base or sugar moieties strongly impair ligand binding. Based on structural differences between bacterial and human dUTPases, derivatization of dUTP-analogous compounds will be required as a second step to invoke species-specific character. Studies performed with dUTP analogues also offer insights into substrate binding characteristics of this important and structurally peculiar enzyme. In this study, alpha,beta-methylene-dUDP was synthesized and its complex with dUTPase was characterized. Enzymatic phosphorylation of this substrate analogue by pyruvate kinase was not possible in contrast to the successful enzymatic phosphorylation of alpha,beta-imino-dUDP. One explanation for this finding is that the different bond angles and the presence of the methylene group may preclude formation of a catalytically competent complex with the kinase. Crystal structure of E. coli dUTPase:alpha,beta-methylene-dUDP and E. coli dUTPase:dUDP:Mn complexes were determined and analyzed in comparison with previous data. Results show that the "trans" alpha-phosphate conformation of alpha,beta-methylene-dUDP differs from the catalytically competent "gauche" alpha-phosphate conformation of the imino analogue and the oxo substrate, manifested in the shifted position of the alpha-phosphorus by more than 3 A. The three-dimensional structures determined in this work show that the binding of the methylene analogue with the alpha-phosphorus in the "gauche" conformation would result in steric clash of the methylene group with the protein atoms. In addition, the metal ion cofactor was not bound in the crystal of the complex with the methylene analogue while it was clearly visible as coordinated to dUDP, arguing that the altered phosphate chain conformation also perturbs metal ion complexation. Isothermal calorimetry titrations indicate that the binding affinity of alpha,beta-methylene-dUDP toward dUTPase is drastically decreased when compared with that of dUDP. In conclusion, the present data suggest that while alpha,beta-methylene-dUDP seems to be practically nonhydrolyzable, it is not a strong binding inhibitor of dUTPase probably due to the altered binding mode of the phosphate chain. Results indicate that in some cases methylene analogues may not faithfully reflect the competent substrate ligand properties, especially if the methylene hydrogens are in steric conflict with the protein.     

Folding transitions in calpain activator peptides studied by solution NMR spectroscopy

Calpastatin, the endogenous inhibitor of calpain, a cysteine protease in eukaryotic cells, is an intrinsically unstructured protein, which upon binding to the enzyme goes through a conformational change. Peptides calpA (SGKSGMDAALDDLIDTLGG) and calpC (SKPIGPDDAIDALSSDFTS), corresponding to the two conserved subdomains of calpastatin, are known to activate calpain and increase the Ca²⁺ sensitivity of the enzyme. Using solution NMR spectroscopy, here we show that calpA and calpC are disordered in water but assume an α‐helical conformation in 50% CD₃OH. The position and length of the helices are in agreement with those described in the literature for the bound state of the corresponding segments of calpastatin suggesting that the latter might be structurally primed for the interaction with its target. According to our data, the presence of Ca²⁺ induces a backbone rearrangement in the peptides, an effect that may contribute to setting the fine conformational balance required for the interaction of the peptides with calpain. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

Helicobacter Pylori's Plasticity Zones Are Novel Transposable Elements

Background

Genes present in only certain strains of a bacterial species can strongly affect cellular phenotypes and evolutionary potentials. One segment that seemed particularly rich in strain-specific genes was found by comparing the first two sequenced Helicobacter pylori genomes (strains 26695 and J99) and was named a “plasticity zone”.

Principal Findings

We studied the nature and evolution of plasticity zones by sequencing them in five more Helicobacter strains, determining their locations in additional strains, and identifying them in recently released genome sequences. They occurred as discrete units, inserted at numerous chromosomal sites, and were usually flanked by direct repeats of 5′AAGAATG, a sequence generally also present in one copy at unoccupied sites in other strains. This showed that plasticity zones are transposable elements, to be called TnPZs. Each full length TnPZ contained a cluster of type IV protein secretion genes (tfs3), a tyrosine recombinase family gene (“xerT”), and a large (≥2800 codon) orf encoding a protein with helicase and DNA methylase domains, plus additional orfs with no homology to genes of known function. Several TnPZ types were found that differed in gene arrangement or DNA sequence. Our analysis also indicated that the first-identified plasticity zones (in strains 26695 and J99) are complex mosaics of TnPZ remnants, formed by multiple TnPZ insertions, and spontaneous and transposable element mediated deletions. Tests using laboratory-generated deletions showed that TnPZs are not essential for viability, but identified one TnPZ that contributed quantitatively to bacterial growth during mouse infection and another that affected synthesis of proinflammatory cytokines in cell culture.

Conclusions

We propose that plasticity zone genes are contained in conjugative transposons (TnPZs) or remnants of them, that TnPZ insertion is mediated by XerT recombinase, and that some TnPZ genes affect bacterial phenotypes and fitness.     

Successful restoration of water level and surface area restored migrant bird populations in a Hungarian wetland

Water level and water surface area fluctuations are important factors determining abundance of bird populations and bird assemblages structure in a wetland habitat. The water level and water surface area of the Marsh T?m?rd (West Hungary) changed drastically between 1998 and 2008, and the marsh dried out because of scarce rainfall in 2000 and 2001. A habitat restoration in winter 2001 repaired the waterholding capacity of the marsh. We analyzed changes in parameters of bird assemblages in investigated wetland area in relation of environmental factors. We used full redundancy analysis (RDA) on number of caugth migratory birds per year, species richness, diversity and evenness of bird assemblages to examine correlations among water level, water surface area and vegetation core. Species like water rail, common snipe, river warbler, Savi’s warbler, great reed warbler, reed warbler, marsh warbler, sedge warbler, reed bunting showed high and positive linear correlations with the water level and water surface area in the postbreeding period. Some wetland species, sedge warbler, Savi’s warbler and reed bunting as well as total number of caugth birds per year and total numbers of caugth species per year were clearly associated with thick marsh vegetation. According to our results the bird species composition of the wetland might have returned to the prerestoration levels and surface areas.     

Salicylic acid and photosynthesis: signalling and effects

Salicylic acid (SA) is a well-known signalling molecule playing a role in local and systemic acquired resistance against pathogens as well as in acclimation to certain abiotic stressors. As a stress-related signalling compound, it may directly or indirectly affect various physiological processes, including photosynthesis. The effects of exogenously applied SA on plant physiological processes under optimal environmental conditions are controversial. Several studies suggest that SA may have a positive effect on germination or plant growth in various plant species. However, SA may also act as a stress factor, having a negative influence on various physiological processes. Its mode of action depends greatly on several factors, such as the plant species, the environmental conditions (light, temperature, etc.) and the concentration. Exogenous SA may also alleviate the damaging effects of various stress factors, and this protection may also be manifested as higher photosynthetic capacity. Unfavourable environmental conditions have also been shown to increase the endogenous SA level in plants. Recent results strongly suggest that controlled SA levels are important in plants for optimal photosynthetic performance and for acclimation to changing environmental stimuli. The present review discusses the effects of exogenous and endogenous SA on the photosynthetic processes under optimal and stress conditions.