Proteoglycan-specific molecular switch for RPTPσ clustering and neuronal extension

Heparan and chondroitin sulfate proteoglycans (HSPGs and CSPGs, respectively) regulate numerous cell surface signaling events, with typically opposite effects on cell function. CSPGs inhibit nerve regeneration through receptor protein tyrosine phosphatase sigma (RPTPσ). Here we report that RPTPσ acts bimodally in sensory neuron extension, mediating CSPG inhibition and HSPG growth promotion. Crystallographic analyses of a shared HSPG-CSPG binding site reveal a conformational plasticity that can accommodate diverse glycosaminoglycans with comparable affinities. Heparan sulfate and analogs induced RPTPσ ectodomain oligomerization in solution, which was inhibited by chondroitin sulfate. RPTPσ and HSPGs colocalize in puncta on sensory neurons in culture, whereas CSPGs occupy the extracellular matrix. These results lead to a model where proteoglycans can exert opposing effects on neuronal extension by competing to control the oligomerization of a common receptor.     

The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.     

Wind dispersal of oribatid mites as a mode of migration

Oribatid mites are important colonizers of young soils, but little is known about their immigration pathways. In this study, one often-stated hypothesis was tested quantitatively: that wind is an important dispersal pathway. The aim was (1) to detect wind dispersal in oribatid mites (using sticky traps at different heights above ground level) and to determine factors influencing wind dispersal, (2) to investigate whether oribatids can survive wind dispersal and immigrate by wind into young soils (using mini-pitfall traps in test plots with oribatid-free substrate, active immigration being prohibited) and (3) to find out whether those oribatids are able to colonize young soils (using soil cores from the test plots). The results demonstrate (1) that mainly arboreal oribatid species were dispersed by wind - even at 160 m height - and can therefore be spread over large distances. Nevertheless, about 10% of the wind-dispersed oribatid mites belonged to species able to live in the soil and may therefore be potential colonizers of young soils. The number of specimen and species transported by wind was the highest close to the soil surface and the number of dispersed individuals was mainly influenced by seasonality and humidity. The results also suggest that the probability of a soil oribatid being dispersed by wind depends on its original microhabitat (tree habitats > soil surface > deeper soil layers) and its body weight. It was also shown that soil-dwelling oribatid mites survived wind dispersal and immigrated by wind into the test plots and that colonization of the test plots took at least 2 months longer than immigration. However, colonization success was low during the first 2 years of investigation and only Trichoribates incisellus was found several times in the nutrient-poor substrate. Therefore, wind dispersal is an important migration pathway, especially for arboreal oribatids. We suggest that immigration into young soils most likely occurs by repeated short-distance dispersal. Only some species are able to survive the hostile conditions of wind dispersal as well as of pioneer soils, but those that do are potentially the founders of new populations.     

Degradability of black carbon and its impact on trace gas fluxes and carbon turnover in paddy soils

Rice paddy soils are characterized by anoxic conditions, anaerobic carbon turnover, and significant emissions of the greenhouse gas methane. A main source for soil organic matter in paddy fields is the rice crop residue that is returned to fields if not burned. We investigated as an alternative treatment the amendment of rice paddies with rice residues that have been charred to black carbon. This treatment might avoid various negative side effects of traditional rice residue treatments. Although charred biomass is seen as almost recalcitrant, its impact on trace gas (CO₂, CH₄) production and emissions in paddy fields has not been studied. We quantified the degradation of black carbon produced from rice husks in four wetland soils in laboratory incubations. In two of the studied soils the addition of carbonised rice husks resulted in a transient increase in carbon mineralisation rates in comparison to control soils without organic matter addition. After almost three years, between 4.4% and 8.5% of the black carbon added was mineralised to CO₂ under aerobic and anaerobic conditions, respectively. The addition of untreated rice husks resulted in a strong increase in carbon mineralisation rates and in the same time period 77%-100% of the added rice husks were mineralised aerobically and 31%-54% anaerobically. The ¹³C-signatures of respired CO₂ gave a direct indication of black carbon mineralisation to CO_2. In field trials we quantified the impact of rice husk black carbon or untreated rice husks on soil respiration and methane emissions. The application of black carbon had no significant effect on soil respiration but significantly enhanced methane emissions in the first rice crop season. The additional methane released accounted for only 0.14% of black carbon added. If the same amount of organic carbon was added as untreated rice husks, 34% of the applied carbon was released as CO₂ and methane in the first season. Furthermore, the addition of fresh harvest residues to paddy fields resulted in a disproportionally high increase in methane emissions. Estimating the carbon budget of the different rice crop residue treatments indicated that charring of rice residues and adding the obtained black carbon to paddy fields instead of incorporating untreated harvest residues may reduce field methane emissions by as much as 80%. Hence, the production of black carbon from rice harvest residues could be a powerful strategy for mitigating greenhouse gas emissions from rice fields.     

Does tree seedling growth and survival require weeding of Himalayan balsam (Impatiens glandulifera)?

The effect of Himalayan balsam (Impatiens glandulifera) on survival and growth of naturally regenerated silver birch (Betula pendula) and planted Norway spruce (Picea abies) and silver fir (Abies alba) seedlings was studied in a weeding experiment over 3 years. Three different treatments were applied: control, mowing, and hand weeding by pulling out the entire plant. There were no consistent treatment effects on height and diameter of the tree seedlings. The coverage of Rubus fruticosus had a negative impact on diameter increment of Norway spruce and silver fir. As opposed to growth, treatment effects on seedling survival could be found for planted Norway spruce and silver fir. However, it is very likely that these effects, namely higher seedling survival after mowing, have to be attributed to the control of bramble (Rubus fruticosus) rather than to that of Himalayan balsam. It is concluded that Himalayan balsam is not able to seriously affect the growth of already established seedlings.     

A method of preparing mesocosms for assessing complex biotic processes in soils

Equipment and handling methods for the preparation of soil mesocosms were developed. The mesocosms were used to investigate the interrelationships between mesofauna and microflora in a coniferous forest soil. Soil monoliths were taken from the ground, defaunated by deep-freezing, wrapped in nets to control reimmigration of different faunal size-classes, and replanted in the field for 8 months. in a practical test the technique described here proved to be an inexpensive field method for producing a replicated series of mesocosm in a short time. Deep-freezing is appropriate for defaunating soil monoliths. The fine nets effectively exluded meso-and macrofauna. No significant differences were found in the abundance of Enchytraeids and Collembola between recolonized mesocosms and the undisturbed control at the end of the study period. In contrast, oribatid mite abundace was still greatly reduced in the recolonized esocosms. Dominance structure and species composition of the more dominant oribatid species in the different treatments were apparently similar. To compensate for the low colonization ability of oribatids, a reintroduction of selected animal size-classes to defaunated monoliths is recommended.     

Salt‐resistant and salt‐sensitive wheat genotypes show similar biochemical reaction at protein level in the first phase of salt stress

Salinity has a two‐phase effect on plant growth, an osmotic effect due to salts in the outside solution and ion toxicity in a second phase due to salt build‐up in transpiring leaves. To elucidate salt‐resistance mechanisms in the first phase of salt stress, we studied the biochemical reaction of salt‐resistant and salt‐sensitive wheat (Triticum aestivum L.) genotypes at protein level after 10 d exposure to 125 mM–NaCl salinity (first phase of salt stress) and the variation of salt resistance among the genotypes after 30 d exposure to 125 mM–NaCl salinity (second phase of salt stress) in solution culture experiments in a growth chamber. The three genotypes differed significantly in absolute and relative shoot and root dry weights after 30 d exposure to NaCl salinity. SARC‐1 produced the maximum and 7‐Cerros the minimum shoot dry weights under salinity relative to control. A highly significant negative correlation (r² = –0.99) was observed between salt resistance (% shoot dry weight under salinity relative to control) and shoot Na⁺ concentration of the wheat genotypes studied. However, the salt‐resistant and salt‐sensitive genotypes showed a similar biochemical reaction at the level of proteins after 10 d exposure to 125 mM NaCl. In both genotypes, the expression of more than 50% proteins was changed, but the difference between the genotypes in various categories of protein change (up‐regulated, down‐regulated, disappeared, and new‐appeared) was only 1%–8%. It is concluded that the initial biochemical reaction to salinity at protein level in wheat is an unspecific response and not a specific adaptation to salinity.