Model building of a protein-protein complexed structure using saturation transfer and residual dipolar coupling without paired intermolecular NOE

For understanding the precise mechanisms of molecular recognition of proteins, three-dimensional structural analyses of the protein-protein complexes are essential. For this purpose, a new method to reveal complex structures was developed with the assistance of saturation transfer (SAT) and residual dipolar coupling (RDC) by heteronuclear NMR experiments, without any paired intermolecular NOE information. The SAT and RDC experiments provide the information of the interfacial residues and the relative orientations of the two protein molecules, respectively. Docking simulation was then made to reconstruct a complex conformation, which satisfies the SAT and RDC data. The method was applied to the CAD-ICAD complex structure, which was previously determined by the NOE-distance geometry method. The quality of the current model was evaluated.     

Interspecific difference in the photosynthesis–nitrogen relationship: patterns,physiological causes,and ecological importance

The photosynthesis–nitrogen relationship is significantly different among species. Photosynthetic capacity per unit leaf nitrogen, termed as photosynthetic nitrogen-use efficiency (PNUE), has been considered an important leaf trait to characterise species in relation to their leaf economics, physiology, and strategy. In this review, I discuss (1) relations between PNUE and species ecology, (2) physiological causes and (3) ecological implications of the interspecific difference in PNUE. Species with a high PNUE tend to have high growth rates and occur in disturbed or high productivity habitats, while those with a low PNUE occur in stressful or low productivity habitats. PNUE is an important leaf trait that correlates with other leaf traits, such as leaf mass per area (LMA) and leaf life span, irrespective of life form, phylogeny, and biomes. Various factors are involved in the interspecific difference. In particular, nitrogen allocation within leaves and the mesophyll conductance for CO₂ diffusion are important. To produce tough leaves, plants need to allocate more biomass and nitrogen to make thick cell walls, leading to a reduction in the mesophyll conductance and in nitrogen allocation to the photosynthetic apparatus. Allocation of biomass and nitrogen to cell walls may cause the negative relationship between PNUE and LMA. Since plants cannot maximise both PNUE and leaf toughness, there is a trade-off between photosynthesis and persistence, which enables the existence of species with various leaf characteristics on the earth.     

Scale-dependent relationships between the spatial distribution of a limiting resource and plant species diversity in an African grassland ecosystem

One cornerstone of ecological theory is that nutrient availability limits the number of species that can inhabit a community. However, the relationship between the spatial distribution of limiting nutrients and species diversity is not well established because there is no single scale appropriate for measuring variation in resource distribution. Instead, the correct scale for analyzing resource variation depends on the range of species sizes within the community. To quantify the relationship between nutrient distribution and plant species diversity, we measured NO₃^- distribution and plant species diversity in 16 paired, modified Whittaker grassland plots in Serengeti National Park, Tanzania. Semivariograms were used to quantify the spatial structure of NO₃^- from scales of 0.4–26 m. Plant species diversity (Shannon-Weiner diversity index; H ) was quantified in 1-m² plots, while plant species richness was measured at multiple spatial scales between 1 and 1,000 m². Small-scale variation in NO₃^- (<0.4 m) was positively correlated with 1-m² H , while 1,000-m² species richness was a log-normal function of average NO₃^- patch size. Nine of the 16 grassland plots had a fractal (self-similar across scales) NO₃^- spatial distribution; of the nine fractal plots, five were adjacent to plots that had a non-fractal distribution of NO₃^-. This finding offered the unique opportunity to test predictions of Ritchie and Olff (1999): when the spatial distribution of limiting resources is fractal, communities should display a left-skewed log-size distribution and a log-normal relationship between net primary production and species richness. These predictions were supported by comparisons of plant size distributions and biomass-richness relationships in paired plots, one with a fractal and one with a non-fractal distribution of NO₃^-. In addition, fractal plots had greater large-scale richness than paired non-fractal plots (1,0–1000 m²), but neither species diversity (H ) nor richness was significantly different at small scales (1 m²). This result is most likely explained by differences in the scale of resource variation among plots: fractal and non-fractal plots had equivalent NO₃^- variation at small scales but differed in NO₃^- variation at large scales (as measured by the fractal dimension). We propose that small-scale variation in NO₃^- is largely due to the direct effects of plants on soil, while patterns of species richness at large scales is controlled by the patch size and fractal dimension of NO₃^- in the landscape. This study provides an important empirical step in understanding the relationship between the spatial distribution of resources and patterns of species diversity across multiple spatial scales.     

Mycorrhiza does not alter low temperature impact on <Emphasis Type="Italic">Gnaphalium norvegicum</Emphasis>

Extreme arctic-alpine vegetation has relatively low affinity to form mycorrhizal symbiosis. We asked whether the mycorrhizal growth benefit for the host plant is lower at low temperatures. We investigated the role of two root-associated fungi and temperature in growth, carbon–nitrogen relations and germination of an arctic-alpine herb. Seeds of Gnaphalium norvegicum were germinated at 8° or 15°C with or without arbuscular mycorrhizal (AM, Glomus claroideum) and dark septate endophytic (DSE, Phialocephala fortinii) inocula in a climate chamber. We found that germination percentage, shoot and root biomass, shoot N% and root AM colonization were lower at 8°C than at 15°C. P. fortinii inoculation had a positive impact on germination at both temperatures, whereas G. claroideum produced no effect. N% was lower in AM plants at both temperatures. Plant biomass and shoot N content were higher in AM plants than in control plants at 15°C, but not at 8°C. DSE inoculation tended also to have positive effects on plant biomass and N content at 15°C. At 15°C, rate of photosynthesis, photosynthetic nutrient use efficiency and specific leaf area were positively affected by G. claroideum, which suggests that G. claroideum formed a carbon sink and possibly enhanced the seedling water economy. The positive effects of P. fortinii were probably due to its saprotrophic function in the substrate because it did not colonize the roots. These results suggest that the effects of AM and DSE on plant growth are affected by temperature and that the mycorrhizal benefit for the host plant was lower at the lower temperature. Low saprotrophic activity and decreased mycorrhiza-mediated nutrient acquisition may thus constrain plant nutrient acquisition in cold environments. Decreased mycorrhizal benefit may be related to the comparatively low mycotrophy of cold environment vegetation.     

Spatio-temporal patterns of soil available nutrients following experimental disturbance in a pine forest

Although disturbance is known to alter soil nutrient heterogeneity, it remains unclear whether spatial patterns in soil nutrients after disturbance follow predictable temporal changes that reflect underlying processes. This study examined the effects of tree harvesting and girdling on overall variability, geostatistical patterns, and resource congruence of soil available nutrients in a mature Pinus elliottii Engelm. forest. The two disturbances led to different patterns of vegetation removal, forest floor redistribution, and revegetation, but showed similar post-disturbance changes in overall soil nutrient variability. Soil nutrient variability increased after both disturbances by more than 5-fold, and then decreased, returning to the undisturbed level in 4 years. Spatial structures assessed using geostatistics did not show predictable temporal trends. However, girdled plots showed more persistent spatial structures in soil nutrients than harvested plots, and had semivariogram ranges mostly equal to or less than 10 m, reflecting effects of persistent and spatially stable patches of undisturbed hardwoods that had an average patch size of 10 m. Resource congruence examined with Spearman rank correlations was nil before disturbance, increased after disturbance and then became nil again by the 4th year post-disturbance. The timing of the increase was related to treatment, occurring in the 1st year after disturbance in the girdled plots, but not until the 2nd year in the harvested plots. These two patterns of congruence were potentially caused by different rates of nutrient patch formation and resource uptake by plants during early succession. Although temporal changes in soil heterogeneity have been documented previously, the present study indicates that temporal trends in nutrient variability after disturbance may be predictable, and that the marked changes in spatio-temporal patterns of soil nutrients as a result of disturbance are ephemeral.Electronic Supplementary Material Supplementary material is available in the online version of this article at     

Successional changes in soil nitrogen availability,non-symbiotic nitrogen fixation and carbon/nitrogen ratios in southern Chilean forest ecosystems

Vast areas of southern Chile are now covered by second-growth forests because of fire and logging. To study successional patterns after moderate-intensity, anthropogenic fire disturbance, we assessed differences in soil properties and N fluxes across a chronosequence of seven successional stands (2–130 years old). We examined current predictions of successional theory concerning changes in the N cycle in forest ecosystems. Seasonal fluctuations of net N mineralization (N_min) in surface soil and N availability (N_a; N_a=NH ₄ ⁺ –N+NO ₃ ^– –N) in upper and deep soil horizons were positively correlated with monthly precipitation. In accordance with theoretical predictions, stand age was positively, but weakly related to both N_a (r ²=0.282, P<0.001) and total N (N_tot; r ²=0.192, P<0.01), and negatively related to soil C/N ratios (r ²=0.187, P<0.01) in surface soils. A weak linear increase in soil N_min (upper plus deep soil horizons) was found across the chronosequence (r ²=0.124, P<0.022). N_min occurred at modest rates in early successional stands, suggesting that soil disturbance did not impair microbial processes. The relationship between N fixation (N_fix) in the litter layer and stand age best fitted a quadratic model (r ²=0.228, P<0.01). In contrast to documented successional trends for most temperate, tropical and Mediterranean forests, non-symbiotic N_fix in the litter layer is a steady N input to unpolluted southern temperate forests during mid and late succession, which may compensate for hydrological losses of organic N from old-growth ecosystems.     

Nitrogen uptake and turnover in riparian woody vegetation

The nutrient balance of streams and adjacent riparian ecosystems may be modified by the elimination of anadromous fish runs and perhaps by forest fertilization. To better understand nitrogen (N) dynamics within stream and riparian ecosystems we fertilized two streams and their adjacent riparian corridors in central Idaho. On each stream two nitrogen doses were applied to a swathe approximately 35 m wide centered on the stream. The fertilizer N was enriched in ¹⁵N to 18. This enrichment is light relative to many previous labeling studies, yet sufficient to yield a traceable signal in riparian and stream biota. This paper reports pre-treatment differences in ¹⁵N and the first-year N response to fertilizer within the riparian woody plant community. Future papers will describe the transfer of allochthonous litter N to the stream and its subsequent processing by stream biota. Pre-treatment ¹⁵N differed between the two creeks (P=0.0002), possibly due to residual salmon nitrogen in one of the creeks. Pre-treatment ¹⁵N of current-year needles was enriched compared to leaf litter, which was in turn enriched compared to needles aged 4 years and older. We conclude that fractionation due to retranslocation occurs in at least two phases. The first phase, which optimizes allocation of N in younger needle age classes, is distinctly different from the second, which conserves N prior to abscission. The ¹⁵N difference between creeks was eliminated by the fertilization (P=0.42). In the two dominant conifer species, Abies lasiocarpa and Picea engelmannii, most fertilizer N was found in the current-year foliage; little was found in older needles and none was detected in litter (P=0.53). The only N-fixing shrub species, Alnus incana, took up only a small amount of fertilizer N [mean percent N derived from fertilizer (%Ndff) 5.0±1.6% (SE)]. Far more fertilizer N was taken up by other deciduous shrubs (mean %Ndff=33.9±4.5%). Fertilizer N made up 25% (±4.2%) of the N in deciduous shrub litter. These results demonstrate the feasibility of light labeling with ¹⁵N and the potential influence of riparian plant species composition on stream nutrient dynamics via allochthonous leaf litter inputs.     

Rapid development of phosphorus limitation in temperate rainforest along the Franz Josef soil chronosequence

The aim of this study was to examine how shifts in soil nutrient availability along a soil chronosequence affected temperate rainforest vegetation. Soil nutrient availability, woody plant diversity, composition and structure, and woody species leaf and litter nutrient concentrations were quantified along the sequence through ecosystem progression and retrogression. In this super-wet, high leaching environment, the chronosequence exhibited rapid soil development and decline within 120,000 years. There were strong gradients of soil pH, N, P and C, and these had a profound effect on vegetation. N:P_leaf increased along the chronosequence as vegetation shifted from being N- to P- limited. However, high N:P_leaf ratios, which indicate P-limitation, were obtained on soils with both high and low soil P availability. This was because the high N-inputs from an N-fixing shrub caused vegetation to be P-limited in spite of high soil P availability. Woody species nutrient resorption increased with site age, as availability of N and P declined. Soil P declined 8-fold along the sequence and P resorption proficiency decreased from 0.07 to 0.01%, correspondingly. N resorption proficiency decreased from 1.54 to 0.26%, corresponding to shifts in mineralisable N. Woody plant species richness, vegetation cover and tree height increased through ecosystem progression and then declined. During retrogression, the forest became shorter, more open and less diverse, and there were compositional shifts towards stress-tolerant species. Conifers (of the Podocarpaceae) were the only group to increase in richness along the sequence. Conifers maintained a lower N:P_leaf than other groups, suggesting superior acquisition of P on poor soils. In conclusion, there was evidence that P limitation and retrogressive forests developed on old soils, but N limitation on very young soils was not apparent because of inputs from an abundant N-fixing shrub.Electronic Supplementary Material Supplementary material is available in the online version of this article at .     

Interactions of abscisic acid and sugar signalling in the regulation of leaf senescence

Leaf senescence can be triggered by a high availability of carbon relative to nitrogen or by external application of abscisic acid (ABA). Most Arabidopsis mutants with decreased sugar sensitivity during early plant development are either ABA insensitive (abi mutants) or ABA deficient (aba mutants). To analyse the interactions of carbon, nitrogen and ABA in the regulation of senescence, wild-type Arabidopsis thaliana (L.) Heynh. and aba and abi mutants were grown on medium with varied glucose and nitrogen supply. On medium containing glucose in combination with low, but not in combination with high nitrogen supply, senescence was accelerated and sucrose, glucose and fructose accumulated strongly. In abi mutants that are not affected in sugar responses during early development (abi1-1 and abi2-1), we observed no difference in the sugar-dependent regulation of senescence compared to wild-type plants. Similarly, senescence was not affected in the sugar-insensitive abi4-1 mutant. In contrast, the abi5-1 mutant did exhibit a delay in senescence compared to its wild type. As ABA has been reported to induce senescence and ABA deficiency results in sugar insensitivity during early development, we expected senescence to be delayed in aba mutants. However, the aba1-1 and aba2-1 mutants showed accelerated senescence compared to their wild types on glucose-containing medium. Our results show that, in contrast to sugar signalling in seedlings, ABA is not required for the sugar-dependent induction of leaf senescence. Instead, increased sensitivity to osmotic stress could have triggered early senescence in the aba mutants.Abbreviations ABA Abscisic acid - aba Abscisic acid deficient - abi Abscisic acid insensitive - F_v/F_m Maximum efficiency of photosystem II photochemistry