Flavonoid Responses in Wheat Grown at Elevated CO2: Green Versus Senescent Leaves

We compared flavonoids in green, mature, and senescing flag leaves of wheat grown under ambient (AC - 370 mol mol^-1) and elevated (EC - 550 mol mol^-1) concentrations of CO₂ in a FACE (Free Air CO₂ Enrichment) system. The concentrations of flag leaf flavonoids (e.g., isoorientin and tricin) decreased to one third in mature leaves, and the majoritary isoorientin almost disappeared in senescing leaves. Flavonoid concentrations increased in green well-developed flag leaves under EC (46 % isoorientin and 55 % tricin), whereas the differences disappeared in mature and senescing flag leaves. Predictions of changes in litter phenolic concentrations and their effects on decomposition rates under EC based on changes in green leaves need to be revised.     

Scoring functions in protein folding and design

We present an analysis of the assumptions behind some of the most commonly used methods for evaluating the goodness of the fit between a sequence and a structure. Our studies on a lattice model show that methods based on statistical considerations are easy to use and can capture some of the features of protein-like sequences and their corresponding native states, but unfortunately are incapable of recognizing, with certainty, the native-like conformation of a sequence among a set of decoys. Meanwhile, an optimization method, entailing the determination of the parameters of an effective free energy of interaction, is much more reliable in recognizing the native state of a sequence. However, the statistical method is shown to perform quite well in tests of protein design.     

Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles

Specific binding of antigenic peptides to major histocompatibility complex (MHC) class I molecules is a prerequisite for their recognition by cytotoxic T-cells. Prediction of MHC-binding peptides must therefore be incorporated in any predictive algorithm attempting to identify immunodominant T-cell epitopes, based on the amino acid sequence of the protein antigen. Development of predictive algorithms based on experimental binding data requires experimental testing of a very large number of peptides. A complementary approach relies on the structural conservation observed in crystallographically solved peptide-MHC complexes. By this approach, the peptide structure in the MHC groove is used as a template upon which peptide candidates are threaded, and their compatibility to bind is evaluated by statistical pairwise potentials. Our original algorithm based on this approach used the pairwise potential table of Miyazawa and Jernigan (Miyazawa S, Jernigan RL, 1996, J Mol Biol 256:623-644) and succeeded to correctly identify good binders only for MHC molecules with hydrophobic binding pockets, probably because of the high emphasis of hydrophobic interactions in this table. A recently developed pairwise potential table by Betancourt and Thirumalai (Betancourt MR, Thirumalai D, 1999, Protein Sci 8:361-369) that is based on the Miyazawa and Jernigan table describes the hydrophilic interactions more appropriately. In this paper, we demonstrate how the use of this table, together with a new definition of MHC contact residues by which only residues that contribute exclusively to sequence specific binding are included, allows the development of an improved algorithm that can be applied to a wide range of MHC class I alleles.     

作物最高理论产量计算方法的应用——以合肥地区水稻为例

本文以合肥地区水稻为例,探讨了作物最高理论产量的计算方法,即首先根据“ＦＡＯ”农业生态带理论,计算出作物光温生产力指数,再根据当地的气候（主要是水分状况）对作物的光温生产力指数进行订正,从而求出作物的最高理论产量。     

Responses of N fluxes and pools to elevated atmospheric CO2 in model forest ecosystems with acidic and calcareous soils

The objectives of this study were to estimate how soil type, elevated N deposition (0.7 vs. 7 g N m^–2y^–1) and tree species influence the potential effects of elevated CO₂ (370 vs. 570 mol CO₂ mol^–1) on N pools and fluxes in forest soils. Model spruce-beech forest ecosystems were established on a nutrient-rich calcareous sand and on a nutrient-poor acidic loam in large open-top chambers. In the fourth year of treatment, we measured N concentrations in the soil solution at different depths, estimated N accumulation by ion exchange resin (IER) bags, and quantified N export in drainage water, denitrification, and net N uptake by trees. Under elevated CO₂, concentrations of N in the soil solution were significantly reduced. In the nutrient-rich calcareous sand, CO₂ enrichment decreased N concentrations in the soil solution at all depths (–45 to –100%). In the nutrient-poor acidic loam, the negative CO₂ effect was restricted to the uppermost 5 cm of the soil. Increasing the N deposition stimulated the negative impact of CO₂ enrichment on soil solution N in the acidic loam at 5 cm depth from –20% at low N inputs to –70% at high N inputs. In the nutrient-rich calcareous sand, N additions did not influence the CO₂ effect on soil solution N. Accumulation of N by IER bags, which were installed under individual trees, was decreased at high CO₂ levels under spruce in both soil types. Under beech, this decrease occurred only in the calcareous sand. N accumulation by IER bags was negatively correlated with current-years foliage biomass, suggesting that the reduction of soil N availability indices was related to a CO₂-induced growth enhancement. However, the net N uptake by trees was not significantly increased by elevated CO₂. Thus, we suppose that the reduced N concentrations in the soil solution at elevated CO₂ concentrations were rather caused by an increased N immobilisation in the soil. Denitrification was not influenced by atmospheric CO₂ concentrations. CO₂ enrichment decreased nitrate leaching in drainage by 65%, which suggests that rising atmospheric CO₂ potentially increases the N retention capacity of forest ecosystems.     

Oak canopy effects on the distribution patterns of two annual grasses: the role of competition and soil nutrients

Within the oak woodlands of California there is often a distinct shift in the botanical composition between the open grassland and the herbaceous understory beneath oak canopy. Botanical sampling at two woodland sites indicated that the annual grass Bromus diandrus was dominant under deciduous blue oak canopy, while a congener, Bromus hordeaceus, was dominant in open grassland. We examined the relative importance of congeneric competition and edaphic factors in creating these differences in species distribution in two separate field experiments that manipulated both congeneric and intraspecific competition, as well as soil type. We used the demographic measure of relative reproductive rate as an index of population growth. In general, demographic performance correctly predicted the distribution of the two annual grasses in the field. Our results indicate that reduced abundance of B. hordeaceus under canopy reflects the negative effects of competition with B. diandrus. In contrast, B. diandrus is little affected by competition from B. hordeaceus. The reduced abundance of B. diandrus in open grassland may result, in part, from its inability to adapt as well as B. hordeaceus to lower nutrient availability in soils of the open grassland.     

Seedbed and moisture availability determine safe sites for early Thuja occidentalis (Cupressaceae) regeneration

Regeneration of many late-successional tree species depends on specialized safe sites. The primary objective was to investigate the roles of seedbed and moisture retention as dimensions of safe sites for the early regeneration of drought-sensitive northern white cedar (Thuja occidentalis). We hypothesized that rates of germination, survival, and growth of T. occidentalis are unlikely to differ among seedbed types under conditions of abundant water, but that differences are likely to emerge as water becomes more limited. In a 67-d greenhouse experiment, cedar seeds were sown on logs, leaf litter, and soil of cedar and paper birch (Betula papyrifera) canopy origin. Seedbeds were subjected to three water treatments. Among the water treatments, highest germination rates occurred within the high water treatment, although germination on cedar litter was comparable to that of the low water treatment. Higher germination and survival rates occurred on decayed logs than other natural seedbeds for medium (P = 0.001) and low (P < 0.0001) water treatments. Germination on birch logs occurred at higher rates than on cedar logs within the low water treatment (P = 0.04). Seedling growth for the medium water treatment was lower on leaf litter than any other type of seedbed (P < 0.01). Results generally demonstrated that the interplay between seedbed and moisture retention is a component of safe sites for T. occidentalis regeneration.     

Altered G protein-coupling functions of RNA editing isoform and splicing variant serotonin2C receptors

Different isoforms of serotonin subtype 2C receptor (5-HT(2C)R) with altered G protein-coupling efficacy are generated by RNA editing, which converts genomically encoded adenosine residues into inosines. In combination, editing of five sites all located within the second intracellular loop region of 5-HT(2C)R mRNA changes the gene-encoded Ile, Asn, and Ile at positions 156, 158, and 160, respectively. We analyzed the G protein-coupling functions of previously unreported editing isoform receptors. An approximately 13-fold reduction in the agonist potency for G protein-coupling stimulation as well as a significantly reduced basal level activity was observed with the thalamus-specific isoform carrying Ile156, Gly158, and Val160 (5-HT(2C)R-IGV). In contrast, the agonist was four- to five-fold less potent with 5-HT(2C)R-MSV and -IDV, detected in the amygdala and choroid plexus, respectively, indicating a dominant role for the amino acid residue at position 158 in receptor functions. We also identified a splicing variant receptor with a truncated C terminus that displayed no ligand binding capacity or G protein-coupling activity. Examination of the alternatively spliced RNA encoding this truncated receptor suggests that editing of this variant RNA occurs after completion of splicing, resulting in complete editing at all five sites.     

Microbial removal of nitrogen monoxide (NO) under aerobic conditions

Nitrogen oxide gas (NO_x), consisting of nitrogen monoxide (NO) and nitrogen dioxide (NO₂), at a low concentration corresponding to that on roads as a result of exhaust from automobiles, was supplied for 25 days through a laboratory-scale biofilter packed with soil as a packing material. The removal efficiency of NO₂ by soil was almost 100%, and the removal efficiency of NO was 60% on average and 86% at maximum. By using -irradiated soil as a packing material, NO₂ was completely removed mainly by adsorption onto or absorption into the packing material. However, the removal efficiency of NO in the sterilized soil was only 20%, suggesting that NO in soil was removed microbiologically under aerobic conditions.     

Impact of crop management on intraspecific diversity of Pseudomonas corrugata in bulk soil

Colonization at sugar beet root surfaces by seedling-inoculated biocontrol strain Pseudomonas fluorescens DR54 and native soil bacteria was followed over a period of 3 weeks using a combination of immunofluorescence (DR54-targeting specific antibody) and fluorescence in situ hybridization (rRNA-targeting Eubacteria EUB338 probe) techniques with confocal laser scanning microscopy. The dual staining protocol allowed cellular activity (ribosomal number) to be recorded in both single cells and microcolonies of strain DR54 during establishment on the root. After 2 days, the population density of strain DR54 reached a constant level at the root basis. From this time, however, high cellular activity was only found in few bacteria located as single cells, whereas all microcolony-forming cells occurring in aggregates were still active. In contrast, a low density of strain DR54 was observed at the root tip, but here many of the bacteria located as single cells were active. The native population of soil bacteria, comprising a diverse assembly of morphologically different forms and size classes, initiated colonization at the root basis only after 2 days of incubation. Hence the dual staining protocol allowed direct microscopic studies of early root colonization by both inoculant and native soil bacteria, including their differentiation into active and non-active cells and into single or microcolony-forming cells.