Regional Assessment of N Saturation using Foliar and Root $\varvec {\delta}^{\bf 15}{\bf N}$\varvec {\delta}^{\bf 15}{\bf N}

N saturation induced by atmospheric N deposition can have serious consequences for forest health in many regions. In order to evaluate whether foliar may be a robust, regional-scale measure of the onset of N saturation in forest ecosystems, we assembled a large dataset on atmospheric N deposition, foliar and root and N concentration, soil C:N, mineralization and nitrification. The dataset included sites in northeastern North America, Colorado, Alaska, southern Chile and Europe. Local drivers of N cycling (net nitrification and mineralization, and forest floor and soil C:N) were more closely coupled with foliar than the regional driver of N deposition. Foliar increased non-linearly with nitrification:mineralization ratio and decreased with forest floor C:N. Foliar was more strongly related to nitrification rates than was foliar N concentration, but concentration was more strongly correlated with N deposition. Root was more tightly coupled to forest floor properties than was foliar . We observed a pattern of decreasing foliar values across the following species: American beech>yellow birch>sugar maple. Other factors that affected foliar included species composition and climate. Relationships between foliar and soil variables were stronger when analyzed on a species by species basis than when many species were lumped. European sites showed distinct patterns of lower foliar , due to the importance of ammonium deposition in this region. Our results suggest that examining values of foliage may improve understanding of how forests respond to the cascading effects of N deposition.     

Regional Assessment of N Saturation using Foliar and Root \varvec {\delta}^{\bf 15}{\bf N}

N saturation induced by atmospheric N deposition can have serious consequences for forest health in many regions. In order to evaluate whether foliar may be a robust, regional-scale measure of the onset of N saturation in forest ecosystems, we assembled a large dataset on atmospheric N deposition, foliar and root and N concentration, soil C:N, mineralization and nitrification. The dataset included sites in northeastern North America, Colorado, Alaska, southern Chile and Europe. Local drivers of N cycling (net nitrification and mineralization, and forest floor and soil C:N) were more closely coupled with foliar than the regional driver of N deposition. Foliar increased non-linearly with nitrification:mineralization ratio and decreased with forest floor C:N. Foliar was more strongly related to nitrification rates than was foliar N concentration, but concentration was more strongly correlated with N deposition. Root was more tightly coupled to forest floor properties than was foliar . We observed a pattern of decreasing foliar values across the following species: American beech>yellow birch>sugar maple. Other factors that affected foliar included species composition and climate. Relationships between foliar and soil variables were stronger when analyzed on a species by species basis than when many species were lumped. European sites showed distinct patterns of lower foliar , due to the importance of ammonium deposition in this region. Our results suggest that examining values of foliage may improve understanding of how forests respond to the cascading effects of N deposition.     

Effects of common soil anions and pH on the uptake and accumulation of perchlorate in lettuce

A mechanistic understanding of perchlorate () entry into plants is important for establishing the human health risk associated with consumption of contaminated produce and for assessing the effectiveness of phytoremediation. To determine whether common soil anions affect uptake and accumulation in higher plants, a series of competition experiments using lettuce (Lactuca sativa L.) were conducted between (50 nM) and (4–12 mM), (1–10 mM), or Cl⁻ (5–15 mM) in hydroponic solution. The effects of (0–5 mM) and pH (5.5–7.5) on uptake were also examined. Increasing in solution significantly reduced the amount of taken up by green leaf, butter head, and crisphead lettuces. Sulfate and Cl⁻ had no significant effects on uptake in lettuce over the concentrations tested. Increasing pH significantly reduced the amount of taken up by crisphead and green leaf lettuces, whereas increasing significantly reduced uptake in butter head lettuce. The inhibition by across all lettuce genotypes suggests that may share an ion carrier with , and the decrease in uptake with increasing pH or provides macroscopic evidence for cotransport across the plasma membrane.     

Long-term changes in nutrient concentrations of the Changjiang River and principal tributaries

We present long-term nutrient data on the Changjiang River (Yangtze River) at six hydrological stations and eight principal tributaries during the period 1958–1985. Three patterns of temporal changes were observed in nitrate and nitrite : minimal variations in the upper catchment area, rapid increases in the middle watershed towards the end of the 1970s, and a gradual increase in the lower drainage basin. Prior to the 1970s, the level of throughout the Changjiang River system remained fairly constant. In the 1980s, however, this changed, with the lowest values in the upper Changjiang changing rapidly to the highest in the middle reaches and then declining slowly but steadily in the lower courses. Compared to and ammonium and soluble reactive phosphorus (SRP) showed smaller increases or no long-term variations, while dissolved silica (DSi) concentration generally decreased at most stations. These three patterns of and changes in the Changjiang River system were reflective of the difference in chemical fertilizer use and landscape features (e.g., slope, soil type and water body area) of the drainage basins of the primary tributaries. The decreases in DSi were most likely attributed to a reduction in suspended sediment loading due to dam constructions and increasing diatom consumption. The increase in and with a reduction in DSi concentrations in the Changjiang River could have significant effects on the stoichiometric balance of nutrients delivered to the East China Sea and the ecosystem in this dynamic region.     

Probing the interactions of the solvated electron with DNA by molecular dynamics simulations: bromodeoxyuridine substituted DNA

Solvated electrons () are produced during water radiolysis and can interact with biological substrates, including DNA. To augment DNA damage, radiosensitizers such as bromo-deoxyuridine (BUdR), often referred to as an “electron affinic radiosensitizer”, are incorporated in place of isosteric thymidine. However, little is known about the primary interactions of with DNA. In the present study we addressed this problem by applying molecular modeling and molecular dynamics (MD) simulations to a system of normal (BUdR·A)-DNA and a hydrated electron, where the excess electron was modeled as a localized (H₂O)₆ anionic cluster. Our goals were to evaluate the suitability of the MD simulations for this application; to characterize the motion of around DNA (e.g., diffusion coefficients); to identify and describe configurational states of close localization to DNA; and to evaluate the structural dynamics of DNA in the presence of . The results indicate that has distinct space-preferences for forming close contacts with DNA and is more likely to interact directly with nucleotides other than BUdR. Several classes of DNA - contact sites, all within the major groove, were distinguished depending on the structure of the intermediate water layer H-bonding pattern (or its absence, i.e., a direct H-bonding of with DNA bases). Large-scale structural perturbations were identified during and after the approached the DNA from the major groove side, coupled with deeper penetration of sodium counterions in the minor groove. Figure A rare configuration showing direct interaction between the solvated electron and DNA, where (yellow) and N7(A16) are H-bonded. The close approach from the major groove side invokes deep Na⁺ (magenta) penetration into the minor DNA groove (Fig. 7a).     

Alternate-site isotopic labeling of ribonucleotides for NMR studies of ribose conformational dynamics in RNA

Heteronuclear NMR spin relaxation studies of conformational dynamics are coming into increasing use to help understand the functions of ribozymes and other RNAs. Due to strong magnetic interactions within the ribose ring, however, these studies have thus far largely been limited to ¹³C and ¹⁵N resonances on the nucleotide base side chains. We report here the application of the alternate-site ¹³C isotopic labeling scheme, pioneered by LeMaster for relaxation studies of amino acid side chains, to nucleic acid systems. We have used different strains of E. coli to prepare mononucleotides containing ¹³C label in one of two patterns: Either C1′ or C2′ in addition to C4′, termed (1′/2′,4′) labeling, or nearly complete labeling at the C2′ and C4′ sites only, termed (2′,4′) labeling. These patterns provide isolated H spin systems on the labeled carbon atoms and thus allow spin relaxation studies without interference from scalar or dipolar coupling. Using relaxation studies of AMP dissolved in glycerol at varying temperature to produce systems with correlation times characteristic of different size RNAs, we demonstrate the removal of errors due to interaction in T ₁ measurements of larger nucleic acids and in T _1ρ measurements in RNA molecules. By extending the applicability of spin relaxation measurements to backbone ribose groups, this technology should greatly improve the flexibility and completeness of NMR analyses of conformational dynamics in RNA.     

Isolation and Characterization of Hieronymain II, Another Peptidase Isolated from Fruits of Bromelia hieronymi Mez (Bromeliaceae)

From unripe fruits of Bromelia hieronymi Mez (Bromeliaceae), a partially purified protease preparation was obtained by acetone fractionation of the crude extract. Purification was achieved by anionic exchange chromatography (FPLC) on Q-Sepharose HP followed by cationic exchange chromatography (SP-Sepharose HP). Homogeneity of the new enzyme, named hieronymain II, was confirmed by SDS-PAGE and mass spectroscopy (MALDI-TOF-TOF). The molecular mass of was 23,411 Da, and maximum proteolytic activity (more than 90% of maximum activity) was achieved at pH 7.5–9.0 on casein and at pH 7.3–8.3 on Z-Phe-Arg-p-nitroanilide. The enzyme was completely inhibited by E-64 and iodoacetic acid and activated by the addition of cysteine. The N-terminal sequence of hieronymain II (AVPQSIDWRVYGAV) was compared with those of 12 plant cysteine proteases which showed more than 70% of identity. Kinetic enzymatic assays were made on Z-Phe-Arg-p-nitroanilide ( / ). No detectable activity could be found on PFLNA or Z-Arg-Arg-p-nitroanilide.     

Topological research on diamagnetic susceptibilities of organic compounds

A novel molecular connectivity index, , based on the adjacency matrix of molecular graphs and novel atomic valence connectivities, , for predicting the molar diamagnetic susceptibilities of organic compounds is proposed. The is defined as: , where and E_i are the atomic valence connectivity and the valence orbital energy of atom i, respectively. A good QSPR model for molar diamagnetic susceptibilities can be constructed from and using multivariate linear regression (MLR). The correlation coefficient r, standard error, and average absolute deviation of the MLR model are 0.9918, 5.56 cgs, and 4.26 cgs, respectively, for the 721 organic compounds tested (training set). Cross-validation using the leave-one-out method demonstrates that the MLR model is highly reliable statistically. Using the MLR model, the average absolute deviations of the predicted values of molar diamagnetic susceptibility of another 360 organic compounds (test set) is 4.34 cgs. The results show that the current method is more effective than literature methods for estimating the molar diamagnetic susceptibility of an organic compound. The MLR method thus provides an acceptable model for the prediction of molar diamagnetic susceptibilities of organic compounds. Figure Plot of calculated vs experimental values of molar diamagnetic susceptibilities using the multivariate linear regression (MLR) model (Eq. 8)     

Improvement of pistillate flowers yield with GA3 in heavy metals treated plants

GA₃ can be beneficial to improve the flowering yield in Lagenaria siceraria (Mol.) Standl. and Luffa cylindrica L. (Roem) treated with HgCl₂ and . This paper reviews the literature on the possible involvement of gibberellins in flower development and suggests that plants under the stress of heavy metals can be treated with GA₃ to improve growth parameters, to avoid delay in flowering and likewise quality of fruit can be improved. Applied GA₃ (400 mg/l) caused precocious flowering, increasing the number of flowers in the treated plants. All data was compared with control plants grown under similar conditions. Both heavy metals caused significant delay in flowering, consequently leading to reduction in the number of flowers. However, when GA₃ was applied with HgCl₂ and , there was less decrease in staminate and pistillate flowers, revealing the dominant effect of GA₃. Current work reveals that inhibitory effects of heavy metals on flowering can be partially restored with GA₃ application.     

Quantifying Lipari–Szabo modelfree parameters from 13CO NMR relaxation experiments

It is proposed to obtain effective Lipari–Szabo order parameters and local correlation times for relaxation vectors of protein ¹³CO nuclei by carrying out a ¹³CO-R₁ auto relaxation experiment, a transverse CSA/dipolar cross correlation and a transverse ¹³CO CSA/¹³CO–¹⁵N CSA/dipolar cross correlation experiment. Given the global rotational correlation time from ¹⁵N relaxation experiments, a new program COMFORD (CO-Modelfree Fitting Of Relaxation Data) is presented to fit the ¹³CO data to an effective order parameter , an effective local correlation time and the orientation of the CSA tensor with respect to the molecular frame. It is shown that the effective is least sensitive to rotational fluctuations about an imaginary axis and most sensitive to rotational fluctuations about an imaginary axis parallel to the NH bond direction. As such, the information is fully complementary to the ¹⁵N relaxation order parameter, which is least sensitive to fluctuations about the NH axis and most sensitive to fluctuations about the axis. The new paradigm is applied on data of Ca²⁺ saturated Calmodulin, and on available literature data for Ubiquitin. Our data indicate that the order parameters rapport on slower, and sometimes different, motions than the ¹⁵N relaxation order parameters. The CO local correlation times correlate well with the calmodulin’s secondary structure. Electronic Supplementary Material Supplementary material is available to authorized users in the online version of this article at .     

Genetic structure of an insect-pollinated and bird-dispersed tropical tree in vegetation fragments and corridors: implications for conservation

In the vegetation corridors that connect small remnants of undisturbed primary forest in the Lavras landscape (Brazil), Protium spruceanum is a representative of a mass-flowering insect-pollinated and bird-dispersed tree. Allozyme variation was quantified from five forest remnants (N = 150) from secondary vegetation corridors linking them (N = 80) to generate information for genetic conservation. The species adhered to H-W equilibrium in all fragments in most of the loci. The results indicated high gene diversity in the fragments and corridors positively correlated with the plant density (r = 0.742, R ² = 0.551, d.f. = 4). We did not find evidence of inbreeding within fragments nor overall The genetic differentiation among remnants was low Evidence of recent bottlenecks by anthropogenic disturbance was detected in fragments (P < 0.05, Wilcoxon sign-rank test). The minimal viable population was estimated for conservation in situ, indicating fragments with possibilities of maintaining genetic equilibrium diversity in the short term (except F3) and in the long term (only F5). The ratios was also calculated to contribute to vegetation enrichment, area recovery or creation of new vegetation corridors. We found high levels of gene diversity in the vegetation corridors, genetic identity with the fragments and absence of inbreeding. Thus, our results suggest that landscape management strategies should therefore consider both the creation of new vegetation corridors and the protection of extant ones.     

A linked hydrodynamic and water quality model for the Salton Sea

A linked hydrodynamic and water quality model was developed and applied to the Salton Sea. The hydrodynamic component is based on the one-dimensional numerical model, DLM. The water quality model is based on a new conceptual model for nutrient cycling in the Sea, and simulates temperature, total suspended sediment concentration, nutrient concentrations, including and DO concentration and chlorophyll a concentration as functions of depth and time. Existing water temperature data from 1997 were used to verify that the model could accurately represent the onset and breakup of thermal stratification. 1999 is the only year with a near-complete dataset for water quality variables for the Salton Sea. The linked hydrodynamic and water quality model was run for 1999, and by adjustment of rate coefficients and other water quality parameters, a good match with the data was obtained. In this article, the model is fully described and the model results for reductions in external phosphorus load on chlorophyll a distribution are presented. Guest editor: S. H. Hurlbert The Salton Sea Centennial Symposium. Proceedings of a Symposium Celebrating a Century of Symbiosis Among Agriculture, Wildlife and People, 1905–2005, held in San Diego, California, USA, March 2005     

The humus layer determines SO<Subscript>4</Subscript><Superscript>2−</Superscript> isotope values in the mineral soil

Biocycling of sulfur (S) has been proposed to play an important role in the recovery of ecosystems following anthropogenic S deposition. Here, we investigated the importance of the humus layer in the biocycling of S in three forested catchments in the Gårdsjön area of southwestern Sweden with differing S inputs and S isotope signature values. These experimental sites consisted of two reference catchments and the Gårdsjön roof experiment catchment (G1), where anthropogenic deposition was intercepted from 1991 until May 2002 by a roof placed over the entire catchment area. Under the roof, controlled levels of deposition were applied, using a sprinkler system, and the only form of S added was marine SO₄²⁻ with a δ of +19.5‰.We installed ion exchange resin bags at the interface between the humus layer and mineral soil at each of the catchments to collect SO₄²⁻ passing through the humus. The resin bags were installed on four occasions, in 1999 and 2000, covering two summer and two winter periods. The ions collected by each bag during these sampling periods were then eluted and their δ values and SO₄²⁻ concentrations determined. The most striking result is that the average δ value in the resin bags was more than 12‰ lower compared to that of the sprinkler water in the G1 roof catchment. There was no increasing trend in the isotope value in the resin bag SO₄²⁻ despite that the roof treatment has been on-going for almost 10 years; the average value for all resin bags was +7.1‰. The highest δ values found in the G1 roof catchment were between +11‰ and +12‰. However, these values were all obtained from resin bags installed at a single sampling location. Throughfall and resin bag δ values were more similar in the two reference catchments: about +7.5‰ in both cases. There was, however, an increase in resin bag δ values during the first winter period, from about +7‰ to +9‰. The resin bag δ value was linearly and positively related (r² = 0.26, p < 0.001) to the amount of SO₄²⁻ extracted from the resin bags, if relatively high amounts (>50 mmol m⁻²) were excluded. High amounts of resin bag SO₄²⁻ seemed to be related to groundwater inputs, as indicated by the δ value. Our results suggest that rapid immobilization of SO₄²⁻ into a large organic S pool may alter the S isotope value and affect the δ values measured in the mineral soil and runoff.     

Effect of nickel on ROS content and antioxidative enzyme activities in wheat leaves

Influence of 100 μM Ni on growth, Ni accumulation,, H₂O₂ and lipid peroxides contents as well as the activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), guaiacol peroxidase (POD) and glutathione peroxidase (GSH-Px) were studied in the leaves of wheat plants on the 3rd, 6th and 9th days after treatment. Exposure of the plants to Ni for only 3 days led to almost 200-fold increase in this metal concentration in the leaf tissue but later the rate of Ni accumulation was much slower. Length and fresh weight of the leaves were substantially reduced, up to 25% and 39%, respectively at the end of experiment. Visible symptoms of Ni toxicity: chlorosis and necrosis were observed following the 3rd day. Treatment with Ni resulted in the increase in and H₂O₂ contents in the leaves. Both showed their highest values, approximately 250% of those of the control, on the 3rd day and then their levels decreased but still markedly exceeded the control values. SOD and CAT activities decreased significantly in response to Ni treatment, however a several-fold increase in APX and POD activities was found. No significant changes in lipid peroxides content were observed in the leaves after Ni application. The activity of GSH-Px showed a 29% induction on the 3rd day. Our results indicated that despite prolonged increases in and H₂O₂ levels, oxidative damage, measured as the level of lipid peroxidation, did not occur in the leaves of Ni-treated wheat.     

Cell-to-cell pathway dominates xylem-epidermis hydraulic connection in<Emphasis Type="Italic"> Tradescantia fluminensis</Emphasis> (Vell. Conc.) leaves

A steady supply of water is indispensable for leaves to fulfil their photosynthetic function. Understanding water movement in leaves, especially factors that regulate the movement of water flux from xylem to epidermis, requires that the nature of the transport pathway be elucidated. To determine the hydraulic linkage between xylem and epidermis, epidermal cell turgor pressure (P _t) in leaves of Tradescantia fluminensis was monitored using a cell pressure probe in response to a 0.2 MPa step change in xylem pressure applied at the leaf petiole. Halftime of P _t changes were 10–30 times greater than that of water exchange across an individual cell membrane suggesting that cell-to-cell water transport constitutes a significant part of the leaf hydraulic path from xylem to epidermis. Furthermore, perfusion of H₂O₂ resulted in increases of both and by a factor of 2.5, indicating that aquaporins may play a role in the xylem to epidermis hydraulic link. The halftime for water exchange did not differ significantly between cells located at the leaf base (2.5 s), middle (2.6 s) and tip (2.5 s), indicating that epidermal cell hydraulic properties are similar along the length of the leaf. Following the pressure application to the xylem (0.2 MPa), P _t changed by 0.12, 0.06 and 0.04 MPa for epidermal cells at the base, middle and the tip of the leaf, respectively. This suggests that pressure dissipation between xylem and epidermis is significant, and that the pressure drop along the vein may be due to its structural similarities to a porous pipe, an idea which was further supported by measurements of xylem hydraulic resistance using a perfusion technique.     

Inferential backbone assignment for sparse data

This paper develops an approach to protein backbone NMR assignment that effectively assigns large proteins while using limited sets of triple-resonance experiments. Our approach handles proteins with large fractions of missing data and many ambiguous pairs of pseudoresidues, and provides a statistical assessment of confidence in global and position-specific assignments. The approach is tested on an extensive set of experimental and synthetic data of up to 723 residues, with match tolerances of up to 0.5 ppm for and resonance types. The tests show that the approach is particularly helpful when data contain experimental noise and require large match tolerances. The keys to the approach are an empirical Bayesian probability model that rigorously accounts for uncertainty in the data at all stages in the analysis, and a hybrid stochastic tree-based search algorithm that effectively explores the large space of possible assignments.     

A graph-theoretic method for the basic reproduction number in continuous time epidemiological models

In epidemiological models of infectious diseases the basic reproduction number is used as a threshold parameter to determine the threshold between disease extinction and outbreak. A graph-theoretic form of Gaussian elimination using digraph reduction is derived and an algorithm given for calculating the basic reproduction number in continuous time epidemiological models. Examples illustrate how this method can be applied to compartmental models of infectious diseases modelled by a system of ordinary differential equations. We also show with these examples how lower bounds for can be obtained from the digraphs in the reduction process.     

A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci*

Analysis of linkage disequilibrium (=mean squared correlation of allele frequencies at different gene loci) provides a means of estimating effective population size (N _e) from a single sample, but this method has seen much less use than the temporal method (which requires at least two samples). It is shown that for realistic numbers of loci and alleles, the linkage disequilibrium method can provide precision comparable to that of the temporal method. However, computer simulations show that estimates of N _e based on for unlinked, diallelic gene loci are sharply biased downwards ( in some cases) if sample size (S) is less than true N _e. The bias is shown to arise from inaccuracies in published formula for when S and/or N _e are small. Empirically derived modifications to for two mating systems (random mating and lifetime monogamy) effectively eliminate the bias (residual bias in % in most cases). The modified method also performs well in estimating N _e in non-ideal populations with skewed sex ratio or non-random variance in reproductive success. Recent population declines are not likely to seriously affect , but if N has recently increased from a bottleneck can be biased downwards for a few generations. These results should facilitate application of the disequilibrium method for estimating contemporary N _e in natural populations. However, a comprehensive assessment of performance of with highly polymorphic markers such as microsatellites is needed.The US Governmentȁ9s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.