Nitrogen processes in aquatic ecosystems

Executive summary Nature of the problem (science/management/policy) ��� Freshwater ecosystems play a key role in the European nitrogen (N) cycle, both as a reactive agent that transfers, stores and processes N loadings from the atmosphere and terrestrial ecosystems, and as a natural environment severely impacted by the increase of these loadings. Approaches ��� This chapter is a review of major processes and factors controlling N transport and transformations for running waters, standing waters, groundwaters and riparian wetlands. Key findings/state of knowledge ��� The major factor controlling N processes in freshwater ecosystems is the residence time of water, which varies widely both in space and in time, and which is sensitive to changes in climate, land use and management. ��� The effects of increased N loadings to European freshwaters include acidification in semi-natural environments, and eutrophication in more disturbed ecosystems, with associated loss of biodiversity in both cases. ��� An important part of the nitrogen transferred by surface waters is in the form of organic N, as dissolved organic N (DON) and particulate organic N (PON). This part is dominant in semi-natural catchments throughout Europe and remains a significant component of the total N load even in nitrate enriched rivers. ��� In eutrophicated standing freshwaters N can be a factor limiting or co-limiting biological production, and control of both N and phosphorus (P) loading is oft en needed in impacted areas, if ecological quality is to be restored. Major uncertainties/challenges ��� The importance of storage and denitrifi cation in aquifers is a major uncertainty in the global N cycle, and controls in part the response of catchments to land use or management changes. In some aquifers, the increase of N concentrations will continue for decades even if efficient mitigation measures are implemented now. ��� Nitrate retention by riparian wetlands has oft en been highlighted. However, their use for mitigation must be treated with caution, since their effectiveness is difficult to predict, and side effects include increased DON emissions to adjacent open waters, N2O emissions to the atmosphere, and loss of biodiversity. ��� In fact, the character and specific spatial origins of DON are not fully understood, and similarly the quantitative importance of indirect N2O emissions from freshwater ecosystems as a result of N leaching losses from agricultural soils is still poorly known at the regional scale. ��� These major uncertainties remain due to the lack of adequate monitoring (all forms of N at a relevant frequency), especially ��� but not only ��� in the southern and eastern EU countries. Recommendations (research/policy) ��� The great variability of transfer pathways, buffering capacity and sensitivity of the catchments and of the freshwater ecosystems calls for site specific mitigation measures rather than standard ones applied at regional to national scale. ��� The spatial and temporal variations of the N forms, the processes controlling the transport and transformation of N within freshwaters, require further investigation if the role of N in influencing freshwater ecosystem health is to be better understood, underpinning the implementation of the EU Water Framework Directive for European freshwaters.

Processes controlling DOC in pore water during simulated drought cycles in six different UK peats

The effect of episodic drought on dissolved organic carbon (DOC) dynamics in peatlands has been the subject of considerable debate, as decomposition and DOC production is thought to increase under aerobic conditions, yet decreased DOC concentrations have been observed during drought periods. Decreased DOC solubility due to drought-induced acidification driven by sulphur (S) redox reactions has been proposed as a causal mechanism; however evidence is based on a limited number of studies carried out at a few sites. To test this hypothesis on a range of different peats, we carried out controlled drought simulation experiments on peat cores collected from six sites across Great Britain. Our data show a concurrent increase in sulphate (SO4) and a decrease in DOC across all sites during simulated water table draw-down, although the magnitude of the relationship between SO4 and DOC differed between sites. Instead, we found a consistent relationship across all sites between DOC decrease and acidification measured by the pore water acid neutralising capacity (ANC). ANC provided a more consistent measure of drought-induced acidification than SO4 alone because it accounts for differences in base cation and acid anions concentrations between sites. Rewetting resulted in rapid DOC increases without a concurrent increase in soil respiration, suggesting DOC changes were primarily controlled by soil acidity not soil biota. These results highlight the need for an integrated analysis of hydrologically driven chemical and biological processes in peatlands to improve our understanding and ability to predict the interaction between atmospheric pollution and changing climatic conditions from plot to regional and global scales.

Wiener System identification using B-spline functions with De Boor recursion

A simple and effective algorithm is introduced for the system identi���cation of Wiener system based on the observational input/output data. The B-spline neural network is used to approximate the nonlinear static function in the Wiener system. We incorporate the Gauss-Newton algorithm with De Boor algorithm (both curve and the ���rst order derivatives) for the parameter estimation of the Wiener model, together with the use of a parameter initialization scheme. The ef���cacy of the proposed approach is demonstrated using an illustrative example.

Finite departure from convective quasi-equilibrium: periodic cycle and discharge-recharge mechanism

A simple self���contained theory is proposed for describing life cycles of convective systems as a discharge���recharge process. A closed description is derived for the dynamics of an ensemble of convective plumes based on an energy cycle. The system consists of prognostic equations for the cloud work function and the convective kinetic energy. The system can be closed by intro ducing a functional relationship between the convective kinetic energy and the cloud���base mass ���ux. The behaviour of this system is considered under a bulk simpli���cation. Previous cloud���resolving mo delling as well as bulk statistical theories for ensemble convective systems suggest that a plausible relationship would be to assume that the convective kinetic energy is linearly proportional to the cloud���base mass ���ux. As a result, the system reduces to a nonlinear dynamical system with two dependent variables, the cloud���base mass ���ux and the cloud work function. The fully nonlinear solution of this system always represents a periodic cycle regardless of the initial condition under constant large���scale forcing. Importantly, the inclusion of energy dissipation in this model does not in itself lead the system to an equilibrium.

Production and dissolution rates of earthworm-secreted calcium carbonate

Earthworms secrete granules of calcium carbonate. These are potentially important in soil biogeochemical cycles and are routinely recorded in archaeological studies of Quaternary soils. Production rates of calcium carbonate granules by the earthworm Lumbricus terrestris L. were determined over 27 days in a range of soils with differing chemical properties (pH, organic matter content, water holding capacity, bulk composition, cation exchange capacity and exchangeable cations). Production rate varied between soils, lay in the range 0���0.043 mmolCaCO3 (0���4.3 mg) earthworm���1 d���1 with an average rate of 8 �� 10���3 mmolCaCO3 (0.8 mg) earthworm���1 d���1 and was significantly correlated (r = 0.68, P ��� 0.01) with soil pH. In a second experiment lasting 315 days earthworms repeatedly (over periods of 39���57 days) produced comparable masses of granules. Converting individual earthworm granule production rates into fluxes expressed on per hectare of land per year basis depends heavily on estimates of earthworm numbers. Using values of 10���20 L. terrestris m���2 suggests a rate of 18��� 3139 molCaCO3 ha���1 yr���1. Data obtained from flow-through dissolution experiments suggest that at near neutral pH, granule geometric surface areanormalised dissolution rates are similar to those for other biogenic and inorganic calcium carbonate. Fits of the data to the dissolution relationship r = k(1 ��� ��)n where r = dissolution rate, k = a rate constant, �� = relative saturation and n = the reaction order gave values of k = 1.72 �� 10���10 mol cm���2 s���1 and n = 1.8 for the geometric surface area-normalised rates and k = 3.51 �� 10���13 mol cm���2 s���1 and n = 1.8 for the BET surface area-normalised rates. In 196 day leaching column experiments trends in granule dissolution rate referenced to soil chemistry corresponded to predictions made by the SLIM model for dissolution of limestone in soil. If soil solution approaches saturation with respect to calcium carbonate granule dissolution will slow or even stop and granules be preserved indefinitely. Granules have the potential to be a small but significant component of the biogeochemical cycling of C and Ca in soil.

Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand

We describe a crystal structure, at atomic resolution (1.1 ��, 100 K), of a ruthenium polypyridyl complex bound to duplex DNA, in which one ligand acts as a wedge in the minor groove, resulting in the 51�� kinking of the double helix. The complex cation ��-[Ru(1,4,5,8-tetraazaphenanthrene)2(dipyridophenazine)]2+ crystallizes in a 1���1 ratio with the oligonucleotide d(TCGGCGCCGA) in the presence of barium ions. Each complex binds to one duplex by intercalation of the dipyridophenazine ligand and also by semiintercalation of one of the orthogonal tetraazaphenanthrene ligands into a second symmetrically equivalent duplex. The result is noncovalent cross-linking and marked kinking of DNA.

Synthesis of water-soluble and ether-soluble tetra-��-acetatodiruthenium(II,III) complexes and X-ray crystal structure of [Ru2(��-O2CC6H5)4(C2H5OH)2][Ru2(��-O2CC6H5)4(HSO4)2]

[Ru2(��-O2CCH3)4Cl] reacts readily with aqueous Ag2SO4 (2: 1 molar ratio) to give the sulphate salt [Ru2(��-O2CCH3)4(H2O)2]2(SO4) (1). Addition of NaBPh4 to an aqueous solution of 1 produces the ether-soluble tetraphenylborate salt [Ru2(��-O2CCH3)4(H2O)2][BPh4] (2). A methanolic solution of 1 reacts with Ba(C6H5C���CCO2)2 �� H2O to give the tetraacetatemonophenylpropynoate complex [Ru2(��-O2CCH3)4(O2CC���CC6H5)] �� H2O (3). The reaction of an ethanolic suspension of [Ru2(��-O2CC6H5)4Cl] with Ag2SO4 and H2SO4 (2 : 1 : 1 molar ratio) leads to the tetra-��-benzoatodiruthenium(II,III) double complex salt [Ru2(��-O2CC6H5)4(C2H5OH)2][Ru2(��-O2CC6H5)4(HSO4)2] (4). Complex 4 is also obtained by reacting an ethanolic solution of 1 with an excess of benzoic acid in the presence of H2SO4. The X-ray crystal structure of 4 shows it to consist of [Ru2(��-O2CC6H5)4(C2H5OH)2]+ and [Ru2(��-O2CC6H5)4(HSO4)2]��� ions, which are linked together by hydrogen bonds into an infinite polymeric chain. The Ru���Ru distances in the cation and anion are very similar [2.265(2) and 2.272(2) ��, respectively]. Spectroscopic, magnetic, conductivity and cyclic voltammetry data are given for the complexes.

��-dimerization of pleiadiene radical cations at low temperatures revealed by UV���vis spectroelectrochemistry and quantum theory

One-electron oxidation of the non-alternant polycyclic aromatic hydrocarbon pleiadiene and related cyclohepta[ c,d]pyrene and cyclohepta[c,d]fluoranthene in THF produces corresponding radical cations detectable in the temperature range of 293���263 K only on the subsecond time scale of cyclic voltammetry. Although the EPR-active red-coloured pleiadiene radical cation is stable according to the literature in concentrated sulfuric acid, spectroelectrochemical measurements reported in this study provide convincing evidence for its facile conversion into the green-coloured, formally closed shell and, hence, EPRsilent ��-bound dimer dication stable in THF at 253 K. The unexpected formation of the thermally unstable dimeric product featuring a characteristic intense low-energy absorption band at 673 nm (1.84 eV; log��max=4.0) is substantiated by ab initio calculations on the parent pleiadiene molecule and the PF6 ��� salts of the corresponding radical cation and dimer dication. The latter is stabilized with respect to the radical cation by 14.40 kcal mol���1 (DFT B3LYP) [37.64 kcal mol���1 (CASPT2/DFT B3LYP)]. An excellent match has been obtained between the experimental and TDDFT- calculated UV���vis spectra of the PF6 ��� salt of the pleiadiene dimer dication, considering solvent (THF) effects.

Adjuvant-free immunization with hemagglutinin-Fc fusion proteins as an approach to influenza vaccines

The hemagglutinins (HAs) of human H1 and H3 influenza viruses and avian H5 influenza virus were produced as recombinant fusion proteins with the human immunoglobulin Fc domain. Recombinant HA-human immunoglobulin Fc domain (HA-HuFc) proteins were secreted from baculovirus-infected insect cells as glycosylated oligomer HAs of the anticipated molecular mass, agglutinated red blood cells, were purified on protein A, and were used to immunize mice in the absence of adjuvant. Immunogenicity was demonstrated for all subtypes, with the serum samples demonstrating subtype-specific hemagglutination inhibition, epitope specificity similar to that seen with virus infection, and neutralization. HuFc-tagged HAs are potential candidates for gene-to-vaccine approaches to influenza vaccination.

Reaping the benefits: science and the sustainable intensification of global agriculture

Food security is one of this century���s key global challenges. By 2050 the world will require increased crop production in order to feed its predicted 9 billion people. This must be done in the face of changing consumption patterns, the impacts of climate change and the growing scarcity of water and land. Crop production methods will also have to sustain the environment, preserve natural resources and support livelihoods of farmers and rural populations around the world. There is a pressing need for the ���sustainable intensifi cation��� of global agriculture in which yields are increased without adverse environmental impact and without the cultivation of more land. Addressing the need to secure a food supply for the whole world requires an urgent international effort with a clear sense of long-term challenges and possibilities. Biological science, especially publicly funded science, must play a vital role in the sustainable intensifi cation of food crop production. The UK has a responsibility and the capacity to take a leading role in providing a range of scientifi c solutions to mitigate potential food shortages. This will require signifi cant funding of cross-disciplinary science for food security. The constraints on food crop production are well understood, but differ widely across regions. The availability of water and good soils are major limiting factors. Signifi cant losses in crop yields occur due to pests, diseases and weed competition. The effects of climate change will further exacerbate the stresses on crop plants, potentially leading to dramatic yield reductions. Maintaining and enhancing the diversity of crop genetic resources is vital to facilitate crop breeding and thereby enhance the resilience of food crop production. Addressing these constraints requires technologies and approaches that are underpinned by good science. Some of these technologies build on existing knowledge, while others are completely radical approaches, drawing on genomics and high-throughput analysis. Novel research methods have the potential to contribute to food crop production through both genetic improvement of crops and new crop and soil management practices. Genetic improvements to crops can occur through breeding or genetic modifi cation to introduce a range of desirable traits. The application of genetic methods has the potential to refi ne existing crops and provide incremental improvements. These methods also have the potential to introduce radical and highly signifi cant improvements to crops by increasing photosynthetic effi ciency, reducing the need for nitrogen or other fertilisers and unlocking some of the unrealised potential of crop genomes. The science of crop management and agricultural practice also needs to be given particular emphasis as part of a food security grand challenge. These approaches can address key constraints in existing crop varieties and can be applied widely. Current approaches to maximising production within agricultural systems are unsustainable; new methodologies that utilise all elements of the agricultural system are needed, including better soil management and enhancement and exploitation of populations of benefi cial soil microbes. Agronomy, soil science and agroecology���the relevant sciences���have been neglected in recent years. Past debates about the use of new technologies for agriculture have tended to adopt an either/or approach, emphasising the merits of particular agricultural systems or technological approaches and the downsides of others. This has been seen most obviously with respect to genetically modifi ed (GM) crops, the use of pesticides and the arguments for and against organic modes of production. These debates have failed to acknowledge that there is no technological panacea for the global challenge of sustainable and secure global food production. There will always be trade-offs and local complexities. This report considers both new crop varieties and appropriate agroecological crop and soil management practices and adopts an inclusive approach. No techniques or technologies should be ruled out. Global agriculture demands a diversity of approaches, specific to crops, localities, cultures and other circumstances. Such diversity demands that the breadth of relevant scientific enquiry is equally diverse, and that science needs to be combined with social, economic and political perspectives. In addition to supporting high-quality science, the UK needs to maintain and build its capacity to innovate, in collaboration with international and national research centres. UK scientists and agronomists have in the past played a leading role in disciplines relevant to agriculture, but training in agricultural sciences and related topics has recently suffered from a lack of policy attention and support. Agricultural extension services, connecting farmers with new innovations, have been similarly neglected in the UK and elsewhere. There is a major need to review the support for and provision of extension services, particularly in developing countries. The governance of innovation for agriculture needs to maximise opportunities for increasing production, while at the same time protecting societies, economies and the environment from negative side effects. Regulatory systems need to improve their assessment of benefits. Horizon scanning will ensure proactive consideration of technological options by governments. Assessment of benefi ts, risks and uncertainties should be seen broadly, and should include the wider impacts of new technologies and practices on economies and societies. Public and stakeholder dialogue���with NGOs, scientists and farmers in particular���needs to be a part of all governance frameworks.

Integrating nitrogen fluxes at the European scale

Executive summary Nature of the problem ��� Environmental problems related to nitrogen concern all economic sectors and impact all media: atmosphere, pedosphere, hydrosphere and anthroposphere. ��� Therefore, the integration of fluxes allows an overall coverage of problems related to reactive nitrogen (Nr) in the environment, which is not accessible from sectoral approaches or by focusing on specific media. Approaches ��� This chapter presents a set of high resolution maps showing key elements of the N flux budget across Europe, including N2 and Nr fluxes. ��� Comparative nitrogen budgets are also presented for a range of European countries, highlighting the most efficient strategies for mitigating Nr problems at a national scale. A new European Nitrogen Budget (EU-27) is presented on the basis of state-of-the-art Europe-wide models and databases focusing on different segments of Europe���s society. Key findings ��� From c. 18 Tg Nr yr ���1 input to agriculture in the EU-27, only about 7 Tg Nr yr��� 1 find their way to the consumer or are further processed by industry. ��� Some 3.7 Tg Nr yr���1 is released by the burning of fossil fuels in the EU-27, whereby the contribution of the industry and energy sectors is equal to that of the transport sector. More than 8 Tg Nr yr���1 are disposed of to the hydrosphere, while the EU-27 is a net exporter of reactive nitrogen through atmospheric transport of c. 2.3 Tg Nr yr���1. ��� The largest single sink for Nr appears to be denitrifi cation to N2 in European coastal shelf regions (potentially as large as the input of mineral fertilizer, about 11 Tg N yr���1 for the EU-27); however, this sink is also the most uncertain, because of the uncertainty of Nr import from the open ocean. Major uncertainties ��� National nitrogen budgets are diffi cult to compile using a large range of data sources and are currently available only for a limited number of countries. ��� Modelling approaches have been used to fill in the data gaps in some of these budgets, but it became obvious during this study that further research is needed in order to collect necessary data and make national nitrogen budgets inter-comparable across Europe. ��� In some countries, due to inconsistent or contradictory information coming from different data sources, closure of the nitrogen budget was not possible. Recommendations ��� The large variety of problems associated with the excess of Nr in the European environment,including adverse impacts, requires an integrated nitrogen management approach that would allow for creation and closure of N budgets within European environments. ��� Development of nitrogen budgets nationwide, their assessment and management could become an effective tool to prioritize measures and prevent unwanted side effects.

Characterization of the Salmonella typhimurium proteome by semi-automated two dimensional HPLC-mass spectrometry: detection of proteins implicated in multiple antibiotic resistance

The proteome of Salmonella enterica serovar Typhimurium was characterized by 2-dimensional HPLC mass spectrometry to provide a platform for subsequent proteomic investigations of low level multiple antibiotic resistance (MAR). Bacteria (2.15 +/- 0.23 x 10(10) cfu; mean +/- s.d.) were harvested from liquid culture and proteins differentially fractionated, on the basis of solubility, into preparations representative of the cytosol, cell envelope and outer membrane proteins (OMPs). These preparations were digested by treatment with trypsin and peptides separated into fractions (n = 20) by strong cation exchange chromatography (SCX). Tryptic peptides in each SCX fraction were further separated by reversed-phase chromatography and detected by mass spectrometry. Peptides were assigned to proteins and consensus rank listings compiled using SEQUEST. A total of 816 +/- 11 individual proteins were identified which included 371 +/- 33, 565 +/- 15 and 262 +/- 5 from the cytosolic, cell envelope and OMP preparations, respectively. A significant correlation was observed (r(2) = 0.62 +/- 0.10; P < 0.0001) between consensus rank position for duplicate cell preparations and an average of 74 +/- 5% of proteins were common to both replicates. A total of 34 outer membrane proteins were detected, 20 of these from the OMP preparation. A range of proteins (n = 20) previously associated with the mar locus in E. coli were also found including the key MAR effectors AcrA, TolC and OmpF.

Protease-activated receptor 2 sensitizes the capsaicin receptor transient receptor potential vanilloid receptor 1 to induce hyperalgesia

Inflammatory proteases (mast cell tryptase and trypsins) cleave protease-activated receptor 2 (PAR2) on spinal afferent neurons and cause persistent inflammation and hyperalgesia by unknown mechanisms. We determined whether transient receptor potential vanilloid receptor 1 (TRPV1), a cation channel activated by capsaicin, protons, and noxious heat, mediates PAR2-induced hyperalgesia. PAR2 was coexpressed with TRPV1 in small- to medium-diameter neurons of the dorsal root ganglia (DRG), as determined by immunofluorescence. PAR2 agonists increased intracellular [Ca2+] ([Ca2+]i) in these neurons in culture, and PAR2-responsive neurons also responded to the TRPV1 agonist capsaicin, confirming coexpression of PAR2 and TRPV1. PAR2 agonists potentiated capsaicin-induced increases in [Ca2+]i in TRPV1-transfected human embryonic kidney (HEK) cells and DRG neurons and potentiated capsaicin-induced currents in DRG neurons. Inhibitors of phospholipase C and protein kinase C (PKC) suppressed PAR2-induced sensitization of TRPV1-mediated changes in [Ca2+]i and TRPV1 currents. Activation of PAR2 or PKC induced phosphorylation of TRPV1 in HEK cells, suggesting a direct regulation of the channel. Intraplantar injection of a PAR2 agonist caused persistent thermal hyperalgesia that was prevented by antagonism or deletion of TRPV1. Coinjection of nonhyperalgesic doses of PAR2 agonist and capsaicin induced hyperalgesia that was inhibited by deletion of TRPV1 or antagonism of PKC. PAR2 activation also potentiated capsaicin-induced release of substance P and calcitonin gene-related peptide from superfused segments of the dorsal horn of the spinal cord, where they mediate hyperalgesia. We have identified a novel mechanism by which proteases that activate PAR2 sensitize TRPV1 through PKC. Antagonism of PAR2, TRPV1, or PKC may abrogate protease-induced thermal hyperalgesia.

Ligand substituents effect on 10Dq

Reaction of 5,6-dihydro-5,6-epoxy-1,10-phenanthroline (L) with Ni(ClO4)(2)center dot 6H(2)O in methanol in 3:1 M proportion at room temperature yields [NiL3](ClO4)(2)center dot 2H(2)O. The X-ray crystal structure of the cation Nil(3)(2+) has been determined. Aminolysis of the three epoxide rings in NiL32+ by 4-substituted anilines in boiling water without any Lewis acid catalyst gives a family of Ni(II) complexes with octahedral NiL62+ core. In these complexes, crystal field splitting 10Dq varies from 11601 to 15798 cm(-1) in acetonitrile. The variation in 10Dq is found to be satisfactorily linear (r(2) = 0.951) with the Hammett sigma(R) parameter of the substituent on the anilino fragment. 10Dq increases with the increase in the electron donation ability of the substituent.

Cryopreservation of cocoa (Theobroma cacao L.) somatic embryos by vitrification

Losses of cultivated cocoa (Theobroma cacao L.) due to diseases and continued depletion of forests that harbour the wild progenitors of the crop make ex situ conservation of cocoa germplasm of paramount importance. In order to enhance security of in situ germplasm collections, 2-3 mm floral-derived secondary somatic embryos were cryopreserved by vitrification. This work demonstrates the most uncomplicated clonal cocoa cryopreservation. Optimal post-cryostorage survival (74.5%) was achieved by 5 d preculture of SSEs on 0.5 M sucrose medium followed by 60 min dehydration in cold PVS2. To minimise free radical related cryo-injury, cation sources were removed from the embryo development solution and/or the recovery medium, the former treatment resulting in a significant benefit. After optimisation with cocoa genotype AMAZ 15, the same protocol was effective across all five additional cocoa genotypes tested. For the multiplication of clones, embryos regenerated following cryopreservation were used as explant sources, and vitrification was found to maintain their embryogenic potential.