Deposition of ammonia to the forest floor under spruce and beech at the Höglwald site

Laboratory and field measurements of the flux of ammonia to forest floor canopies of spruce and beech stands at the Höglwald site in southern Bavaria are reported. Measurements were performed with an open chamber method. A linearity between ammonia concentration and ammonia flux from the atmosphere to the ground floor canopy was detected. Deposition of ammonia showed no saturation even at air concentrations up to 50 g NH₃ m^–3 air. Temperature, water content and the moss layer of the ground floor canopy had a minor influence on the deposition velocity in laboratory experiments. Deposition velocity of ammonia was higher to the spruce (1.3 cm s^–1), and limed spruce ground floor canopy (1.17 cm s^–1) compared to the beech stand (0.79 cm s^–1). In field studies, a diurnal course of the deposition velocity was detected with highest velocities in midday and minor during night times, but not in the climatic chamber. The flux of ammonia to the ground floor canopy was estimated of app. 10 kg N ha^–1 yr^–1 for the soil under spruce, 9 kg N ha^–1 yr^–1 for the limed spruce and 6 kg N ha^–1yr^–1 for the soil under beech. The fluxes are interpreted as fluxes from the atmosphere to the ground canopies of the stands.     

Anaerobic energy metabolism of the sulfur-reducing bacterium “Spirillum” 5175 during dissimilatory nitrate reduction to ammonia

In a batch culture experiment the microaerophilic Campylobacter-like bacterium “Spirillum” 5175 derived its energy for growth from the reduction of nitrate to nitrite and nitrite to ammonia. Hereby, formate served as electron donor, acetate as carbon source, and l-cysteine as sulfur source. Nitrite was quantitatively accumulated in the medium during the reduction of nitrate; reduction of nitrite began only after nitrate was exhausted from the medium. The molar growth yield per mol formate consumed, Y_m, was 2.4g/mol for the reduction of nitrate to nitrite and 2.0 g/mol for the conversion of nitrite to ammonia. The gain of ATP per mol of oxidized formate was 20% higher for the reduction of nitrate to nitrite, compared to the reduction of nitrite to ammonia. With succinate as carbon source and nitrite as electron acceptor, Y_m was 3.2g/mol formate, i.e. 60% higher than with acetate as carbon source. No significant amount of nitrous oxide or dinitrogen was produced during growth with nitrate or nitrite both in the presence or absence of acetylene. No growth on nitrous oxide was found. The hexaheme c nitrite reductase of “Spirillum” 5175 was an inducible enzyme. It was present in cells cultivated with nitrate or nitrite as electron acceptor. It was absent in cells grown with fumarate, but appeared in high concentration in “Spirillum” 5175 grown on elemental sulfur. Furthermore, the dissimilatory enzymes nitrate reductase and hexaheme c nitrite reductase were localized in the periplasmic part of the cytoplasmic membrane.     

Excited-state proton-transfer reactions of 7-azaindole with water,ammonia and mixed water–ammonia: microsolvated dynamics simulation

Dynamics simulations of excited-state multiple proton transfer (ESMPT) reactions in 7-azaindole (7AI) with ammonia, mixed water–ammonia, and water molecules were investigated by quantum dynamics simulations in the first-excited state using RI-ADC(2)/SVP-SV(P) in the gas phase. 7AI(WW), 7AI(WA), 7AI(AW) and 7AI(AA) clusters (W, water and A, ammonia) show very high probability of the excited-state triple proton transfer (ESTPT) occurrence in ranges from 20% for 7AI(WA) to 60% for 7AI(AW), respectively. Furthermore, 7AI(AW) clusters with ammonia placed near N–H of 7AI has the highest probability among other isomers. In 7AI with three molecules of bridged-planar of water, ammonia and mixed water–ammonia clusters, the excited-state quadruple proton transfer reactions occur ineffectively and rearrangement of hydrogen-bonded network on solvents also takes place prior to either ESTPT or excited-state double proton transfer. The role played by mixed-solvent is revealed with replacing H₂O with NH₃ in which the ESMPT is found to be more efficient corresponding to lower barrier in the excited state. The preferential number of solvent surrounding 7AI that facilitates the proton transfer process is two for methanol and water but this preferential number for ammonia is one.

Highlights: (i) replacing H₂O with NH₃ assists ESPT corresponding to lower barrier in the excited state; (ii) the ESMPT time of 7AI with mixed water–ammonia is in the sub-picosecond timescale; (iii) the PT tends to be concerted process with at least one ammonia, but synchronous without ammonia.     

Is ammonia a pathogenetic factor in Alzheimer's disease?

An attempt was made to review experimental evidence in favor of the idea that ammonia plays a role in dementia of the Alzheimer type (DAT). Hyperammonemia causes biochemical and cellular dysfunctions in the brain, which can be found in brains of DAT patients. The most conspicuous among these findings are astrocytosis, impairment of glucose utilization, and a decreased rate of energy metabolism, and the impairment of neurotransmission, with a net increase in excitability and glutamate release. The derangement of lysosomal processing of proteins is another potential site of ammonia action. This aspect is especially important in view of the growing evidence for the role of the endosomal-lysosomal system in the formation of amyloidogenic fragments from -amyloid precursor protein. Ammonia is not considered a primary factor of the disease. However, since hyperammonemia and release of ammonia from the brains of DAT patients is well supported by published observations, ammonia should be taken into account as a factor that contributes to manifestations and the progression of DAT. If elevated ammonia concentrations turn out to be indeed as important in DAT, as is suggested in this review, rational therapeutic avenues can be envisaged that lead to the amelioration of symptoms and progression of the disease.Abbreviations -AP -amyloid protein - -APP -amyloid precursor protein - CNS central nervous system - DAT dementia of the Alzheimer type - GABA -aminobutyrate - MAO monoamine oxidase - NAD nicotinamide adenine dinucleotide This paper is dedicated to Rudi Vrba, a pioneer of the neurochemistry of ammonia, and a friend, at the occasion of his 68th birthday.     

Purification and properties of adenylyl sulphate:ammonia adenylyltransferase from Chlorella catalysing the formation of adenosine 5′-phosphoramidate from adenosine 5′-phosphosulphate and ammonia

Extracts of Chlorella pyrenoidosa, Euglena gracilis var. bacillaris, spinach, barley, Dictyostelium discoideum and Escherichia coli form an unknown compound enzymically from adenosine 5′-phosphosulphate in the presence of ammonia. This unknown compound shares the following properties with adenosine 5′-phosphoramidate: molar proportions of constituent parts (1 adenine:1 ribose:1 phosphate:1 ammonia released at low pH), co-electrophoresis in all buffers tested including borate, formation of AMP at low pH through release of ammonia, mass and i.r. spectra and conversion into 5′-AMP by phosphodiesterase. This unknown compound therefore appears to be identical with adenosine 5′-phosphoramidate. The enzyme that catalyses the formation of adenosine 5′-phosphoramidate from ammonia and adenosine 5′-phosphosulphate was purified 1800-fold (to homogeneity) from Chlorella by using (NH₄)₂SO₄ precipitation and DEAE-cellulose, Sephadex and Reactive Blue 2–agarose chromatography. The purified enzyme shows one band of protein, coincident with activity, at a position corresponding to 60000–65000 molecular weight, on polyacrylamide-gel electrophoresis, and yields three subunits on sodium dodecyl sulphate/polyacrylamide-gel electrophoresis of 26000, 21000 and 17000 molecular weight, consistent with a molecular weight of 64000 for the native enzyme. Isoelectrofocusing yields one band of pI4.2. The pH optimum of the enzyme-catalysed reaction is 8.8. ATP, ADP or adenosine 3′-phosphate 5′-phosphosulphate will not replace adenosine 5′-phosphosulphate, and the apparent K_m for the last-mentioned compound is 0.82mm. The apparent K_m for ammonia (assuming NH₃ to be the active species) is about 10mm. A large variety of primary, secondary and tertiary amines or amides will not replace ammonia. One mol.prop. of adenosine 5′-phosphosulphate reacts with 1 mol.prop. of ammonia to yield 1 mol.prop. each of adenosine 5′-phosphoramidate and sulphate; no AMP is found. The highly purified enzyme does not catalyse any of the known reactions of adenosine 5′-phosphosulphate, including those catalysed by ATP sulphurylase, adenosine 5′-phosphosulphate kinase, adenosine 5′-phosphosulphate sulphotransferase or ADP sulphurylase. Adenosine 5′-phosphoramidate is found in old samples of the ammonium salt of adenosine 5′-phosphosulphate and can be formed non-enzymically if adenosine 5′-phosphosulphate and ammonia are boiled. In the non-enzymic reaction both adenosine 5′-phosphoramidate and AMP are formed. Thus the enzyme forms adenosine 5′-phosphoramidate by selectively speeding up an already favoured reaction.     

Biochar’s role as an alternative N-fertilizer: ammonia capture

Background

Biochar’s role as a carbon sequestration agent, while simultaneously providing soil fertility improvements when used as an amendment, has been receiving significant attention across all sectors of society, ranging from academia, industry, government, as well as the general public. This has lead to some exaggeration and possible confusion regarding biochar’s actual effectiveness as a soil amendment. One sparsely explored area where biochar appears to have real potential for significant impact is the soil nitrogen cycle.

Scope

Taghizadeh-Toosi et al. (this issue) examined ammonia sorption on biochar as a means of providing a nitrogen-enriched soil amendment. The longevity of the trapped ammonia was particularly remarkable; it was sequestered in a stable form for at least 12?days under laboratory air flow. Furthermore, the authors observed increased ¹⁵N uptake by plants grown in soil amended with the ¹⁵N-enriched biochar, indicating that the ¹⁵N was not irreversibly bound, but, was plant-available.

Conclusions

Their observations add credence to utilizing biochar as a carrier for nitrogen fertilization, while potentially reducing the undesired environmental consequences through gas emissions, overland flow, and leaching.     

Abundance of archaeal and bacterial ammonia oxidizers – Possible bioindicator for soil monitoring

Many soil functions are driven by soil microorganisms and they have therefore been identified as appropriate indicators for monitoring of soil status. Genetic profiling of the bacterial ammonia oxidizing community was recently top-scored as soil biological indicator (Ritz et al., 2009). However, ammonia oxidation is not only performed by bacteria, but also ammonia oxidizing archaea. Based on the suggested niche differentiation between these two groups and findings that they are susceptible to environmental change in soil ecosystems at varying scales, we suggest that the abundance of these two communities rather than community profiling of the ammonia oxidizing bacteria could serve as a relevant and cost-effective bioindicator for soil monitoring.     

Complete ammonia oxidation: an important control on nitrification in engineered ecosystems?

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Cold-temperate climate: a factor for selection of ammonia oxidizers in upland soil?

Ammonia-oxidizing bacteria in various upland soils show a rather large diversity with respect to their amoA genes (coding for a subunit of the ammonium monooxygenase). It is known that the community structure of ammonia-oxidizing bacteria in upland soils is influenced by different selective factors, such as pH, gravimetric water content, fertilizer treatment, and temperature. The question, from an ecological point of view, is whether a particular ecophysiological factor, such as temperature, could select for a particular community structure of ammonia oxidizers in upland soils that would be represented by distinct clusters of the amoA gene (AmoA cluster). Studying the literature, including recent publications and our own unpublished results, we found that AmoA clusters 3a, 3b, and 9-12 apparently exhibited no preference for either subtropical/tropical soils (i.e., warm regions) or temperate cold soils. However, AmoA clusters 1 and 4 (and perhaps cluster 2) seem to occur predominantly in soils from cold-temperate regions. Here we review the evidence for a temperature effect on the global distribution of amoA genes in warm- and cold-temperate soils.     

N–H bond cleavage of ammonia on graphene-like B36 borophene: DFT studies

The prediction of domain/linker residues in protein sequences is a crucial task in the functional classification of proteins, homology-based protein structure prediction, and high-throughput structural genomics. In this work, a novel consensus-based machine-learning technique was applied for residue-level prediction of the domain/linker annotations in protein sequences using ordered/disordered regions along protein chains and a set of physicochemical properties. Six different classifiers—decision tree, Gaussian naïve Bayes, linear discriminant analysis, support vector machine, random forest, and multilayer perceptron—were exhaustively explored for the residue-level prediction of domain/linker regions. The protein sequences from the curated CATH database were used for training and cross-validation experiments. Test results obtained by applying the developed PDP-CON tool to the mutually exclusive, independent proteins of the CASP-8, CASP-9, and CASP-10 databases are reported. An n-star quality consensus approach was used to combine the results yielded by different classifiers. The average PDP-CON accuracy and F-measure values for the CASP targets were found to be 0.86 and 0.91, respectively. The dataset, source code, and all supplementary materials for this work are available at https://cmaterju.org/cmaterbioinfo/ for noncommercial use.

     

Characteristics of ammonia oxidation potentials and ammonia oxidizers in mineral soil under <Emphasis Type="Italic">Salix polaris</Emphasis>–moss vegetation in Ny-Ålesund,Svalbard

Although nitrification is a unique and important process in the nitrogen cycle with respect to ammonium consumption and nitrate production, limited information on this process is available for high-Arctic soils. We elucidated the ammonia oxidation potentials (AOPs) and characteristics of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in mineral soils under climax vegetation, i.e., Salix polaris (polar willow)–moss vegetation, on a coastal hill in Ny-Ålesund, Svalbard. AOPs at 10 °C were determined by incubation with sufficient substrate (2 mM ammonium). The ammonia monooxygenase subunit A (amoA) genes of AOB and AOA were analyzed by using quantitative polymerase chain reaction and pyrosequencing. AOPs ranged from 1.1 to 14.1 ng N g^?1 dry soil h^?1—relatively low but of a similar order to the gross nitrification rates reported in another Svalbard study. AOP was positively correlated with thickness of the moss layer (P < 0.01), soil water content, and ammonium nitrogen content (P < 0.05). The population sizes of both AOB and AOA were not significantly related to AOP or edaphic factors. For AOB-amoA, six major operational taxonomic units (OTUs) were identified, all of which were classified into the Nitrosospira Mount Everest cluster. For AOA-amoA, six major OTUs were also identified, five of which were grouped with sequences from cold environments within clade A of the Nitrososphaera cluster, i.e., species known to have low, or no, AOP. It is, therefore, possible that the AOPs measured at the study site were driven mainly by psychrotolerant AOB.     

How to regulate a gene: to repress or to activate?

Gene-expression responses to an input can depend on growth conditions; in this issue, Sasson et al. (2012) show that this dependence is lower when the input results in a high degree of promoter occupancy.     

Production of aromatic d-amino acids from α-keto acids and ammonia by coupling of four enzyme reactions

A multi-enzyme system composed of glutamate racemase, thermostable d-amino acid aminotransferase, glutamate dehydrogenase and formate dehydrogenase was employed for the production of aromatic d-amino acids, d-phenylalanine and d-tyrosine, from the corresponding α-keto acids, phenylpyruvate and hydroxyphenylpyruvate, respectively. The optimal concentration of ammonium formate for the production of these d-amino acids was found in the range of 0.25–1.0 M. The optimal concentration of α-keto acid was determined to be 50 mM, above which the productivity greatly decreased. To keep the concentration of α-keto acid around this concentration, α-keto acid was intermittently fed into the multi-enzyme system during the production period. By running the multi-enzyme system for 35 h, 48 g l⁻¹ of d-phenylalanine and 60 g l⁻¹ of d-tyrosine were produced with 100% of optical purity from the equimolar amounts of phenylpyruvate and hydroxyphenylpyruvate, respectively. The production levels of both aromatic d-amino acids were demonstrated to be dependent on the stability of glutamate racemase.     

Study on properties of liquid ammonia via molecular dynamics simulation based on ABEEMσπ polarisable force field

Abstract

The molecular dynamics simulation has been performed to investigate the charge distribution, structural and dynamical properties of liquid ammonia at 273 K using a polarisable force field of the atom-bond electronegativity equalisation method (ABEEMσπ). One ammonia molecule in this model has eight charge sites, one N atomic site, three H atomic sites, three N–H bond sites and one lone-pair electron site. ABEEMσπ model can present the quantitative site charges of molecular ammonias in liquid and their changing in response to their surroundings. The radial distribution functions and dynamical properties are in fair agreement with the available experimental data. The first peak of g_NN(r) appears at N–N distance of ~3.50 ± 0.05 Å where most hydrogen bonds are formed. The average coordination number of the first shell is 13.0 ± 0.1 among which a central ammonia molecule intimately connects 3 ~ 4 ammonia molecules by hydrogen bonds. The power spectrum shows the vibrations of hydrogen bonds. For a reference, a simple estimation of the average hydrogen bonding energy in liquid ammonia is 6.5 ± 0.1 kcal/mol larger than 3.8 ± 0.3 kcal/mol in dimer ammonia. Our simulation results provide more detailed information about liquid ammonia.     

Novel formation of α-amino acid from α-oxo acids and ammonia in an aqueous medium

In the course of a study of possible mechanisms for chemical evolution in the primeval sea, we found the novel formation of -amino acids and N-acylamino acids from -oxo acids and ammonia in an aqueous medium. Glyoxylic acid reacted with ammonia to form N-oxalylglycine, which gave glycine in a 5–39% yield after hydrolysis with 6N HCl. Pyruvic acid and ammonia reacted to give N-acetylalanine, which formed alanine in a 3–7% overall yield upon hydrolysis. The pH optima in these reactions were between pH 3 and 4. These reactions were further extended to the formation of other amino acids. Glutamic acid, phenylalanine and alanine were formed from -ketoglutaric acid, phenylpyruvic acid and oxaloacetic acid, respectively, under similar conditions. N-Succinylglutamic acid was obtained as an intermediate in glutamic acid synthesis. Phenylacetylphenyl-alanineamide was also isolated as an intermediate in phenylalanine synthesis. Alanine, rather than aspartic acid, was produced from oxaloacetic acid. These reactions provide a novel route for the prebiotic synthesis of amino acids. A mechanism for the reactions will be proposed.     

Disgust sensitivity relates to affective responses to – but not ability to detect – olfactory cues to pathogens

Hundreds of studies have assessed variation in the degree to which people experience disgust toward substances associated with pathogens, but little is known about the mechanistic sources of this variation. The current investigation uses olfactory perception and threshold methods to test whether it is apparent at the cue-detection level, at the cue-interpretation level, or both. It further tests whether relations between disgust sensitivity and olfactory perception are specific to odors associated with pathogens. Two studies (N's = 119 and 160) of individuals sampled from a Dutch university each revealed that pathogen disgust sensitivity relates to valence perceptions of odors found in pathogen sources, but not to valence perceptions of odors not associated with pathogens, nor to intensity perceptions of odors of either type. Study 2, which also assessed olfactory thresholds via a three-alternative forced-choice staircase method, did not reveal a relation between pathogen disgust sensitivity and the ability to detect an odor associated with pathogens, nor an odor not associated with pathogens. In total, results are consistent with the idea that pathogen disgust sensitivity relates to how olfactory pathogen cues are interpreted after detection, but not necessarily to the ability to detect such cues.