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PubMed1995

Characterization of nuclear factors for elicitor-mediated activation of the promoter of the pea phenylalanine ammonia-lyase gene 1.

The nuclear factors presumably associated with the activation of the gene encoding phenylalanine ammonia-lyase by a fungal elicitor were characterized in pea (Pisum sativum L.) epicotyls. The TATA-proximal region was dissected and putative cis-regulatory elements in the promoter of pea phenylalanine ammonia-lyase gene 1 were examined by gel-mobility shift and in vitro footprinting analyses. Specific binding of the nuclear factors to the promoter-proximal regions of pea phenylalanine ammonia-lyase gene 1 associated with elicitor-mediated activation was detected at a region containing consensus sequence motifs of boxes 2 and 4 and other AT-rich sequences. The analyses of DNA fragments containing the deleted promoter regions suggested that a residue from -183 to -173 (ATTAGTAAGTGAT) was essential for a maximal activity of forming low-mobility complex (LMC) in the gel-mobility shift assay, and synthetic oligonucleotides confirmed the presence of at least one nuclear component associated with the formation of an active LMC. Competition experiments and treatment with Hoechst 33258 provided direct evidence that the formation of LMC with the promoter fragments from genes encoding phenylalanine ammonia-lyase and chalcone synthase in pea contained one or more of the same proteins that recognize AT-rich sequence motifs for binding. It also suggests that common high-mobility group-like proteins might be involved in the regulation of elicitor-inducible genes in pea.

Base Sequence↗
PubMedDate not supplied

The toxicity to rat cerebral cortex or topical applications of acetaldehyde, ammonia or bilirubin.

The relative toxicity of acetaldehyde, ammonia and bilirubin to cerebral cortex of rats has been tested by superfusion of the intact dura for 1 h with each toxin separately. The cortex was examined histologically after 6 days survival using a silver strain which selectively impregnates degenerating axons and their synaptic terminals. A tissue concentration of 30 mM acetaldehyde was found to cause axonal and terminal degeneration, whereas 11 mM acetaldehyde was not toxic, and did not produce any structural changes detectable by electron microscopy. In terms of tissue concentrations, acetaldehyde was at least 27 times more toxic than ethanol on a molar basis. However, the acetaldehyde concentration necessary to produce neuronal degeneration in a 1 h exposure is many times greater than ever reported in CSF in human alcoholism. Both ammonia and bilirubin are capable of causing neuronal degeneration, but we have not measured the tissue concentrations that are toxic. Comparison of molar concentrations in the superfusing fluids showed that ammonia is at least 39 times more toxic than acetaldehyde, and at least 1000 times more toxic than ethanol. Superfusion with an ethanolic solution of bilirubin (2.5mM) was strongly toxic, but this solution diluted to 50% with saline was not toxic. The possibility exists that ammonia or bilirubin may reach concentrations toxic to neurons in alcoholism, especially in the presence of liver damage.

Acetaldehyde↗
PubMed1988

Role of cyclic AMP and ammonia in induction and maintenance of post-aggregative differentiation in a suspension culture of Dictyostelium discoideum.

The effects of ammonia and cAMP on prespore and prestalk differentiation of Dictyostelium discoideum were investigated by monitoring eight developmentally regulated proteins as differentiation markers under the shake culture conditions in glucose/albumin medium. In the medium containing cAMP, cells form small agglomerates and undergo prespore differentiation [19]. Under the conditions where agglomeration was prevented, ammonia induced four marker proteins out of eight tested in the presence of cAMP, which included not only a prespore specific enzyme but also cell-type non-specific proteins. No inhibitory effect of ammonia was observed in presumptive cell differentiation. These results suggest that ammonia is an inducer of differentiation at the protein level as well as the mRNA level as found previously [24]. The effects of cAMP were examined with special attention to the difference between induction of differentiation and maintenance of differentiated state in this specific medium. The induction of differentiation from early aggregative cells was cAMP-dependent with all the marker proteins tested. This agrees with the observations so far obtained in other culture systems. However, when already differentiated cell masses (slugs) were dissociated and shaken in this specific medium, only two enzymes required cAMP to maintain the activity while five out of eight kinds of the proteins continued to be expressed as in undisturbed slugs even without cAMP. This suggests that for the maintenance of the differentiated state after slug disaggregation cAMP may not be required with respect to the majority of proteins, if cells are provided with some favorable conditions such as glucose/albumin medium.

Ammonia↗
PubMed1987

Use of a bioreactor consisting of sequentially aligned L-glutamate dehydrogenase and L-glutamate oxidase for the determination of ammonia by chemiluminescence.

A chemiluminometric method for the automated flow injection analysis of ammonia is described. The essence of the invention is the use of a bioreactor consisting of both immobilized L-glutamate dehydrogenase (GLDH) and L-glutamate oxidase (GLXD), which are sequentially aligned in this order in a minicolumn measuring 2.0 X 20 mm. The unidirectional constant flow of liquid through the column reactor minimizes the reversed diffusion of the solutes so that the following sequence of reactions is ensured. Thus, ammonia to be determined is first transformed by GLDH into L-glutamate, which then produces hydrogen peroxide by GLXD. Hydrogen peroxide in the effluent from the column is then determined by its chemiluminescence upon admixing with luminol and potassium ferricyanide. The present method gives linearity of the standard curve for ammonia up to 1.0 mM. It is at least 100 times more sensitive than the conventional method for ammonia assay using ultraviolet absorption measurement.

Amino Acid Oxidoreductases↗
PubMed2006

Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples.

PCR-based techniques are commonly used to characterize microbial communities, but are subject to bias that is difficult to assess. This study aimed to evaluate bias of several PCR primer-based strategies used to study diversity of autotrophic ammonia oxidizers. 16S rRNA genes from soil- or sediment-DNA were amplified using primers considered either selective or specific for betaproteobacterial ammonia oxidizers. Five approaches were assessed: (a) amplification with primers betaAMO143f-betaAMO1315r; (b) amplification with primers CTO189f-CTO654r; (c) nested amplification with betaAMO143f-betaAMO1315r followed by CTO189f-CTO654r primers; (d) nested amplification with betaAMO143f-betaAMO1315r and CTO189f-Pf1053r primers; (e) nested amplification with 27f-1492r and CTO189f-CTO654r primers. Amplification products were characterized by denaturing gradient gel electrophoresis (DGGE) analysis after further amplification with 357f-GC-518r primers. DGGE profiles of soil communities were heterogeneous and depended on the approach followed. Ammonia oxidizer diversity was higher using approaches (b), (c) and (e) than using (a) and (d), where sequences of the most prominent bands showed similarities to nonammonia oxidizers. Profiles from marine sediments were more consistent, regardless of the approach adopted, and sequence analysis of excised bands indicated that these consisted of ammonia oxidizers only. The study demonstrates the importance of choice of primer, of screening for sequences of nontarget organisms and use of several approaches when characterizing microbial communities in natural environments.

Ammonia↗
PubMed2000

The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae.

Saccharomyces cerevisiae is able to use a wide variety of nitrogen sources for growth. Not all nitrogen sources support growth equally well. In order to select the best out of a large diversity of available nitrogen sources, the yeast has developed molecular mechanisms. These mechanisms consist of a sensing mechanism and a regulatory mechanism which includes induction of needed systems, and repression of systems that are not beneficial. The first step in use of most nitrogen sources is its uptake via more or less specific permeases. Hence the first level of regulation is encountered at this level. The next step is the degradation of the nitrogen source to useful building blocks via the nitrogen metabolic pathways. These pathways can be divided into routes that lead to the degradation of the nitrogen source to ammonia and glutamate, and routes that lead to the synthesis of nitrogen containing compounds in which glutamate and glutamine are used as nitrogen donor. Glutamine is synthesized out of ammonia and glutamate. The expression of the specific degradation routes is also regulated depending on the availability of a particular nitrogen source. Ammonia plays a central role as intermediate between degradative and biosynthetic pathways. It not only functions as a metabolite in metabolic reactions but is also involved in regulation of metabolic pathways at several levels. This review describes the central role of ammonia in nitrogen metabolism. This role is illustrated at the level of enzyme activity, translation and transcription.

Ammonia↗
PubMed1981

Cerebrovascular effects of ammonia in vitro.

The effect of ammonia (ammonium salts) upon human and rabbit cerebral arteries was studied in vitro. Ammonia (NH3/NH4+) caused relaxation of cerebrovascular smooth muscle which was transient and occurred irrespective of how the vessels were preconstricted (potassium-Krebs solution, noradrenaline, serotonin, prostaglandin F2 alpha). The effect was independent of ammonia-induced extracellular changes in pH. It is concluded that ammonia may contribute to the vasodilatation and increase in cerebral blood flow which occurs under certain pathophysiological conditions.

Ammonia↗
PubMed1992

Amperometric assay of creatinine in urine by flow injection analysis based on conjugated reactions of immobilized enzymes. Simultaneous compensation of endogenous ammonia.

A flow-injection analysis biosensor system was developed for the amperometric assay of creatinine based on coupled reactions of three immobilized enzymes, using an oxygen electrode as the detection device. The ammonia produced by creatinine deiminase-catalyzed hydrolysis of creatinine was further converted into L-glutamate with two sequentially aligned enzyme reactors: glutamate dehydrogenase and glutamate oxidase. Endogenous ammonia was simultaneously compensated with a double peak recording system, where the flow was split after sample injection and rejoined before the glutamate dehydrogenase reactor. The system gave linear calibration in a range of 0.1-2.0 mM for creatinine and the first peak of ammonia, and 0.1-3.0 mM for the second peak of ammonia. One run was completed within two minutes. The system can be readily applied to the assay of creatinine in urine and showed good correlation with that from the currently used Jaffe method.

Amino Acid Oxidoreductases↗
PubMed1995

A multifunctional flow-injection biosensor for the simultaneous determination of ammonia, creatinine, and urea.

A strategy for the multifunctionalization of the FIA biosensor was developed. The described multifunctional FIA system offers a fast and simple method for the simultaneous determination of ammonia, creatinine, and urea. The hydrolysis of creatinine by creatinine deiminase (CRDI) or of urea by urease forms ammonia, which is amperometrically detected by an oxygen electrode, based on an enzyme conversion system, glutamate dehydrogenase (GLDH)/glutamate oxidase (GLOD). The split of the stream into three after sample injection and confluence before the GLDH reactor resulted in a three-channel system, into which were set three parallel columns, respectively, filled with immobilized CRDI, urease, and CPG. A triple-peak recording was obtained by putting two delay coils at the channels involving CRDI and urease. Thus the interfering of the endogenous ammonia on the creatinine and urea assay is simultaneously compensated. Furthermore, the problem of great difference in concentration between urea and the other two components is resolved by taking advantage of the differentiated dilution effect for each channel caused from the split-stream, flow-injection system. Linear calibration ranges for ammonia, creatinine, and urea were 0.1-5, 0.2-10, and 2-40 mM, respectively. One run was finished within 5 minutes, and the system was reproducibility good (3 to 5%). The results of the urine assay obtained by the present method will be described in the near future.

Amino Acid Oxidoreductases↗
PubMedDate not supplied

Ammonia metabolism and the urea cycle: function and clinical implications.

Disposal of waste products accumulated during metabolic processes is integral to the health of any living organism. Disposal of excess nitrogen and ammonia is no exception. Although nitrogen is essential for growth and maintenance in animals, an excess of some nitrogenous compounds can quickly lead to toxicity and death. Because of the correlation between ammonia accumulation and clinical disease, it is important for veterinary clinicians to understand the physiological mechanisms used to dispose of nitrogen and ammonia. Therefore, the purposes of this article are to review ammonia metabolism, the urea cycle, and the clinical implications of urea cycle dysfunction in diseases of companion animals.

Acid-Base Equilibrium↗
PubMed1994

Studies on the transport in vitro of lysine, histidine, arginine and ammonia across the mucosa of the equine colon.

Discs of stripped mucosa from the proximal ventral colon were prepared immediately after slaughter of 8 Shetland cross-breed ponies. The mucosae were fixed in incubation chambers and used in incubation experiments to study the transmucosal fluxes of the amino acids lysine, histidine and arginine (150 min) and of ammonia (90 min). When the amino acid concentrations in the mucosal solution were in the physiological range (2.8-3.0 mmol/l) no transport to the serosal side of the tissue was found. When the concentrations were raised 10-fold, less than 2% of the mucosal amino acid pool was recovered in the serosal solution. Ammonia was transported across the mucosa at significant rates although only 63% of the ammonia that disappeared from the mucosal solution was found in the serosal solution. The findings show that the equine proximal colon is virtually impermeable to luminal free amino acids whereas ammonia is transported at rates equal to, or higher than those observed with rumen mucosa from sheep.

Amino Acids, Essential↗
PubMed1981

Effects of increased blood ammonia concentrations on the concentrations of some metabolites in rat tissues.

Rats were given ammonium chloride intravenously (5 and 10 mg per 100 g body weight) and sacrificed 30 sec, 5 min and 30 min after injection. Ammonia concentrations were determined in brain, liver, skeletal muscle and epididymial fat, and glycogen, glucose, pyruvate, lactate, ATP and cyclic AMP were assayed in brain, liver and muscle. In control animals, muscle and fat showed a high capacity for ammonia accumulation. After injection of NH4Cl the ammonia concentration increased in all tissues analysed, particularly in muscle and fat, where ammonia concentrations remained elevated for 30 min. In brain, glycogen was reduced whereas glucose, pyruvate, lactate and cyclic AMP levels were raised. In liver, glycogen was lower and glucose higher than in controls. ATP concentrations were unchanged in both tissues. In muscle samples taken 30 sec and 5 min after dosing, glycogen concentrations were not affected but glucose, pyruvate and lactate concentrations were reduced and ATP concentrations were increased. In muscle samples taken after 30 min metabolite concentrations were normal again but glycogen concentrations had dropped.

Adenosine Triphosphate↗
PubMed1972

Air containing nitrogen-15 ammonia: foliar absorption by corn seedlings.

Thirty-day-old corn seedlings, grown in the greenhouse with different concentrations of supplemental nitrate nitrogen, were moved to a constant-temperature growth chamber and sealed in a 560-liter tent made of polyvinyl chloride. The plants were exposed to air containing ammonia labeled with nitrogen-15 (1, 10, and 20 parts per million) for 24 hours and then harvested. The nitrogen-15 content of the tops and roots showed that at 1 part per million 43 percent of the ammonia was absorbed, whereas at 10 and 20 parts per million, 30 percent of the ammonia was absorbed. The results demonstrate that growing plants may be a natural sink for atmospheric ammonia.

Air↗
PubMed1999

Superionic and metallic states of water and ammonia at giant planet conditions.

The phase diagrams of water and ammonia were determined by constant pressure ab initio molecular dynamic simulations at pressures (30 to 300 gigapascal) and temperatures (300 to 7000 kelvin) of relevance for the middle ice layers of the giant planets Neptune and Uranus. Along the planetary isentrope water and ammonia behave as fully dissociated ionic, electronically insulating fluid phases, which turn metallic at temperatures exceeding 7000 kelvin for water and 5500 kelvin for ammonia. At lower temperatures, the phase diagrams of water and ammonia exhibit a superionic solid phase between the solid and the ionic liquid. These simulations improve our understanding of the properties of the middle ice layers of Neptune and Uranus.

Ammonia↗
PubMed2006

Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahía del Tóbari, Mexico.

Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase alpha-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterial amoA gene was PCR amplifiable from only 40% of samples. Bacterial amoA libraries were dominated by a few widely distributed Nitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaeal amoA diversity in estuarine sediments and demonstrate that diverse communities of Crenarchaeota capable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.

Ammonia↗
PubMed1989

More monensin-sensitive, ammonia-producing bacteria from the rumen.

Two monensin-sensitive bacteria which utilized carbohydrates poorly and grew rapidly on amino acids were isolated from the bovine rumen. The short rods (strain SR) fermented arginine, serine, lysine, glutamine, and threonine rapidly (greater than 158 nmol/mg of protein per h) and grew faster on casein digest containing short peptides than on free amino acids ().34 versus 0.29 h(-1)). Gelatin hydrolysate, an amino acid source containing an abundance of long peptides, was unable to support growth or ammonia production, but there was a large increase in ammonia production if strain SR was cocultured with peptidase-producing ruminal bacteria (Bacteroides ruminicola or Streptococcus bovis). Cocultures showed no synergism with short peptides. Strain SR washed out of continuous culture ().1 h(-1)) at pH 5.9. The irregularly shaped organisms (strain F) deaminated glutamine, histidine, glutamate, and serine rapidly (greater than 137 nmol/mg of protein per min) and grew faster on free amino acids than on short peptides ().43 versus 0.21 h(-1)). When strain F was provided with casein or gelatin hydrolysate and cocultured with peptidase-producing bacteria, there was a more than additive increase in ammonia production. Strain F grew in continuous culture (0.1 h(-1)) when the pH was as low as 5.3. The irregularly shaped cells and short rods were present at less than 10(9)/ml in vivo, but they ahd very high specific activities of ammonia production (greater than 310 nmol of ammonia/mg of protein per min) and could play an important role in ruminal amino acid fermentation.

Amino Acids↗
PubMed1990

Detection and analysis of two serotypes of ammonia-oxidizing bacteria in sewage plants by flow cytometry.

Two different serotypes of the genus Nitrosomonas were isolated from samples of the sewage plant Heidelberg. These nitrifiers were enumerated in activated sludge of various other sewage plants after immunofluorescent labeling and staining with propidium iodide by flow cytometry. The concentrations of these serotypes of Nitrosomonas spp. were in the range of 0.1 to 2%. Also, a test for the determination of the activity of ammonia-oxidizing bacteria was developed. Nitrite-oxidizing bacteria were specifically inhibited with sodium chlorate, and the activity of ammonia-oxidizing bacteria could be calculated from the increase of nitrite. Concentrations and activities of ammonia oxidizers were measured for a period of 6 months in the sewage plant Heidelberg. With one exception, activities and concentrations of ammonia-oxidizing bacteria decreased and increased in parallel.

Ammonia↗
PubMed1998

Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools.

Biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. Although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. In this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. Both 16S rRNA and ammonia monooxygenase (amoA) genes were used to characterize the heterotrophic and ammonia-oxidizing bacteria collected from the biofilter during a 102-day experiment. The overall diversity of the heterotrophic microbial population appeared to decrease by 38% at the end of the experiment. The community structure of the heterotrophic population also shifted from predominantly members of two subdivisions of the Proteobacteria (the beta and gamma subdivisions) to members of one subdivision (the gamma subdivision). An overall decrease in the diversity of ammonia monooxygenase genes was not observed. However, a shift from groups dominated by organisms containing Nitrosomonas-like and Nitrosospira-like amoA genes to groups dominated by organisms containing only Nitrosospira-like amoA genes was observed. In addition, a new amoA gene was discovered. This new gene is the first freshwater amoA gene that is closely affiliated with Nitrosococcus oceanus and the particulate methane monooxygenase gene from the methane oxidizers belonging to the gamma subdivision of the Proteobacteria.

Amino Acid Sequence↗