Identifying pathways and processes affecting nitrate and orthophosphate inputs to streams in agricultural watersheds

USGS Publications Warehouse

Tesoriero, A.J.; Duff, J.H.; Wolock, D.M.; Spahr, N.E.; Almendinger, J.E.

2009-01-01

Understanding nutrient pathways to streams will improve nutrient management strategies and estimates of the time lag between when changes in land use practices occur and when water quality effects that result from these changes are observed. Nitrate and orthophosphate (OP) concentrations in several environmental compartments were examined in watersheds having a range of base flow index (BFI) values across the continental United States to determine the dominant pathways for water and nutrient inputs to streams. Estimates of the proportion of stream nitrate that was derived from groundwater increased as BFI increased. Nitrate concentration gradients between groundwater and surface water further supported the groundwater source of nitrate in these high BFI streams. However, nitrate concentrations in stream-bed pore water in all settings were typically lower than stream or upland groundwater concentrations, suggesting that nitrate discharge to streams was not uniform through the bed. Rather, preferential pathways (e.g., springs, seeps) may allow high nitrate groundwater to bypass sites of high biogeochemical transformation. Rapid pathway compartments (e.g., overland flow, tile drains) had OP concentrations that were typically higher than in streams and were important OP conveyers in most of these watersheds. In contrast to nitrate, the proportion of stream OP that is derived from ground water did not systematically increase as BFI increased. While typically not the dominant source of OP, groundwater discharge was an important pathway of OP transport to streams when BFI values were very high and when geochemical conditions favored OP mobility in groundwater. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis.

PubMed

Hyde, Embriette R; Andrade, Fernando; Vaksman, Zalman; Parthasarathy, Kavitha; Jiang, Hong; Parthasarathy, Deepa K; Torregrossa, Ashley C; Tribble, Gena; Kaplan, Heidi B; Petrosino, Joseph F; Bryan, Nathan S

2014-01-01

The microbiota of the human lower intestinal tract helps maintain healthy host physiology, for example through nutrient acquisition and bile acid recycling, but specific positive contributions of the oral microbiota to host health are not well established. Nitric oxide (NO) homeostasis is crucial to mammalian physiology. The recently described entero-salivary nitrate-nitrite-nitric oxide pathway has been shown to provide bioactive NO from dietary nitrate sources. Interestingly, this pathway is dependent upon oral nitrate-reducing bacteria, since humans lack this enzyme activity. This pathway appears to represent a newly recognized symbiosis between oral nitrate-reducing bacteria and their human hosts in which the bacteria provide nitrite and nitric oxide from nitrate reduction. Here we measure the nitrate-reducing capacity of tongue-scraping samples from six healthy human volunteers, and analyze metagenomes of the bacterial communities to identify bacteria contributing to nitrate reduction. We identified 14 candidate species, seven of which were not previously believed to contribute to nitrate reduction. We cultivated isolates of four candidate species in single- and mixed-species biofilms, revealing that they have substantial nitrate- and nitrite-reduction capabilities. Colonization by specific oral bacteria may thus contribute to host NO homeostasis by providing nitrite and nitric oxide. Conversely, the lack of specific nitrate-reducing communities may disrupt the nitrate-nitrite-nitric oxide pathway and lead to a state of NO insufficiency. These findings may also provide mechanistic evidence for the oral systemic link. Our results provide a possible new therapeutic target and paradigm for NO restoration in humans by specific oral bacteria.

Metagenomic Analysis of Nitrate-Reducing Bacteria in the Oral Cavity: Implications for Nitric Oxide Homeostasis

PubMed Central

Hyde, Embriette R.; Andrade, Fernando; Vaksman, Zalman; Parthasarathy, Kavitha; Jiang, Hong; Parthasarathy, Deepa K.; Torregrossa, Ashley C.; Tribble, Gena; Kaplan, Heidi B.; Petrosino, Joseph F.; Bryan, Nathan S.

2014-01-01

The microbiota of the human lower intestinal tract helps maintain healthy host physiology, for example through nutrient acquisition and bile acid recycling, but specific positive contributions of the oral microbiota to host health are not well established. Nitric oxide (NO) homeostasis is crucial to mammalian physiology. The recently described entero-salivary nitrate-nitrite-nitric oxide pathway has been shown to provide bioactive NO from dietary nitrate sources. Interestingly, this pathway is dependent upon oral nitrate-reducing bacteria, since humans lack this enzyme activity. This pathway appears to represent a newly recognized symbiosis between oral nitrate-reducing bacteria and their human hosts in which the bacteria provide nitrite and nitric oxide from nitrate reduction. Here we measure the nitrate-reducing capacity of tongue-scraping samples from six healthy human volunteers, and analyze metagenomes of the bacterial communities to identify bacteria contributing to nitrate reduction. We identified 14 candidate species, seven of which were not previously believed to contribute to nitrate reduction. We cultivated isolates of four candidate species in single- and mixed-species biofilms, revealing that they have substantial nitrate- and nitrite-reduction capabilities. Colonization by specific oral bacteria may thus contribute to host NO homeostasis by providing nitrite and nitric oxide. Conversely, the lack of specific nitrate-reducing communities may disrupt the nitrate-nitrite-nitric oxide pathway and lead to a state of NO insufficiency. These findings may also provide mechanistic evidence for the oral systemic link. Our results provide a possible new therapeutic target and paradigm for NO restoration in humans by specific oral bacteria. PMID:24670812

It is rocket science - why dietary nitrate is hard to 'beet'! Part II: further mechanisms and therapeutic potential of the nitrate-nitrite-NO pathway.

PubMed

Mills, Charlotte Elizabeth; Khatri, Jibran; Maskell, Perry; Odongerel, Chimed; Webb, Andrew James

2017-01-01

Dietary nitrate (found in green leafy vegetables such as rocket and in beetroot) is now recognized to be an important source of nitric oxide, via the nitrate-nitrite-NO pathway. Dietary nitrate confers several cardiovascular beneficial effects on blood pressure, platelets, endothelial function, mitochondrial efficiency and exercise. Having described key twists and turns in the elucidation of the pathway and the underlying mechanisms in Part I, we explore the more recent developments which have served to confirm mechanisms, extend our understanding, and discover new properties and potential therapeutic uses of the pathway in Part II. Even the established dependency on low oxygen states for bioactivation of nitrite has recently been challenged. Dietary nitrate appears to be an important component of 'healthy diets', such as the DASH diet to lower blood pressure and the Mediterranean diet, with its potential to lower cardiovascular risk, possibly through beneficial interactions with a range of other constituents. The World Cancer Research Foundation report strong evidence for vegetables including spinach and lettuce (high nitrate-containing) decreasing cancer risk (mouth, pharynx, larynx, oesophagus and stomach), summarized in a 'Nitrate-Cancer Risk Veg-Table'. The European Space Agency recommends that beetroot, lettuce, spinach and rocket (high-nitrate vegetables) are grown to provide food for long-term space missions. Nitrate, an ancient component of rocket fuel, could support sustainable crops for healthy humans. © 2016 The British Pharmacological Society.

Nitrate-dependent shoot sodium accumulation and osmotic functions of sodium in Arabidopsis under saline conditions.

PubMed

Álvarez-Aragón, Rocío; Rodríguez-Navarro, Alonso

2017-07-01

Improving crop plants to be productive in saline soils or under irrigation with saline water would be an important technological advance in overcoming the food and freshwater crises that threaten the world population. However, even if the transformation of a glycophyte into a plant that thrives under seawater irrigation was biologically feasible, current knowledge about Na + effects would be insufficient to support this technical advance. Intriguingly, crucial details about Na + uptake and its function in the plant have not yet been well established. We here propose that under saline conditions two nitrate-dependent transport systems in series that take up and load Na + into the xylem constitute the major pathway for the accumulation of Na + in Arabidopsis shoots; this pathway can also function with chloride at high concentrations. In nrt1.1 nitrate transport mutants, plant Na + accumulation was partially defective, which suggests that NRT1.1 either partially mediates or modulates the nitrate-dependent Na + transport. Arabidopsis plants exposed to an osmotic potential of -1.0 MPa (400 mOsm) for 24 h showed high water loss and wilting in sorbitol or Na/MES, where Na + could not be accumulated. In contrast, in NaCl the plants that accumulated Na + lost a low amount of water, and only suffered transitory wilting. We discuss that in Arabidopsis plants exposed to high NaCl concentrations, root Na + uptake and tissue accumulation fulfil the primary function of osmotic adjustment, even if these processes lead to long-term toxicity. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Modeled aerosol nitrate formation pathways during wintertime in the Great Lakes region of North America

NASA Astrophysics Data System (ADS)

Kim, Yoo Jung; Spak, Scott N.; Carmichael, Gregory R.; Riemer, Nicole; Stanier, Charles O.

2014-11-01

Episodic wintertime particle pollution by ammonium nitrate is an important air quality concern across the Midwest U.S. Understanding and accurately forecasting PM2.5 episodes are complicated by multiple pathways for aerosol nitrate formation, each with uncertain rate parameters. Here, the Community Multiscale Air Quality model (CMAQ) simulated regional atmospheric nitrate budgets during the 2009 LADCO Winter Nitrate Study, using integrated process rate (IPR) and integrated reaction rate (IRR) tools to quantify relevant processes. Total nitrate production contributing to PM2.5 episodes is a regional phenomenon, with peak production over the Ohio River Valley and southern Great Lakes. Total nitrate production in the lower troposphere is attributed to three pathways, with 57% from heterogeneous conversion of N2O5, 28% from the reaction of OH and NO2, and 15% from homogeneous conversion of N2O5. TNO3 formation rates varied day-to-day and on synoptic timescales. Rate-limited production does not follow urban-rural gradients and NOx emissions due, to counterbalancing of urban enhancement in daytime HNO3 production with nocturnal reductions. Concentrations of HNO3 and N2O5 and nighttime TNO3 formation rates have maxima aloft (100-500 m), leading to net total nitrate vertical flux during episodes, with substantial vertical gradients in nitrate partitioning. Uncertainties in all three pathways are relevant to wintertime aerosol modeling and highlight the importance of interacting transport and chemistry processes during ammonium nitrate episodes, as well as the need for additional constraint on the system through field and laboratory experiments.

Role of nitrite, urate and pepsin in the gastroprotective effects of saliva

PubMed Central

Rocha, Bárbara S.; Lundberg, Jon O; Radi, Rafael; Laranjinha, João

2016-01-01

Dietary nitrate is now recognized as an alternative substrate for nitric oxide (•NO) production in the gut. This novel pathway implies the sequential reduction of nitrate to nitrite, •NO and other bioactive nitrogen oxides but the physiological relevance of these oxidants has remained elusive. We have previously shown that dietary nitrite fuels an hitherto unrecognized nitrating pathway at acidic gastric pH, through which pepsinogen is nitrated in the gastric mucosa, yielding a less active form of pepsin in vitro. Here, we demonstrate that pepsin is nitrated in vivo and explore the functional impact of protein nitration by means of peptic ulcer development. Upon administration of pentagastrin and human nitrite-rich saliva or sodium nitrite to rats, nitrated pepsin was detected in the animal's stomach by immunoprecipitation. •NO was measured in the gastric headspace before and after nitrite instillation by chemiluminescence. At the end of each procedure, the stomach's lesions, ranging from gastric erosions to haemorrhagic ulcers, were scored. Nitrite increased gastric •NO by 200-fold (p<0.05) and nitrated pepsin was detected both in the gastric juice and the mucosa (p<0.05). Exogenous urate, a scavenger of nitrogen dioxide radical, blunted •NO detection and inhibited pepsin nitration, suggesting an underlining free radical-dependent mechanism for nitration. Functionally, pepsin nitration prevented the development of gastric ulcers, as the lesions were only apparent when pepsin nitration was inhibited by urate. In sum, this work unravels a novel dietary-dependent nitrating pathway in which pepsin is nitrated and inactivated in the stomach, preventing the progression of gastric ulcers. PMID:27156250

Identifying functional zones of denitrification in heterogeneous aquifer systems by numerical simulations - a case study

NASA Astrophysics Data System (ADS)

Jang, E.; Kalbacher, T.; He, W.; Shao, H.; Schueth, C.; Kolditz, O.

2014-12-01

Nitrate contamination in shallow groundwater is still one of the common problems in many countries. Because of its high solubility and anionic nature, nitrate can easily leach through soil and persist in groundwater for decades. High nitrate concentration has been suggested as a major cause of accelerated eutrophication, methemoglobinemia and gastric cancer. There are several factors influencing the fate of nitrate in groundwater system, which is e.g. distribution of N- sources to soil and groundwater, distribution and amount of reactive substances maintaining denitrification, rate of nitrate degradation and its kinetics, and geological characteristics of the aquifer. Nitrate transport and redox transformation processes are closely linked to complex and spatially distributed physical and chemical interaction, therefore it is difficult to predict and quantify in the field and laboratory experiment. Models can play a key role in elucidation of nitrate reduction pathway in groundwater system and in the design and evaluation of field tests to investigate in situ remediation technologies as well. The goal of the current study is to predict groundwater vulnerability to nitrate, to identify functional zones of denitrification in heterogeneous aquifer systems and to describe the uncertainty of the predictions due to scale effects. For this aim, we developed a kinetic model using multi-component mass transport code OpenGeoSys coupling with IPhreeqc module of the geochemical solver PHREEQC. The developed model included sequential aerobic and nitrate-based respiration, multi-Monod kinetics, multi-species biogeochemical reactions, and geological characteristics of the groundwater aquifer. Moreover water-rock interaction such as secondary mineral precipitation was also included in this model. In this presentation, we focused on the general modelling approach and present the simulation results of nitrate transport simulation in a hypothetical aquifer systems based on data from Hessian Ried, an important groundwater resource for the densely populated Rhine-Main region in Germany.

Comment on Egami's concept of the evolution of nitrate respiration

NASA Technical Reports Server (NTRS)

Rambler, M.; Margulis, L.

1976-01-01

Recent results suggest that the presence of common nitrogen salts (sodium nitrite and nitrate) in the irradiation medium can markedly protect filamentous blue-green algae from potentially lethal ultraviolet irradiation. The present results as well as general biological arguments of Egami support and extend Egami's original view that anaerobic respiratory pathways using nitrite and nitrate as terminal electron acceptors evolved prior to oxygen requiring aerobic respiratory pathways.

Dietary nitrate and nitrite modulate blood and organ nitrite and the cellular ischemic stress response

PubMed Central

Raat, Nicolaas J.H.; Noguchi, Audrey C.; Liu, Virginia B.; Raghavachari, Nalini; Liu, Delong; Xu, Xiuli; Shiva, Sruti; Munson, Peter J.; Gladwin, Mark T.

2009-01-01

Dietary nitrate, found in abundance in green vegetables, can be converted to the cytoprotective molecule nitrite by oral bacteria, suggesting that nitrate and nitrite may represent active cardioprotective constituents of the Mediterranean diet. We therefore tested the hypothesis that dietary nitrate and nitrite levels modulate tissue damage and ischemic gene expression in a mouse liver ischemia-reperfusion model. We found that stomach content, plasma, heart and liver nitrite levels were significantly reduced after dietary nitrate and nitrite depletion, and could be restored to normal levels with nitrite supplementation in water. Remarkably, we confirmed that basal nitrite levels significantly reduced liver injury after ischemia-reperfusion. Consistent with an effect of nitrite on the post-translational modification of complex I of the mitochondrial electron transport chain, the severity of liver infarction was inversely proportional to complex I activity after nitrite repletion in the diet. The transcriptional response of dietary nitrite after ischemia was more robust than after normoxia, suggesting a hypoxic potentiation of nitrite-dependent transcriptional signaling. Our studies indicate that normal dietary nitrate and nitrite levels modulate ischemic stress responses and hypoxic gene expression programs, supporting the hypothesis that dietary nitrate and nitrite are cytoprotective components of the diet. PMID:19464364

Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments

PubMed Central

Canales, Javier; Moyano, Tomás C.; Villarroel, Eva; Gutiérrez, Rodrigo A.

2014-01-01

Nitrogen (N) is an essential macronutrient for plant growth and development. Plants adapt to changes in N availability partly by changes in global gene expression. We integrated publicly available root microarray data under contrasting nitrate conditions to identify new genes and functions important for adaptive nitrate responses in Arabidopsis thaliana roots. Overall, more than 2000 genes exhibited changes in expression in response to nitrate treatments in Arabidopsis thaliana root organs. Global regulation of gene expression by nitrate depends largely on the experimental context. However, despite significant differences from experiment to experiment in the identity of regulated genes, there is a robust nitrate response of specific biological functions. Integrative gene network analysis uncovered relationships between nitrate-responsive genes and 11 highly co-expressed gene clusters (modules). Four of these gene network modules have robust nitrate responsive functions such as transport, signaling, and metabolism. Network analysis hypothesized G2-like transcription factors are key regulatory factors controlling transport and signaling functions. Our meta-analysis highlights the role of biological processes not studied before in the context of the nitrate response such as root hair development and provides testable hypothesis to advance our understanding of nitrate responses in plants. PMID:24570678

It is rocket science – why dietary nitrate is hard to ‘beet’! Part II: further mechanisms and therapeutic potential of the nitrate‐nitrite‐NO pathway

PubMed Central

Mills, Charlotte Elizabeth; Khatri, Jibran; Maskell, Perry; Odongerel, Chimed

2016-01-01

Dietary nitrate (found in green leafy vegetables such as rocket and in beetroot) is now recognized to be an important source of nitric oxide, via the nitrate‐nitrite‐NO pathway. Dietary nitrate confers several cardiovascular beneficial effects on blood pressure, platelets, endothelial function, mitochondrial efficiency and exercise. Having described key twists and turns in the elucidation of the pathway and the underlying mechanisms in Part I, we explore the more recent developments which have served to confirm mechanisms, extend our understanding, and discover new properties and potential therapeutic uses of the pathway in Part II. Even the established dependency on low oxygen states for bioactivation of nitrite has recently been challenged. Dietary nitrate appears to be an important component of ‘healthy diets’, such as the DASH diet to lower blood pressure and the Mediterranean diet, with its potential to lower cardiovascular risk, possibly through beneficial interactions with a range of other constituents. The World Cancer Research Foundation report strong evidence for vegetables including spinach and lettuce (high nitrate‐containing) decreasing cancer risk (mouth, pharynx, larynx, oesophagus and stomach), summarized in a ‘Nitrate‐Cancer Risk Veg‐Table’. The European Space Agency recommends that beetroot, lettuce, spinach and rocket (high‐nitrate vegetables) are grown to provide food for long‐term space missions. Nitrate, an ancient component of rocket fuel, could support sustainable crops for healthy humans. PMID:26914827

Protein kinase Cδ oxidation contributes to ERK inactivation in lupus T cells.

PubMed

Gorelik, Gabriela J; Yarlagadda, Sushma; Patel, Dipak R; Richardson, Bruce C

2012-09-01

CD4+ T cells from patients with active lupus have impaired ERK pathway signaling that decreases DNA methyltransferase expression, resulting in DNA demethylation, overexpression of immune genes, and autoimmunity. The ERK pathway defect is due to impaired phosphorylation of T(505) in the protein kinase Cδ (PKCδ) activation loop. However, the mechanisms that prevent PKCδ T(505) phosphorylation in lupus T cells are unknown. Others have reported that oxidative modifications, and nitration in particular, of T cells as well as serum proteins correlate with lupus disease activity. We undertook this study to test our hypothesis that nitration inactivates PKCδ, contributing to impaired ERK pathway signaling in lupus T cells. CD4+ T cells were purified from lupus patients and controls and then stimulated with phorbol myristate acetate (PMA). Signaling protein levels, nitration, and phosphorylation were quantitated by immunoprecipitation and immunoblotting of T cell lysates. Transfections were performed by electroporation. Treating CD4+ T cells with peroxynitrite nitrated PKCδ, preventing PKCδ T(505) phosphorylation and inhibiting ERK pathway signaling similar to that observed in lupus T cells. Patients with active lupus had higher nitrated T cell PKCδ levels than did controls, which correlated directly with disease activity, and antinitrotyrosine immunoprecipitations demonstrated that nitrated PKCδ, but not unmodified PKCδ, was refractory to PMA-stimulated T(505) phosphorylation, similar to PKCδ in peroxynitrite-treated cells. Oxidative stress causes PKCδ nitration, which prevents its phosphorylation and contributes to the decreased ERK signaling in lupus T cells. These results identify PKCδ as a link between oxidative stress and the T cell epigenetic modifications in lupus. Copyright © 2012 by the American College of Rheumatology.

Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate.

PubMed

Carlson, Hans K; Kuehl, Jennifer V; Hazra, Amrita B; Justice, Nicholas B; Stoeva, Magdalena K; Sczesnak, Andrew; Mullan, Mark R; Iavarone, Anthony T; Engelbrektson, Anna; Price, Morgan N; Deutschbauer, Adam M; Arkin, Adam P; Coates, John D

2015-06-01

We investigated perchlorate (ClO(4)(-)) and chlorate (ClO(3)(-)) (collectively (per)chlorate) in comparison with nitrate as potential inhibitors of sulfide (H(2)S) production by mesophilic sulfate-reducing microorganisms (SRMs). We demonstrate the specificity and potency of (per)chlorate as direct SRM inhibitors in both pure cultures and undefined sulfidogenic communities. We demonstrate that (per)chlorate and nitrate are antagonistic inhibitors and resistance is cross-inducible implying that these compounds share at least one common mechanism of resistance. Using tagged-transposon pools we identified genes responsible for sensitivity and resistance in Desulfovibrio alaskensis G20. We found that mutants in Dde_2702 (Rex), a repressor of the central sulfate-reduction pathway were resistant to both (per)chlorate and nitrate. In general, Rex derepresses its regulon in response to increasing intracellular NADH:NAD(+) ratios. In cells in which respiratory sulfate reduction is inhibited, NADH:NAD(+) ratios should increase leading to derepression of the sulfate-reduction pathway. In support of this, in (per)chlorate or nitrate-stressed wild-type G20 we observed higher NADH:NAD(+) ratios, increased transcripts and increased peptide counts for genes in the core Rex regulon. We conclude that one mode of (per)chlorate and nitrate toxicity is as direct inhibitors of the central sulfate-reduction pathway. Our results demonstrate that (per)chlorate are more potent inhibitors than nitrate in both pure cultures and communities, implying that they represent an attractive alternative for controlling sulfidogenesis in industrial ecosystems. Of these, perchlorate offers better application logistics because of its inhibitory potency, solubility, relative chemical stability, low affinity for mineral cations and high mobility in environmental systems.

Nitrate foraging by Arabidopsis roots is mediated by the transcription factor TCP20 through the systemic signaling pathway

PubMed Central

Guan, Peizhu; Wang, Rongchen; Nacry, Philippe; Breton, Ghislain; Kay, Steve A.; Pruneda-Paz, Jose L.; Davani, Ariea; Crawford, Nigel M.

2014-01-01

To compete for nutrients in diverse soil microenvironments, plants proliferate lateral roots preferentially in nutrient-rich zones. For nitrate, root foraging involves local and systemic signaling; however, little is known about the genes that function in the systemic signaling pathway. By using nitrate enhancer DNA to screen a library of Arabidopsis transcription factors in the yeast one-hybrid system, the transcription factor gene TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1-20 (TCP20) was identified. TCP20, which belongs to an ancient, plant-specific gene family that regulates shoot, flower, and embryo development, was implicated in nitrate signaling by its ability to bind DNA in more than 100 nitrate-regulated genes. Analysis of insertion mutants of TCP20 showed that they had normal primary and lateral root growth on homogenous nitrate media but were impaired in preferential lateral root growth (root foraging) on heterogeneous media in split-root plates. Inhibition of preferential lateral root growth was still evident in the mutants even when ammonium was uniformly present in the media, indicating that the TCP20 response was to nitrate. Comparison of tcp20 mutants with those of nlp7 mutants, which are defective in local control of root growth but not in the root-foraging response, indicated that TCP20 function is independent of and distinct from NLP7 function. Further analysis showed that tcp20 mutants lack systemic control of root growth regardless of the local nitrate concentrations. These results indicate that TCP20 plays a key role in the systemic signaling pathway that directs nitrate foraging by Arabidopsis roots. PMID:25288754

Estimating discharge and non-point source nitrate loading to streams from three end-member pathways using high-frequency water quality and streamflow data

NASA Astrophysics Data System (ADS)

Miller, M. P.; Tesoriero, A. J.; Hood, K.; Terziotti, S.; Wolock, D.

2017-12-01

The myriad hydrologic and biogeochemical processes taking place in watersheds occurring across space and time are integrated and reflected in the quantity and quality of water in streams and rivers. Collection of high-frequency water quality data with sensors in surface waters provides new opportunities to disentangle these processes and quantify sources and transport of water and solutes in the coupled groundwater-surface water system. A new approach for separating the streamflow hydrograph into three components was developed and coupled with high-frequency specific conductance and nitrate data to estimate time-variable watershed-scale nitrate loading from three end-member pathways - dilute quickflow, concentrated quickflow, and slowflow groundwater - to two streams in central Wisconsin. Time-variable nitrate loads from the three pathways were estimated for periods of up to two years in a groundwater-dominated and a quickflow-dominated stream, using only streamflow and in-stream water quality data. The dilute and concentrated quickflow end-members were distinguished using high-frequency specific conductance data. Results indicate that dilute quickflow contributed less than 5% of the nitrate load at both sites, whereas 89±5% of the nitrate load at the groundwater-dominated stream was from slowflow groundwater, and 84±13% of the nitrate load at the quickflow-dominated stream was from concentrated quickflow. Concentrated quickflow nitrate concentrations varied seasonally at both sites, with peak concentrations in the winter that were 2-3 times greater than minimum concentrations during the growing season. Application of this approach provides an opportunity to assess stream vulnerability to non-point source nitrate loading and expected stream responses to current or changing conditions and practices in watersheds.

Differential molecular response of monodehydroascorbate reductase and glutathione reductase by nitration and S-nitrosylation

PubMed Central

Begara-Morales, Juan C.; Sánchez-Calvo, Beatriz; Chaki, Mounira; Mata-Pérez, Capilla; Valderrama, Raquel; Padilla, María N.; Luque, Francisco; Corpas, Francisco J.; Barroso, Juan B.

2015-01-01

The ascorbate–glutathione cycle is a metabolic pathway that detoxifies hydrogen peroxide and involves enzymatic and non-enzymatic antioxidants. Proteomic studies have shown that some enzymes in this cycle such as ascorbate peroxidase (APX), monodehydroascorbate reductase (MDAR), and glutathione reductase (GR) are potential targets for post-translational modifications (PMTs) mediated by nitric oxide-derived molecules. Using purified recombinant pea peroxisomal MDAR and cytosolic and chloroplastic GR enzymes produced in Escherichia coli, the effects of peroxynitrite (ONOO–) and S-nitrosoglutathione (GSNO) which are known to mediate protein nitration and S-nitrosylation processes, respectively, were analysed. Although ONOO– and GSNO inhibit peroxisomal MDAR activity, chloroplastic and cytosolic GR were not affected by these molecules. Mass spectrometric analysis of the nitrated MDAR revealed that Tyr213, Try292, and Tyr345 were exclusively nitrated to 3-nitrotyrosine by ONOO–. The location of these residues in the structure of pea peroxisomal MDAR reveals that Tyr345 is found at 3.3 Å of His313 which is involved in the NADP-binding site. Site-directed mutagenesis confirmed Tyr345 as the primary site of nitration responsible for the inhibition of MDAR activity by ONOO–. These results provide new insights into the molecular regulation of MDAR which is deactivated by nitration and S-nitrosylation. However, GR was not affected by ONOO– or GSNO, suggesting the existence of a mechanism to conserve redox status by maintaining the level of reduced GSH. Under a nitro-oxidative stress induced by salinity (150mM NaCl), MDAR expression (mRNA, protein, and enzyme activity levels) was increased, probably to compensate the inhibitory effects of S-nitrosylation and nitration on the enzyme. The present data show the modulation of the antioxidative response of key enzymes in the ascorbate–glutathione cycle by nitric oxide (NO)-PTMs, thus indicating the close involvement of NO and reactive oxygen species metabolism in antioxidant defence against nitro-oxidative stress situations in plants. PMID:26116026

Aromatic hydrocarbon nitration under tropospheric and combustion conditions. A theoretical mechanistic study.

PubMed

Ghigo, Giovanni; Causà, Mauro; Maranzana, Andrea; Tonachini, Glauco

2006-12-14

The viability of some nitration pathways is explored for benzene (B), naphthalene (N), and in part pyrene (P). In principle, functionalization can either take place by direct nitration (NO2 or N2O5 attack) or be initiated by more reactive species, as the nitrate and hydroxyl radicals. The direct attack of the NO2 radical on B and N, followed by abstraction of the H geminal to the nitro group (most likely accomplished by 3O2) could yield the final nitro-derivatives. Nevertheless, the initial step (NO2 attack) involves significant free energy barriers. N2O5 proves to be an even worst nitrating agent. These results rule out direct nitration at room temperature. Instead, NO3 and, even more easily, HO can form pi-delocalized nitroxy- or hydroxycyclohexadienyl radicals. A subsequent NO2 attack can produce several regio- and diastereoisomers of nitroxy-nitro or hydroxy-nitro cyclohexadienes. In this respect, the competition between NO2 and O2 is considered: the rate ratios are such to indicate that the NO3 and HO initiated pathways are the major source of nitroarenes. Finally, if the two substituents are 1,2-trans, either a HNO3 or a H2O concerted elimination can give the nitro-derivatives. Whereas HNO3 elimination is feasible, H2O elimination presents, by contrast, a high barrier. Under combustion conditions the NO2 direct nitration pathway is more feasible, but remains a minor channel.

Roles of oxyanions in promoting the partial oxidation of styrene on Ag(110): nitrate, carbonate, sulfite, and sulfate.

PubMed

Zhou, Ling; Madix, Robert J

2010-11-02

The promotion roles of nitrate, carbonate, sulfite, and sulfate in oxidation of styrene on Ag(110) have been studied by means of temperature-programmed reaction spectroscopy (TPRS) and X-ray photoelectron spectroscopy (XPS). While isolated nitrate leads only to the secondary oxidation of styrene, a surface co-covered by nitrate, oxygen, and 0.1 ML cesium promotes a low-temperature epoxidation pathway. XPS indicates that adsorbed surface oxygen is the oxidant in this selective reaction pathway, and, though it affects the reactivity of the surface oxygen, nitrate is a spectator. Carbonate acts as an oxygen transfer agent and exhibits similar reactivity and selectivity as an oxidant for styrene as does atomic oxygen on Ag(110). The reactivities of sulfite and sulfate are strongly dependent on their surface structures, the c(6 × 2) sulfite showing the capacity to transfer oxygen to styrene.

Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC.

PubMed

Oosterkamp, Margreet J; Boeren, Sjef; Atashgahi, Siavash; Plugge, Caroline M; Schaap, Peter J; Stams, Alfons J M

2015-06-01

Alicycliphilus denitrificans strain BC grows anaerobically on acetone with nitrate as electron acceptor. Comparative proteomics of cultures of A. denitrificans strain BC grown on either acetone or acetate with nitrate was performed to study the enzymes involved in the acetone degradation pathway. In the proposed acetone degradation pathway, an acetone carboxylase converts acetone to acetoacetate, an AMP-dependent synthetase/ligase converts acetoacetate to acetoacetyl-CoA, and an acetyl-CoA acetyltransferase cleaves acetoacetyl-CoA to two acetyl-CoA. We also found a putative aldehyde dehydrogenase associated with acetone degradation. This enzyme functioned as a β-hydroxybutyrate dehydrogenase catalyzing the conversion of surplus acetoacetate to β-hydroxybutyrate that may be converted to the energy and carbon storage compound, poly-β-hydroxybutyrate. Accordingly, we confirmed the formation of poly-β-hydroxybutyrate in acetone-grown cells of strain BC. Our findings provide insight in nitrate-dependent acetone degradation that is activated by carboxylation of acetone. This will aid studies of similar pathways found in other microorganisms degrading acetone with nitrate or sulfate as electron acceptor. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

SPATIO-TEMPORAL ANALYSIS OF TOTAL NITRATE CONCENTRATIONS USING DYNAMIC STATISTICAL MODELS

EPA Science Inventory

Atmospheric concentrations of total nitrate (TNO₃), defined here as gas-phase nitric acid plus particle-phase nitrate, are difficult to simulate in numerical air quality models due to the presence of a variety of formation pathways and loss mechanisms, some of which ar...

Gallium nitrate ameliorates type II collagen-induced arthritis in mice.

PubMed

Choi, Jae-Hyeog; Lee, Jong-Hwan; Roh, Kug-Hwan; Seo, Su-Kil; Choi, Il-Whan; Park, Sae-Gwang; Lim, Jun-Goo; Lee, Won-Jin; Kim, Myoung-Hun; Cho, Kwang-rae; Kim, Young-Jae

2014-05-01

Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease. Gallium nitrate has been reported to reserve immunosuppressive activities. Therefore, we assessed the therapeutic effects of gallium nitrate in the mouse model of developed type II collagen-induced arthritis (CIA). CIA was induced by bovine type II collagen with Complete Freund's adjuvant. CIA mice were intraperitoneally treated from day 36 to day 49 after immunization with 3.5mg/kg/day, 7mg/kg/day gallium nitrate or vehicle. Gallium nitrate ameliorated the progression of mice with CIA. The clinical symptoms of collagen-induced arthritis did not progress after treatment with gallium nitrate. Gallium nitrate inhibited the increase of CD4(+) T cell populations (p<0.05) and also inhibited the type II collagen-specific IgG2a-isotype autoantibodies (p<0.05). Gallium nitrate reduced the serum levels of TNF-α, IL-6 and IFN-γ (p<0.05) and the mRNA expression levels of these cytokine and MMPs (MMP2 and MMP9) in joint tissues. Western blotting of members of the NF-κB signaling pathway revealed that gallium nitrate inhibits the activation of NF-κB by blocking IκB degradation. These data suggest that gallium nitrate is a potential therapeutic agent for autoimmune inflammatory arthritis through its inhibition of the NF-κB pathway, and these results may help to elucidate gallium nitrate-mediated mechanisms of immunosuppression in patients with RA. Copyright © 2014 Elsevier B.V. All rights reserved.

Vascular effects of dietary nitrate (as found in green leafy vegetables and beetroot) via the nitrate-nitrite-nitric oxide pathway.

PubMed

Lidder, Satnam; Webb, Andrew J

2013-03-01

The discovery that dietary (inorganic) nitrate has important vascular effects came from the relatively recent realization of the 'nitrate-nitrite-nitric oxide (NO) pathway'. Dietary nitrate has been demonstrated to have a range of beneficial vascular effects, including reducing blood pressure, inhibiting platelet aggregation, preserving or improving endothelial dysfunction, enhancing exercise performance in healthy individuals and patients with peripheral arterial disease. Pre-clinical studies with nitrate or nitrite also show the potential to protect against ischaemia-reperfusion injury and reduce arterial stiffness, inflammation and intimal thickness. However, there is a need for good evidence for hard endpoints beyond epidemiological studies. Whilst these suggest reduction in cardiovascular risk with diets high in nitrate-rich vegetables (such as a Mediterranean diet), others have suggested possible small positive and negative associations with dietary nitrate and cancer, but these remain unproven. Interactions with other nutrients, such as vitamin C, polyphenols and fatty acids may enhance or inhibit these effects. In order to provide simple guidance on nitrate intake from different vegetables, we have developed the Nitrate 'Veg-Table' with 'Nitrate Units' [each unit being 1 mmol of nitrate (62 mg)] to achieve a nitrate intake that is likely to be sufficient to derive benefit, but also to minimize the risk of potential side effects from excessive ingestion, given the current available evidence. The lack of data concerning the long term effects of dietary nitrate is a limitation, and this will need to be addressed in future trials. © 2012 The Authors. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

Nitrate ammonification in mangrove soils: a hidden source of nitrite?

PubMed Central

Balk, Melike; Laverman, Anniet M.; Keuskamp, Joost A.; Laanbroek, Hendrikus J.

2015-01-01

Nitrate reduction is considered to be a minor microbial pathway in the oxidation of mangrove-derived organic matter due to a limited supply of nitrate in mangrove soils. At a limited availability of this electron acceptor compared to the supply of degradable carbon, nitrate ammonification is thought to be the preferential pathway of nitrate reduction. Mangrove forest mutually differ in their productivity, which may lead to different available carbon to nitrate ratios in their soil. Hence, nitrate ammonification is expected to be of more importance in high- compared to low-productive forests. The hypothesis was tested in flow-through reactors that contain undisturbed mangrove soils from high-productive Avicennia germinans and Rhizophora mangle forests in Florida and low-productive Avicennia marina forests in Saudi Arabia. Nitrate was undetectable in the soils from both regions. It was assumed that a legacy of nitrate ammonification would be reflected by a higher ammonium production from these soils upon the addition of nitrate. Unexpectedly, the soils from the low-productive forests in Saudi Arabia produced considerably more ammonium than the soils from the high-productive forests in Florida. Hence, other environmental factors than productivity must govern the selection of nitrate ammonification or denitrification. A rather intriguing observation was the 1:1 production of nitrite and ammonium during the consumption of nitrate, more or less independent from sampling region, location, sampling depth, mangrove species and from the absence or presence of additional degradable carbon. This 1:1 ratio points to a coupled production of ammonium and nitrite by one group of nitrate-reducing microorganisms. Such a production of nitrite will be hidden by the presence of active nitrite-reducing microorganisms under the nitrate-limited conditions of most mangrove forest soils. PMID:25784903

Nitrate ammonification in mangrove soils: a hidden source of nitrite?

PubMed

Balk, Melike; Laverman, Anniet M; Keuskamp, Joost A; Laanbroek, Hendrikus J

2015-01-01

Nitrate reduction is considered to be a minor microbial pathway in the oxidation of mangrove-derived organic matter due to a limited supply of nitrate in mangrove soils. At a limited availability of this electron acceptor compared to the supply of degradable carbon, nitrate ammonification is thought to be the preferential pathway of nitrate reduction. Mangrove forest mutually differ in their productivity, which may lead to different available carbon to nitrate ratios in their soil. Hence, nitrate ammonification is expected to be of more importance in high- compared to low-productive forests. The hypothesis was tested in flow-through reactors that contain undisturbed mangrove soils from high-productive Avicennia germinans and Rhizophora mangle forests in Florida and low-productive Avicennia marina forests in Saudi Arabia. Nitrate was undetectable in the soils from both regions. It was assumed that a legacy of nitrate ammonification would be reflected by a higher ammonium production from these soils upon the addition of nitrate. Unexpectedly, the soils from the low-productive forests in Saudi Arabia produced considerably more ammonium than the soils from the high-productive forests in Florida. Hence, other environmental factors than productivity must govern the selection of nitrate ammonification or denitrification. A rather intriguing observation was the 1:1 production of nitrite and ammonium during the consumption of nitrate, more or less independent from sampling region, location, sampling depth, mangrove species and from the absence or presence of additional degradable carbon. This 1:1 ratio points to a coupled production of ammonium and nitrite by one group of nitrate-reducing microorganisms. Such a production of nitrite will be hidden by the presence of active nitrite-reducing microorganisms under the nitrate-limited conditions of most mangrove forest soils.

Regulation of nitrate assimilation in cyanobacteria.

PubMed

Ohashi, Yoshitake; Shi, Wei; Takatani, Nobuyuki; Aichi, Makiko; Maeda, Shin-ichi; Watanabe, Satoru; Yoshikawa, Hirofumi; Omata, Tatsuo

2011-02-01

Nitrate assimilation by cyanobacteria is inhibited by the presence of ammonium in the growth medium. Both nitrate uptake and transcription of the nitrate assimilatory genes are regulated. The major intracellular signal for the regulation is, however, not ammonium or glutamine, but 2-oxoglutarate (2-OG), whose concentration changes according to the change in cellular C/N balance. When nitrogen is limiting growth, accumulation of 2-OG activates the transcription factor NtcA to induce transcription of the nitrate assimilation genes. Ammonium inhibits transcription by quickly depleting the 2-OG pool through its metabolism via the glutamine synthetase/glutamate synthase cycle. The P(II) protein inhibits the ABC-type nitrate transporter, and also nitrate reductase in some strains, by an unknown mechanism(s) when the cellular 2-OG level is low. Upon nitrogen limitation, 2-OG binds to P(II) to prevent the protein from inhibiting nitrate assimilation. A pathway-specific transcriptional regulator NtcB activates the nitrate assimilation genes in response to nitrite, either added to the medium or generated intracellularly by nitrate reduction. It plays an important role in selective activation of the nitrate assimilation pathway during growth under a limited supply of nitrate. P(II) was recently shown to regulate the activity of NtcA negatively by binding to PipX, a small coactivator protein of NtcA. On the basis of accumulating genome information from a variety of cyanobacteria and the molecular genetic data obtained from the representative strains, common features and group- or species-specific characteristics of the response of cyanobacteria to nitrogen is summarized and discussed in terms of ecophysiological significance.

Modulation of Hypercholesterolemia-Induced Oxidative/Nitrative Stress in the Heart

PubMed Central

Sárközy, Márta; Pipicz, Márton; Dux, László; Csont, Tamás

2016-01-01

Hypercholesterolemia is a frequent metabolic disorder associated with increased risk for cardiovascular morbidity and mortality. In addition to its well-known proatherogenic effect, hypercholesterolemia may exert direct effects on the myocardium resulting in contractile dysfunction, aggravated ischemia/reperfusion injury, and diminished stress adaptation. Both preclinical and clinical studies suggested that elevated oxidative and/or nitrative stress plays a key role in cardiac complications induced by hypercholesterolemia. Therefore, modulation of hypercholesterolemia-induced myocardial oxidative/nitrative stress is a feasible approach to prevent or treat deleterious cardiac consequences. In this review, we discuss the effects of various pharmaceuticals, nutraceuticals, some novel potential pharmacological approaches, and physical exercise on hypercholesterolemia-induced oxidative/nitrative stress and subsequent cardiac dysfunction as well as impaired ischemic stress adaptation of the heart in hypercholesterolemia. PMID:26788247

Impact of elevated nitrate on sulfate-reducing bacteria: A comparative study of Desulfovibrio vulgaris

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Q.; He, Z.; Joyner, D.C.

2010-07-15

Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation thatmore » significant growth inhibition was effected by 70 mM NaNO{sub 3} but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level.« less

It is rocket science – why dietary nitrate is hard to ‘beet’! Part I: twists and turns in the realization of the nitrate–nitrite–NO pathway

PubMed Central

Khatri, Jibran; Mills, Charlotte Elizabeth; Maskell, Perry; Odongerel, Chimed

2016-01-01

Dietary nitrate (found in green leafy vegetables, such as rocket, and in beetroot) is now recognized to be an important source of nitric oxide (NO), via the nitrate–nitrite–NO pathway. Dietary nitrate confers several cardiovascular beneficial effects on blood pressure, platelets, endothelial function, mitochondrial efficiency and exercise. While this pathway may now seem obvious, its realization followed a rather tortuous course over two decades. Early steps included the discovery that nitrite was a source of NO in the ischaemic heart but this appeared to have deleterious effects. In addition, nitrate‐derived nitrite provided a gastric source of NO. However, residual nitrite was not thought to be absorbed systemically. Nitrite was also considered to be physiologically inert but potentially carcinogenic, through N‐nitrosamine formation. In Part 1 of a two‐part Review on the nitrate‐nitrite‐NO pathway we describe key twists and turns in the elucidation of the pathway and the underlying mechanisms. This provides the critical foundation for the more recent developments in the nitrate–nitrite–NO pathway which are covered in Part 2. PMID:26896747

From Nitrate to Nitric Oxide: The Role of Salivary Glands and Oral Bacteria.

PubMed

Qu, X M; Wu, Z F; Pang, B X; Jin, L Y; Qin, L Z; Wang, S L

2016-12-01

The salivary glands and oral bacteria play an essential role in the conversion process from nitrate (NO 3 - ) and nitrite (NO 2 - ) to nitric oxide (NO) in the human body. NO is, at present, recognized as a multifarious messenger molecule with important vascular and metabolic functions. Besides the endogenous L-arginine pathway, which is catalyzed by complex NO synthases, nitrate in food contributes to the main extrinsic generation of NO through a series of sequential steps (NO 3 - -NO 2 - -NO pathway). Up to 25% of nitrate in circulation is actively taken up by the salivary glands, and as a result, its concentration in saliva can increase 10- to 20-fold. However, the mechanism has not been clearly illustrated until recently, when sialin was identified as an electrogenic 2NO 3 - /H + transporter in the plasma membrane of salivary acinar cells. Subsequently, the oral bacterial species located at the posterior part of the tongue reduce nitrate to nitrite, as catalyzed by nitrate reductase enzymes. These bacteria use nitrate and nitrite as final electron acceptors in their respiration and meanwhile help the host to convert nitrate to NO as the first step. This review describes the role of salivary glands and oral bacteria in the metabolism of nitrate and in the maintenance of NO homeostasis. The potential therapeutic applications of oral inorganic nitrate and nitrite are also discussed. © International & American Associations for Dental Research 2016.

Global isotope metabolomics reveals adaptive strategies for nitrogen assimilation

DOE PAGES

Kurczy, Michael E.; Forsberg, Erica M.; Thorgersen, Michael P.; ...

2016-04-05

Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using 15NO 3 as a nitrogen source. In contrast to a control ( Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee ( Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2more » strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. In conclusion, the use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.« less

Global isotope metabolomics reveals adaptive strategies for nitrogen assimilation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurczy, Michael E.; Forsberg, Erica M.; Thorgersen, Michael P.

Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using 15NO 3 as a nitrogen source. In contrast to a control ( Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee ( Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2more » strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. In conclusion, the use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.« less

Nitrate Transport, Sensing, and Responses in Plants.

PubMed

O'Brien, José A; Vega, Andrea; Bouguyon, Eléonore; Krouk, Gabriel; Gojon, Alain; Coruzzi, Gloria; Gutiérrez, Rodrigo A

2016-06-06

Nitrogen (N) is an essential macronutrient that affects plant growth and development. N is an important component of chlorophyll, amino acids, nucleic acids, and secondary metabolites. Nitrate is one of the most abundant N sources in the soil. Because nitrate and other N nutrients are often limiting, plants have developed sophisticated mechanisms to ensure adequate supply of nutrients in a variable environment. Nitrate is absorbed in the root and mobilized to other organs by nitrate transporters. Nitrate sensing activates signaling pathways that impinge upon molecular, metabolic, physiological, and developmental responses locally and at the whole plant level. With the advent of genomics technologies and genetic tools, important advances in our understanding of nitrate and other N nutrient responses have been achieved in the past decade. Furthermore, techniques that take advantage of natural polymorphisms present in divergent individuals from a single species have been essential in uncovering new components. However, there are still gaps in our understanding of how nitrate signaling affects biological processes in plants. Moreover, we still lack an integrated view of how all the regulatory factors identified interact or crosstalk to orchestrate the myriad N responses plants typically exhibit. In this review, we provide an updated overview of mechanisms by which nitrate is sensed and transported throughout the plant. We discuss signaling components and how nitrate sensing crosstalks with hormonal pathways for developmental responses locally and globally in the plant. Understanding how nitrate impacts on plant metabolism, physiology, and growth and development in plants is key to improving crops for sustainable agriculture. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate

PubMed Central

Thorup, Casper; Schramm, Andreas

2017-01-01

ABSTRACT This study demonstrates that the deltaproteobacterium Desulfurivibrio alkaliphilus can grow chemolithotrophically by coupling sulfide oxidation to the dissimilatory reduction of nitrate and nitrite to ammonium. Key genes of known sulfide oxidation pathways are absent from the genome of D. alkaliphilus. Instead, the genome contains all of the genes necessary for sulfate reduction, including a gene for a reductive-type dissimilatory bisulfite reductase (DSR). Despite this, growth by sulfate reduction was not observed. Transcriptomic analysis revealed a very high expression level of sulfate-reduction genes during growth by sulfide oxidation, while inhibition experiments with molybdate pointed to elemental sulfur/polysulfides as intermediates. Consequently, we propose that D. alkaliphilus initially oxidizes sulfide to elemental sulfur, which is then either disproportionated, or oxidized by a reversal of the sulfate reduction pathway. This is the first study providing evidence that a reductive-type DSR is involved in a sulfide oxidation pathway. Transcriptome sequencing further suggests that nitrate reduction to ammonium is performed by a novel type of periplasmic nitrate reductase and an unusual membrane-anchored nitrite reductase. PMID:28720728

Nitric Oxide Production by the Human Intestinal Microbiota by Dissimilatory Nitrate Reduction to Ammonium

PubMed Central

Vermeiren, Joan; Van de Wiele, Tom; Verstraete, Willy; Boeckx, Pascal; Boon, Nico

2009-01-01

The free radical nitric oxide (NO) is an important signaling molecule in the gastrointestinal tract. Besides eukaryotic cells, gut microorganisms are also capable of producing NO. However, the exact mechanism of NO production by the gut microorganisms is unknown. Microbial NO production was examined under in vitro conditions simulating the gastrointestinal ecosystem using L-arginine or nitrate as substrates. L-arginine did not influence the microbial NO production. However, NO concentrations in the order of 90 ng NO-N per L feed medium were produced by the fecal microbiota from nitrate. 15N tracer experiments showed that nitrate was mainly reduced to ammonium by the dissimilatory nitrate reduction to ammonium (DNRA) pathway. To our knowledge, this is the first study showing that gastrointestinal microbiota can generate substantial amounts of NO by DNRA and not by the generally accepted denitrification or L-arginine pathway. Further work is needed to elucidate the exact role between NO produced by the gastrointestinal microbiota and host cells. PMID:19888436

Nitric oxide production by the human intestinal microbiota by dissimilatory nitrate reduction to ammonium.

PubMed

Vermeiren, Joan; Van de Wiele, Tom; Verstraete, Willy; Boeckx, Pascal; Boon, Nico

2009-01-01

The free radical nitric oxide (NO) is an important signaling molecule in the gastrointestinal tract. Besides eukaryotic cells, gut microorganisms are also capable of producing NO. However, the exact mechanism of NO production by the gut microorganisms is unknown. Microbial NO production was examined under in vitro conditions simulating the gastrointestinal ecosystem using L-arginine or nitrate as substrates. L-arginine did not influence the microbial NO production. However, NO concentrations in the order of 90 ng NO-N per L feed medium were produced by the fecal microbiota from nitrate. (15)N tracer experiments showed that nitrate was mainly reduced to ammonium by the dissimilatory nitrate reduction to ammonium (DNRA) pathway. To our knowledge, this is the first study showing that gastrointestinal microbiota can generate substantial amounts of NO by DNRA and not by the generally accepted denitrification or L-arginine pathway. Further work is needed to elucidate the exact role between NO produced by the gastrointestinal microbiota and host cells.

Mammalian Nitrate Biosynthesis: Incorporation of 15NH3 into Nitrate is Enhanced by Endotoxin Treatment

NASA Astrophysics Data System (ADS)

Wagner, David A.; Young, Vernon R.; Tannenbaum, Steven R.

1983-07-01

Incorporation of an oral dose of [15N]ammonium acetate into urinary [15N]nitrate has been demonstrated in the rat. Investigation of the regulation of nitrate synthesis has shown that Escherichia coli lipopolysaccharide potently stimulates urinary nitrate excretion (9-fold increase). It was further shown that the enhanced rate of nitrate excretion by lipopolysaccharide was due not to a reduction in nitrate metabolic loss but rather to an increased rate of synthesis. This conclusion was based on finding a proportionally increased incorporation of [15N]ammonium into nitrate nitrogen with lipopolysaccharide treatment. Nitrate biosynthesis was also increased by intraperitoneal injection of carrageenan and subcutaneous injection of turpentine. It is proposed that the pathway of nitrate biosynthesis may be the result of oxidation of reduced nitrogen compounds by oxygen radicals generated by an activated reticuloendothelial system.

Interaction of Yna1 and Yna2 Is Required for Nuclear Accumulation and Transcriptional Activation of the Nitrate Assimilation Pathway in the Yeast Hansenula polymorpha.

PubMed

Silvestrini, Lucia; Rossi, Beatrice; Gallmetzer, Andreas; Mathieu, Martine; Scazzocchio, Claudio; Berardi, Enrico; Strauss, Joseph

2015-01-01

A few yeasts, including Hansenula polymorpha are able to assimilate nitrate and use it as nitrogen source. The genes necessary for nitrate assimilation are organised in this organism as a cluster comprising those encoding nitrate reductase (YNR1), nitrite reductase (YNI1), a high affinity transporter (YNT1), as well as the two pathway specific Zn(II)2Cys2 transcriptional activators (YNA1, YNA2). Yna1p and Yna2p mediate induction of the system and here we show that their functions are interdependent. Yna1p activates YNA2 as well as its own (YNA1) transcription thus forming a nitrate-dependent autoactivation loop. Using a split-YFP approach we demonstrate here that Yna1p and Yna2p form a heterodimer independently of the inducer and despite both Yna1p and Yna2p can occupy the target promoter as mono- or homodimer individually, these proteins are transcriptionally incompetent. Subsequently, the transcription factors target genes containing a conserved DNA motif (termed nitrate-UAS) determined in this work by in vitro and in vivo protein-DNA interaction studies. These events lead to a rearrangement of the chromatin landscape on the target promoters and are associated with the onset of transcription of these target genes. In contrast to other fungi and plants, in which nuclear accumulation of the pathway-specific transcription factors only occur in the presence of nitrate, Yna1p and Yna2p are constitutively nuclear in H. polymorpha. Yna2p is needed for this nuclear accumulation and Yna1p is incapable of strictly positioning in the nucleus without Yna2p. In vivo DNA footprinting and ChIP analyses revealed that the permanently nuclear Yna1p/Yna2p heterodimer only binds to the nitrate-UAS when the inducer is present. The nitrate-dependent up-regulation of one partner protein in the heterodimeric complex is functionally similar to the nitrate-dependent activation of nuclear accumulation in other systems.

Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort

PubMed Central

Gonzalez, Antonio; Hyde, Embriette; Sangwan, Naseer; Gilbert, Jack A.; Viirre, Erik

2016-01-01

ABSTRACT Nitrates, such as cardiac therapeutics and food additives, are common headache triggers, with nitric oxide playing an important role. Facultative anaerobic bacteria in the oral cavity may contribute migraine-triggering levels of nitric oxide through the salivary nitrate-nitrite-nitric oxide pathway. Using high-throughput sequencing technologies, we detected observable and significantly higher abundances of nitrate, nitrite, and nitric oxide reductase genes in migraineurs versus nonmigraineurs in samples collected from the oral cavity and a slight but significant difference in fecal samples. IMPORTANCE Recent work has demonstrated a potentially symbiotic relationship between oral commensal bacteria and humans through the salivary nitrate-nitrite-nitric oxide pathway (C. Duncan et al., Nat Med 1:546–551, 1995, http://dx.doi.org/10.1038/nm0695-546). Oral nitrate-reducing bacteria contribute physiologically relevant levels of nitrite and nitric oxide to the human host that may have positive downstream effects on cardiovascular health (V. Kapil et al., Free Radic Biol Med 55:93–100, 2013, http://dx.doi.org/10.1016/j.freeradbiomed.2012.11.013). In the work presented here, we used 16S rRNA Illumina sequencing to determine whether a connection exists between oral nitrate-reducing bacteria, nitrates for cardiovascular disease, and migraines, which are a common side effect of nitrate medications (U. Thadani and T. Rodgers, Expert Opin Drug Saf 5:667–674, 2006, http://dx.doi.org/10.1517/14740338.5.5.667). PMID:27822557

Nitrate-Regulated Glutaredoxins Control Arabidopsis Primary Root Growth1[OPEN

PubMed Central

Walters, Laura A.; Cooper, Andrew M.; Olvera, Jocelyn G.; Rosas, Miguel A.; Rasmusson, Allan G.

2016-01-01

Nitrogen is an essential soil nutrient for plants, and lack of nitrogen commonly limits plant growth. Soil nitrogen is typically available to plants in two inorganic forms: nitrate and ammonium. To better understand how nitrate and ammonium differentially affect plant metabolism and development, we performed transcriptional profiling of the shoots of ammonium-supplied and nitrate-supplied Arabidopsis (Arabidopsis thaliana) plants. Seven genes encoding class III glutaredoxins were found to be strongly and specifically induced by nitrate. RNA silencing of four of these glutaredoxin genes (AtGRXS3/4/5/8) resulted in plants with increased primary root length (approximately 25% longer than the wild type) and decreased sensitivity to nitrate-mediated inhibition of primary root growth. Increased primary root growth is also a well-characterized phenotype of many cytokinin-deficient plant lines. We determined that nitrate induction of glutaredoxin gene expression was dependent upon cytokinin signaling and that cytokinins could activate glutaredoxin gene expression independent of plant nitrate status. In addition, crosses between “long-root” cytokinin-deficient plants and “long-root” glutaredoxin-silenced plants generated hybrids that displayed no further increase in primary root length (i.e. epistasis). Collectively, these findings suggest that AtGRXS3/4/5/8 operate downstream of cytokinins in a signal transduction pathway that negatively regulates plant primary root growth in response to nitrate. This pathway could allow Arabidopsis to actively discriminate between different nitrogen sources in the soil, with the preferred nitrogen source, nitrate, acting to suppress primary root growth (vertical dimension) in concert with its well-characterized stimulatory effect on lateral root growth (horizontal dimension). PMID:26662603

Thyroid Cancer Induction: Nitrates as Independent Risk Factors or Risk Modulators after Radiation Exposure, with a Focus on the Chernobyl Accident.

PubMed

Drozd, Valentina M; Branovan, Igor; Shiglik, Nikolay; Biko, Johannes; Reiners, Christoph

2018-03-01

In recent decades, differentiated thyroid cancer (DTC) incidence has been increasing worldwide. The important contributions to this phenomenon of "overdiagnosis" driven by wider use of improved ultrasound systems are amply documented, notwithstanding the "real" carcinogenic effects of ionizing radiation, e.g., from the Chernobyl accident or health care interventions. Less well understood is the role of nitrates - as environmental pollutants, in diet, and in medication - in thyroid carcinogenesis. Increasing exposure to nitrates is associated with rising incidence of esophageal, stomach, bladder, and colon cancers. Recent data suggest that in agricultural areas with higher mean nitrate levels in groundwater, DTC risk is also elevated. Our work in Belarus after Chernobyl has shown that children in districts with high nitrate concentrations in drinking water had significantly higher thyroid cancer incidence after irradiation than did their counterparts in areas with lower nitrate concentrations. Notwithstanding thyroid shielding, increasing use of computed tomography and dental X-rays heightens radiation exposure of the salivary glands in the general population, especially in children and adolescents. When nitrate intake is increased, salivary gland irradiation may potentially result in carcinogenic elevations in plasma nitric oxide concentrations. In conclusion, excess nitrate intake seems to be an independent risk factor for DTC. Additionally, we hypothesize from our data that high nitrate levels modulate the carcinogenic effect of radiation on the thyroid. Cohort studies, case-control studies, or both, are needed to quantify the effects of nitrates on DTC risk in the presence or absence of radiation exposure, e.g., that associated with diagnostic or therapeutic health care interventions.

Lack of modulation of gastric emptying by dietary nitrate in healthy volunteers.

PubMed

Terai, Shiho; Iijima, Katsunori; Asanuma, Kiyotaka; Ara, Nobuyuki; Uno, Kaname; Abe, Yasuhiko; Koike, Tomoyuki; Imatani, Akira; Ohara, Shuichi; Shimosegawa, Tooru

2009-05-01

Nitric oxide produced endogenously in vagal neurons modulates gastrointestinal motor activity as an important non-adrenergic and non-cholinergic neurotransmitter. Other than through endogenous biosynthesis, a high concentration of nitric oxide also occurs by chemical reactions within the stomach in the presence of gastric acid through the entero-salivary re-circulation of dietary nitrate. Although dietary nitrate can be a potential source of nitric oxide in the human stomach, there has been no report on the effect of dietary nitrate on gastric motor function. The aim of this study is to investigate the effect of dietary nitrate on gastric emptying, one of the major parameters for the gastric motor function. Fifteen healthy volunteers underwent a placebo-controlled (310 mg sodium nitrate or placebo), double-blind, crossover trial. Since a sufficient amount of gastric acid is essential for dietary nitrate-derived nitric oxide generation in the stomach, the same protocol was repeated after 1-week treatment with a proton pump inhibitor, rabeprazole. Gastric emptying was evaluated by (13)C-octanoate breath test. The sodium nitrate ingestion did not affect gastric emptying either prior to or during rabeprazole treatment, although rabeprazole treatment itself significantly delayed gastric emptying, being independent of the dietary nitrate load. Confirmation of the delayed gastric emptying with rabeprazole indicates the sensitivity of the breath test employed in the present study. In conclusion, despite the potential nitrogen source of exogenous nitric oxide, the ingestion of 310 mg sodium nitrate, which is equivalent to the average daily intake of Japanese adults, does not affect gastric emptying in healthy volunteers.

Number of nitrate groups determines reactivity and potency of organic nitrates: a proof of concept study in ALDH-2−/− mice

PubMed Central

Wenzel, P; Hink, U; Oelze, M; Seeling, A; Isse, T; Bruns, K; Steinhoff, L; Brandt, M; Kleschyov, A L; Schulz, E; Lange, K; Weiner, H; Lehmann, J; Lackner, K J; Kawamoto, T; Münzel, T; Daiber, A

2007-01-01

Background and purpose: Mitochondrial aldehyde dehydrogenase (ALDH-2) has been shown to provide a pathway for bioactivation of organic nitrates and to be prone to desensitization in response to highly potent, but not to less potent, nitrates. We therefore sought to support the hypothesis that bioactivation by ALDH-2 critically depends on the number of nitrate groups within the nitrovasodilator. Experimental approach: Nitrates with one (PEMN), two (PEDN; GDN), three (PETriN; glyceryl trinitrate, GTN) and four (pentaerithrityl tetranitrate, PETN) nitrate groups were investigated. Vasodilatory potency was measured in isometric tension studies using isolated aortic segments of wild type (WT) and ALDH-2−/− mice. Activity of the cGMP-dependent kinase-I (reflected by levels of phosphorylated VAsodilator Stimulated Phosphoprotein, P-VASP) was quantified by Western blot analysis, mitochondrial dehydrogenase activity by HPLC. Following incubation of isolated mitochondria with PETN, PETriN-chromophore and PEDN, metabolites were quantified using chemiluminescence nitrogen detection and mass spectrometry. Key results: Compared to WT, vasorelaxation in response to PETN, PETriN and GTN was attenuated about 10fold in ALDH-2−/− mice, identical to WT vessels preincubated with inhibitors of ALDH-2. Reduced vasodilator potency correlated with reduced P-VASP formation and diminished biotransformation of the tetranitrate- and trinitrate-compounds. None of these findings were observed for PEDN, GDN and PEMN. Conclusions and implications: Our results support the crucial role of ALDH-2 in bioactivating highly reactive nitrates like GTN, PETN and PETriN. ALDH-2-mediated relaxation by organic nitrates therefore depends mainly on the number of nitrate groups. Less potent nitrates like PEDN, GDN and PEMN are apparently biotransformed by other pathways. PMID:17220910

Dietary inorganic nitrate: From villain to hero in metabolic disease?

PubMed Central

McNally, Ben; Griffin, Julian L.

2015-01-01

Historically, inorganic nitrate was believed to be an inert by‐product of nitric oxide (NO) metabolism that was readily excreted by the body. Studies utilising doses of nitrate far in excess of dietary and physiological sources reported potentially toxic and carcinogenic effects of the anion. However, nitrate is a significant component of our diets, with the majority of the anion coming from green leafy vegetables, which have been consistently shown to offer protection against obesity, type 2 diabetes and metabolic diseases. The discovery of a metabolic pathway in mammals, in which nitrate is reduced to NO, via nitrite, has warranted a re‐examination of the physiological role of this small molecule. Obesity, type 2 diabetes and the metabolic syndrome are associated with a decrease in NO bioavailability. Recent research suggests that the nitrate‐nitrite‐NO pathway may be harnessed as a therapeutic to supplement circulating NO concentrations, with both anti‐obesity and anti‐diabetic effects, as well as improving vascular function. In this review, we examine the key studies that have led to the re‐evaluation of the physiological function of inorganic nitrate, from toxic and carcinogenic metabolite, to a potentially important and beneficial agent in the treatment of metabolic disease. PMID:26227946

Dancing with Hormones: A Current Perspective of Nitrate Signaling and Regulation in Arabidopsis

PubMed Central

Guan, Peizhu

2017-01-01

In nature and agriculture, nitrate availability is a main environmental cue for plant growth, development and stress responses. Nitrate signaling and regulation are hence at the center of communications between plant intrinsic programs and the environment. It is also well known that endogenous phytohormones play numerous critical roles in integrating extrinsic cues and intrinsic responses, regulating and refining almost all aspects of plant growth, development and stress responses. Therefore, interaction between nitrate and phytohormones, such as auxins, cytokinins, abscisic acid, gibberellins, and ethylene, is prevalent. The growing evidence indicates that biosynthesis, de-conjugation, transport, and signaling of hormones are partly controlled by nitrate signaling. Recent advances with nitrate signaling and transcriptional regulation in Arabidopsis give rise to new paradigms. Given the comprehensive nitrate transport, sensing, signaling and regulations at the level of the cell and organism, nitrate itself is a local and long-distance signal molecule, conveying N status at the whole-plant level. A direct molecular link between nitrate signaling and cell cycle progression was revealed with TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1-20 (TCP20) – NIN-LIKE PROTEIN 6/7 (NLP6/7) regulatory nexus. NLPs are key regulators of nitrogen responses in plants. TCPs function as the main regulators of plant morphology and architecture, with the emerging role as integrators of plant developmental responses to the environment. By analogy with auxin being proposed as a plant morphogen, nitrate may be an environmental morphogen. The morphogen-gradient-dependent and cell-autonomous mechanisms of nitrate signaling and regulation are an integral part of cell growth and cell identification. This is especially true in root meristem growth that is regulated by intertwined nitrate, phytohormones, and glucose-TOR signaling pathways. Furthermore, the nitrate transcriptional hierarchy is emerging. Nitrate regulators in primary nitrate signaling can individually and combinatorially control downstream transcriptional networks and hormonal pathways for signal propagation and amplification. Under the new paradigms, nitrate-induced hormone metabolism and signaling deserve fresh examination. The close interplay and convergent regulation of nitrate and hormonal signaling at morphological, physiological, and molecular levels have significant effects on important agronomic traits, especially nutrient-dependent adaptive root system growth and architecture. PMID:29033968

Understanding nitrate assimilation and its regulation in microalgae

PubMed Central

Sanz-Luque, Emanuel; Chamizo-Ampudia, Alejandro; Llamas, Angel; Galvan, Aurora; Fernandez, Emilio

2015-01-01

Nitrate assimilation is a key process for nitrogen (N) acquisition in green microalgae. Among Chlorophyte algae, Chlamydomonas reinhardtii has resulted to be a good model system to unravel important facts of this process, and has provided important insights for agriculturally relevant plants. In this work, the recent findings on nitrate transport, nitrate reduction and the regulation of nitrate assimilation are presented in this and several other algae. Latest data have shown nitric oxide (NO) as an important signal molecule in the transcriptional and posttranslational regulation of nitrate reductase and inorganic N transport. Participation of regulatory genes and proteins in positive and negative signaling of the pathway and the mechanisms involved in the regulation of nitrate assimilation, as well as those involved in Molybdenum cofactor synthesis required to nitrate assimilation, are critically reviewed. PMID:26579149

Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen-starved Arabidopsis seedlings.

PubMed

Engelsberger, Wolfgang R; Schulze, Waltraud X

2012-03-01

Nitrogen is an essential macronutrient for plant growth and development. Inorganic nitrogen and its assimilation products control various metabolic, physiological and developmental processes. Although the transcriptional responses induced by nitrogen have been extensively studied in the past, our work here focused on the discovery of candidate proteins for regulatory events that are complementary to transcriptional changes. Most signaling pathways involve modulation of protein abundance and/or activity by protein phosphorylation. Therefore, we analyzed the dynamic changes in protein phosphorylation in membrane and soluble proteins from plants exposed to rapid changes in nutrient availability over a time course of 30 min. Plants were starved of nitrogen and subsequently resupplied with nitrogen in the form of nitrate or ammonium. Proteins with maximum change in their phosphorylation level at up to 5 min after nitrogen resupply (fast responses) included GPI-anchored proteins, receptor kinases and transcription factors, while proteins with maximum change in their phosphorylation level after 10 min of nitrogen resupply (late responses) included proteins involved in protein synthesis and degradation, as well as proteins with functions in central metabolism and hormone metabolism. Resupply of nitrogen in the form of nitrate or ammonium resulted in distinct phosphorylation patterns, mainly of proteins with signaling functions, transcription factors and transporters. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

Dietary nitrate as modulator of physical performance and cardiovascular health.

PubMed

Kerley, Conor P

2017-11-01

Early interventional trials reported improvements in cardiac and exercise outcomes with inorganic nitrate ingestion. The current review aims to provide a brief update of recent evidence regarding ergogenic and cardiovascular effects of dietary nitrate and practical recommendations. Recent evidence has been inconsistent and questions remain regarding effective dose, duration, and source of nitrate and cohorts likely to benefit. Dietary nitrate may be most relevant to those with vascular/metabolic impairments, those engaging in short-term, intense exercise, deconditioned individuals, and those with a low dietary nitrate intake. The evidence for cardiovascular/exercise benefit is plausible but inconsistent. However, dietary nitrate, in contrast to pharmacological nitrate, has a high benefit-risk ratio. Although nitrate supplementation has grown in popularity, it is suggested that increased green vegetables consumption may provide similar/superior benefits to nitrate supplementation in a cheaper, safer, and potentially tastier context.

Nitrate and nitrite in biology, nutrition and therapeutics

PubMed Central

Lundberg, Jon O.; Gladwin, Mark T.; Ahluwalia, Amrita; Benjamin, Nigel; Bryan, Nathan S.; Butler, Anthony; Cabrales, Pedro; Fago, Angela; Feelisch, Martin; Ford, Peter C.; Freeman, Bruce A.; Frenneau, Michael; Friedman, Joel; Kelm, Malte; Kevil, Christopher G.; Kim-Shapiro, Daniel B.; Kozlov, Andrey V.; Lancaster, Jack R.; Lefer, David J.; McColl, Kenneth; McCurry, Kenneth; Patel, Rakesh; Petersson, Joel; Rassaf, Tienush; Reutov, Valentin P.; Richter-Addo, George B.; Schechter, Alan; Shiva, Sruti; Tsuchiya, Koichiro; van Faassen, Ernst E.; Webb, Andrew J.; Zuckerbraun, Brian S.; Zweier, Jay L.; Weitzberg, Eddie

2014-01-01

Inorganic nitrate and nitrite from endogenous or dietary sources are metabolized in vivo to nitric oxide (NO) and other bioactive nitrogen oxides. The nitrate-nitrite-NO pathway is emerging as an important mediator of blood flow regulation, cell signaling, energetics and tissue responses to hypoxia. The latest advances in our understanding of the biochemistry, physiology and therapeutics of nitrate, nitrite and NO were discussed during a recent two-day meeting at the Nobel Forum, Karolinska Institutet in Stockholm. PMID:19915529

Photodegradation of Paracetamol in Nitrate Solution

NASA Astrophysics Data System (ADS)

Meng, Cui; Qu, Ruijuan; Liang, Jinyan; Yang, Xi

2010-11-01

The photodegradation of paracetamol in nitrate solution under simulated solar irradiation has been investigated. The degradation rates were compared by varying environmental parameters including concentrations of nitrate ion, humic substance and pH values. The quantifications of paracetamol were conducted by HPLC method. The results demonstrate that the photodegradation of paracetamol followed first-order kinetics. The photoproducts and intermediates of paracetamol in the presence of nitrate ions were identified by extensive GC-MS method. The photodegradation pathways involving. OH radicals as reactive species were proposed.

Photodegradation of Paracetamol in Nitrate Solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng Cui; Qu Ruijuan; Liang Jinyan

2010-11-24

The photodegradation of paracetamol in nitrate solution under simulated solar irradiation has been investigated. The degradation rates were compared by varying environmental parameters including concentrations of nitrate ion, humic substance and pH values. The quantifications of paracetamol were conducted by HPLC method. The results demonstrate that the photodegradation of paracetamol followed first-order kinetics. The photoproducts and intermediates of paracetamol in the presence of nitrate ions were identified by extensive GC-MS method. The photodegradation pathways involving. OH radicals as reactive species were proposed.

[Mechanisms of nitroxide-ergic dysregulation in tissues of parodontium in rats under combined excessive sodium nitrate and fluoride intake].

PubMed

Богданов, Алексей В; Гришко, Юлия М; Костенко, Виталий А

2016-01-01

intake of inorganic nitrates is typically accompanied by production of excessive amount of nitric oxide (NO), which level is maintained by the mechanism of autoregulation known as the NO cycle. Hypothetically, this process may be disrupted with fluorides that are able to suppress arginase pathway of L-arginine metabolism, which competes with NO-synthase pathway. to study mechanisms of disregulation of oxidative (NO-synthase) and non-oxidative (arginase) metabolic pathways of L-arginine in the tissues of periodontium under combined excessive sodium nitrate and fluoride intake. these investigations were carried out on 90 white Wistar rats. Homogenates of parodontium soft tissues were used to assess spectrophotometrically the total activities of NO-synthase (NOS), arginase, ornithine decarboxylase as well as the peroxynitrite concentration. typical for the isolated sodium nitrate administration inhibition of total NOS activity varies under combined administration of nitrate and sodium fluoride and is usually manifested by its hyperactivation that is accompanied by an increase in peroxynitrite concentration. At this time arginase and ornithine decarboxylase activity is observed to be substantially reduced. The administration of aminoguanidine, an iNOS inhibitor, (20 mg/kg, twice a week during the experiment) increases arginase and ornithine decarboxylase activities, and the administration of L-arginine (500 mg/kg, twice a week) results in the increase of arginase activity. The administration of L-selenomethionine, a peroxynitrite scavenger (3 mg/kg, twice a week), and JSH-23 (4-methyl-N-(3-phenylpropyl) benzene-1,2-diamine, an inhibitor of NF-κB activation (1 mg/kg, twice a week) for modeling binary nitrate and fluoride intoxication reduces the total concentration of NOS activity and peroxynitrite concentration, and increases ornithine decarboxylase activity. the combined effect of nitrate and sodium fluoride for 30 days leads to disregulatory increased activity of NO-synthase enzymes and reduction of arginase pathway of L-arginine in the soft tissues of parodontium that is promoted by hyperactivation of iNOS and NF-κB, and increased peroxynitrite production.

[Mechanisms of nitroxide-ergic dysregulation in tissues of parodontium in rats under combined excessive sodium nitrate and fluoride intake].

PubMed

Богданов, Алексей В; Гришко, Юлия М; Костенко, Виталий А

intake of inorganic nitrates is typically accompanied by production of excessive amount of nitric oxide (NO), which level is maintained by the mechanism of autoregulation known as the NO cycle. Hypothetically, this process may be disrupted with fluorides that are able to suppress arginase pathway of L-arginine metabolism, which competes with NO-synthase pathway. to study mechanisms of disregulation of oxidative (NO-synthase) and non-oxidative (arginase) metabolic pathways of L-arginine in the tissues of periodontium under combined excessive sodium nitrate and fluoride intake. these investigations were carried out on 90 white Wistar rats. Homogenates of parodontium soft tissues were used to assess spectrophotometrically the total activities of NO-synthase (NOS), arginase, ornithine decarboxylase as well as the peroxynitrite concentration. typical for the isolated sodium nitrate administration inhibition of total NOS activity varies under combined administration of nitrate and sodium fluoride and is usually manifested by its hyperactivation that is accompanied by an increase in peroxynitrite concentration. At this time arginase and ornithine decarboxylase activity is observed to be substantially reduced. The administration of aminoguanidine, an iNOS inhibitor, (20 mg/kg, twice a week during the experiment) increases arginase and ornithine decarboxylase activities, and the administration of L-arginine (500 mg/kg, twice a week) results in the increase of arginase activity. The administration of L-selenomethionine, a peroxynitrite scavenger (3 mg/kg, twice a week), and JSH-23 (4-methyl-N-(3-phenylpropyl) benzene-1,2-diamine, an inhibitor of NF-κB activation (1 mg/kg, twice a week) for modeling binary nitrate and fluoride intoxication reduces the total concentration of NOS activity and peroxynitrite concentration, and increases ornithine decarboxylase activity. the combined effect of nitrate and sodium fluoride for 30 days leads to disregulatory increased activity of NO-synthase enzymes and reduction of arginase pathway of L-arginine in the soft tissues of parodontium that is promoted by hyperactivation of iNOS and NF-κB, and increased peroxynitrite production.

The Nitrate-nitrite-NO pathway and its implications for Heart Failure and Preserved Ejection Fraction

PubMed Central

Chirinos, Julio A.; Zamani, Payman

2016-01-01

The pathogenesis of exercise intolerance in patients with heart failure and preserved ejection fraction (HFpEF) is likely multifactorial. In addition to cardiac abnormalities (diastolic dysfunction, abnormal contractile reserve, chronotropic incompetence), several peripheral abnormalities are likely to be involved. These include abnormal pulsatile hemodynamics, abnormal arterial vasodilatory responses to exercise, and abnormal peripheral O2 delivery, extraction and utilization. The nitrate-nitrite-NO pathway is emerging as a potential target to modify key physiologic abnormalities, including late systolic LV load from arterial wave reflections (which has deleterious short- and long-term consequences for the LV), arterial vasodilatory reserve, muscle O2 delivery, and skeletal muscle mitochondrial function. In a recently completed randomized trial, the administration of a single dose of exogenous inorganic nitrate has been shown exert various salutary arterial hemodynamic effects, ultimately leading to enhanced aerobic capacity in patients with HFpEF. These effects have the potential for both immediate improvements in exercise tolerance and for long-term “disease-modifying” effects. In this review, we provide an overview of key mechanistic contributors to exercise intolerance in HFpEF, and of the potential therapeutic role of drugs that target the nitrate-nitrite-NO pathway. PMID:26792295

Thyroid Cancer Induction: Nitrates as Independent Risk Factors or Risk Modulators after Radiation Exposure, with a Focus on the Chernobyl Accident

PubMed Central

Drozd, Valentina M.; Branovan, Igor; Shiglik, Nikolay; Biko, Johannes; Reiners, Christoph

2018-01-01

In recent decades, differentiated thyroid cancer (DTC) incidence has been increasing worldwide. The important contributions to this phenomenon of “overdiagnosis” driven by wider use of improved ultrasound systems are amply documented, notwithstanding the “real” carcinogenic effects of ionizing radiation, e.g., from the Chernobyl accident or health care interventions. Less well understood is the role of nitrates – as environmental pollutants, in diet, and in medication – in thyroid carcinogenesis. Increasing exposure to nitrates is associated with rising incidence of esophageal, stomach, bladder, and colon cancers. Recent data suggest that in agricultural areas with higher mean nitrate levels in groundwater, DTC risk is also elevated. Our work in Belarus after Chernobyl has shown that children in districts with high nitrate concentrations in drinking water had significantly higher thyroid cancer incidence after irradiation than did their counterparts in areas with lower nitrate concentrations. Notwithstanding thyroid shielding, increasing use of computed tomography and dental X-rays heightens radiation exposure of the salivary glands in the general population, especially in children and adolescents. When nitrate intake is increased, salivary gland irradiation may potentially result in carcinogenic elevations in plasma nitric oxide concentrations. In conclusion, excess nitrate intake seems to be an independent risk factor for DTC. Additionally, we hypothesize from our data that high nitrate levels modulate the carcinogenic effect of radiation on the thyroid. Cohort studies, case-control studies, or both, are needed to quantify the effects of nitrates on DTC risk in the presence or absence of radiation exposure, e.g., that associated with diagnostic or therapeutic health care interventions. PMID:29594057

Isotopic composition of atmospheric nitrate in a tropical marine boundary layer.

PubMed

Savarino, Joel; Morin, Samuel; Erbland, Joseph; Grannec, Francis; Patey, Matthew D; Vicars, William; Alexander, Becky; Achterberg, Eric P

2013-10-29

Long-term observations of the reactive chemical composition of the tropical marine boundary layer (MBL) are rare, despite its crucial role for the chemical stability of the atmosphere. Recent observations of reactive bromine species in the tropical MBL showed unexpectedly high levels that could potentially have an impact on the ozone budget. Uncertainties in the ozone budget are amplified by our poor understanding of the fate of NOx (= NO + NO2), particularly the importance of nighttime chemical NOx sinks. Here, we present year-round observations of the multiisotopic composition of atmospheric nitrate in the tropical MBL at the Cape Verde Atmospheric Observatory. We show that the observed oxygen isotope ratios of nitrate are compatible with nitrate formation chemistry, which includes the BrNO3 sink at a level of ca. 20 ± 10% of nitrate formation pathways. The results also suggest that the N2O5 pathway is a negligible NOx sink in this environment. Observations further indicate a possible link between the NO2/NOx ratio and the nitrogen isotopic content of nitrate in this low NOx environment, possibly reflecting the seasonal change in the photochemical equilibrium among NOx species. This study demonstrates the relevance of using the stable isotopes of oxygen and nitrogen of atmospheric nitrate in association with concentration measurements to identify and constrain chemical processes occurring in the MBL.

Isotopic composition of atmospheric nitrate in a tropical marine boundary layer

PubMed Central

Savarino, Joel; Morin, Samuel; Erbland, Joseph; Grannec, Francis; Patey, Matthew D.; Vicars, William; Alexander, Becky; Achterberg, Eric P.

2013-01-01

Long-term observations of the reactive chemical composition of the tropical marine boundary layer (MBL) are rare, despite its crucial role for the chemical stability of the atmosphere. Recent observations of reactive bromine species in the tropical MBL showed unexpectedly high levels that could potentially have an impact on the ozone budget. Uncertainties in the ozone budget are amplified by our poor understanding of the fate of NOx (= NO + NO2), particularly the importance of nighttime chemical NOx sinks. Here, we present year-round observations of the multiisotopic composition of atmospheric nitrate in the tropical MBL at the Cape Verde Atmospheric Observatory. We show that the observed oxygen isotope ratios of nitrate are compatible with nitrate formation chemistry, which includes the BrNO3 sink at a level of ca. 20 ± 10% of nitrate formation pathways. The results also suggest that the N2O5 pathway is a negligible NOx sink in this environment. Observations further indicate a possible link between the NO2/NOx ratio and the nitrogen isotopic content of nitrate in this low NOx environment, possibly reflecting the seasonal change in the photochemical equilibrium among NOx species. This study demonstrates the relevance of using the stable isotopes of oxygen and nitrogen of atmospheric nitrate in association with concentration measurements to identify and constrain chemical processes occurring in the MBL. PMID:23431201

Short-term effects of a high nitrate diet on nitrate metabolism in healthy individuals.

PubMed

Bondonno, Catherine P; Liu, Alex H; Croft, Kevin D; Ward, Natalie C; Puddey, Ian B; Woodman, Richard J; Hodgson, Jonathan M

2015-03-12

Dietary nitrate, through the enterosalivary nitrate-nitrite-NO pathway, can improve blood pressure and arterial stiffness. How long systemic nitrate and nitrite remain elevated following cessation of high nitrate intake is unknown. In 19 healthy men and women, the time for salivary and plasma nitrate and nitrite to return to baseline after 7 days increased nitrate intake from green leafy vegetables was determined. Salivary and plasma nitrate and nitrite was measured at baseline [D0], end of high nitrate diet [D7], day 9 [+2D], day 14 [+7D] and day 21 [+14D]. Urinary nitrite and nitrate was assessed at D7 and +14D. Increased dietary nitrate for 7 days resulted in a more than fourfold increase in saliva and plasma nitrate and nitrite (p < 0.001) measured at [D7]. At [+2D] plasma nitrite and nitrate had returned to baseline while saliva nitrate and nitrite were more than 1.5 times higher than at baseline levels. By [+7D] all metabolites had returned to baseline levels. The pattern of response was similar between men and women. Urinary nitrate and nitrate was sevenfold higher at D7 compared to +14D. These results suggest that daily ingestion of nitrate may be required to maintain the physiological changes associated with high nitrate intake.

Formation of the formate-nitrate electron transport pathway from inactive components in Escherichia coli.

PubMed Central

Scott, R H; DeMoss, J A

1976-01-01

When Escherichia coli was grown on medium containing 10 mM tungstate the formation of active formate dehydrogenase, nitrate reductase, and the complete formate-nitrate electron transport pathway was inhibited. Incubation of the tungstate-grown cells with 1 mM molybdate in the presence of chloramphenicol led to the rapid activation of both formate dehydrogenase and nitrate reductase, and, after a considerable lag, the complete electron transport pathway. Protein bands which corresponded to formate dehydrogenase and nitrate reductase were identified on polyacrylamide gels containing Triton X-100 after the activities were released from the membrane fraction and partially purified Cytochrome b1 was associated with the protein band corresponding to formate dehydrogenase but was not found elsewhere on the gels. When a similar fraction was prepared from cells grown on 10 mM tungstate, an inactive band corresponding to formate dehydrogenase was not observed on polyacrylamide gels; rather, a new faster migrating band was present. Cytochrome b1 was not associated with this band nor was it found anywhere else on the gels. This new band disappeared when the tungstate-grown cells were incubated with molybdate in the presence of chloramphenicol. The formate dehydrogenase activity which was formed, as well as a corresponding protein band, appeared at the original position on the gels. Cytochrome b1 was again associated with this band. The protein band which corresponded to nitrate reductase also was severely depressed in the tungstate-grown cells and a new faster migrating band appeared on the polyacrylamide gels. Upon activation of the nitrate reductase by incubation of the cells with molybdate, the new band diminished and protein reappeared at the original position. Most of the nitrate reductase activity which was formed appeared at the original position of nitrate reductase on gels although some was present at the position of the inactive band formed by tungstate-grown cells. Apparently, inactive forms of both formate dehydrogenase and nitrate reductase accumulate during growth on tungstate which are electrophoretically distinct from the active enzymes. Activation by molybdate results in molecular changes which include the reassociation of cytochrome b1 with formate dehydrogenase and restoration of both enzymes to their original electrophoretic mobilities. Images PMID:770433

Phenotypic Restoration by Molybdate of Nitrate Reductase Activity in chlD Mutants of Escherichia coli

PubMed Central

Glaser, J. H.; DeMoss, J. A.

1971-01-01

ChlD mutants of Escherichia coli are pleiotropic, lacking formate-nitrate reductase activity as well as formate-hydrogenlyase activity. Whole-chain formate-nitrate reductase activity, assayed with formate as the electron donor and measuring the amount of nitrite produced, was restored to wild-type levels in the mutants by addition of 10−4m molybdate to the growth medium. Under these conditions, the activity of each of the components of the membrane-bound nitrate reductase chain increased after molybdate supplementation. In the absence of nitrate, the activities of the formate-hydrogenlyase system were also restored by molybdate. Strains deleted for the chlD gene responded in a similar way to molybdate supplementation. The concentration of molybdenum in the chlD mutant cells did not differ significantly from that in the wild-type cells at either low or high concentrations of molybdate in the medium. However, the distribution of molybdenum between the soluble protein and membrane fractions differed significantly from wild type. We conclude that the chlD gene product cannot be a structural component of the formate-hydrogenlyase pathway or the formate-nitrate reductase pathway, but that it must have an indirect role in processing molybdate to a form necessary for both electron transport systems. PMID:4942767

SMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana.

PubMed

Gras, Diana E; Vidal, Elena A; Undurraga, Soledad F; Riveras, Eleodoro; Moreno, Sebastián; Dominguez-Figueroa, José; Alabadi, David; Blázquez, Miguel A; Medina, Joaquín; Gutiérrez, Rodrigo A

2018-01-23

The reproductive success of plants largely depends on the correct programming of developmental phase transitions, particularly the shift from vegetative to reproductive growth. The timing of this transition is finely regulated by the integration of an array of environmental and endogenous factors. Nitrogen is the mineral macronutrient that plants require in the largest amount, and as such its availability greatly impacts on many aspects of plant growth and development, including flowering time. We found that nitrate signaling interacts with the age-related and gibberellic acid pathways to control flowering time in Arabidopsis thaliana. We revealed that repressors of flowering time belonging to the AP2-type transcription factor family including SCHLAFMUTZE (SMZ) and SCHNARCHZAPFEN (SNZ) are important regulators of flowering time in response to nitrate. Our results support a model whereby nitrate activates SMZ and SNZ via the gibberellin pathway to repress flowering time in Arabidopsis thaliana. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Variation of isomer distribution in electrophilic nitration of toluene, anisole, and o-xylene: Independence of high regioselectivity from reactivity of reagent*

PubMed Central

Olah, George A.; Lin, Henry C.; Olah, Judith A.; Narang, Subhash C.

1978-01-01

The nitration of toluene and anisole was studied with nitrating systems of varying reactivity. High regioselectivity of ortho-para over meta substitution was maintained in all nitrations, regardless of the reactivity of the nitrating system. At the same time, the amount of meta substitution stayed low (3% or less), even when the fast reactions may have reached the encounter-controlled limit. Because the nitration of o-xylene, in which both ring positions are activated by the effect of a methyl group, also does not show any diminishing of regioselectivity, the possibility of a dual mechanistic pathway, in which the activated position would react by a fast, encounter-controlled path, whereas the nonactivated meta position by a slower σ-type path, can be ruled out. The data unambiguously prove that the high regioselectivity of electrophilic aromatic nitration is independent of the reactivity of the reagent, because no significant increase of meta substitution of toluene or anisole was observed, regardless of the activity of the nitrating system. No selectivity-reactivity relationship is thus evident and the ortho-para directing effect of primary substituents over meta substitution is always maintained. The variation in the amount of the meta isomer, up to the observed limit of about 3% in the case of toluene and <2% for anisole, is probably significant but, at the present time, cannot be quantitatively evaluated with the ±0.5% overall reproducible accuracy of the nitrations. Steric factors, such as increasing bulkiness of the nitrating agent, also can affect the ortho-para isomer ratios but are not considered to be the only reason for the observed variations, which reflect the specific nitrating systems, affecting the nature and position of the transition state of highest energy on the reaction pathway. PMID:16592489

Methylammonium-resistant mutants of Nicotiana plumbaginifolia are affected in nitrate transport.

PubMed

Godon, C; Krapp, A; Leydecker, M T; Daniel-Vedele, F; Caboche, M

1996-02-25

This work reports the isolation and preliminary characterization of Nicotiana plumbaginifolia mutants resistant to methylammonium. Nicotiana plumbaginifolia plants cannot grow on low levels of nitrate in the presence of methylammonium. Methylammonium is not used as a nitrogen source, although it can be efficiently taken up by Nicotiana plumbaginifolia cells and converted into methylglutamine, an analog of glutamine. Glutamine is known to repress the expression of the enzymes that mediate the first two steps in the nitrate assimilatory pathway, nitrate reductase (NR) and nitrite reductase (NiR). Methylammonium has therefore been used, in combination with low concentrations of nitrate, as a selective agent in order to screen for mutants in which the nitrate pathway is de-repressed. Eleven semi-dominant mutants, all belonging to the same complementation group, were identified. The mutant showing the highest resistance to methylammonium was not affected either in the utilization of ammonium, accumulation of methylammonium or in glutamine synthase activity. A series of experiments showed that utilization of nitrite by the wild-type and the mutant was comparable, in the presence or the absence of methylammonium, thus suggesting that the mutation specifically affected nitrate transport or reduction. Although NR mRNA levels were less repressed by methylammonium treatment of the wild-type than the mutant, NR activities of the mutant remained comparable with or without methylammonium, leading to the hypothesis that modified expression of NR is probably not responsible for resistance to methylammonium. Methylammonium inhibited nitrate uptake in the wild-type but had only a limited effect in the mutant. The implications of these results are discussed.

Brain Damage Caused by Chemical Warfare Agents: Are Free Radicals a Final Common Pathway?

DTIC Science & Technology

1998-08-01

to methemoglobin (Fe(III); MetHb), simultaneously releasing nitrate (Feelisch and Noack, 1987; Archer, 1993,). An analytical approach to measure NO...NO analysis such as measurement of nitrite and nitrate by the Griess assay or HPLC-conductivity detection (Green et al., 1982; Lippsmeyer et al., 1990...enzyme nitrate reductase. Although other groups have claimed to use the Griess reaction with microdialysis samples, we have found the Griess reaction

Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant

PubMed Central

Bourion, Virginie

2014-01-01

To complement N2 fixation through symbiosis, legumes can efficiently acquire soil mineral N through adapted root architecture. However, root architecture adaptation to mineral N availability has been little studied in legumes. Therefore, this study investigated the effect of nitrate availability on root architecture in Medicago truncatula and assessed the N-uptake potential of a new highly branched root mutant, TR185. The effects of varying nitrate supply on both root architecture and N uptake were characterized in the mutant and in the wild type. Surprisingly, the root architecture of the mutant was not modified by variation in nitrate supply. Moreover, despite its highly branched root architecture, TR185 had a permanently N-starved phenotype. A transcriptome analysis was performed to identify genes differentially expressed between the two genotypes. This analysis revealed differential responses related to the nitrate acquisition pathway and confirmed that N starvation occurred in TR185. Changes in amino acid content and expression of genes involved in the phenylpropanoid pathway were associated with differences in root architecture between the mutant and the wild type. PMID:24706718

Long-term fertilization alters the relative importance of nitrate reduction pathways in salt marsh sediments

NASA Astrophysics Data System (ADS)

Peng, Xuefeng; Ji, Qixing; Angell, John H.; Kearns, Patrick J.; Yang, Hannah J.; Bowen, Jennifer L.; Ward, Bess B.

2016-08-01

Salt marshes provide numerous valuable ecological services. In particular, nitrogen (N) removal in salt marsh sediments alleviates N loading to the coastal ocean. N removal reduces the threat of eutrophication caused by increased N inputs from anthropogenic sources. It is unclear, however, whether chronic nutrient overenrichment alters the capacity of salt marshes to remove anthropogenic N. To assess the effect of nutrient enrichment on N cycling in salt marsh sediments, we examined important N cycle pathways in experimental fertilization plots in a New England salt marsh. We determined rates of nitrification, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) using sediment slurry incubations with 15N labeled ammonium or nitrate tracers under oxic headspace (20% oxygen/80% helium). Nitrification and denitrification rates were more than tenfold higher in fertilized plots compared to control plots. By contrast, DNRA, which retains N in the system, was high in control plots but not detected in fertilized plots. The relative contribution of DNRA to total nitrate reduction largely depends on the carbon/nitrate ratio in the sediment. These results suggest that long-term fertilization shifts N cycling in salt marsh sediments from predominantly retention to removal.

Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant.

PubMed

Bourion, Virginie; Martin, Chantal; de Larambergue, Henri; Jacquin, Françoise; Aubert, Grégoire; Martin-Magniette, Marie-Laure; Balzergue, Sandrine; Lescure, Geoffroy; Citerne, Sylvie; Lepetit, Marc; Munier-Jolain, Nathalie; Salon, Christophe; Duc, Gérard

2014-06-01

To complement N2 fixation through symbiosis, legumes can efficiently acquire soil mineral N through adapted root architecture. However, root architecture adaptation to mineral N availability has been little studied in legumes. Therefore, this study investigated the effect of nitrate availability on root architecture in Medicago truncatula and assessed the N-uptake potential of a new highly branched root mutant, TR185. The effects of varying nitrate supply on both root architecture and N uptake were characterized in the mutant and in the wild type. Surprisingly, the root architecture of the mutant was not modified by variation in nitrate supply. Moreover, despite its highly branched root architecture, TR185 had a permanently N-starved phenotype. A transcriptome analysis was performed to identify genes differentially expressed between the two genotypes. This analysis revealed differential responses related to the nitrate acquisition pathway and confirmed that N starvation occurred in TR185. Changes in amino acid content and expression of genes involved in the phenylpropanoid pathway were associated with differences in root architecture between the mutant and the wild type. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Short-Term Effects of a High Nitrate Diet on Nitrate Metabolism in Healthy Individuals

PubMed Central

Bondonno, Catherine P.; Liu, Alex H.; Croft, Kevin D.; Ward, Natalie C.; Puddey, Ian B.; Woodman, Richard J.; Hodgson, Jonathan M.

2015-01-01

Dietary nitrate, through the enterosalivary nitrate-nitrite-NO pathway, can improve blood pressure and arterial stiffness. How long systemic nitrate and nitrite remain elevated following cessation of high nitrate intake is unknown. In 19 healthy men and women, the time for salivary and plasma nitrate and nitrite to return to baseline after 7 days increased nitrate intake from green leafy vegetables was determined. Salivary and plasma nitrate and nitrite was measured at baseline [D0], end of high nitrate diet [D7], day 9 [+2D], day 14 [+7D] and day 21 [+14D]. Urinary nitrite and nitrate was assessed at D7 and +14D. Increased dietary nitrate for 7 days resulted in a more than fourfold increase in saliva and plasma nitrate and nitrite (p < 0.001) measured at [D7]. At [+2D] plasma nitrite and nitrate had returned to baseline while saliva nitrate and nitrite were more than 1.5 times higher than at baseline levels. By [+7D] all metabolites had returned to baseline levels. The pattern of response was similar between men and women. Urinary nitrate and nitrate was sevenfold higher at D7 compared to +14D. These results suggest that daily ingestion of nitrate may be required to maintain the physiological changes associated with high nitrate intake. PMID:25774606

Formate and Nitrate Utilization in Enterobacter aerogenes for Semi-Anaerobic Production of Isobutanol.

PubMed

Jung, Hwi-Min; Kim, Yong Hwan; Oh, Min-Kyu

2017-11-01

Anaerobic bioprocessing is preferred because of its economic advantages. However, low productivity and decreased growth of the host strain have limited the use of the anaerobic process. Anaerobic respiration can be applied to anoxic processing using formate and nitrate metabolism to improve the productivity of value-added metabolites. A isobutanol-producing strains is constructed using Enterobacter aerogenes as a host strain by metabolic engineering approaches. The byproduct pathway (ldhA, budA, and pflB) is knocked out, and heterologous keto-acid decarboxylase (kivD) and alcohol dehydrogenase (adhA) are expressed along with the L-valine synthesis pathway (ilvCD and budB). The pyruvate formate-lyase mutant shows decreased growth rates when cultivated in semi-anaerobic conditions, which results in a decline in productivity. When formate and nitrate are supplied in the culture medium, the growth rates and amount of isobutanol production is restored (4.4 g L -1 , 0.23 g g -1 glucose, 0.18 g L -1  h -1 ). To determine the function of the formate and nitrate coupling reaction system, the mutant strains that could not utilize formate or nitrate is contructed. Decreased growth and productivity are observed in the nitrate reductase (narG) mutant strain. This is the first report of engineering isobutanol-producing E. aerogenes to increase strain fitness via augmentation of formate and nitrate metabolism during anaerobic cultivation. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Direct transcriptional activation of BT genes by NLP transcription factors is a key component of the nitrate response in Arabidopsis.

PubMed

Sato, Takeo; Maekawa, Shugo; Konishi, Mineko; Yoshioka, Nozomi; Sasaki, Yuki; Maeda, Haruna; Ishida, Tetsuya; Kato, Yuki; Yamaguchi, Junji; Yanagisawa, Shuichi

2017-01-29

Nitrate modulates growth and development, functioning as a nutrient signal in plants. Although many changes in physiological processes in response to nitrate have been well characterized as nitrate responses, the molecular mechanisms underlying the nitrate response are not yet fully understood. Here, we show that NLP transcription factors, which are key regulators of the nitrate response, directly activate the nitrate-inducible expression of BT1 and BT2 encoding putative scaffold proteins with a plant-specific domain structure in Arabidopsis. Interestingly, the 35S promoter-driven expression of BT2 partially rescued growth inhibition caused by reductions in NLP activity in Arabidopsis. Furthermore, simultaneous disruption of BT1 and BT2 affected nitrate-dependent lateral root development. These results suggest that direct activation of BT1 and BT2 by NLP transcriptional activators is a key component of the molecular mechanism underlying the nitrate response in Arabidopsis. Copyright © 2016 Elsevier Inc. All rights reserved.

Inorganic Nitrite Therapy: Historical perspective and future directions

PubMed Central

Kevil, Christopher G.; Kolluru, Gopi K.; Pattillo, Christopher B.; Giordano, Tony

2015-01-01

Over the past several years, investigators studying nitric oxide (NO) biology and metabolism have come to learn that the one electron oxidation product of NO, nitrite anion, serves as a unique player in modulating tissue NO bioavailability. Numerous studies have examined how this oxidized metabolite of NO can act as a salvage pathway for maintaining NO equivalents through multiple reduction mechanisms in permissive tissue environments. Moreover, it is now clear that nitrite anion production and distribution throughout the body can act in an endocrine manner to augment NO bioavailability that is important for physiological and pathological processes. These discoveries have led to renewed hope and efforts for an effective NO based therapeutic agent through the unique action of sodium nitrite as an NO pro-drug. More recent studies also indicate that sodium nitrate may also increase plasma nitrite levels via the enterosalivary circulatory system resulting in nitrate reduction to nitrite by microorganisms found within the oral cavity. In this review, we discuss the importance of nitrite anion in several disease models along with an appraisal of sodium nitrite therapy in the clinic, potential caveats of such clinical uses, and future possibilities of nitrite based therapies. PMID:21619929

Vertical segregation among pathways mediating nitrogen loss (N2 and N2O production) across the oxygen gradient in a coastal upwelling ecosystem

NASA Astrophysics Data System (ADS)

Galán, Alexander; Thamdrup, Bo; Saldías, Gonzalo S.; Farías, Laura

2017-10-01

The upwelling system off central Chile (36.5° S) is seasonally subjected to oxygen (O2)-deficient waters, with a strong vertical gradient in O2 (from oxic to anoxic conditions) that spans a few metres (30-50 m interval) over the shelf. This condition inhibits and/or stimulates processes involved in nitrogen (N) removal (e.g. anammox, denitrification, and nitrification). During austral spring (September 2013) and summer (January 2014), the main pathways involved in N loss and its speciation, in the form of N2 and/or N2O, were studied using 15N-tracer incubations, inhibitor assays, and the natural abundance of nitrate isotopes along with hydrographic information. Incubations were developed using water retrieved from the oxycline (25 m depth) and bottom waters (85 m depth) over the continental shelf off Concepción, Chile. Results of 15N-labelled incubations revealed higher N removal activity during the austral summer, with denitrification as the dominant N2-producing pathway, which occurred together with anammox at all times. Interestingly, in both spring and summer maximum potential N removal rates were observed in the oxycline, where a greater availability of oxygen was observed (maximum O2 fluctuation between 270 and 40 µmol L-1) relative to the hypoxic bottom waters ( < 20 µmol O2 L-1). Different pathways were responsible for N2O produced in the oxycline and bottom waters, with ammonium oxidation and dissimilatory nitrite reduction, respectively, as the main source processes. Ammonium produced by dissimilatory nitrite reduction to ammonium (DNiRA) could sustain both anammox and nitrification rates, including the ammonium utilized for N2O production. The temporal and vertical variability of δ15N-NO3- confirms that multiple N-cycling processes are modulating the isotopic nitrate composition over the shelf off central Chile during spring and summer. N removal processes in this coastal system appear to be related to the availability and distribution of oxygen and particles, which are a source of organic matter and the fuel for the production of other electron donors (i.e. ammonium) and acceptors (i.e. nitrate and nitrite) after its remineralization. These results highlight the links between several pathways involved in N loss. They also establish that different mechanisms supported by alternative N substrates are responsible for substantial accumulation of N2O, which are frequently observed as hotspots in the oxycline and bottom waters. Considering the extreme variation in oxygen observed in several coastal upwelling systems, these findings could help to understand the ecological and biogeochemical implications due to global warming where intensification and/or expansion of the oceanic OMZs is projected.

Transformation of benzalkonium chloride under nitrate reducing conditions.

PubMed

Tezel, Ulas; Pavlostathis, Spyros G

2009-03-01

The effect and transformation potential of benzalkonium chlorides (BAC) under nitrate reducing conditions were investigated at concentrations up to 100 mg/L in batch assays using a mixed, mesophilic (35 degrees C) methanogenic culture. Glucose was used as the carbon and energy source and the initial nitrate concentration was 70 mg N/L Dissimilatory nitrate reduction to ammonia (DNRA) and to dinitrogen (DNRN) were observed at BAC concentrations up to 25 mg/L At and above 50 mg BAC/L, DNRA was inhibited and DNRN was incomplete resulting in accumulation of nitrous oxide. Long-term inhibition of methanogenesis and accumulation of volatile fatty acids were observed at and above 50 mg BAC/L Over 99% of the added BAC was recovered from all cultures except the one amended with 100 mg BAC/L where 37% of the initially added BAC was transformed during the 100 day incubation period. Abiotic and biotic assays performed with 100 mg/L of BAC and 5 mM (in the liquid phase) of either nitrate, nitrite, or nitric oxide demonstrated that BAC transformation was abiotic and followed the modified Hofmann degradation pathway, i.e., bimolecular nucleophilic substitution with nitrite. Alkyl dimethyl amines (tertiary amines) were produced at equamolar levels to BAC transformed, but were not further degraded. This is the first report demonstrating the transformation of BAC under nitrate reducing conditions and elucidating the BAC transformation pathway.

Effects of Parental Temperature and Nitrate on Seed Performance are Reflected by Partly Overlapping Genetic and Metabolic Pathways.

PubMed

He, Hanzi; Willems, Leo A J; Batushansky, Albert; Fait, Aaron; Hanson, Johannes; Nijveen, Harm; Hilhorst, Henk W M; Bentsink, Leónie

2016-03-01

Seed performance is affected by the seed maturation environment, and previously we have shown that temperature, nitrate and light intensity were the most influential environmental factors affecting seed performance. Seeds developed in these environments were selected to assess the underlying metabolic pathways, using a combination of transcriptomics and metabolomics. These analyses revealed that the effects of the parental temperature and nitrate environments were reflected by partly overlapping genetic and metabolic networks, as indicated by similar changes in the expression levels of metabolites and transcripts. Nitrogen metabolism-related metabolites (asparagine, γ-aminobutyric acid and allantoin) were significantly decreased in both low temperature (15 °C) and low nitrate (N0) maturation environments. Correspondingly, nitrogen metabolism genes (ALLANTOINASE, NITRATE REDUCTASE 1, NITRITE REDUCTASE 1 and NITRILASE 4) were differentially regulated in the low temperature and nitrate maturation environments, as compared with control conditions. High light intensity during seed maturation increased galactinol content, and displayed a high correlation with seed longevity. Low light had a genotype-specific effect on cell surface-encoding genes in the DELAY OF GERMINATION 6-near isogenic line (NILDOG6). Overall, the integration of phenotypes, metabolites and transcripts led to new insights into the regulation of seed performance. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Plasma levels of nitrate and risk of prostate cancer: a prospective study.

PubMed

Wu, Tianying; Wang, Yushan; Ho, Shuk-Mei; Giovannucci, Edward

2013-07-01

Nitrate and nitrite supplements have recently been shown to improve cardiovascular health, but there is concern that these supplements could contribute to the development of cancer. Previous small, cross-sectional studies reported positive associations between circulating nitrate/nitrite levels and cancer. Prospective studies examining the association between plasma nitrate and cancer, especially prostate cancer, are lacking. We conducted a nested case-control study within the Health Professionals Follow-up Study. Baseline blood samples were collected in 1994, and incident cases of prostate cancer were identified from 1997 to 2005. Baseline plasma levels of nitrate were measured in the 630 cases and 630 matched controls. We have found that baseline levels of plasma nitrate were not associated with risk of prostate cancer. Compared to quintile 1, the relative risk from quintiles 2 to 5 were 1.13 [95% confidence interval (CI), 0.78-1.63], 0.93 (95% CI, 0.63-1.38), 0.95 (95% CI, 0.65-1.39), and 0.99 (95% CI, 0.68-1.48); Ptrend was 0.9 after adjustment of multivariate risk factors. When analyses were restricted to men fasting more than 6 hours, the trend was similar. Furthermore, plasma nitrate seemed to be inversely associated with advanced-stage prostate cancer. The relative risk across extreme quartiles was 0.44 (95% CI, 0.17-1.12; Ptrend = 0.07) for the whole dataset and 0.30 (95% CI, 0.09-0.99; Ptrend = 0.05) for the fasting dataset. In summary, we did not find an increased risk of prostate cancer associated with higher plasma nitrate levels. A potential protective association between nitrate and aggressive forms of prostate cancer requires confirmation. Nitrate-nitrite-nitric oxide pathway has emerged as a new therapeutic pathway for chronic diseases. The results of this study certainly merit replications in other prospective studies.

Plasma levels of nitrate and risk of prostate cancer: a prospective study

PubMed Central

Wu, Tianying; Wang, Yushan; Ho, Shuk-Mei; Giovannucci, Edward

2013-01-01

Background Nitrate and nitrite supplements have recently been shown to improve cardiovascular health, but there is concern that these supplements could contribute to the development of cancer.Previous small, cross-sectional studies reported positive associations between circulating nitrate/nitrite levels and cancer. Prospective studies examining the association between plasma nitrate and cancer, especially prostate cancer (PCa), are lacking. Methods We conducted a nested case-control study within the Health Professionals Follow-up Study. Baseline blood samples were collected in 1994, and incident cases of PCa were identified from 1997–2005. Baseline plasma levels of nitrate were measured in the 630 cases and 630 matched controls. Results We have found that baseline levels of plasma nitrate were not associated with risk of PCa. Compared to quintile 1, the relative risk from quintiles 2–5 were 1.13 (95% CI, 0.78–1.63), 0.93 (95% CI, 0.63–1.38), 0.95 (95% CI, 0.65–1.39), and 0.99 (95% CI, 0.68–1.48); p for trend was 0.9 after adjustment of multivariate risk factors. When analyses were restricted to men fasting more than 6 hrs, the trend was similar. Further, plasma nitrate appeared to be inversely associated with advanced-stage PCa. The relative risk across extreme quartiles was 0.44 (95% CI, 0.17–1.12; p for trend = 0.07) for the whole data set and 0.30 (95% CI, 0.09–0.99; p for trend = 0.05) for the fasting data set. Conclusions In summary, we did not find an increased risk of PCa associated with higher plasma nitrate levels. A potential protective association between nitrate and aggressive forms of PCa requires confirmation. Impact Nitrate-nitrite-nitric oxide pathway has emerged as a new therapeutic pathway for chronic diseases. The results of this study certainly merit replications in other prospective studies. PMID:23677578

Estimating Discharge and Nonpoint Source Nitrate Loading to Streams From Three End-Member Pathways Using High-Frequency Water Quality Data

NASA Astrophysics Data System (ADS)

Miller, Matthew P.; Tesoriero, Anthony J.; Hood, Krista; Terziotti, Silvia; Wolock, David M.

2017-12-01

The myriad hydrologic and biogeochemical processes taking place in watersheds occurring across space and time are integrated and reflected in the quantity and quality of water in streams and rivers. Collection of high-frequency water quality data with sensors in surface waters provides new opportunities to disentangle these processes and quantify sources and transport of water and solutes in the coupled groundwater-surface water system. A new approach for separating the streamflow hydrograph into three components was developed and coupled with high-frequency nitrate data to estimate time-variable nitrate loads from chemically dilute quick flow, chemically concentrated quick flow, and slowflow groundwater end-member pathways for periods of up to 2 years in a groundwater-dominated and a quick-flow-dominated stream in central Wisconsin, using only streamflow and in-stream water quality data. The dilute and concentrated quick flow end-members were distinguished using high-frequency specific conductance data. Results indicate that dilute quick flow contributed less than 5% of the nitrate load at both sites, whereas 89 ± 8% of the nitrate load at the groundwater-dominated stream was from slowflow groundwater, and 84 ± 25% of the nitrate load at the quick-flow-dominated stream was from concentrated quick flow. Concentrated quick flow nitrate concentrations varied seasonally at both sites, with peak concentrations in the winter that were 2-3 times greater than minimum concentrations during the growing season. Application of this approach provides an opportunity to assess stream vulnerability to nonpoint source nitrate loading and expected stream responses to current or changing conditions and practices in watersheds.

Nitrate in groundwater and water sources used by riparian trees in an agricultural watershed: A chemical and isotopic investigation in southern Minnesota

USGS Publications Warehouse

Komor, Stephen C.; Magner, Joseph A.

1996-01-01

This study evaluates processes that affect nitrate concentrations in groundwater beneath riparian zones in an agricultural watershed. Nitrate pathways in the upper 2 m of groundwater were investigated beneath wooded and grass-shrub riparian zones next to cultivated fields. Because trees can be important components of the overall nitrate pathway in wooded riparian zones, water sources used by riparian trees and possible effects of trees on nitrate concentrations in groundwater were also investigated. Average nitrate concentrations in shallow groundwater beneath the cultivated fields were 5.5 mg/L upgradient of the wooded riparian zone and 3.5 mg/L upgradient of the grass-shrub zone. Shallow groundwater beneath the fields passed through the riparian zones and discharged into streams that had average nitrate concentrations of 8.5 mg/L (as N). Lateral variations of δD values in groundwater showed that mixing among different water sources occurred beneath the riparian zones. In the wooded riparian zone, nitrate concentrations in shallow groundwater were diluted by upwelling, nitrate-poor, deep groundwater. Upwelling deep groundwater contained ammonium with a δ15N of 5‰ that upon nitrification and mixing with nitrate in shallow groundwater caused nitrate δ15N values in shallow groundwater to decrease by as much as 19.5‰. Stream water penetrated laterally beneath the wooded riparian zone as far as 19 m from the stream's edge and beneath the grass-shrub zone as far as 27 m from the stream's edge. Nitrate concentrations in shallow groundwater immediately upgradient of where it mixed with stream water averaged 0.4 mg/L in the wooded riparian zone and 0.8 mg/L near the grass-shrub riparian zone. Nitrate concentrations increased toward the streams because of mixing with nitrate-rich stream water. Because nitrate concentrations were larger in stream water than shallow groundwater, concentrated nitrate in the streams cannot have come from shallow groundwater at these sites. Water sources of riparian trees were identified by comparing δD values of sap water, soil water, groundwater, and stream water. Soil water was the main water source for trees in the outer 4 to 6 m of one part of the wooded riparian zone and outer 10 m of another part. Groundwater was a significant water source for trees closer to the streams where the water table was less than about 2.1 to 2.7 m below the surface. No evidence was found in the nitrate concentration profiles that trees close to the streams that took up groundwater through their roots also took up nitrate from groundwater. The lack of such evidence is attributed to the nitrate concentration profiles being insufficiently sensitive indicators of nitrate removal by trees.

Single Pd Atoms on θ-Al2O3 (010) Surface do not Catalyze NO Oxidation.

PubMed

Narula, Chaitanya K; Allard, Lawrence F; Moses-DeBusk, Melanie; Stocks, G Malcom; Wu, Zili

2017-04-03

New convenient wet-chemistry synthetic routes have made it possible to explore catalytic activities of a variety of single supported atoms, however, the single supported atoms on inert substrates (e.g. alumina) are limited to adatoms and cations of Pt, Pd, and Ru. Previously, we have found that single supported Pt atoms are remarkable NO oxidation catalysts. In contrast, we report that Pd single atoms are completely inactive for NO oxidation. The diffuse reflectance infra-red spectroscopy (DRIFTS) results show the absence of nitrate formation on catalyst. To explain these results, we explored modified Langmuir-Hinshelwood type pathways that have been proposed for oxidation reactions on single supported atom. In the first pathway, we find that there is energy barrier for the release of NO 2 which prevent NO oxidation. In the second pathway, our results show that there is no driving force for the formation of O=N-O-O intermediate or nitrate on single supported Pd atoms. The decomposition of nitrate, if formed, is an endothermic event.

Modeling denitrification in a tile-drained, corn and soybean agroecosystem of Illinois, USA

USDA-ARS?s Scientific Manuscript database

Denitrification is known as an important pathway for nitrate loss in agroecosystems. It is important to estimate denitrification fluxes to close field and watershed N mass balances, determine greenhouse gas emissions (N2O), and help constrain estimates of other major N fluxes (e.g., nitrate leaching...

Nitrate removal from drinking water with a focus on biological methods: a review.

PubMed

Rezvani, Fariba; Sarrafzadeh, Mohammad-Hossein; Ebrahimi, Sirous; Oh, Hee-Mock

2017-05-31

This article summarizes several developed and industrial technologies for nitrate removal from drinking water, including physicochemical and biological techniques, with a focus on autotrophic nitrate removal. Approaches are primarily classified into separation-based and elimination-based methods according to the fate of the nitrate in water treatment. Biological denitrification as a cost-effective and promising method of biological nitrate elimination is reviewed in terms of its removal process, applicability, efficiency, and associated disadvantages. The various pathways during biological nitrate removal, including assimilatory and dissimilatory nitrate reduction, are also explained. A comparative study was carried out to provide a better understanding of the advantages and disadvantages of autotrophic and heterotrophic denitrification. Sulfur-based and hydrogen-based denitrifications, which are the most common autotrophic processes of nitrate removal, are reviewed with the aim of presenting the salient features of hydrogenotrophic denitrification along with some drawbacks of the technology and research areas in which it could be used but currently is not. The application of algae-based water treatment is also introduced as a nature-inspired approach that may broaden future horizons of nitrate removal technology.

Two tales of legacy effects on stream nutrient behaviour

NASA Astrophysics Data System (ADS)

Bieroza, M.; Heathwaite, A. L.

2017-12-01

Intensive agriculture has led to large-scale land use conversion, shortening of flow pathways and increased loads of nutrients in streams. This legacy results in gradual build-up of nutrients in agricultural catchments: in soil for phosphorus (biogeochemical legacy) and in the unsaturated zone for nitrate (hydrologic legacy), controlling the water quality in the long-term. Here we investigate these effects on phosphorus and nitrate stream concentrations using high-frequency (10-5 - 100 Hz) sampling with in situ wet-chemistry analysers and optical sensors. Based on our 5 year study, we observe that storm flow responses differ for both nutrients: phosphorus shows rapid increases (up to 3 orders of magnitude) in concentrations with stream flow, whereas nitrate shows both dilution and concentration effects with increasing flow. However, the range of nitrate concentrations change is narrow (up to 2 times the mean) and reflects chemostatic behaviour. We link these nutrient responses with their dominant sources and flow pathways in the catchment. Nitrate from agriculture (with the peak loading in 1983) is stored in the unsaturated zone of the Penrith Sandstone, which can reach up to 70 m depth. Thus nitrate legacy is related to a hydrologic time lag with long travel times in the unsaturated zone. Phosphorus is mainly sorbed to soil particles, therefore it is mobilised rapidly during rainfall events (biogeochemical legacy). The phosphorus stream response will however depend on how well connected is the stream to the catchment sources (driven by soil moisture distribution) and biogeochemical activity (driven by temperature), leading to both chemostatic and non-chemostatic responses, alternating on a storm-to-storm and seasonal basis. Our results also show that transient within-channel storage is playing an important role in delivery of phosphorus, providing an additional time lag component. These results show, that consistent agricultural legacy in the catchment (high historical loads of nutrients) has different effects on nutrients stream responses, depending on their dominant sources and pathways. Both types of time lags, biogeochemical for phosphorus and hydrologic for nitrate, need to be taken into account when designing and evaluating the effectiveness of the agri-environmental mitigation measures.

Enhanced XOR activity in eNOS-deficient mice: Effects on the nitrate-nitrite-NO pathway and ROS homeostasis.

PubMed

Peleli, Maria; Zollbrecht, Christa; Montenegro, Marcelo F; Hezel, Michael; Zhong, Jianghong; Persson, Erik G; Holmdahl, Rikard; Weitzberg, Eddie; Lundberg, Jon O; Carlström, Mattias

2016-10-01

Xanthine oxidoreductase (XOR) is generally known as the final enzyme in purine metabolism and as a source of reactive oxygen species (ROS). In addition, this enzyme has been suggested to mediate nitric oxide (NO) formation via reduction of inorganic nitrate and nitrite. This NO synthase (NOS)-independent pathway for NO generation is of particular importance during certain conditions when NO bioavailability is diminished due to reduced activity of endothelial NOS (eNOS) or increased oxidative stress, including aging and cardiovascular disease. The exact interplay between NOS- and XOR-derived NO generation is not fully elucidated yet. The aim of the present study was to investigate if eNOS deficiency is associated with changes in XOR expression and activity and the possible impact on nitrite, NO and ROS homeostasis. Plasma levels of nitrate and nitrite were similar between eNOS deficient (eNOS -/- ) and wildtype (wt) mice. XOR activity was upregulated in eNOS -/- compared with wt, but not in nNOS -/- , iNOS -/- or wt mice treated with the non-selective NOS inhibitor L-NAME. Following an acute dose of nitrate, plasma nitrite increased more in eNOS -/- compared with wt, and this augmented response was abolished by the selective XOR inhibitor febuxostat. Livers from eNOS -/- displayed higher nitrite reducing capacity compared with wt, and this effect was attenuated by febuxostat. Dietary supplementation with nitrate increased XOR expression and activity, but concomitantly reduced superoxide generation. The latter effect was also seen in vitro after nitrite administration. Treatment with febuxostat elevated blood pressure in eNOS -/- , but not in wt mice. A high dose of dietary nitrate reduced blood pressure in naïve eNOS -/- mice, and again this effect was abolished by febuxostat. In conclusion, eNOS deficiency is associated with an upregulation of XOR facilitating the nitrate-nitrite-NO pathway and decreasing the generation of ROS. This interplay between XOR and eNOS is proposed to play a significant role in NO homeostasis and blood pressure regulation. Copyright © 2016 Elsevier Inc. All rights reserved.

Attenuated vasodilatation in lambs with endogenous and exogenous activation of cGMP signaling: Role of protein kinase G nitration

PubMed Central

Aggarwal, Saurabh; Gross, Christine M.; Kumar, Sanjiv; Datar, Sanjeev; Oishi, Peter; Kalka, Gokhan; Schreiber, Christian; Fratz, Sohrab; Fineman, Jeffrey R.; Black, Stephen M.

2012-01-01

Pulmonary vasodilation is mediated through the activation of protein kinase G (PKG) via a signaling pathway involving nitric oxide (NO), natriuretic peptides (NP), and cyclic guanosine monophosphate (cGMP). In pulmonary hypertension secondary to congenital heart disease, this pathway is endogenously activated by an early vascular upregulation of NO and increased myocardial B-type NP expression and release. In the treatment of pulmonary hypertension, this pathway is exogenously activated using inhaled NO or other pharmacological agents. Despite this activation of cGMP, vascular dysfunction is present, suggesting that NO-cGMP independent mechanisms are involved and were the focus of this study. Exposure of pulmonary artery endothelial or smooth muscle cells to the NO donor, Spermine NONOate (SpNONOate), increased peroxynitrite (ONOO−) generation and PKG-1α nitration, while PKG-1α activity was decreased. These changes were prevented by superoxide dismutase (SOD) or manganese(III)tetrakis(1-methyl-4-pyridyl)porphyrin (MnTMPyP) and mimicked by the ONOO− donor, 3-morpholinosydnonimine N-ethylcarbamide (SIN-1). Peripheral lung extracts from 4-week old lambs with increased pulmonary blood flow and pulmonary hypertension (Shunt lambs with endogenous activation of cGMP) or juvenile lambs treated with inhaled NO for 24h (with exogenous activation of cGMP) revealed increased ONOO− levels, elevated PKG-1α nitration, and decreased kinase activity without changes in PKG-1α protein levels. However, in Shunt lambs treated with L-arginine or lambs administered polyethylene glycol conjugated-SOD (PEG-SOD) during inhaled NO exposure, ONOO− and PKG-1α nitration were diminished and kinase activity was preserved. Together our data reveal that vascular dysfunction can occur, despite elevated levels of cGMP, due to PKG-1α nitration and subsequent attenuation of activity. PMID:21351102

Role of sulfate, chloride, and nitrate anions on the degradation of fluoroquinolone antibiotics by photoelectro-Fenton.

PubMed

Villegas-Guzman, Paola; Hofer, Florian; Silva-Agredo, Javier; Torres-Palma, Ricardo A

2017-12-01

Taking ciprofloxacin (CIP) as a fluoroquinolone antibiotic model, this work explores the role of common anions (sulfate, nitrate, and chloride) during the application of photoelectro-Fenton (PEF) at natural pH to degrade this type of compound in water. The system was composed of an IrO 2 anode, Ti, or gas diffusion electrode (GDE) as cathode, Fe 2+ , and UV (254 nm). To determine the implications of these anions, the degradation pathway and efficiency of the PEF sub-processes (UV photolysis, anodic oxidation, and electro-Fenton at natural pH) were studied in the individual presence of the anions. The results highlight that degradation routes and kinetics are strongly dependent on electrolytes. When chloride and nitrate ions were present, indirect electro-chemical oxidation was identified by electro-generated HOCl and nitrogenated oxidative species, respectively. Additionally, direct photolysis and direct oxidation at the anode surface were identified as degradation routes. As a consequence of the different pathways, six primary CIP by-products were identified. Therefore, a scheme was proposed representing the pathways involved in the degradation of CIP when submitted to PEF in water with chloride, nitrate, and sulfate ions, showing the complexity of this process. Promoted by individual and synergistic actions of this process, the PEF system leads to a complete elimination of CIP with total removal of antibiotic activity against Staphylococcus aureus and Escherichia coli, and significant mineralization. Finally, the role of the anions was tested in seawater containing CIP, in which the positive contributions of the anions were partially suppressed by its OH radical scavenger action. The findings are of interest for the understanding of the degradation of antibiotics via the PEF process in different matrices containing sulfate, nitrate, and chloride ions.

The Modular Organization of Protein Interactions in Escherichia coli

PubMed Central

Peregrín-Alvarez, José M.; Xiong, Xuejian; Su, Chong; Parkinson, John

2009-01-01

Escherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a ‘systems’ view of E. coli. Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins (∼45% of its proteome). These were combined with a recently generated set of 3,888 high-quality physical interactions between 918 proteins and clustered to reveal 316 discrete modules. In addition to known protein complexes (e.g., RNA and DNA polymerases), we identified modules that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes. To aid the interpretation of modular relationships, several case examples are presented, including both well characterized and novel biochemical systems. Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks. PMID:19798435

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate.

PubMed

Thorup, Casper; Schramm, Andreas; Findlay, Alyssa J; Finster, Kai W; Schreiber, Lars

2017-07-18

This study demonstrates that the deltaproteobacterium Desulfurivibrio alkaliphilus can grow chemolithotrophically by coupling sulfide oxidation to the dissimilatory reduction of nitrate and nitrite to ammonium. Key genes of known sulfide oxidation pathways are absent from the genome of D. alkaliphilus Instead, the genome contains all of the genes necessary for sulfate reduction, including a gene for a reductive-type dissimilatory bisulfite reductase (DSR). Despite this, growth by sulfate reduction was not observed. Transcriptomic analysis revealed a very high expression level of sulfate-reduction genes during growth by sulfide oxidation, while inhibition experiments with molybdate pointed to elemental sulfur/polysulfides as intermediates. Consequently, we propose that D. alkaliphilus initially oxidizes sulfide to elemental sulfur, which is then either disproportionated, or oxidized by a reversal of the sulfate reduction pathway. This is the first study providing evidence that a reductive-type DSR is involved in a sulfide oxidation pathway. Transcriptome sequencing further suggests that nitrate reduction to ammonium is performed by a novel type of periplasmic nitrate reductase and an unusual membrane-anchored nitrite reductase. IMPORTANCE Sulfide oxidation and sulfate reduction, the two major branches of the sulfur cycle, are usually ascribed to distinct sets of microbes with distinct diagnostic genes. Here we show a more complex picture, as D. alkaliphilus , with the genomic setup of a sulfate reducer, grows by sulfide oxidation. The high expression of genes typically involved in the sulfate reduction pathway suggests that these genes, including the reductive-type dissimilatory bisulfite reductases, are also involved in as-yet-unresolved sulfide oxidation pathways. Finally, D. alkaliphilus is closely related to cable bacteria, which grow by electrogenic sulfide oxidation. Since there are no pure cultures of cable bacteria, D. alkaliphilus may represent an exciting model organism in which to study the physiology of this process. Copyright © 2017 Thorup et al.

Thermal Decomposition Of Hydroxylamine Nitrate

NASA Astrophysics Data System (ADS)

Oxley, Jimmie C.; Brower, Kay R.

1988-05-01

used hydroxylamine nitrate decomposes within a few minutes in the temperature range 130-140°C. Added ammonium ion is converted to N2, while hydrazinium ion is converted to HN3. Nitrous acid is an intermediate and its formation is rate-determining. A hygride transfer process is postulated. The reaction pathways have been elucidated by use of N tracers.

[Photodegradation of UV filter PABA in nitrate solution].

PubMed

Meng, Cui; Ji, Yue-Fei; Zeng, Chao; Yang, Xi

2011-09-01

The aqueous photolysis of a UV filter p-aminobenzoic acid (PABA) using Xe lamp as simulated solar irradiation source was investigated in the presence of nitrate ions. The effects of pH, concentration of nitrate ions and concentration of humic substance in natural water on the photodegradation of PABA were studied. The results showed that photodegradation of PABA in nitrate solution followed the first order kinetics. The increasing concentration of nitrate ion increased favored the photodegradaton of PABA, of which the first order constant increased from 0.002 2 min(-10 to 0.017 9 min(-1). The photodegradation of PABA promoted with the increase of pH while the increasing concentration of humic substance showed inhibiting effect. Hydroxyl radicals determined by the molecular probe method played a very importnant role in the photolysis process of PABA. Photoproducts upon irradiation of PABA in nitrate solution were isolated by means of solid-phase extraction (SPE) and identified by LC-MS techniques. The probable photoinduced degradation pathways in nitrate solution were proposed.

Triosephosphate isomerase tyrosine nitration induced by heme-NaNO2 -H2 O2 or peroxynitrite: Effects of different natural phenolic compounds.

PubMed

Gao, Wanxia; Zhao, Jie; Li, Hailing; Gao, Zhonghong

2017-06-01

Peroxynitrite and heme peroxidases (or heme)-H 2 O 2 -NaNO 2 system are the two common ways to cause protein tyrosine nitration in vitro, but the effects of antioxidants on reducing these two pathways-induced protein nitration and oxidation are controversial. Both nitrating systems can dose-dependently induce triosephosphate isomerase (TIM) nitration, however, heme-H 2 O 2 -NaNO 2 was less destructive to protein secondary structures and led to more nitrated tyrosine residue than 3-morpholinosydnonimine hydrochloride (SIN-1, a peroxynitrite donor). Both of desferrioxamine and catechin could inhibit TIM nitration induced by heme-H 2 O 2 -NaNO 2 and SIN-1 and protein oxidation induced by SIN-1, but promoted heme-H 2 O 2 -NaNO 2 -induced protein oxidation. Moreover, the antagonism of natural phenolic compounds on SIN-1-induced tyrosine nitration was consistent with their radical scavenging ability, but no similar consensus was found in heme-H 2 O 2 -NaNO 2 -induced nitration. Our results indicated that peroxynitrite and heme-H 2 O 2 -NaNO 2 -induced protein nitration was different, and the later one could be a better model for anti-nitration compounds screening. © 2017 Wiley Periodicals, Inc.

The Arabidopsis NRG2 Protein Mediates Nitrate Signaling and Interacts with and Regulates Key Nitrate Regulators[OPEN

PubMed Central

Zhao, Lufei; Zhang, Chengfei; Li, Zehui; Lei, Zhao; Liu, Fei; Guan, Peizhu; Crawford, Nigel M.

2016-01-01

We show that NITRATE REGULATORY GENE2 (NRG2), which we identified using forward genetics, mediates nitrate signaling in Arabidopsis thaliana. A mutation in NRG2 disrupted the induction of nitrate-responsive genes after nitrate treatment by an ammonium-independent mechanism. The nitrate content in roots was lower in the mutants than in the wild type, which may have resulted from reduced expression of NRT1.1 (also called NPF6.3, encoding a nitrate transporter/receptor) and upregulation of NRT1.8 (also called NPF7.2, encoding a xylem nitrate transporter). Genetic and molecular data suggest that NRG2 functions upstream of NRT1.1 in nitrate signaling. Furthermore, NRG2 directly interacts with the nitrate regulator NLP7 in the nucleus, but nuclear retention of NLP7 in response to nitrate is not dependent on NRG2. Transcriptomic analysis revealed that genes involved in four nitrogen-related clusters including nitrate transport and response to nitrate were differentially expressed in the nrg2 mutants. A nitrogen compound transport cluster containing some members of the NRT/PTR family was regulated by both NRG2 and NRT1.1, while no nitrogen-related clusters showed regulation by both NRG2 and NLP7. Thus, NRG2 plays a key role in nitrate regulation in part through modulating NRT1.1 expression and may function with NLP7 via their physical interaction. PMID:26744214

Influence of growing system on nitrate accumulation in two varieties of lettuce and red radicchio of Treviso.

PubMed

Lucarini, Massimo; D'Evoli, Laura; Tufi, Sara; Gabrielli, Paolo; Paoletti, Sara; Di Ferdinando, Sandra; Lombardi-Boccia, Ginevra

2012-11-01

Green leafy vegetables contribute greatly to the total intake of nitrates from the daily diet. This study evaluates the influence of different cultivation systems on nitrate accumulation in leafy vegetables. Two varieties of lettuce (Lactuca sativa L.) (Lattuga Romana, Foglia di Quercia) and two varieties of red radicchio of Treviso (Cychorium intibus L.) (Early, Late) were selected. Lettuce varieties were both organically and biodynamically grown; red radicchio varieties were conventionally grown both in the field and in spring water. Both lettuce varieties biodynamically grown accumulated 1.3-2 times less nitrate than the respective organically grown plants. The two lettuce varieties showed differences in nitrate accumulating capacity: Foglia di Quercia was almost three times richer in nitrate than Lattuga Romana. The traditional growing systems applied to the red radicchio of Treviso varieties strongly influenced nitrate accumulation in leaves, the Early variety having up to 15 times higher nitrate than the Late variety. Our findings on nitrate levels in both lettuce and red radicchio of Treviso varieties suggest that both genetic factors and cultivation systems strongly affect the nitrate accumulation capacity. This study also highlights how the cultivation strategy can reduce nitrate levels in leafy vegetables, suggesting the possibility of modulating the N supply along the harvesting time. Copyright © 2011 Society of Chemical Industry.

Nitrate-induced photodegradation of atenolol in aqueous solution: kinetics, toxicity and degradation pathways.

PubMed

Ji, Yuefei; Zeng, Chao; Ferronato, Corinne; Chovelon, Jean-Marc; Yang, Xi

2012-07-01

The extensive utilization of β-blockers worldwide led to frequent detection in natural water. In this study the photolysis behavior of atenolol (ATL) and toxicity of its photodegradation products were investigated in the presence of nitrate ions. The results showed that ATL photodegradation followed pseudo-first-order kinetics upon simulated solar irradiation. The photodegradation was found to be dependent on nitrate concentration and increasing the nitrate from 0.5 mML(-1) to 10 mML(-1) led to the enhancement of rate constant from 0.00101 min(-1) to 0.00716 min(-1). Hydroxyl radical was determined to play a key role in the photolysis process by using isopropanol as molecular probe. Increasing the solution pH from 4.8 to 10.4, the photodegradation rate slightly decreased from 0.00246 min(-1) to 0.00195 min(-1), probably due to pH-dependent effect of nitrate-induced .OH formation. Bicarbonate decreased the photodegradation of ATL in the presence of nitrate ions mainly through pH effect, while humic substance inhibited the photodegradation via both attenuating light and competing radicals. Upon irradiation for 240 min, only 10% reduction of total organic carbon (TOC) can be achieved in spite of 72% transformation rate of ATL, implying a majority of ATL transformed into intermediate products rather than complete mineralization. The main photoproducts of ATL were identified by using solid phase extraction-liquid chromatography-mass spectrometry (SPE-LC-MS) techniques and possible nitrate-induced photodegradation pathways were proposed. The toxicity of the phototransformation products was evaluated using aquatic species Daphnia magna, and the results revealed that photodegradation was an effective mechanism for ATL toxicity reduction in natural waters. Copyright © 2012 Elsevier Ltd. All rights reserved.

Overexpression of the PP2A regulatory subunit Tap46 leads to enhanced plant growth through stimulation of the TOR signalling pathway

PubMed Central

Ahn, Chang Sook; Ahn, Hee-Kyung; Pai, Hyun-Sook

2015-01-01

Tap46, a regulatory subunit of protein phosphatase 2A (PP2A), plays an essential role in plant growth and development through a functional link with the Target of Rapamycin (TOR) signalling pathway. Here, we have characterized the molecular mechanisms behind a gain-of-function phenotype of Tap46 and its relationship with TOR to gain further insights into Tap46 function in plants. Constitutive overexpression of Tap46 in Arabidopsis resulted in overall growth stimulation with enlarged organs, such as leaves and siliques. Kinematic analysis of leaf growth revealed that increased cell size was mainly responsible for the leaf enlargement. Tap46 overexpression also enhanced seed size and viability under accelerated ageing conditions. Enhanced plant growth was also observed in dexamethasone (DEX)-inducible Tap46 overexpression Arabidopsis lines, accompanied by increased cellular activities of nitrate-assimilating enzymes. DEX-induced Tap46 overexpression and Tap46 RNAi resulted in increased and decreased phosphorylation of S6 kinase (S6K), respectively, which is a sensitive indicator of endogenous TOR activity, and Tap46 interacted with S6K in planta based on bimolecular fluorescence complementation and co-immunoprecipitation. Furthermore, inactivation of TOR by estradiol-inducible RNAi or rapamycin treatment decreased Tap46 protein levels, but increased PP2A catalytic subunit levels. Real-time quantitative PCR analysis revealed that Tap46 overexpression induced transcriptional modulation of genes involved in nitrogen metabolism, ribosome biogenesis, and lignin biosynthesis. These findings suggest that Tap46 modulates plant growth as a positive effector of the TOR signalling pathway and Tap46/PP2Ac protein abundance is regulated by TOR activity. PMID:25399018

Photochemically assisted fast abiotic oxidation of manganese and formation of δ-MnO 2 nanosheets in nitrate solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jung, Haesung; Chadha, Tandeep S.; Kim, Doyoon

This study introduces a new and previously unconsidered fast abiotic formation of Mn(IV) oxides. We report photochemically assisted fast abiotic oxidation of Mn 2+ (aq) to Mn(IV) (s) by superoxide radicals generated from nitrate photolysis. This photochemical pathway generates randomly stacked layered birnessite (δ-MnO 2) nanosheets.

Nitration Enzyme Toolkit for the Biosynthesis of Energetic Materials

DTIC Science & Technology

by - products that degrade performance of the energetic products . To reduce the...bionitration mechanisms used by microorganisms to produce nitro-containing natural products . We investigated biosynthetic pathways for 2-nitroimidazole...producing a diverse set of nitrophenols. This growing bionitration toolkit represents a diverse range of nitration mechanisms and products that can be adapted for the green chemistry production of nitro compounds and

Membrane cytochromes of Escherichia coli chl mutants.

PubMed Central

Hackett, N R; Bragg, P D

1983-01-01

The cytochromes present in the membranes of Escherichia coli cells having defects in the formate dehydrogenase-nitrate reductase system have been analyzed by spectroscopic, redox titration, and enzyme fractionation techniques. Four phenotypic classes differing in cytochrome composition were recognized. Class I is represented by strains with defects in the synthesis or insertion of molybdenum cofactor. Cytochromes of the formate dehydrogenase-nitrate reductase pathway are present. Class II strains map in the chlC-chlI region. The cytochrome associated with nitrate reductase (cytochrome bnr) is absent in these strains, whereas that associated with formate dehydrogenase (cytochrome bfdh) is the major cytochrome in the membranes. Class III strains lack both cytochromes bfdh and bnr but overproduce cytochrome d of the aerobic pathway even under anaerobic conditions in the presence of nitrate. Class III strains have defects in the regulation of cytochrome synthesis. An fdhA mutant produced cytochrome bnr but lacked cytochrome bfdh. These results support the view that chlI (narI) is the structural gene for cytochrome bnr and that chlC (narG) and chlI(narI) are in the same operon, and they provide evidence of the complexity of the regulation of cytochrome synthesis. PMID:6302081

Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus.

PubMed

Yang, Jhung-Ahn; Yang, Sung-Hyun; Kim, Junghee; Kwon, Kae Kyoung; Oh, Hyun-Myung

2017-07-01

Here we report the comparative genomic analysis of strain UJ101 with 15 strains from the family Flavobacteriaceae, using the CGExplorer program. Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus, from the East Sea near Korea. The complete genome of strain UJ101 is a 3,074,209 bp, single, circular chromosome with 30.74% GC content. While the UJ101 genome contains a number of annotated genes for many metabolic pathways, such as the Embden-Meyerhof pathway, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, genes for the Entner-Douddoroff pathway are not found in the UJ101 genome. Overall, carbon fixation processes were absent but nitrate reduction and denitrification pathways were conserved. The UJ101 genome was compared to genomes from other marine animals (three invertebrate strains and 5 fish strains) and other marine animal- derived genera. Notable results by genome comparisons showed that UJ101 is capable of denitrification and nitrate reduction, and that biotin-thiamine pathway participation varies among marine bacteria; fish-dwelling bacteria, freeliving bacteria, invertebrate-dwelling bacteria, and strain UJ101. Pan-genome analysis of the 16 strains in this study included 7,220 non-redundant genes that covered 62% of the pan-genome. A core-genome of 994 genes was present and consisted of 8% of the genes from the pan-genome. Strain UJ101 is a symbiotic hetero-organotroph isolated from xanthid crab, and is a metabolic generalist with nitrate-reducing abilities but without the ability to synthesize biotin. There is a general tendency of UJ101 and some fish pathogens to prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin and thiamine auxotrophy or prototrophy may be used as important markers in microbial community studies.

Investigation of the chemical pathway of gaseous nitrogen dioxide formation during flue gas desulfurization with dry sodium bicarbonate injection

NASA Astrophysics Data System (ADS)

Stein, Antoinette Weil

The chemical reaction pathway for the viable flue gas desulfurization process, dry sodium bicarbonate injection, was investigated to mitigate undesirable plume discoloration. Based on a foundation of past findings, a simplified three-step reaction pathway was hypothesized for the formation of the plume-discoloring constituent, NO2. As the first step, it was hypothesized that sodium sulfite formed by sodium bicarbonate reaction with flue gas SO 2. As the second step, it was hypothesized that sodium nitrate formed by sodium sulfite reaction with flue gas NO. And as the third step, it was hypothesized that NO2 and sodium sulfate formed by sodium nitrate reaction with SO2. The second and third hypothesized steps were experimentally investigated using an isothermal fixed bed reactor. As reported in the past, technical grade sodium sulfite was found to be un-reactive with NO and O2. Freshly prepared sodium sulfite, maintained unexposed to moist air, was shown to react with NO and O2 resulting in a mixture of sodium nitrite and sodium nitrate together with a significant temperature rise. This reaction was found to proceed only when oxygen was present in the flue gas. As reported in the past, technical grade sodium nitrate was shown to be un-reactive with SO2. But freshly formed sodium nitrate kept unexposed to humidity was found to be reactive with SO2 and O 2 resulting in the formation of NO2 and sodium sulfate polymorphic Form I. The NO2 formation by this reaction was shown to be temperature dependent with maximum formation at 175°C. Plume mitigation methods were studied based on the validated three-step reaction pathway. Mitigation of NO2 was exhibited by limiting oxygen concentration in the flue gas to a level below 5%. It was also shown that significant NO2 mitigation was achieved by operating below 110°C or above 250°C. An innovative NO2 mitigation method was patented as a result of the findings of this study. The patented process incorporated a process step of sodium sulfite injection to remove flue gas NO prior to sodium bicarbonate injection.

Wastewater polishing by a channelized macrophyte-dominated wetland and anaerobic digestion of the harvested phytomass.

PubMed

Cohen, Michael F; Hare, Caden; Kozlowski, John; McCormick, Rachel S; Chen, Lily; Schneider, Linden; Parish, Meghan; Knight, Zane; Nelson, Timothy A; Grewell, Brenda J

2013-01-01

Constructed wetlands (CW) offer a mechanism to meet increasingly stringent regulatory standards for wastewater treatment while minimizing energy inputs. Additionally, harvested wetland phytomass subjected to anaerobic digestion can serve as a source of biogas methane. To investigate CW wastewater polishing activities and potential energy yield we constructed a pair of secondary wastewater-fed channelized CW modules designed to retain easily harvestable floating aquatic vegetation and maximize exposure of water to roots and sediment. Modules that were regularly harvested averaged a nitrate removal rate of 1.1 g N m(-2) d(-1); harvesting, sedimentation and gasification were responsible for 30.5%, 8.0% and 61.5% of the N losses, respectively. Selective harvesting of a module to maintain dominance of filamentous algae had no effect on nitrate removal rate but lowered productivity by one-half. The average monthly productivity for unselectively harvested modules was 9.3 ± 1.7 g dry wt. m(-2) d(-1) (±SE). Cessation of harvesting in one module resulted in a significant increase in nitrate removal rate and decrease in phosphate removal rate. Compared to the influent, the effluent of the harvested module had significantly lower levels of estrogenic activity, as determined by a quantitative PCR-based juvenile trout bioassay, and significantly lower densities of E. coli. In mixed vertical-flow reactors anaerobic co-digestion of equal dry weight proportions of harvested aquatic vegetation, wine yeast lees and dairy manure was greatly improved when the manure was replaced with the crude glycerol by-product of biodiesel production. Remaining solids were vermicomposted for use as a soil amendment. Our results indicate that incorporation of constructed wetlands into an integrated treatment system can simultaneously enhance the economic and energetic feasibility of wastewater and organic waste treatment processes.

Nitrite and Nitrate Concentrations and Metabolism in Breast Milk, Infant Formula, and Parenteral Nutrition

PubMed Central

Jones, Jesica A.; Ninnis, Janet R.; Hopper, Andrew O.; Ibrahim, Yomna; Merritt, T. Allen; Wan, Kim-Wah; Power, Gordon G.; Blood, Arlin B.

2015-01-01

Dietary nitrate and nitrite are sources of gastric NO, which modulates blood flow, mucus production, and microbial flora. However, the intake and importance of these anions in infants is largely unknown. Nitrate and nitrite levels were measured in breast milk of mothers of preterm and term infants, infant formulas, and parenteral nutrition. Nitrite metabolism in breast milk was measured after freeze-thawing, at different temperatures, varying oxygen tensions, and after inhibition of potential nitrite-metabolizing enzymes. Nitrite concentrations averaged 0.07 ± 0.01 μM in milk of mothers of preterm infants, less than that of term infants (0.13 ± 0.02 μM) (P < .01). Nitrate concentrations averaged 13.6 ± 3.7 μM and 12.7 ± 4.9 μM, respectively. Nitrite and nitrate concentrations in infant formulas varied from undetectable to many-fold more than breast milk. Concentrations in parenteral nutrition were equivalent to or lower than those of breast milk. Freeze-thawing decreased nitrite concentration ∼64%, falling with a half-life of 32 minutes at 37°C. The disappearance of nitrite was oxygen-dependent and prevented by ferricyanide and 3 inhibitors of lactoperoxidase. Nitrite concentrations in breast milk decrease with storage and freeze-thawing, a decline likely mediated by lactoperoxidase. Compared to adults, infants ingest relatively little nitrite and nitrate, which may be of importance in the modulation of blood flow and the bacterial flora of the infant GI tract, especially given the protective effects of swallowed nitrite. PMID:23894175

Nitrite and nitrate concentrations and metabolism in breast milk, infant formula, and parenteral nutrition.

PubMed

Jones, Jesica A; Ninnis, Janet R; Hopper, Andrew O; Ibrahim, Yomna; Merritt, T Allen; Wan, Kim-Wah; Power, Gordon G; Blood, Arlin B

2014-09-01

Dietary nitrate and nitrite are sources of gastric NO, which modulates blood flow, mucus production, and microbial flora. However, the intake and importance of these anions in infants is largely unknown. Nitrate and nitrite levels were measured in breast milk of mothers of preterm and term infants, infant formulas, and parenteral nutrition. Nitrite metabolism in breast milk was measured after freeze-thawing, at different temperatures, varying oxygen tensions, and after inhibition of potential nitrite-metabolizing enzymes. Nitrite concentrations averaged 0.07 ± 0.01 μM in milk of mothers of preterm infants, less than that of term infants (0.13 ± 0.02 μM) (P < .01). Nitrate concentrations averaged 13.6 ± 3.7 μM and 12.7 ± 4.9 μM, respectively. Nitrite and nitrate concentrations in infant formulas varied from undetectable to many-fold more than breast milk. Concentrations in parenteral nutrition were equivalent to or lower than those of breast milk. Freeze-thawing decreased nitrite concentration ~64%, falling with a half-life of 32 minutes at 37°C. The disappearance of nitrite was oxygen-dependent and prevented by ferricyanide and 3 inhibitors of lactoperoxidase. Nitrite concentrations in breast milk decrease with storage and freeze-thawing, a decline likely mediated by lactoperoxidase. Compared to adults, infants ingest relatively little nitrite and nitrate, which may be of importance in the modulation of blood flow and the bacterial flora of the infant GI tract, especially given the protective effects of swallowed nitrite. © 2013 American Society for Parenteral and Enteral Nutrition.

Respiration of Nitrate and Nitrite.

PubMed

Cole, Jeffrey A; Richardson, David J

2008-09-01

Nitrate reduction to ammonia via nitrite occurs widely as an anabolic process through which bacteria, archaea, and plants can assimilate nitrate into cellular biomass. Escherichia coli and related enteric bacteria can couple the eight-electron reduction of nitrate to ammonium to growth by coupling the nitrate and nitrite reductases involved to energy-conserving respiratory electron transport systems. In global terms, the respiratory reduction of nitrate to ammonium dominates nitrate and nitrite reduction in many electron-rich environments such as anoxic marine sediments and sulfide-rich thermal vents, the human gastrointestinal tract, and the bodies of warm-blooded animals. This review reviews the regulation and enzymology of this process in E. coli and, where relevant detail is available, also in Salmonella and draws comparisons with and implications for the process in other bacteria where it is pertinent to do so. Fatty acids may be present in high levels in many of the natural environments of E. coli and Salmonella in which oxygen is limited but nitrate is available to support respiration. In E. coli, nitrate reduction in the periplasm involves the products of two seven-gene operons, napFDAGHBC, encoding the periplasmic nitrate reductase, and nrfABCDEFG, encoding the periplasmic nitrite reductase. No bacterium has yet been shown to couple a periplasmic nitrate reductase solely to the cytoplasmic nitrite reductase NirB. The cytoplasmic pathway for nitrate reduction to ammonia is restricted almost exclusively to a few groups of facultative anaerobic bacteria that encounter high concentrations of environmental nitrate.

Enhanced nitrogen selectivity for nitrate reduction on Cu-nZVI by TiO2 photocatalysts under UV irradiation

NASA Astrophysics Data System (ADS)

Krasae, Nalinee; Wantala, Kitirote

2016-09-01

The aims of this work were to study the effect of Cu-nZVI with and without TiO2 on nitrate reduction and to study the pathway of nitrate reduction utilizing to nitrogen gas. The chemical and physical properties of Cu-nZVI and Cu-nZVI/TiO2 such as specific surface area, crystalline phase, oxidation state of Cu and Fe and morphology were determined by N2 adsorption-desorption Brunauer-Emmett-Teller (BET) analytical technique, X-ray diffraction (XRD), X-ray Absorption Near Edge Structure (XANES) technique and Transmittance Electron Microscopy (TEM). The full factorial design (FFD) was used in this experiment for the effect of Cu-nZVI with and without TiO2, where the initial solution pH was varied at 4, 5.5, and 7 and initial nitrate concentration was varied at 50, 75, and 100 ppm. Finally, the pathway of nitrate reduction was examined to calculate the nitrogen gas selectivity. The specific area of Cu-nZVI and Cu-nZVI/TiO2 was found to be about 4 and 36 m2/g, respectively. The XRD pattern of Fe0 in Cu-nZVI was found at 45° (2θ), whereas Cu-nZVI/TiO2 cannot be observed. TEM images can confirm the position of the core and the shell of nZVI for Fe0 and ferric oxide. Cu-nZVI/TiO2 proved to have higher activity in nitrogen reduction performance than that without TiO2 and nitrate can be completely degraded in both of solution pH of 4 and 7 in 75 ppm of initial nitrate concentration. It can be highlighted that the nitrogen gas selectivity of Cu-nZVI/TiO2 greater than 82% was found at an initial solution pH of 4 and 7. The main effects of Cu-nZVI with and without TiO2 and the initial nitrate concentration on nitrate reduction were significant. The interaction between solution pH and initial nitrate concentration and the interaction of all effects at a reaction time of 15 min on nitrate reduction were also significant.

Electrical activity of the cingulate cortex. II. Cholinergic modulation.

PubMed

Borst, J G; Leung, L W; MacFabe, D F

1987-03-24

The role of the cholinergic innervation in the modulation of cingulate electrical activity was studied by means of pharmacological manipulations and brain lesions. In the normal rat, an irregular slow activity (ISA) accompanied with EEG-spikes was recorded in the cingulate cortex during immobility as compared to walking. Atropine sulfate, but not atropine methyl nitrate, increased ISA and the frequency of cingulate EEG-spikes. Pilocarpine suppressed ISA and EEG-spikes during immobility, and induced a slow (4-7 Hz) theta rhythm. Unilateral or bilateral lesions of the substantia innominata and ventral globus pallidus area using kainic acid did not significantly change the cingulate EEG or its relation to behavior. Large electrolytic lesions of the medial septal nuclei and vertical limbs of the diagonal band generally decreased or abolished all theta activity in the cingulate cortex and the hippocampus. However, in 5 rats the cingulate theta rhythm increased while the hippocampal theta disappeared after a medial septal lesion. The large, postlesion cingulate theta, accompanied by sharp EEG-spikes during its negative phase, is an unequivocal demonstration of the existence of a theta rhythm in the cingulate cortex, independent of the hippocampal rhythm. Cholinergic afferents from the medial septum and diagonal band nuclei are inferred to be responsible for the behavioral suppression of cingulate EEG-spikes and ISA, and partially for the generation of a local cingulate theta rhythm. However, an atropine-resistant pathway and a theta-suppressing pathway, possibly coming from the medial septum or the hippocampus, may also be important in cingulate theta generation.

Enterocyte protein tyrosine nitration in response to Eimeria infection in broilers

USDA-ARS?s Scientific Manuscript database

Activation of pathogen-sensing mechanisms in intestinal cells initiate the generation of pathway effectors that perturb normal nutritional enterocyte (ETC) functions. Among the conserved pathway mediator molecules generated are nitric oxide (NO) and superoxide anion (SOA) which are known to interac...

Structural aspects of denitrifying enzymes.

PubMed

Moura, I; Moura, J J

2001-04-01

The reduction of nitrate to nitrogen gas via nitrite, nitric oxide and nitrous oxide is the metabolic pathway usually known as denitrification, a key step in the nitrogen cycle. As observed for other elemental cycles, a battery of enzymes are utilized, namely the reductases for nitrate, nitrite, nitric oxide and nitrous oxide, as well as multiple electron donors that interact with these enzymes, in order to carry out the stepwise reactions that involve key intermediates. Because of the importance of this pathway (of parallel importance to the nitrogen-fixation pathway), efforts are underway to understand the structures of the participating enzymes and to uncover mechanistic aspects. Three-dimensional structures have been solved for the majority of these enzymes in the past few years, revealing the architecture of the active metal sites as well as global structural aspects, and possible mechanistic aspects. In addition, the recognition of specific electron-transfer partners raises important questions regarding specific electron-transfer pathways, partner recognition and control of metabolism.

Dissimilatory nitrate reduction to nitrate, nitrous oxide, and ammonium by Pseudomonas putrefaciens.

PubMed

Samuelsson, M O

1985-10-01

The influence of redox potential on dissimilatory nitrate reduction to ammonium was investigated on a marine bacterium, Pseudomonas putrefaciens. Nitrate was consumed (3.1 mmol liter-1), and ammonium was produced in cultures with glucose and without sodium thioglycolate. When sodium thioglycolate was added, nitrate was consumed at a lower rate (1.1 mmol liter-1), and no significant amounts of nitrite or ammonium were produced. No growth was detected in glucose media either with or without sodium thioglycolate. When grown on tryptic soy broth, the production of nitrous oxide paralleled growth. In the same medium, but with sodium thioglycolate, nitrous oxide was first produced during growth and then consumed. Acetylene caused the nitrous oxide to accumulate. These results and the mass balance calculations for different nitrogen components indicate that P. putrefaciens has the capacity to dissimilate nitrate to ammonium as well as to dinitrogen gas and nitrous oxide (denitrification). The dissimilatory pathway to ammonium dominates except when sodium thioglycolate is added to the medium.

Investigating ego modules and pathways in osteosarcoma by integrating the EgoNet algorithm and pathway analysis.

PubMed

Chen, X Y; Chen, Y H; Zhang, L J; Wang, Y; Tong, Z C

2017-02-16

Osteosarcoma (OS) is the most common primary bone malignancy, but current therapies are far from effective for all patients. A better understanding of the pathological mechanism of OS may help to achieve new treatments for this tumor. Hence, the objective of this study was to investigate ego modules and pathways in OS utilizing EgoNet algorithm and pathway-related analysis, and reveal pathological mechanisms underlying OS. The EgoNet algorithm comprises four steps: constructing background protein-protein interaction (PPI) network (PPIN) based on gene expression data and PPI data; extracting differential expression network (DEN) from the background PPIN; identifying ego genes according to topological features of genes in reweighted DEN; and collecting ego modules using module search by ego gene expansion. Consequently, we obtained 5 ego modules (Modules 2, 3, 4, 5, and 6) in total. After applying the permutation test, all presented statistical significance between OS and normal controls. Finally, pathway enrichment analysis combined with Reactome pathway database was performed to investigate pathways, and Fisher's exact test was conducted to capture ego pathways for OS. The ego pathway for Module 2 was CLEC7A/inflammasome pathway, while for Module 3 a tetrasaccharide linker sequence was required for glycosaminoglycan (GAG) synthesis, and for Module 6 was the Rho GTPase cycle. Interestingly, genes in Modules 4 and 5 were enriched in the same pathway, the 2-LTR circle formation. In conclusion, the ego modules and pathways might be potential biomarkers for OS therapeutic index, and give great insight of the molecular mechanism underlying this tumor.

Investigating ego modules and pathways in osteosarcoma by integrating the EgoNet algorithm and pathway analysis

PubMed Central

Chen, X.Y.; Chen, Y.H.; Zhang, L.J.; Wang, Y.; Tong, Z.C.

2017-01-01

Osteosarcoma (OS) is the most common primary bone malignancy, but current therapies are far from effective for all patients. A better understanding of the pathological mechanism of OS may help to achieve new treatments for this tumor. Hence, the objective of this study was to investigate ego modules and pathways in OS utilizing EgoNet algorithm and pathway-related analysis, and reveal pathological mechanisms underlying OS. The EgoNet algorithm comprises four steps: constructing background protein-protein interaction (PPI) network (PPIN) based on gene expression data and PPI data; extracting differential expression network (DEN) from the background PPIN; identifying ego genes according to topological features of genes in reweighted DEN; and collecting ego modules using module search by ego gene expansion. Consequently, we obtained 5 ego modules (Modules 2, 3, 4, 5, and 6) in total. After applying the permutation test, all presented statistical significance between OS and normal controls. Finally, pathway enrichment analysis combined with Reactome pathway database was performed to investigate pathways, and Fisher's exact test was conducted to capture ego pathways for OS. The ego pathway for Module 2 was CLEC7A/inflammasome pathway, while for Module 3 a tetrasaccharide linker sequence was required for glycosaminoglycan (GAG) synthesis, and for Module 6 was the Rho GTPase cycle. Interestingly, genes in Modules 4 and 5 were enriched in the same pathway, the 2-LTR circle formation. In conclusion, the ego modules and pathways might be potential biomarkers for OS therapeutic index, and give great insight of the molecular mechanism underlying this tumor. PMID:28225867

Absence of an effect of high nitrate intake from beetroot juice on blood pressure in treated hypertensive individuals: a randomized controlled trial.

PubMed

Bondonno, Catherine P; Liu, Alex H; Croft, Kevin D; Ward, Natalie C; Shinde, Sujata; Moodley, Yuben; Lundberg, Jon O; Puddey, Ian B; Woodman, Richard J; Hodgson, Jonathan M

2015-08-01

Dietary nitrate, which is in green leafy vegetables and beetroot, decreases blood pressure through the enterosalivary nitrate-nitrite-nitric oxide pathway in healthy individuals. Whether similar effects would occur in individuals with treated hypertension and, therefore, at increased risk of cardiovascular disease is unclear. We assessed whether increased dietary nitrate intake by using beetroot juice for 1 wk lowers blood pressure in treated hypertensive men and women. Participants (n = 27) were recruited to a randomized, placebo-controlled, double-blind crossover trial. The effect of 1-wk intake of nitrate-rich beetroot juice was compared with 1-wk intake of nitrate-depleted beetroot juice (placebo). The primary outcome was blood pressure assessed by measuring home blood pressure during the intervention and 24-h ambulatory blood pressure on day 7 of the intervention. Other outcomes included nitrate metabolism assessed by measuring nitrate and nitrite in plasma, saliva, and urine. Relative to the placebo, 1-wk intake of nitrate-rich beetroot juice resulted in a 3-fold increase in plasma nitrite and nitrate, a 7-fold increase in salivary nitrite, an 8-fold higher salivary nitrate, and a 4-fold increase in both urinary nitrite and nitrate (P < 0.001). However, no differences in home blood pressure and 24-h ambulatory blood pressure were observed with 1-wk intake of nitrate-rich beetroot juice in comparison with the placebo. An increase in dietary nitrate intake may not be an effective short-term approach to further lower blood pressure in treated hypertensive subjects. © 2015 American Society for Nutrition.

A comparison of organic and inorganic nitrates/nitrites.

PubMed

Omar, Sami A; Artime, Esther; Webb, Andrew J

2012-05-15

Although both organic and inorganic nitrates/nitrites mediate their principal effects via nitric oxide, there are many important differences. Inorganic nitrate and nitrite have simple ionic structures and are produced endogenously and are present in the diet, whereas their organic counterparts are far more complex, and, with the exception of ethyl nitrite, are all medicinally synthesised products. These chemical differences underlie the differences in pharmacokinetic properties allowing for different modalities of administration, particularly of organic nitrates, due to the differences in their bioavailability and metabolic profiles. Whilst the enterosalivary circulation is a key pathway for orally ingested inorganic nitrate, preventing an abrupt effect or toxic levels of nitrite and prolonging the effects, this is not used by organic nitrates. The pharmacodynamic differences are even greater; while organic nitrates have potent acute effects causing vasodilation, inorganic nitrite's effects are more subtle and dependent on certain conditions. However, in chronic use, organic nitrates are considerably limited by the development of tolerance and endothelial dysfunction, whereas inorganic nitrate/nitrite may compensate for diminished endothelial function, and tolerance has not been reported. Also, while inorganic nitrate/nitrite has important cytoprotective effects against ischaemia-reperfusion injury, continuous use of organic nitrates may increase injury. While there are concerns that inorganic nitrate/nitrite may induce carcinogenesis, direct evidence of this in humans is lacking. While organic nitrates may continue to dominate the therapeutic arena, this may well change with the increasing recognition of their limitations, and ongoing discovery of beneficial effects and specific advantages of inorganic nitrate/nitrite. Copyright © 2012 Elsevier Inc. All rights reserved.

Observations of fine and coarse particle nitrate at several rural locations in the United States

NASA Astrophysics Data System (ADS)

Lee, Taehyoung; Yu, Xiao-Ying; Ayres, Benjamin; Kreidenweis, Sonia M.; Malm, William C.; Collett, Jeffrey L.

Nitrate comprises an important part of aerosol mass at many non-urban locations during some times of the year. Little is known, however, about the chemical form and size distribution of particulate nitrate in these environments. While submicron ammonium nitrate is often assumed to be the dominant species, this assumption is rarely tested. Properties of aerosol nitrate were characterized at several IMPROVE monitoring sites during a series of field studies. Study sites included Bondville, Illinois (February 2003), San Gorgonio Wilderness Area, California (April and July 2003), Grand Canyon National Park, Arizona (May 2003), Brigantine National Wildlife Refuge, New Jersey (November 2003), and Great Smoky Mountains National Park, Tennessee (July/August 2004). Nitrate was found predominantly in submicron ammonium nitrate particles during the Bondville and San Gorgonio (April) campaigns. Coarse mode nitrate particles, resulting from reactions of nitric acid or its precursors with sea salt or soil dust, were more important at Grand Canyon and Great Smoky Mountains. Both fine and coarse mode nitrate were important during the studies at Brigantine and San Gorgonio (July). These results, which complement earlier findings about the importance of coarse particle nitrate at Yosemite and Big Bend National Parks, suggest a need to more closely examine common assumptions regarding the importance of ammonium nitrate at non-urban sites, to include pathways for coarse mode nitrate formation in regional models, and to consider impacts of coarse particle nitrate on visibility. Because coarse particle nitrate modes often extend well below 2.5 μm aerodynamic diameter, measurements of PM 2.5 nitrate in these environments should not automatically be assumed to contain only ammonium nitrate.

Nitrate induction of root hair density is mediated by TGA1/TGA4 and CPC transcription factors in Arabidopsis thaliana.

PubMed

Canales, Javier; Contreras-López, Orlando; Álvarez, José M; Gutiérrez, Rodrigo A

2017-10-01

Root hairs are specialized cells that are important for nutrient uptake. It is well established that nutrients such as phosphate have a great influence on root hair development in many plant species. Here we investigated the role of nitrate on root hair development at a physiological and molecular level. We showed that nitrate increases root hair density in Arabidopsis thaliana. We found that two different root hair defective mutants have significantly less nitrate than wild-type plants, suggesting that in A. thaliana root hairs have an important role in the capacity to acquire nitrate. Nitrate reductase-null mutants exhibited nitrate-dependent root hair phenotypes comparable with wild-type plants, indicating that nitrate is the signal that leads to increased formation of root hairs. We examined the role of two key regulators of root hair cell fate, CPC and WER, in response to nitrate treatments. Phenotypic analyses of these mutants showed that CPC is essential for nitrate-induced responses of root hair development. Moreover, we showed that NRT1.1 and TGA1/TGA4 are required for pathways that induce root hair development by suppression of longitudinal elongation of trichoblast cells in response to nitrate treatments. Our results prompted a model where nitrate signaling via TGA1/TGA4 directly regulates the CPC root hair cell fate specification gene to increase formation of root hairs in A. thaliana. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Variability and prediction of freshwater and nitrate fluxes for the Louisiana-Texas shelf: Mississippi and Atchafalaya River source functions

USGS Publications Warehouse

Bratkovich, A.; Dinnel, S.P.; Goolsby, D.A.

1994-01-01

Time histories of riverine water discharge, nitrate concentration, and nitrate, flux have been analyzed for the Mississippi and Atchafalaya rivers. Results indicate that water discharge variability is dominated by the annual cycle and shorter-time-scale episodic events presumably associated with snowmelt runoff and spring or summer rains. Interannual variability in water discharge is relatively small compared to the above. In contrast, nitrate concentration exhibits strongest variability at decadal time scales. The interannual variability is not monotonic but more complicated in structure. Weak covariability between water discharge and nitrate concentration leads to a relatively “noisy” nitrate flux signal. Nitrate flux variations exhibit a low-amplitude, long-term modulation of a dominant annual cycle. Predictor-hindcastor analyses indicate that skilled forecasts of nitrate concentration and nitrate flux fields are feasible. Water discharge was the most reliably hindcast (on seasonal to interannual time scales) due to the fundamental strength of the annual hydrologic cycle. However, the forecasting effort for this variable was less successful than the hindcasting effort, mostly due to a phase shift in the annual cycle during our relatively short test period (18 mo). Nitrate concentration was more skillfully predicted (seasonal to interannual time scales) due to the relative dominance of the decadal-scale portion of the signal. Nitrate flux was also skillfully forecast even though historical analyses seemed to indicate that it should be more difficult to predict than either water discharge or nitrate concentration.

Modulation of anaerobic energy metabolism of Bacillus subtilis by arfM (ywiD).

PubMed

Marino, M; Ramos, H C; Hoffmann, T; Glaser, P; Jahn, D

2001-12-01

Bacillus subtilis grows under anaerobic conditions utilizing nitrate ammonification and various fermentative processes. The two-component regulatory system ResDE and the redox regulator Fnr are the currently known parts of the regulatory system for anaerobic adaptation. Mutation of the open reading frame ywiD located upstream of the respiratory nitrate reductase operon narGHJI resulted in elimination of the contribution of nitrite dissimilation to anaerobic nitrate respiratory growth. Significantly reduced nitrite reductase (NasDE) activity was detected, while respiratory nitrate reductase activity was unchanged. Anaerobic induction of nasDE expression was found to be significantly dependent on intact ywiD, while anaerobic narGHJI expression was ywiD independent. Anaerobic transcription of hmp, encoding a flavohemoglobin-like protein, and of the fermentative operons lctEP and alsSD, responsible for lactate and acetoin formation, was partially dependent on ywiD. Expression of pta, encoding phosphotransacetylase involved in fermentative acetate formation, was not influenced by ywiD. Transcription of the ywiD gene was anaerobically induced by the redox regulator Fnr via the conserved Fnr-box (TGTGA-6N-TCACT) centered 40.5 bp upstream of the transcriptional start site. Anaerobic induction of ywiD by resDE was found to be indirect via resDE-dependent activation of fnr. The ywiD gene is subject to autorepression and nitrite repression. These results suggest a ResDE --> Fnr --> YwiD regulatory cascade for the modulation of genes involved in the anaerobic metabolism of B. subtilis. Therefore, ywiD was renamed arfM for anaerobic respiration and fermentation modulator.

Distinguishing summertime atmospheric production of nitrate across the East Antarctic Ice Sheet

NASA Astrophysics Data System (ADS)

Shi, G.; Buffen, A. M.; Ma, H.; Hu, Z.; Sun, B.; Li, C.; Yu, J.; Ma, T.; An, C.; Jiang, S.; Li, Y.; Hastings, M. G.

2018-06-01

Surface snow and atmospheric samples collected along a traverse from the coast to the ice sheet summit (Dome A) are used to investigate summertime atmospheric production of nitrate (NO3-) across East Antarctica. The strong relationship observed between δ15N and δ18O of nitrate in the surface snow suggests a large (lesser) extent of nitrate photolysis in the interior (coastal) region. A linear correlation between the oxygen isotopes of nitrate (δ18O and Δ17O) indicates mixing of various oxidants that react with NOx (NOx = NO + NO2) to produce atmospheric nitrate. On the plateau, the isotopes of snow nitrate are best explained by local reoxidation chemistry of NOx, possibly occurring in both condensed and gas phases. Nitrate photolysis results in redistribution of snow nitrate, and the plateau snow is a net exporter of nitrate and its precursors. Our results suggest that while snow-sourced NOx from the plateau due to photolysis is a significant input to the nitrate budget in coastal snow (up to ∼35%), tropospheric transport from mid-low latitudes dominates (∼65%) coastal snow nitrate. The linear relationship of δ18O vs. Δ17O of the snow nitrate suggests a predominant role of hydroxyl radical (OH) and ozone (O3) in nitrate production, although a high Δ17O(O3) is required to explain the observations. Across Antarctica the oxygen isotope composition of OH appears to be dominated by exchange with water vapor, despite the very dry environment. One of the largest uncertainties in quantifying nitrate production pathways is the limited knowledge of atmospheric oxidant isotopic compositions.

In low transpiring conditions, uncoupling the BnNrt2.1 and BnNrt1.1 NO3- transporters by glutamate treatment reveals the essential role of BnNRT2.1 for nitrate uptake and the nitrate-signaling cascade during growth

PubMed Central

Leblanc, Antonin; Segura, Raphaël; Deleu, Carole; Le Deunff, Erwan

2013-01-01

In plants, the nitrate transporters, NRT1.1 and NRT2.1, are mainly responsible for nitrate uptake. Intriguingly, both nitrate transporters are located in a complementary manner in different cells layers of the mature root suggesting that their coordination should occur during nitrate uptake and plant growth. This hypothesis was examined on 5-d-old rape seedlings grown on agar medium supplemented with 1 or 5mM nitrate. Seedlings were treated with increasing potassium glutamate concentrations in order to uncouple the two nitrate transporters by inhibiting BnNRT2.1 expression and activity specifically. In both nitrate treatments, increasing the glutamate concentrations from 0.5 to 10mM induced a reduction in 15NO3- uptake and an inhibition of N assimilation. The decrease in 15NO3- uptake was caused by downregulation of BnNRT2.1 expression but surprisingly it was not compensated by the upregulation of BnNRT1.1. This created an unprecedented physiological situation where the effects of the nitrate signal on shoot growth were solely modulated by nitrate absorption. In these conditions, the osmotic water flow for volumetric shoot growth was mainly dependent on active nitrate transport and nitrate signaling. This behavior was confirmed by the allometric relationships found between changes in the root length with 15N and water accumulation in the shoot. These findings demonstrate that the BnNRT2.1 transporter is essential for nitrate uptake and growth, and renew the question of the respective roles of the NRT2.1 and NRT1.1 transporters in nitrate uptake and sensing at the whole plant level. PMID:23299418

The Role of Thaumarchaeota in N2O generation in an unconfined basalt-sandstone aquifer system, Western Victoria (Australia)

NASA Astrophysics Data System (ADS)

Moreau, J. W.; Hepburn, E.

2015-12-01

The mechanisms by which nitrous oxide is produced and transformed in groundwater are poorly understood. Here we used GC-MS and nitrogen and oxygen isotope analyses to quantify nitrate, ammonia and nitrous oxide levels in nitrate-contaminated aquifers in the Newer Volcanics province of Western Victoria. Quantitative polymerase chain reaction (Q-PCR), and phylogenetic analyses of functional nitrogen-cycling and 16S rRNA genes, of whole community microbial DNA from groundwater samples obtained from different depths within different aquifers with low-flow pumping revealed nitrate, ammonia and nitrous oxide levels of up to ~40 mg/L, up to ~0.85 mg/L, and up to ~770 nM, respectively in several groundwater samples. Delta 15N and delta 18O values ranged from -2.68‰ to 68.19‰ and -3.37‰ to 26.83‰, respectively. Nitrate and nitrous oxide concentrations decreased with depth in the unconfined aquifer, while TOC generally increased. Higher ammonia levels were observed in more heavily ferruginized sandstones. Increaased nitrate and nitrous oxide levels were found within the principal basaltic aquifers. Q-PCR results showed variable concentrations of nir, nar, nos and amo genes associated with different redox transformations along the nitrification and denitrification pathways, indicating potential nitrous oxide formation via both pathways within different depths in the aquifer. 16S rRNA gene analyses implicated an important role for the Thaumarchaeota in groundwater nitrogen cycling.

Cardiac-specific overexpression of catalase prevents diabetes-induced pathological changes by inhibiting NF-κB signaling activation in the heart.

PubMed

Cong, Weitao; Ruan, Dandan; Xuan, Yuanhu; Niu, Chao; Tao, Youli; Wang, Yang; Zhan, Kungao; Cai, Lu; Jin, Litai; Tan, Yi

2015-12-01

Catalase is an antioxidant enzyme that specifically catabolizes hydrogen peroxide (H2O2). Overexpression of catalase via a heart-specific promoter (CAT-TG) was reported to reduce diabetes-induced accumulation of reactive oxygen species (ROS) and further prevent diabetes-induced pathological abnormalities, including cardiac structural derangement and left ventricular abnormity in mice. However, the mechanism by which catalase overexpression protects heart function remains unclear. This study found that activation of a ROS-dependent NF-κB signaling pathway was downregulated in hearts of diabetic mice overexpressing catalase. In addition, catalase overexpression inhibited the significant increase in nitration levels of key enzymes involved in energy metabolism, including α-oxoglutarate dehydrogenase E1 component (α-KGD) and ATP synthase α and β subunits (ATP-α and ATP-β). To assess the effects of the NF-κB pathway activation on heart function, Bay11-7082, an inhibitor of the NF-κB signaling pathway, was injected into diabetic mice, protecting mice against the development of cardiac damage and increased nitrative modifications of key enzymes involved in energy metabolism. In conclusion, these findings demonstrated that catalase protects mouse hearts against diabetic cardiomyopathy, partially by suppressing NF-κB-dependent inflammatory responses and associated protein nitration. Copyright © 2015 Elsevier Ltd. All rights reserved.

Glucose Elevates NITRATE TRANSPORTER2.1 Protein Levels and Nitrate Transport Activity Independently of Its HEXOKINASE1-Mediated Stimulation of NITRATE TRANSPORTER2.1 Expression1[W][OPEN

PubMed Central

de Jong, Femke; Thodey, Kate; Lejay, Laurence V.; Bevan, Michael W.

2014-01-01

Mineral nutrient uptake and assimilation is closely coordinated with the production of photosynthate to supply nutrients for growth. In Arabidopsis (Arabidopsis thaliana), nitrate uptake from the soil is mediated by genes encoding high- and low-affinity transporters that are transcriptionally regulated by both nitrate and photosynthate availability. In this study, we have studied the interactions of nitrate and glucose (Glc) on gene expression, nitrate transport, and growth using glucose-insensitive2-1 (gin2-1), which is defective in sugar responses. We confirm and extend previous work by showing that HEXOKINASE1-mediated oxidative pentose phosphate pathway (OPPP) metabolism is required for Glc-mediated NITRATE TRANSPORTER2.1 (NRT2.1) expression. Treatment with pyruvate and shikimate, two products derived from intermediates of the OPPP that are destined for amino acid production, restores wild-type levels of NRT2.1 expression, suggesting that metabolites derived from OPPP metabolism can, together with Glc, directly stimulate high levels of NRT2.1 expression. Nitrate-mediated NRT2.1 expression is not influenced by gin2-1, showing that Glc does not influence NRT2.1 expression through nitrate-mediated mechanisms. We also show that Glc stimulates NRT2.1 protein levels and transport activity independently of its HEXOKINASE1-mediated stimulation of NRT2.1 expression, demonstrating another possible posttranscriptional mechanism influencing nitrate uptake. In gin2-1 plants, nitrate-responsive biomass growth was strongly reduced, showing that the supply of OPPP metabolites is essential for assimilating nitrate for growth. PMID:24272701

A new class of organic nitrates: investigations on bioactivation, tolerance and cross-tolerance phenomena.

PubMed

Schuhmacher, S; Schulz, E; Oelze, M; König, A; Roegler, C; Lange, K; Sydow, L; Kawamoto, T; Wenzel, P; Münzel, T; Lehmann, J; Daiber, A

2009-09-01

The chronic use of organic nitrates is limited by serious side effects including oxidative stress, nitrate tolerance and/or endothelial dysfunction. The side effects and potency of nitroglycerine depend on mitochondrial aldehyde dehydrogenase (ALDH-2). We sought to determine whether this concept can be extended to a new class of organic nitrates with amino moieties (aminoalkyl nitrates). Vasodilator potency of the organic nitrates, in vitro tolerance and in vivo tolerance (after continuous infusion for 3 days) were assessed in wild-type and ALDH-2 knockout mice by isometric tension studies. Mitochondrial oxidative stress was analysed by L-012-dependent chemiluminescence and protein tyrosine nitration. Aminoethyl nitrate (AEN) showed an almost similar potency to glyceryl trinitrate (GTN), even though it is only a mononitrate. AEN-dependent vasodilatation was mediated by cGMP and nitric oxide. In contrast to triethanolamine trinitrate (TEAN) and GTN, AEN bioactivation did not depend on ALDH-2 and caused no in vitro tolerance. In vivo treatment with TEAN and GTN, but not with AEN, induced cross-tolerance to acetylcholine (ACh)-dependent and GTN-dependent relaxation. Although all nitrates tested induced tolerance to themselves, only TEAN and GTN significantly increased mitochondrial oxidative stress in vitro and in vivo. The present results demonstrate that not all high potency nitrates are bioactivated by ALDH-2 and that high potency of a given nitrate is not necessarily associated with induction of oxidative stress or nitrate tolerance. Obviously, there are distinct pathways for bioactivation of organic nitrates, which for AEN may involve xanthine oxidoreductase rather than P450 enzymes.

Hydrochemical profiles in urban groundwater systems: New insights into contaminant sources and pathways in the subsurface from legacy and emerging contaminants.

PubMed

White, D; Lapworth, D J; Stuart, M E; Williams, P J

2016-08-15

It has long been known that groundwaters beneath urban areas carry a fingerprint from urban activities but finding a consistent tracer for anthropogenic influence has proved elusive. The varied sources of urban contaminants means that a single consistent and inexpensive means of tracing the fate of urban contaminants is not generally possible and multiple tracers are often required to understand the contaminant sources and pathways in these complex systems. This study has utilized a combination of micro-organic (MO) contaminants and inorganic hydrochemistry to trace recharge pathways and quantify the variability of groundwater quality in multi-level piezometers in the city of Doncaster, UK. A total of 23 MOs were detected during this study, with more compounds consistently detected during higher groundwater table conditions highlighting the importance of sampling under different hydrological conditions. Four of the compounds detected are EU Water Framework Directive priority substances: atrazine, simazine, naphthalene and DEHP, with a maximum concentration of 0.18, 0.03, 0.2, 16μg/l respectively. Our study shows that the burden of the banned pesticide atrazine persists in the Sherwood Sandstone and is detected at two of the three study sites. Emerging contaminants are seen throughout the borehole profiles and provide insights into transient pathways for contaminant migration in the sub-surface. Long term changes in inorganic hydrochemistry show possible changes in contaminant input or the dissolution of minerals. Nitrate was detected above 50mg/l but on the whole nitrate concentrations have declined in the intervening years either due to a reduction of nitrate application at the surface or a migration of peak nitrate concentrations laterally or to greater depth. This study shows that multiple tracers together with multi-level piezometers can give a better resolution of contaminant pathways and variable flow regimes within the relatively uncomplicated aquifer of the Sherwood Sandstone compared with single long screened wells. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Nitric oxide generated by nitrate reductase increases nitrogen uptake capacity by inducing lateral root formation and inorganic nitrogen uptake under partial nitrate nutrition in rice

PubMed Central

Sun, Huwei; Li, Jiao; Song, Wenjing; Tao, Jinyuan; Huang, Shuangjie; Chen, Si; Hou, Mengmeng; Xu, Guohua; Zhang, Yali

2015-01-01

Increasing evidence shows that partial nitrate nutrition (PNN) can be attributed to improved plant growth and nitrogen-use efficiency (NUE) in rice. Nitric oxide (NO) is a signalling molecule involved in many physiological processes during plant development and nitrogen (N) assimilation. It remains unclear whether molecular NO improves NUE through PNN. Two rice cultivars (cvs Nanguang and Elio), with high and low NUE, respectively, were used in the analysis of NO production, nitrate reductase (NR) activity, lateral root (LR) density, and 15N uptake under PNN, with or without NO production donor and inhibitors. PNN increased NO accumulation in cv. Nanguang possibly through the NIA2-dependent NR pathway. PNN-mediated NO increases contributed to LR initiation, 15NH4 +/15NO3 – influx into the root, and levels of ammonium and nitrate transporters in cv. Nanguang but not cv. Elio. Further results revealed marked and specific induction of LR initiation and 15NH4 +/15NO3 – influx into the roots of plants supplied with NH4 ++sodium nitroprusside (SNP) relative to those supplied with NH4 + alone, and considerable inhibition upon the application of cPTIO or tungstate (NR inhibitor) in addition to PNN, which is in agreement with the change in NO fluorescence in the two rice cultivars. The findings suggest that NO generated by the NR pathway plays a pivotal role in improving the N acquisition capacity by increasing LR initiation and the inorganic N uptake rate, which may represent a strategy for rice plants to adapt to a fluctuating nitrate supply and increase NUE. PMID:25784715

Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis.

PubMed

Sun, Yihua; De Vos, Paul; Heylen, Kim

2016-01-19

Firmicutes have the capacity to remove excess nitrate from the environment via either denitrification, dissimilatory nitrate reduction to ammonium or both. The recent renewed interest in their nitrogen metabolism has revealed many interesting features, the most striking being their wide variety of dissimilatory nitrate reduction pathways. In the present study, nitrous oxide production from Bacillus licheniformis, a ubiquitous Gram-positive, spore-forming species with many industrial applications, is investigated. B. licheniformis has long been considered a denitrifier but physiological experiments on three different strains demonstrated that nitrous oxide is not produced from nitrate in stoichiometric amounts, rather ammonium is the most important end-product, produced during fermentation. Significant strain dependency in end-product ratios, attributed to nitrite and ammonium, and medium dependency in nitrous oxide production were also observed. Genome analyses confirmed the lack of a nitrite reductase to nitric oxide, the key enzyme of denitrification. Based on the gene inventory and building on knowledge from other non-denitrifying nitrous oxide emitters, hypothetical pathways for nitrous oxide production, involving NarG, NirB, qNor and Hmp, are proposed. In addition, all publically available genomes of B. licheniformis demonstrated similar gene inventories, with specific duplications of the nar operon, narK and hmp genes as well as NarG phylogeny supporting the evolutionary separation of previously described distinct BALI1 and BALI2 lineages. Using physiological and genomic data we have demonstrated that the common soil bacterium B. licheniformis does not denitrify but is capable of fermentative dissimilatory nitrate/nitrite reduction to ammonium (DNRA) with concomitant production of N2O. Considering its ubiquitous nature and non-fastidious growth in the lab, B. licheniformis is a suitable candidate for further exploration of the actual mechanism of N2O production in DNRA bacteria and its relevance in situ.

Photoinduced degradation of carbaryl in a wetland surface water.

PubMed

Miller, Penney L; Chin, Yu-Ping

2002-11-06

The photoinduced degradation of carbaryl (1-naphthyl-N-methyl carbamate) was studied in a wetland's surface water to examine the photochemical processes influencing its transformation. For this particular wetland water, at high pH, it was difficult to delineate the photolytic contribution to the overall degradation of carbaryl. At lower pH values, the extent of the degradation attributable to indirect pathways, that is, in the presence of naturally occurring photosensitizers, increased significantly. Moreover, the photoenhanced degradation at the lower pH values was found to be seasonally and spatially dependent. Analysis of water samples revealed two primary constituents responsible for the observed indirect photolytic processes: nitrate and dissolved natural organic matter (NOM). Nitrate in the wetland appears at high concentrations (> or =1 mM) seasonally after the application of fertilizers in the watershed and promotes contaminant destruction through the photochemical production of the hydroxyl radical (HO*). The extent of the observed indirect photolysis pathway appears to be dependent upon the concentration of nitrates and the presence of HO* scavengers such as dissolved NOM and carbonate alkalinity. Paradoxically, during low-nitrate events (<50 microM), NOM becomes the principal photosensitizer through either the production of HO*, direct energy transfer from the excited triplet state, and/or production of an unidentified transient species.

Development of a ReaxFF reactive force field for ammonium nitrate and application to shock compression and thermal decomposition.

PubMed

Shan, Tzu-Ray; van Duin, Adri C T; Thompson, Aidan P

2014-02-27

We have developed a new ReaxFF reactive force field parametrization for ammonium nitrate. Starting with an existing nitramine/TATB ReaxFF parametrization, we optimized it to reproduce electronic structure calculations for dissociation barriers, heats of formation, and crystal structure properties of ammonium nitrate phases. We have used it to predict the isothermal pressure-volume curve and the unreacted principal Hugoniot states. The predicted isothermal pressure-volume curve for phase IV solid ammonium nitrate agreed with electronic structure calculations and experimental data within 10% error for the considered range of compression. The predicted unreacted principal Hugoniot states were approximately 17% stiffer than experimental measurements. We then simulated thermal decomposition during heating to 2500 K. Thermal decomposition pathways agreed with experimental findings.

Organic nitrates and nitrate tolerance--state of the art and future developments.

PubMed

Daiber, Andreas; Münzel, Thomas; Gori, Tommaso

2010-01-01

The hemodynamic and antiischemic effects of nitroglycerin (GTN) are lost upon chronic administration due to the rapid development of nitrate tolerance. The mechanism of this phenomenon has puzzled several generations of scientists, but recent findings have led to novel hypotheses. The formation of reactive oxygen and nitrogen species in the mitochondria and the subsequent inhibition of the nitrate-bioactivating enzyme mitochondrial aldehyde dehydrogenase (ALDH-2) appear to play a central role, at least for GTN, that is, bioactivated by ALDH-2. Importantly, these findings provide the opportunity to reconcile the two "traditional" hypotheses of nitrate tolerance, that is, the one postulating a decreased bioactivation and the concurrent one suggesting a role of oxidative stress. Furthermore, recent animal and human experimental studies suggest that the organic nitrates are not a homogeneous group but demonstrate a broad diversity with regard to induction of vascular dysfunction, oxidative stress, and other side effects. In the past, attempts to avoid nitrate-induced side effects have focused on administration schedules that would allow a "nitrate-free interval"; in the future, the role of co-therapies with antioxidant compounds and of activation of endogeneous protective pathways such as the heme oxygenase 1 (HO-1) will need to be explored. However, the development of new nitrates, for example, tolerance-free aminoalkyl nitrates or combination of nitrate groups with established cardiovascular drugs like ACE inhibitors or AT(1)-receptor blockers (hybrid molecules) may be of great clinical interest. Copyright © 2010 Elsevier Inc. All rights reserved.

Microarray and network-based identification of functional modules and pathways of active tuberculosis.

PubMed

Bian, Zhong-Rui; Yin, Juan; Sun, Wen; Lin, Dian-Jie

2017-04-01

Diagnose of active tuberculosis (TB) is challenging and treatment response is also difficult to efficiently monitor. The aim of this study was to use an integrated analysis of microarray and network-based method to the samples from publically available datasets to obtain a diagnostic module set and pathways in active TB. Towards this goal, background protein-protein interactions (PPI) network was generated based on global PPI information and gene expression data, following by identification of differential expression network (DEN) from the background PPI network. Then, ego genes were extracted according to the degree features in DEN. Next, module collection was conducted by ego gene expansion based on EgoNet algorithm. After that, differential expression of modules between active TB and controls was evaluated using random permutation test. Finally, biological significance of differential modules was detected by pathways enrichment analysis based on Reactome database, and Fisher's exact test was implemented to extract differential pathways for active TB. Totally, 47 ego genes and 47 candidate modules were identified from the DEN. By setting the cutoff-criteria of gene size >5 and classification accuracy ≥0.9, 7 ego modules (Module 4, Module 7, Module 9, Module 19, Module 25, Module 38 and Module 43) were extracted, and all of them had the statistical significance between active TB and controls. Then, Fisher's exact test was conducted to capture differential pathways for active TB. Interestingly, genes in Module 4, Module 25, Module 38, and Module 43 were enriched in the same pathway, formation of a pool of free 40S subunits. Significant pathway for Module 7 and Module 9 was eukaryotic translation termination, and for Module 19 was nonsense mediated decay enhanced by the exon junction complex (EJC). Accordingly, differential modules and pathways might be potential biomarkers for treating active TB, and provide valuable clues for better understanding of molecular mechanism of active TB. Copyright © 2017 Elsevier Ltd. All rights reserved.

Profound differences between humans and rodents in the ability to concentrate salivary nitrate: Implications for translational research.

PubMed

Montenegro, Marcelo F; Sundqvist, Michaela L; Nihlén, Carina; Hezel, Michael; Carlström, Mattias; Weitzberg, Eddie; Lundberg, Jon O

2016-12-01

In humans dietary circulating nitrate accumulates rapidly in saliva through active transport in the salivary glands. By this mechanism resulting salivary nitrate concentrations are 10-20 times higher than in plasma. In the oral cavity nitrate is reduced by commensal bacteria to nitrite, which is subsequently swallowed and further metabolized to nitric oxide (NO) and other bioactive nitrogen oxides in blood and tissues. This entero-salivary circulation of nitrate is central in the various NO-like effects observed after ingestion of inorganic nitrate. The very same system has also been the focus of toxicologists studying potential carcinogenic effects of nitrite-dependent nitrosamine formation. Whether active transport of nitrate and accumulation in saliva occurs also in rodents is not entirely clear. Here we measured salivary and plasma levels of nitrate and nitrite in humans, rats and mice after administration of a standardized dose of nitrate. After oral (humans) or intraperitoneal (rodents) sodium nitrate administration (0.1mmol/kg), plasma nitrate levels increased markedly reaching ~300µM in all three species. In humans ingestion of nitrate was followed by a rapid increase in salivary nitrate to >6000µM, ie 20 times higher than those found in plasma. In contrast, in rats and mice salivary nitrate concentrations never exceeded the levels in plasma. Nitrite levels in saliva and plasma followed a similar pattern, ie marked increases in humans but modest elevations in rodents. In mice there was also no accumulation of nitrate in the salivary glands as measured directly in whole glands obtained after acute administration of nitrate. This study suggests that in contrast to humans, rats and mice do not actively concentrate circulating nitrate in saliva. These apparent species differences should be taken into consideration when studying the nitrate-nitrite-nitric oxide pathway in rodents, when calculating doses, exploring physiological, therapeutic and toxicological effects and comparing with human data. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Formation kinetics and abundance of organic nitrates in α-pinene ozonolysis

NASA Astrophysics Data System (ADS)

Berkemeier, Thomas; Ammann, Markus; Pöschl, Ulrich; Shiraiwa, Manabu

2016-04-01

Formation of organic nitrates affects the total atmospheric budget of oxidized nitrogen (NOy) and alters the total aerosol mass yield from secondary sources. We investigated the formation of organic nitrate species during ozonolysis of α-pinene and subsequent formation of secondary organic aerosols (SOA) using the short-lived radioactive tracer 13N inside an aerosol flow reactor (Ammann et al., 2001). The results represent direct measurements of the organic nitrate content of α-pinene secondary aerosol and give insight into the kinetics of organic nitrate formation. Organic nitrates constituted up to 40 % of aerosol mass with a pronounced influence during the initial period of particle growth. Kinetic modelling, as well as additional experiments using OH scavengers and UV irradiation, suggests that organic peroxy radicals (RO2) from the reaction of α-pinene with secondarily produced OH are important intermediates in the organic nitrate formation process. Direct oxidation of α-pinene by NO3 was found to be a less efficient pathway for formation of particle phase nitrate. The organic nitrate content decreased very slightly with an increase of relative humidity on the experimental time scale. The experiments show a tight correlation between organic nitrate content and SOA number concentrations, implying that organic nitrates play an important role in nucleation and growth of nanoparticles. Since present in large amounts in organic aerosol, organic nitrates deposited in the lung might have implications for human health as they release nitric acid upon hydrolysis, especially in regions influenced by urban pollution and large sources of monoterpene SOA precursors. References Ammann et al. (2001) Radiochimica Acta 89, 831.

Nitrate leaching in a winter wheat-summer maize rotation on a calcareous soil as affected by nitrogen and straw management.

PubMed

Huang, Tao; Ju, Xiaotang; Yang, Hao

2017-02-08

Nitrate leaching is one of the most important pathways of nitrogen (N) loss which leads to groundwater contamination or surface water eutrophication. Clarifying the rates, controlling factors and characteristics of nitrate leaching is the pre-requisite for proposing effective mitigation strategies. We investigated the effects of interactions among chemical N fertilizer, straw and manure applications on nitrogen leaching in an intensively managed calcareous Fluvo-aquic soil with winter wheat-summer maize cropping rotations on the North China Plain from October 2010 to September 2013 using ceramic suction cups and seepage water calculations based on a long-term field experiment. Annual nitrate leaching reached 38-60 kg N ha -1 from conventional N managements, but declined by 32-71% due to optimum N, compost manure or municipal waste treatments, respectively. Nitrate leaching concentrated in the summer maize season, and fewer leaching events with high amounts are the characteristics of nitrate leaching in this region. Overuse of chemical N fertilizers, high net mineralization and nitrification, together with predominance of rainfall in the summer season with light soil texture are the main controlling factors responsible for the high nitrate leaching loss in this soil-crop-climatic system.

Nitrate leaching in a winter wheat-summer maize rotation on a calcareous soil as affected by nitrogen and straw management

NASA Astrophysics Data System (ADS)

Huang, Tao; Ju, Xiaotang; Yang, Hao

2017-02-01

Nitrate leaching is one of the most important pathways of nitrogen (N) loss which leads to groundwater contamination or surface water eutrophication. Clarifying the rates, controlling factors and characteristics of nitrate leaching is the pre-requisite for proposing effective mitigation strategies. We investigated the effects of interactions among chemical N fertilizer, straw and manure applications on nitrogen leaching in an intensively managed calcareous Fluvo-aquic soil with winter wheat-summer maize cropping rotations on the North China Plain from October 2010 to September 2013 using ceramic suction cups and seepage water calculations based on a long-term field experiment. Annual nitrate leaching reached 38-60 kg N ha-1 from conventional N managements, but declined by 32-71% due to optimum N, compost manure or municipal waste treatments, respectively. Nitrate leaching concentrated in the summer maize season, and fewer leaching events with high amounts are the characteristics of nitrate leaching in this region. Overuse of chemical N fertilizers, high net mineralization and nitrification, together with predominance of rainfall in the summer season with light soil texture are the main controlling factors responsible for the high nitrate leaching loss in this soil-crop-climatic system.

Heme Oxygenase-1 Induction and Organic Nitrate Therapy: Beneficial Effects on Endothelial Dysfunction, Nitrate Tolerance, and Vascular Oxidative Stress

PubMed Central

Daiber, Andreas; Oelze, Matthias; Wenzel, Philip; Bollmann, Franziska; Pautz, Andrea; Kleinert, Hartmut

2012-01-01

Organic nitrates are a group of very effective anti-ischemic drugs. They are used for the treatment of patients with stable angina, acute myocardial infarction, and chronic congestive heart failure. A major therapeutic limitation inherent to organic nitrates is the development of tolerance, which occurs during chronic treatment with these agents, and this phenomenon is largely based on induction of oxidative stress with subsequent endothelial dysfunction. We therefore speculated that induction of heme oxygenase-1 (HO-1) could be an efficient strategy to overcome nitrate tolerance and the associated side effects. Indeed, we found that hemin cotreatment prevented the development of nitrate tolerance and vascular oxidative stress in response to chronic nitroglycerin therapy. Vice versa, pentaerithrityl tetranitrate (PETN), a nitrate that was previously reported to be devoid of adverse side effects, displayed tolerance and oxidative stress when the HO-1 pathway was blocked pharmacologically or genetically by using HO-1+/– mice. Recently, we identified activation of Nrf2 and HuR as a principle mechanism of HO-1 induction by PETN. With the present paper, we present and discuss our recent and previous findings on the role of HO-1 for the prevention of nitroglycerin-induced nitrate tolerance and for the beneficial effects of PETN therapy. PMID:22506100

Molecular Signals Controlling the Inhibition of Nodulation by Nitrate in Medicago truncatula

PubMed Central

van Noorden, Giel E.; Verbeek, Rob; Dinh, Quy Dung; Jin, Jian; Green, Alexandra; Ng, Jason Liang Pin; Mathesius, Ulrike

2016-01-01

The presence of nitrogen inhibits legume nodule formation, but the mechanism of this inhibition is poorly understood. We found that 2.5 mM nitrate and above significantly inhibited nodule initiation but not root hair curling in Medicago trunatula. We analyzed protein abundance in M. truncatula roots after treatment with either 0 or 2.5 mM nitrate in the presence or absence of its symbiont Sinorhizobium meliloti after 1, 2 and 5 days following inoculation. Two-dimensional gel electrophoresis combined with mass spectrometry was used to identify 106 differentially accumulated proteins responding to nitrate addition, inoculation or time point. While flavonoid-related proteins were less abundant in the presence of nitrate, addition of Nod gene-inducing flavonoids to the Sinorhizobium culture did not rescue nodulation. Accumulation of auxin in response to rhizobia, which is also controlled by flavonoids, still occurred in the presence of nitrate, but did not localize to a nodule initiation site. Several of the changes included defense- and redox-related proteins, and visualization of reactive oxygen species indicated that their induction in root hairs following Sinorhizobium inoculation was inhibited by nitrate. In summary, the presence of nitrate appears to inhibit nodulation via multiple pathways, including changes to flavonoid metabolism, defense responses and redox changes. PMID:27384556

Pseudo-constitutivity of nitrate-responsive genes in nitrate reductase mutants

PubMed Central

Schinko, Thorsten; Gallmetzer, Andreas; Amillis, Sotiris; Strauss, Joseph

2013-01-01

In fungi, transcriptional activation of genes involved in NO3- assimilation requires the presence of an inducer (nitrate or nitrite) and low intracellular concentrations of the pathway products ammonium or glutamine. In Aspergillus nidulans, the two transcription factors NirA and AreA act synergistically to mediate nitrate/nitrite induction and nitrogen metabolite derepression, respectively. In all studied fungi and in plants, mutants lacking nitrate reductase (NR) activity express nitrate-metabolizing enzymes constitutively without the addition of inducer molecules. Based on their work in A. nidulans, Cove and Pateman proposed an “autoregulation control” model for the synthesis of nitrate metabolizing enzymes in which the functional nitrate reductase molecule would act as co-repressor in the absence and as co-inducer in the presence of nitrate. However, NR mutants could simply show “pseudo-constitutivity” due to induction by nitrate which accumulates over time in NR-deficient strains. Here we examined this possibility using strains which lack flavohemoglobins (fhbs), and are thus unable to generate nitrate internally, in combination with nitrate transporter mutations (nrtA, nrtB) and a GFP-labeled NirA protein. Using different combinations of genotypes we demonstrate that nitrate transporters are functional also in NR null mutants and show that the constitutive phenotype of NR mutants is not due to nitrate accumulation from intracellular sources but depends on the activity of nitrate transporters. However, these transporters are not required for nitrate signaling because addition of external nitrate (10 mM) leads to standard induction of nitrate assimilatory genes in the nitrate transporter double mutants. We finally show that NR does not regulate NirA localization and activity, and thus the autoregulation model, in which NR would act as a co-repressor of NirA in the absence of nitrate, is unlikely to be correct. Results from this study instead suggest that transporter-mediated NO3- accumulation in NR deficient mutants, originating from traces of nitrate in the media, is responsible for the constitutive expression of NirA-regulated genes, and the associated phenotype is thus termed “pseudo-constitutive”. PMID:23454548

Low dose dietary nitrate improves endothelial dysfunction and plaque stability in the ApoE-/- mouse fed a high fat diet.

PubMed

Bakker, J R; Bondonno, N P; Gaspari, T A; Kemp-Harper, B K; McCashney, A J; Hodgson, J M; Croft, K D; Ward, N C

2016-10-01

Nitric oxide (NO) is an important vascular signalling molecule. NO is synthesised endogenously by endothelial nitric oxide synthase (eNOS). An alternate pathway is exogenous dietary nitrate, which can be converted to nitrite and then stored or further converted to NO and used immediately. Atherosclerosis is associated with endothelial dysfunction and subsequent lesion formation. This is thought to arise due to a reduction in the bioavailability and/or bioactivity of endogenous NO. To determine if dietary nitrate can protect against endothelial dysfunction and lesion formation in the ApoE -/- mouse fed a high fat diet (HFD). ApoE -/- fed a HFD were randomized to receive (i) high nitrate (10mmol/kg/day, n=12), (ii) moderate nitrate (1mmol/kg/day, n=8), (iii) low nitrate (0.1mmol/kg/day, n=8), or (iv) sodium chloride supplemented drinking water (control, n=10) for 10 weeks. A group of C57BL6 mice (n=6) received regular water and served as a healthy reference group. At 10 weeks, ACh-induced vessel relaxation was significantly impaired in ApoE -/- mice versus C57BL6. Mice supplemented with low or moderate nitrate showed significant improvements in ACh-induced vessel relaxation compared to ApoE -/- mice given the high nitrate or sodium chloride. Plaque collagen expression was increased and lipid deposition reduced following supplementation with low or moderate nitrate compared to sodium chloride, reflecting increased plaque stability with nitrate supplementation. Plasma nitrate and nitrite levels were significantly increased in all three groups fed the nitrate-supplemented water. Low and moderate dose nitrate significantly improved endothelial function and atherosclerotic plaque composition in ApoE -/- mice fed a HFD. Copyright © 2016 Elsevier Inc. All rights reserved.

A new class of organic nitrates: investigations on bioactivation, tolerance and cross-tolerance phenomena

PubMed Central

Schuhmacher, S; Schulz, E; Oelze, M; König, A; Roegler, C; Lange, K; Sydow, L; Kawamoto, T; Wenzel, P; Münzel, T; Lehmann, J; Daiber, A

2009-01-01

Background and purpose: The chronic use of organic nitrates is limited by serious side effects including oxidative stress, nitrate tolerance and/or endothelial dysfunction. The side effects and potency of nitroglycerine depend on mitochondrial aldehyde dehydrogenase (ALDH-2). We sought to determine whether this concept can be extended to a new class of organic nitrates with amino moieties (aminoalkyl nitrates). Experimental approach: Vasodilator potency of the organic nitrates, in vitro tolerance and in vivo tolerance (after continuous infusion for 3 days) were assessed in wild-type and ALDH-2 knockout mice by isometric tension studies. Mitochondrial oxidative stress was analysed by L-012-dependent chemiluminescence and protein tyrosine nitration. Key results: Aminoethyl nitrate (AEN) showed an almost similar potency to glyceryl trinitrate (GTN), even though it is only a mononitrate. AEN-dependent vasodilatation was mediated by cGMP and nitric oxide. In contrast to triethanolamine trinitrate (TEAN) and GTN, AEN bioactivation did not depend on ALDH-2 and caused no in vitro tolerance. In vivo treatment with TEAN and GTN, but not with AEN, induced cross-tolerance to acetylcholine (ACh)-dependent and GTN-dependent relaxation. Although all nitrates tested induced tolerance to themselves, only TEAN and GTN significantly increased mitochondrial oxidative stress in vitro and in vivo. Conclusions and implications: The present results demonstrate that not all high potency nitrates are bioactivated by ALDH-2 and that high potency of a given nitrate is not necessarily associated with induction of oxidative stress or nitrate tolerance. Obviously, there are distinct pathways for bioactivation of organic nitrates, which for AEN may involve xanthine oxidoreductase rather than P450 enzymes. PMID:19563531

Formation, Evaporation, and Hydrolysis of Organic Nitrates from Nitrate Radical Oxidation of Monoterpenes

NASA Astrophysics Data System (ADS)

Ng, N. L.; Takeuchi, M.; Eris, G.; Berkemeier, T.; Boyd, C.; Nah, T.; Xu, L.

2017-12-01

Organic nitrates play an important role in the cycling of NOx and secondary organic aerosol (SOA) formation, yet their formation mechanisms and fates remain highly uncertain. The interactions of biogenic VOCs with NO3 radicals represent a direct way for positively linking anthropogenic and biogenic emissions. Results from ambient studies suggest that organic nitrates have a relatively short lifetime, though corresponding laboratory data are limited. SOA and organic nitrates produced at night may evaporate the following morning due to increasing temperatures or dilution of semi-volatile compounds. Once formed, organic nitrates can also undergo hydrolysis in the presence of particle water. In this work, we investigate the formation, evaporation, and hydrolysis of organic nitrates generated from the nitrate radical oxidation of a-pinene, b-pinene, and limonene. Experiments are conducted in the Georgia Environmental Chamber facility (GTEC) under dry and humid conditions and different temperatures. Experiments are also designed to probe different peroxy radical pathways (RO2+HO2 vs RO2+NO3). Speciated gas-phase and particle-phase organic nitrates are continuously monitored by a Filter Inlet for Gases and AEROsols High Resolution Time-of-Flight Chemical Ionization Mass Spectrometer (FIGAERO-HR-ToF-CIMS). Bulk aerosol composition is measured by a High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS). A large suite of highly oxygenated gas- and particle-phase organic nitrates are formed rapidly. We find a resistance to aerosol evaporation when it is heated. The extent of organic nitrate hydrolysis in the humid experiments is evaluated. The dynamics of the speciated organic nitrates over the course of the experiments will also be discussed. Results from this chamber study provide fundamental data for understanding the dynamics of organic nitrate aerosols over its atmospheric lifetime.

Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome

PubMed Central

Shen, Haoran; Liang, Zhou; Zheng, Saihua; Li, Xuelian

2017-01-01

The purpose of this study was to identify promising candidate genes and pathways in polycystic ovary syndrome (PCOS). Microarray dataset GSE345269 obtained from the Gene Expression Omnibus database includes 7 granulosa cell samples from PCOS patients, and 3 normal granulosa cell samples. Differentially expressed genes (DEGs) were screened between PCOS and normal samples. Pathway enrichment analysis was conducted for DEGs using ClueGO and CluePedia plugin of Cytoscape. A Reactome functional interaction (FI) network of the DEGs was built using ReactomeFIViz, and then network modules were extracted, followed by pathway enrichment analysis for the modules. Expression of DEGs in granulosa cell samples was measured using quantitative RT-PCR. A total of 674 DEGs were retained, which were significantly enriched with inflammation and immune-related pathways. Eight modules were extracted from the Reactome FI network. Pathway enrichment analysis revealed significant pathways of each module: module 0, Regulation of RhoA activity and Signaling by Rho GTPases pathways shared ARHGAP4 and ARHGAP9; module 2, GlycoProtein VI-mediated activation cascade pathway was enriched with RHOG; module 3, Thromboxane A2 receptor signaling, Chemokine signaling pathway, CXCR4-mediated signaling events pathways were enriched with LYN, the hub gene of module 3. Results of RT-PCR confirmed the finding of the bioinformatic analysis that ARHGAP4, ARHGAP9, RHOG and LYN were significantly upregulated in PCOS. RhoA-related pathways, GlycoProtein VI-mediated activation cascade pathway, ARHGAP4, ARHGAP9, RHOG and LYN may be involved in the pathogenesis of PCOS. PMID:28949383

Nitrate uptake and utilization is modulated by exogenous gamma-aminobutyric acid in Arabidopsis thaliana seedlings.

PubMed

Barbosa, Jose M; Singh, Narendra K; Cherry, Joe H; Locy, Robert D

2010-06-01

Exogenously applied GABA modulates root growth by inhibition of root elongation when seedlings were grown in vitro on full-strength Murashige and Skoog (MS) salts, but root elongation was stimulated when seedlings were grown on 1/8 strength MS salts. When the concentration of single ions in MS salts was individually varied, the control of growth between inhibition and stimulation was found to be related to the level of nitrate (NO(3)(-)) in the growth medium. At NO(3)(-) concentrations below 40 mM (full-strength MS salts level), root growth was stimulated by the addition of GABA to the growth medium; whereas at concentrations above 40 mM NO(3)(-), the addition of GABA to the growth medium inhibited root elongation. GABA promoted NO(3)(-) uptake at low NO(3)(-), while GABA inhibited NO(3)(-) uptake at high NO(3)(-). Activities of several enzymes involved in nitrogen and carbon metabolism including nitrate reductase (NR), glutamine synthetase (GS), glutamate synthase (NADH-GOGAT), NADP-dependent isocitrate dehydrogenase (NADP-ICDH), and phosphoenol pyruvate carboxylase (PEPCase) were regulated by GABA in the growth medium. Supplementing 1/8 strength MS medium with 50 mM GABA enhanced the activities of all of the above enzymes except ICDH activities in root tissues. However, at full-strength MS, GABA showed no inhibitory effect on the activities of these enzymes, except on GS in both root and shoot tissues, and PEPCase activity in shoot tissues. Exogenous GABA increased the amount of NR protein rather than its activation status in the tissues. This study shows that GABA affects the growth of Arabidopsis, possibly by acting as a signaling molecule, modulating the activity of enzymes involved in primary nitrogen metabolism and nitrate uptake.

Organic nitrates: past, present and future.

PubMed

França-Silva, Maria S; Balarini, Camille M; Cruz, Josiane C; Khan, Barkat A; Rampelotto, Pabulo H; Braga, Valdir A

2014-09-24

Nitric oxide (NO) is one of the most important vasodilator molecules produced by the endothelium. It has already been established that NO/cGMP signaling pathway deficiencies are involved in the pathophysiological mechanisms of many cardiovascular diseases. In this context, the development of NO-releasing drugs for therapeutic use appears to be an effective alternative to replace the deficient endogenous NO and mimic the role of this molecule in the body. Organic nitrates represent the oldest class of NO donors that have been clinically used. Considering that tolerance can occur when these drugs are applied chronically, the search for new compounds of this class with lower tolerance potential is increasing. Here, we briefly discuss the mechanisms involved in nitrate tolerance and highlight some achievements from our group in the development of new organic nitrates and their preclinical application in cardiovascular disorders.

The formation of nitrogen-containing organic oxidation products in a heavily polluted urban environment

NASA Astrophysics Data System (ADS)

Chen, Q.; Cheng, X.; Zheng, Y.; Li, Y.; Zhu, T.; Zhang, Q.; Canagaratna, M. R.; Nowark, J.; Worsnop, D. R.

2017-12-01

Nitrogen-containing organic oxidation products are important species that may contribute to secondary organic aerosol and to redistribute nitrogen oxides through photolysis and oxidation. We deployed a nitrate ion chemical ionization time-of-flight mass spectrometer and a long time-of-flight aerosol mass spectrometer in Beijing for various seasons to study the nitrogen-containing organic species in both gas and particle phases. High concentrations of nitrated phenols were observed in both winter and summer, due to contributions from both primary and secondary sources. The concentrations of gaseous dinitrophenols tracked the severe haze events and correlated well with many highly oxygenated organic molecules. We also identified mass spectral tracers for quantifying organic nitrates. Significant photochemical production of nitrate and organic nitrates were evident during severe haze events, which may contribute to persistent particle formation. The findings are consistent with observed high OH turnover rates, highlighting the importance of gaseous oxidation pathways on persistent particle formation during haze.

Aniline-induced nitrosative stress in rat spleen: Proteomic identification of nitrated proteins

PubMed Central

Fan, Xiuzhen; Wang, Jianling; Soman, Kizhake V.; Ansari, G. A. S.; Khan, M. Firoze

2011-01-01

Aniline exposure is associated with toxicity to the spleen which is characterized by splenomegaly, hyperplasia, fibrosis, and a variety of sarcomas on chronic exposure in rats. However, mechanisms by which aniline elicits splenotoxic responses are not well understood. Earlier we have shown that aniline exposure leads to increased nitration of proteins in the spleen. However, nitrated proteins remain to be characterized. Therefore, in the current study using proteomic approaches, we focused on characterizing the nitrated proteins in the spleen of aniline-exposed rats. Aniline exposure led to increased tyrosine nitration of proteins, as determined by 2D Western blotting with anti-3-nitrotyrosine specific antibody, compared to the controls. The analyzed nitrated proteins were found in the molecular weight range of 27.7 to 123.6 kDa. A total of 37 nitrated proteins were identified in aniline-treated and control spleens. Among them, 25 were found only in aniline-treated rats, 11 were present in both aniline-treated and control rats, while one was found in controls only. The nitrated proteins identified mainly represent skeletal proteins, chaperones, ferric iron transporter, enzymes, nucleic acids binding protein, and signaling and protein synthesis pathways. Furthermore, aniline exposure led to significantly increased iNOS mRNA and protein expression in the spleen, suggesting its role in increased reactive nitrogen species formation and contribution to increased nitrated proteins. The identified nitrated proteins provide a global map to further investigate alterations in their structural and functional properties, which will lead to a better understanding of the role of protein nitration in aniline-mediated splenic toxicity. PMID:21708182

Vascular effects of dietary nitrate (as found in green leafy vegetables and beetroot) via the nitrate‐nitrite‐nitric oxide pathway

PubMed Central

Lidder, Satnam; Webb, Andrew J.

2013-01-01

The discovery that dietary (inorganic) nitrate has important vascular effects came from the relatively recent realization of the ‘nitrate‐nitrite‐nitric oxide (NO) pathway’. Dietary nitrate has been demonstrated to have a range of beneficial vascular effects, including reducing blood pressure, inhibiting platelet aggregation, preserving or improving endothelial dysfunction, enhancing exercise performance in healthy individuals and patients with peripheral arterial disease. Pre‐clinical studies with nitrate or nitrite also show the potential to protect against ischaemia‐reperfusion injury and reduce arterial stiffness, inflammation and intimal thickness. However, there is a need for good evidence for hard endpoints beyond epidemiological studies. Whilst these suggest reduction in cardiovascular risk with diets high in nitrate‐rich vegetables (such as a Mediterranean diet), others have suggested possible small positive and negative associations with dietary nitrate and cancer, but these remain unproven. Interactions with other nutrients, such as vitamin C, polyphenols and fatty acids may enhance or inhibit these effects. In order to provide simple guidance on nitrate intake from different vegetables, we have developed the Nitrate ‘Veg‐Table’ with ‘Nitrate Units’ [each unit being 1 mmol of nitrate (62 mg)] to achieve a nitrate intake that is likely to be sufficient to derive benefit, but also to minimize the risk of potential side effects from excessive ingestion, given the current available evidence. The lack of data concerning the long term effects of dietary nitrate is a limitation, and this will need to be addressed in future trials. PMID:22882425

Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome.

PubMed

Shen, Haoran; Liang, Zhou; Zheng, Saihua; Li, Xuelian

2017-11-01

The purpose of this study was to identify promising candidate genes and pathways in polycystic ovary syndrome (PCOS). Microarray dataset GSE345269 obtained from the Gene Expression Omnibus database includes 7 granulosa cell samples from PCOS patients, and 3 normal granulosa cell samples. Differentially expressed genes (DEGs) were screened between PCOS and normal samples. Pathway enrichment analysis was conducted for DEGs using ClueGO and CluePedia plugin of Cytoscape. A Reactome functional interaction (FI) network of the DEGs was built using ReactomeFIViz, and then network modules were extracted, followed by pathway enrichment analysis for the modules. Expression of DEGs in granulosa cell samples was measured using quantitative RT-PCR. A total of 674 DEGs were retained, which were significantly enriched with inflammation and immune-related pathways. Eight modules were extracted from the Reactome FI network. Pathway enrichment analysis revealed significant pathways of each module: module 0, Regulation of RhoA activity and Signaling by Rho GTPases pathways shared ARHGAP4 and ARHGAP9; module 2, GlycoProtein VI-mediated activation cascade pathway was enriched with RHOG; module 3, Thromboxane A2 receptor signaling, Chemokine signaling pathway, CXCR4-mediated signaling events pathways were enriched with LYN, the hub gene of module 3. Results of RT-PCR confirmed the finding of the bioinformatic analysis that ARHGAP4, ARHGAP9, RHOG and LYN were significantly upregulated in PCOS. RhoA-related pathways, GlycoProtein VI-mediated activation cascade pathway, ARHGAP4, ARHGAP9, RHOG and LYN may be involved in the pathogenesis of PCOS.

Nitrate supplementation and human exercise performance: too much of a good thing?

PubMed

Poortmans, Jacques R; Gualano, Bruno; Carpentier, Alain

2015-11-01

Ergogenic supplements in sport events are widely used by popular and competitive athletes to enhance performance and reduce oxygen cost. Beetroot juice and nitrate salts have been increasingly used for the past 5-6 years. The present review discusses the scientific background, the efficiency and potential adverse effects of excessive nitrate supplementation. There is clear evidence that nitrate from different food ingredients (such as beetroot juice and other vegetables) is converted into nitrite and possibly into nitric oxide, which may promote vasodilation, angiogenesis and mitochondrial biogenesis. The high affinity of nitric oxide towards different enzyme pathways inhibits excessive mitochondrial respiration and, therefore, tissue oxygen consumption. In addition, L-arginine supplements are proposed to stimulate nitric oxide synthesis in the endothelium. On the basis of these biochemical properties, nitrate supplementation has been suggested to athletes to enhance exercise performance. The recent publications in human individuals based on L-arginine, beetroot juice or nitrate supplementation revealed either a minor positive effect or no systematic effect on exercise performance, especially in trained athletes. Of note, the sugar content of whole beetroot juice might induce a slightly more pronounced effect. Although reasonable intake of nitrate salts (up to 1 g/day) has no detrimental effect on kidney function, the risk and benefit of higher nitrate intake needs to be evaluated to define the optimal range of supplementation.

Relationship Between Urinary Nitrate Excretion and Blood Pressure in the InChianti Cohort.

PubMed

Smallwood, Miranda J; Ble, Alessandro; Melzer, David; Winyard, Paul G; Benjamin, Nigel; Shore, Angela C; Gilchrist, Mark

2017-07-01

Inorganic nitrate from the oxidation of endogenously synthesized nitric oxide (NO) or consumed in the diet can be reduced to NO via a complex enterosalivary circulation pathway. The relationship between total nitrate exposure by measured urinary nitrate excretion and blood pressure in a large population sample has not been assessed previously. For this cross-sectional study, 24-hour urinary nitrate excretion was measured by spectrophotometry in the 919 participants from the InChianti cohort at baseline and blood pressure measured with a mercury sphygmomanometer. After adjusting for age and sex only, diastolic blood pressure was 1.9 mm Hg lower in subjects with ≥2 mmol urinary nitrate excretion compared with those excreting <1 mmol nitrate in 24 hours: systolic blood pressure was 3.4 mm Hg (95% confidence interval (CI): -3.5 to -0.4) lower in subjects for the same comparison. Effect sizes in fully adjusted models (for age, sex, potassium intake, use of antihypertensive medications, diabetes, HS-CRP, or current smoking status) were marginally larger: systolic blood pressure in the ≥2 mmol urinary nitrate excretion group was 3.9 (CI: -7.1 to -0.7) mm Hg lower than in the comparison <1 mmol excretion group. Modest differences in total nitrate exposure are associated with lower blood pressure. These differences are at least equivalent to those seen from substantial (100 mmol) reductions in sodium intake. © American Journal of Hypertension, Ltd 2017. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Biological Oxidation of Fe(II) in Reduced Nontronite Coupled with Nitrate Reduction by Pseudogulbenkiania sp. Strain 2002

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Linduo; Dong, Hailiang; Kukkadapu, Ravi K.

Nitrate contamination in soils, sediments, and water bodies is a significant issue. Although much is known about nitrate degradation in these environments, especially via microbial pathways, a complete understanding of all degradation processes, especially in clay mineral-rich soils, is still lacking. The objective of this study was to study the potential of removing nitrate contaminant using structural Fe(II) in clay mineral nontronite. Specifically, the coupled processes of microbial oxidation of Fe(II) in microbially reduced nontronite (NAu-2) and nitrate reduction by Pseudogulbenkiania species strain 2002 was investigated. Bio-oxidation experiments were conducted in bicarbonate-buffered medium under both growth and nongrowth conditions. Themore » extents of Fe(II) oxidation and nitrate reduction were measured by wet chemical methods. X-ray diffraction (XRD), scanning and transmission electron microscopy (SEM and TEM), and 57Fe-Mössbauer spectroscopy were used to observe mineralogical changes associated with Fe(III) reduction and Fe(II) oxidation in nontronite. The bio-oxidation extent under growth and nongrowth conditions reached 93% and 57%, respectively. Over the same time period, nitrate was completely reduced under both conditions to nitrogen gas (N2), via an intermediate product nitrite. Magnetite was a mineral product of nitrate-dependent Fe(II) oxidation, as evidenced by XRD data and TEM diffraction patterns. The results of this study highlight the importance of iron-bearing clay minerals in the global nitrogen cycle with potential applications in nitrate removal in soils.« less

Vasodilator Therapy: Nitrates and Nicorandil.

PubMed

Tarkin, Jason M; Kaski, Juan Carlos

2016-08-01

Nitrates have been used to treat symptoms of chronic stable angina for over 135 years. These drugs are known to activate nitric oxide (NO)-cyclic guanosine-3',-5'-monophasphate (cGMP) signaling pathways underlying vascular smooth muscle cell relaxation, albeit many questions relating to how nitrates work at the cellular level remain unanswered. Physiologically, the anti-angina effects of nitrates are mostly due to peripheral venous dilatation leading to reduction in preload and therefore left ventricular wall stress, and, to a lesser extent, epicardial coronary artery dilatation and lowering of systemic blood pressure. By counteracting ischemic mechanisms, short-acting nitrates offer rapid relief following an angina attack. Long-acting nitrates, used commonly for angina prophylaxis are recommended second-line, after beta-blockers and calcium channel antagonists. Nicorandil is a balanced vasodilator that acts as both NO donor and arterial K(+) ATP channel opener. Nicorandil might also exhibit cardioprotective properties via mitochondrial ischemic preconditioning. While nitrates and nicorandil are effective pharmacological agents for prevention of angina symptoms, when prescribing these drugs it is important to consider that unwanted and poorly tolerated hemodynamic side-effects such as headache and orthostatic hypotension can often occur owing to systemic vasodilatation. It is also necessary to ensure that a dosing regime is followed that avoids nitrate tolerance, which not only results in loss of drug efficacy, but might also cause endothelial dysfunction and increase long-term cardiovascular risk. Here we provide an update on the pharmacological management of chronic stable angina using nitrates and nicorandil.

Nitrate leaching in a winter wheat-summer maize rotation on a calcareous soil as affected by nitrogen and straw management

PubMed Central

Huang, Tao; Ju, Xiaotang; Yang, Hao

2017-01-01

Nitrate leaching is one of the most important pathways of nitrogen (N) loss which leads to groundwater contamination or surface water eutrophication. Clarifying the rates, controlling factors and characteristics of nitrate leaching is the pre-requisite for proposing effective mitigation strategies. We investigated the effects of interactions among chemical N fertilizer, straw and manure applications on nitrogen leaching in an intensively managed calcareous Fluvo-aquic soil with winter wheat-summer maize cropping rotations on the North China Plain from October 2010 to September 2013 using ceramic suction cups and seepage water calculations based on a long-term field experiment. Annual nitrate leaching reached 38–60 kg N ha−1 from conventional N managements, but declined by 32–71% due to optimum N, compost manure or municipal waste treatments, respectively. Nitrate leaching concentrated in the summer maize season, and fewer leaching events with high amounts are the characteristics of nitrate leaching in this region. Overuse of chemical N fertilizers, high net mineralization and nitrification, together with predominance of rainfall in the summer season with light soil texture are the main controlling factors responsible for the high nitrate leaching loss in this soil-crop-climatic system. PMID:28176865

Impacts of Mesoscale Eddies on the Vertical Nitrate Flux in the Gulf Stream Region

NASA Astrophysics Data System (ADS)

Zhang, Shuwen; Curchitser, Enrique N.; Kang, Dujuan; Stock, Charles A.; Dussin, Raphael

2018-01-01

The Gulf Stream (GS) region has intense mesoscale variability that can affect the supply of nutrients to the euphotic zone (Zeu). In this study, a recently developed high-resolution coupled physical-biological model is used to conduct a 25-year simulation in the Northwest Atlantic. The Reynolds decomposition method is applied to quantify the nitrate budget and shows that the mesoscale variability is important to the vertical nitrate supply over the GS region. The decomposition, however, cannot isolate eddy effects from those arising from other mesoscale phenomena. This limitation is addressed by analyzing a large sample of eddies detected and tracked from the 25-year simulation. The eddy composite structures indicate that positive nitrate anomalies within Zeu exist in both cyclonic eddies (CEs) and anticyclonic eddies (ACEs) over the GS region, and are even more pronounced in the ACEs. Our analysis further indicates that positive nitrate anomalies mostly originate from enhanced vertical advective flux rather than vertical turbulent diffusion. The eddy-wind interaction-induced Ekman pumping is very likely the mechanism driving the enhanced vertical motions and vertical nitrate transport within ACEs. This study suggests that the ACEs in GS region may play an important role in modulating the oceanic biogeochemical properties by fueling local biomass production through the persistent supply of nitrate.

Reactive transport model for bioremediation of nitrate using fumarate in groundwater system: verification and field application

NASA Astrophysics Data System (ADS)

Lee, S.; Yeo, I. W.; Yeum, Y.; Kim, Y.

2016-12-01

Previous studies showed that groundwater of rural areas in Korea is often contaminated with nitrate highly exceeding the drinking water standard of 10 mg/L (NO3-N), which poses a major threat in human and livestock health. In-situ bioremediation method has been developed to reduce high nitrate-nitrogen concentration in groundwater using slowly released encapsulated carbon source. Collaborative research of this study revealed that fumarate was found to be a very effective carbon source in terms of cost and nitrate reduction against formate, propionate, and lactate. For reactive transport modeling of the bioremediation of nitrate using fumarate, the BTEX module of RT3D incorporated in GMS, a commercial groundwater modeling software developed by AQUAVEO, was adopted, where BTEX was replaced with fumarate as a carbon source. Column tests were carried out to determine transport and reaction parameters for numerical modeling such as dispersity and first order degradation rate of nitrate by fumarate. The calibration of the numerical model against column tests strongly indicated that nitrate, known to be not reactive in groundwater system, appeared to be retarded due to sorption by fumarate. The calibrated model was tested for field-scale application to the composting facility in Gimje, Korea. The numerical results showed that the model could simulate the nitrate reduction by fumarate in field scale groundwater system. The reactive transport model for nitrate can be used as a tool for optimum design of in-situ nitrate bioremediation system, such as released depth and amount of fumarate and the spacing of wells that encapsulated fumarate is released through.

Leachate pre-treatment strategies before recirculation in landfill bioreactors.

PubMed

Vigneron, V; Bouchez, T; Bureau, C; Mailly, N; Mazeas, L; Duquennoi, C; Audic, J M; Hébé, L; Bernet, N

2005-01-01

Nitrified leachate recirculation represents a promising strategy for a more sustainable landfill management. Our objective was to determine the reactions involved in nitrate reduction in municipal solid waste batch biodegradation tests. Anaerobic digestion of waste in the three control reactors showed a good reproducibility. In two test reactors, nitrate was added at various moments of the waste degradation process. We observed that: (1) H2S concentration controlled the nitrate reduction pathway: above a certain threshold of H2S, dissimilatory nitrate reduction to ammonium (DNRA) replaced denitrification. (2) N2O/N2 ratio varied with the organic carbon concentration: the lower the easily biodegradable carbon concentration, the higher the N2O/N2 ratio. (3) N2 was consumed after denitrification. The possibility of a nitrogen fixation reaction in the presence of NH4 is discussed. Nitrified leachate recirculation during acidogenesis should be avoided because of higher H2S production which could induce DNRA.

Variation in benthic metabolism and nitrogen cycling across clam aquaculture sites.

PubMed

Murphy, Anna E; Nizzoli, Daniele; Bartoli, Marco; Smyth, Ashley R; Castaldelli, Giuseppe; Anderson, Iris C

2018-02-01

As bivalve aquaculture expands globally, an understanding of how it alters nitrogen is important to minimize impacts. This study investigated nitrogen cycling associated with clam aquaculture in the Sacca di Goro, Italy (Ruditapes philipinarum) and the Eastern Shore, USA (Mercenaria mercenaria). Ammonium and dissolved oxygen fluxes were positively correlated with clam biomass; R. philippinarum consumed ~6 times more oxygen and excreted ~5 times more NH 4 + than M. mercenaria. There was no direct effect of clams on denitrification or dissimilatory nitrate reduction to ammonium (DNRA); rather, nitrate availability controlled the competition between these microbial pathways. Highest denitrification rates were measured at sites where both water column nitrate and nitrification were elevated due to high densities of a burrowing amphipod (Corophium sp.). DNRA exceeded denitrification where water column nitrate was low and nitrification was suppressed in highly reduced sediment, potentially due to low hydrologic flow and high clam densities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Understanding Strategy of Nitrate and Urea Assimilation in a Chinese Strain of Aureococcus anophagefferens through RNA-Seq Analysis

PubMed Central

Dong, Hong-Po; Huang, Kai-Xuan; Wang, Hua-Long; Lu, Song-Hui; Cen, Jing-Yi; Dong, Yue-Lei

2014-01-01

Aureococcus anophagefferens is a harmful alga that dominates plankton communities during brown tides in North America, Africa, and Asia. Here, RNA-seq technology was used to profile the transcriptome of a Chinese strain of A. anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions to understand the molecular mechanisms that underlie nitrate and urea utilization. The number of differentially expressed genes between urea-grown and mixture N-grown cells were much less than those between urea-grown and nitrate-grown cells. Compared with nitrate-grown cells, mixture N-grown cells contained much lower levels of transcripts encoding proteins that are involved in nitrate transport and assimilation. Together with profiles of nutrient changes in media, these results suggest that A. anophagefferens primarily feeds on urea instead of nitrate when urea and nitrate co-exist. Furthermore, we noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid and nucleotide transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source. PMID:25338000

Evaluation of Nitrate Sources and Nitrate Management Strategies in California Suburban Growth Areas

NASA Astrophysics Data System (ADS)

Singleton, M. J.; Moran, J. E.; Esser, B. K.; Leif, R. N.; McNab, W. W.; Carle, S. F.; Moore, K. B.

2005-12-01

Population growth in California has pushed the boundaries of suburban communities into formerly agricultural areas. As a result there is considerable uncertainty as to whether nitrate contamination in groundwater wells results from current sources or is a legacy of agriculture. Fertilizer application for historical agriculture is frequently assumed to be a major source, but septic system leachate, other animal waste, and residential fertilizer application may also contribute. Potential remediation strategies may include improved fertilizer management and/or conversion from septic tanks to sewer systems, but the sources of nitrate and pathways to groundwater must first be identified in order to develop a plan of action. We combine the detection of trace organic compounds that are specific to domestic waste with isotopic compositions of nitrogen and oxygen in nitrate in order to determine nitrate sources. Under anaerobic conditions and in the presence of an electron donor such as organic carbon, microbially mediated denitrification may transform nitrate to harmless nitrogen gas, and fractionate the isotopologues of any residual nitrate. The occurrence of saturated zone denitrification is detected by measuring excess dissolved nitrogen gas with a field-portable membrane inlet mass spectrometer system. Groundwater age dating using the 3H/3He method provides a means of tracking the history of nitrate inputs to groundwater, including changes in nitrate flux after implementation of a remediation program. Groundwater that pre-dates agricultural or suburban activity is used to define natural background levels of nitrate. Study areas in California include Chico, Livermore, and Gilroy. This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48.

Legacy of contaminant N sources to the NO3- signature in rivers: a combined isotopic (δ15N-NO3-, δ18O-NO3-, δ11B) and microbiological investigation

NASA Astrophysics Data System (ADS)

Briand, Cyrielle; Sebilo, Mathieu; Louvat, Pascale; Chesnot, Thierry; Vaury, Véronique; Schneider, Maude; Plagnes, Valérie

2017-02-01

Nitrate content of surface waters results from complex mixing of multiple sources, whose signatures can be modified through N reactions occurring within the different compartments of the whole catchment. Despite this complexity, the determination of nitrate origin is the first and crucial step for water resource preservation. Here, for the first time, we combined at the catchment scale stable isotopic tracers (δ15N and δ18O of nitrate and δ11B) and fecal indicators to trace nitrate sources and pathways to the stream. We tested this approach on two rivers in an agricultural region of SW France. Boron isotopic ratios evidenced inflow from anthropogenic waters, microbiological markers revealed organic contaminations from both human and animal wastes. Nitrate δ15N and δ18O traced inputs from the surface leaching during high flow events and from the subsurface drainage in base flow regime. They also showed that denitrification occurred within the soils before reaching the rivers. Furthermore, this study highlighted the determinant role of the soil compartment in nitrate formation and recycling with important spatial heterogeneity and temporal variability.

Denitrification Temperature Dependence in Remote, Cold, and N-Poor Lake Sediments

NASA Astrophysics Data System (ADS)

Palacin-Lizarbe, Carlos; Camarero, Lluís.; Catalan, Jordi

2018-02-01

The reservoir size and pathway rates of the nitrogen (N) cycle have been deeply modified by the human enhancement of N fixation, atmospheric emissions, and climate warming. Denitrification (DEN) transforms nitrate into nitrogenous gas and thus removes reactive nitrogen (Nr) back to the atmospheric reservoir. There is still a rather limited knowledge of the denitrification rates and their temperature dependence across ecosystems; particularly, for the abundant cold and N-poor freshwater systems (e.g., Arctic and mountain lakes). We experimentally investigated the denitrification rates of mountain lake sediments by manipulating nitrate concentration and temperature on field collected cores. DEN rates were nitrate limited in field conditions and showed a large potential for an immediate DEN increase with both warming and higher Nr load. The estimated activation energy (Ea) for denitrification at nitrate saturation was 46 ± 7 kJ mol-1 (Q10 1.7 ± 0.4). The apparent Ea increased with nitrate (μM) limitation as Ea = 46 + 419 [NO3-]-1. Accordingly, we suggest that climate warming may have a synergistic effect with N emission reduction to readjusting the N cycle. Changes of nitrate availability might be more relevant than direct temperature effects on denitrification.

Electrophoretic Detection and Confocal Microscopic Imaging of Tyrosine Nitrated Proteins in Plant Tissue.

PubMed

Arora, Dhara; Singh, Neha; Bhatla, Satish C

2018-01-01

Tyrosine nitrated proteins can be detected in plant cells electrophoretically and their distribution can be monitored by confocal laser scanning microscopy (CLSM) imaging. One-dimensional polyacrylamide gel electrophoresis (1D PAGE) followed by Western blotting using polyclonal antibody against 3-nitrotyrosine residues enables detection of tyrosine nitrated proteins in plant cells. Here we describe detection of tyrosine nitrated proteins in the homogenates derived from sunflower (Helianthus annuus L.) seedling cotyledons. Total soluble proteins obtained from tissue homogenates are resolved using vertical gel electrophoresis followed by their electrophoretic transfer on to a microporous membrane support for immunodetection. Spatial distribution of tyrosine nitrated proteins can be visualized using an antibody against 3-nitrotyrosine residues. Immunofluorescent localization is performed by cutting 7 μm thick wax sections of tissue followed by incubation in primary anti-nitrotyrosine antibody (dilution 1:200) and secondary Cy-3 labeled anti-rabbit IgG antibody (dilution 1:1500). Confocal laser scanning microscopy analysis is undertaken using argon lasers (ex: 530-550 nm and em: 570 nm) at pinhole 1. Modulation in the abundance and spatial localization of tyrosine nitrated proteins in plant tissues can be monitored using these techniques.

(Per)Chlorate-Reducing Bacteria Can Utilize Aerobic and Anaerobic Pathways of Aromatic Degradation with (Per)Chlorate as an Electron Acceptor

PubMed Central

Carlström, Charlotte I.; Loutey, Dana; Bauer, Stefan; Clark, Iain C.; Rohde, Robert A.; Iavarone, Anthony T.; Lucas, Lauren

2015-01-01

ABSTRACT The pathways involved in aromatic compound oxidation under perchlorate and chlorate [collectively known as (per)chlorate]-reducing conditions are poorly understood. Previous studies suggest that these are oxygenase-dependent pathways involving O2 biogenically produced during (per)chlorate respiration. Recently, we described Sedimenticola selenatireducens CUZ and Dechloromarinus chlorophilus NSS, which oxidized phenylacetate and benzoate, two key intermediates in aromatic compound catabolism, coupled to the reduction of perchlorate or chlorate, respectively, and nitrate. While strain CUZ also oxidized benzoate and phenylacetate with oxygen as an electron acceptor, strain NSS oxidized only the latter, even at a very low oxygen concentration (1%, vol/vol). Strains CUZ and NSS contain similar genes for both the anaerobic and aerobic-hybrid pathways of benzoate and phenylacetate degradation; however, the key genes (paaABCD) encoding the epoxidase of the aerobic-hybrid phenylacetate pathway were not found in either genome. By using transcriptomics and proteomics, as well as by monitoring metabolic intermediates, we investigated the utilization of the anaerobic and aerobic-hybrid pathways on different electron acceptors. For strain CUZ, the results indicated utilization of the anaerobic pathways with perchlorate and nitrate as electron acceptors and of the aerobic-hybrid pathways in the presence of oxygen. In contrast, proteomic results suggest that strain NSS may use a combination of the anaerobic and aerobic-hybrid pathways when growing on phenylacetate with chlorate. Though microbial (per)chlorate reduction produces molecular oxygen through the dismutation of chlorite (ClO2−), this study demonstrates that anaerobic pathways for the degradation of aromatics can still be utilized by these novel organisms. PMID:25805732

Organization of biogeochemical nitrogen pathways with switch-like adjustment in fluctuating soil redox conditions

PubMed Central

Lamba, Sanjay; Bera, Soumen; Rashid, Mubasher; Medvinsky, Alexander B.; Acquisti, Claudia; Li, Bai-Lian

2017-01-01

Nitrogen is cycled throughout ecosystems by a suite of biogeochemical processes. The high complexity of the nitrogen cycle resides in an intricate interplay between reversible biochemical pathways alternatively and specifically activated in response to diverse environmental cues. Despite aggressive research, how the fundamental nitrogen biochemical processes are assembled and maintained in fluctuating soil redox conditions remains elusive. Here, we address this question using a kinetic modelling approach coupled with dynamical systems theory and microbial genomics. We show that alternative biochemical pathways play a key role in keeping nitrogen conversion and conservation properties invariant in fluctuating environments. Our results indicate that the biochemical network holds inherent adaptive capacity to stabilize ammonium and nitrate availability, and that the bistability in the formation of ammonium is linked to the transient upregulation of the amo-hao mediated nitrification pathway. The bistability is maintained by a pair of complementary subsystems acting as either source or sink type systems in response to soil redox fluctuations. It is further shown how elevated anthropogenic pressure has the potential to break down the stability of the system, altering substantially ammonium and nitrate availability in the soil, with dramatic effects on biodiversity. PMID:28280580

Correlation between citric acid and nitrate metabolisms during CAM cycle in the atmospheric bromeliad Tillandsia pohliana.

PubMed

Freschi, Luciano; Rodrigues, Maria Aurineide; Tiné, Marco Aurélio Silva; Mercier, Helenice

2010-12-15

Crassulacean acid metabolism (CAM) confers crucial adaptations for plants living under frequent environmental stresses. A wide metabolic plasticity can be found among CAM species regarding the type of storage carbohydrate, organic acid accumulated at night and decarboxylating system. Consequently, many aspects of the CAM pathway control are still elusive while the impact of this photosynthetic adaptation on nitrogen metabolism has remained largely unexplored. In this study, we investigated a possible link between the CAM cycle and the nitrogen assimilation in the atmospheric bromeliad Tillandsia pohliana by simultaneously characterizing the diel changes in key enzyme activities and metabolite levels of both organic acid and nitrate metabolisms. The results revealed that T. pohliana performed a typical CAM cycle in which phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase phosphorylation seemed to play a crucial role to avoid futile cycles of carboxylation and decarboxylation. Unlike all other bromeliads previously investigated, almost equimolar concentrations of malate and citrate were accumulated at night. Moreover, a marked nocturnal depletion in the starch reservoirs and an atypical pattern of nitrate reduction restricted to the nighttime were also observed. Since reduction and assimilation of nitrate requires a massive supply of reducing power and energy and considering that T. pohliana lives overexposed to the sunlight, we hypothesize that citrate decarboxylation might be an accessory mechanism to increase internal CO₂ concentration during the day while its biosynthesis could provide NADH and ATP for nocturnal assimilation of nitrate. Therefore, besides delivering photoprotection during the day, citrate might represent a key component connecting both CAM pathway and nitrogen metabolism in T. pohliana; a scenario that certainly deserves further study not only in this species but also in other CAM plants that nocturnally accumulate citrate. Copyright © 2010 Elsevier GmbH. All rights reserved.

Impact of Vitamin B12 and Nitrate on Transcript and Metabolite Abundances in Marine Diatoms.

NASA Astrophysics Data System (ADS)

Pound, H. L.; Schanke, N. L.; Penta, W. B.; Zavala, J.; Casu, F.; Bearden, D. W.; Lee, P. A.

2016-02-01

Phytoplankton play countless roles in the support and regulation of marine ecosystems, as well as in global biogeochemical cycling processes. They are also, to varying extents, reliant on other physical and biological processes to supply their nutrient demands, such as the production of vitamin B12 by bacteria and archaea or the regeneration and upwelling of nitrate. One such process in the global biogeochemical sulfur cycle is the pathway that begins with the production of dimethylsulfoniopropionate (DMSP) by marine phytoplankton and leads to the atmospheric formation of sulfate-based cloud condensation nuclei, which contribute to the Earth's albedo. Nutrient limitation is thought to play a major role in the amount of DMSP produced by phytoplankton. Vitamin B12 and nitrate are of particular interest due to their involvement as a co-factor and nitrogen source, respectively, in the synthesis of methionine, the precursor for DMSP. Laboratory-based nutrient limitation experiments have been performed on cultures of the diatom Phaeodactylum tricornutum. In addition to the B12-dependent methionine synthase (MetH) P. tricornutum has a unique B12-independent methionine synthase gene (MetE). Based on classic techniques, B12 limitation had little impact on cell growth, whereas nitrate limitation had a significant effect on both culture health and DMSP concentration. Yet, targeted transcriptomic analysis (using Nanostring nCounter technology) and metabolomics analysis (using Nuclear Magnetic Resonance (NMR)) revealed complex changes in transcript abundance towards upregulated gene expression associated with the MetE gene in B12 limited cultures, and shifts away from nitrogen-based metabolites towards DMSP in nitrate-limited cultures. These experiments help verify the role of B12 in DMSP production and link the underlying metabolic pathways that drive the cellular portion of the sulfur cycle to ecosystem and global scale processes.

Effective connectivity of ascending and descending frontal-thalamic pathways during sustained attention: Complex brain network interactions in adolescence

PubMed Central

Jagtap, Pranav; Diwadkar, Vaibhav A.

2016-01-01

Frontal-thalamic interactions are crucial for bottom-up gating and top-down control, yet have not been well studied from brain network perspectives. We applied network modeling of fMRI signals (Dynamic Causal Modeling; DCM) to investigate frontal-thalamic interactions during an attention task with parametrically varying levels of demand. fMRI was collected while subjects participated in a sustained continuous performance task with low and high attention demands. 162 competing model architectures were employed in DCM to evaluate hypotheses on bilateral frontal-thalamic connections and their modulation by attention demand, selected at a second level using Bayesian Model Selection. The model architecture evinced significant contextual modulation by attention of ascending (thalamus → dPFC) and descending (dPFC → thalamus) pathways. However, modulation of these pathways was asymmetric: While positive modulation of the ascending pathway was comparable across attention demand, modulation of the descending pathway was significantly greater when attention demands were increased. Increased modulation of the (dPFC → thalamus) pathway in response to increased attention demand constitutes novel evidence of attention-related gain in the connectivity of the descending attention pathway. By comparison demand-independent modulation of the ascending (thalamus → dPFC) pathway suggests unbiased thalamic inputs to the cortex in the context of the paradigm. PMID:27145923

Mutation of the regulatory phosphorylation site of tobacco nitrate reductase results in high nitrite excretion and NO emission from leaf and root tissue.

PubMed

Lea, Unni S; Ten Hoopen, Floor; Provan, Fiona; Kaiser, Werner M; Meyer, Christian; Lillo, Cathrine

2004-05-01

In wild-type Nicotiana plumbaginifolia Viv. and other higher plants, nitrate reductase (NR) is regulated at the post-translational level and is rapidly inactivated in response to, for example, a light-to-dark transition. This inactivation is caused by phosphorylation of a conserved regulatory serine residue, Ser 521 in tobacco, and interaction with divalent cations or polyamines, and 14-3-3 proteins. The physiological importance of the post-translational NR modulation is presently under investigation using a transgenic N. plumbaginifolia line. This line expresses a mutated tobacco NR where Ser 521 has been changed into aspartic acid (Asp) by site-directed mutagenesis, resulting in a permanently active NR enzyme. When cut leaves or roots of this line (S(521)) were placed in darkness in a buffer containing 50 mM KNO(3), nitrite was excreted from the tissue at rates of 0.08-0.2 micromol (g FW)(-1) h(-1) for at least 5 h. For the control transgenic plant (C1), which had the regulatory serine of NR intact, nitrite excretion was low and halted completely after 1-3 h. Without nitrate in the buffer in which the tissue was immersed, nitrite excretion was also low for S(521), although 20-40 micromol (g FW)(-1) nitrate was present inside the tissue. Apparently, stored nitrate was not readily available for reduction in darkness. Leaf tissue and root segments of S(521) also emitted much more nitric oxide (NO) than the control. Importantly, NO emission from leaf tissue of S(521) was higher in the dark than in the light, opposite to what was usually observed when post-translational NR modulation was operating.

Simulation of the diurnal variations of the isotope anomaly (?17O) of reactive trace gases (NOx, HOx) and implications for the ?17O of nitrate.

NASA Astrophysics Data System (ADS)

Morin, Samuel; Sander, Rolf; Savarino, Joël.

2010-05-01

The isotope anomaly of secondary atmospheric species such as nitrate (NO3-) has potential to provide useful constrains on their formation pathways. Indeed, the ?17O of their precursors (NOx, HOx etc.) differs and depends on their interactions with ozone, which is the main source of non-zero ?17O in the atmosphere. Interpreting variations of ?17O in nitrate requires an in-depth understanding of the ?17O of its precursors taking into account non-linear chemical regimes operating under various environmental settings. In addition, the role of isotope exchange reactions must be carefully accounted for. To investigate the relevance of various assessments of the isotopic signature of nitrate production pathways that have recently been proposed in the literature, an atmospheric chemistry box model (MECCA, Sander et al., 2005, ACP)) was used to explicitly compute the diurnal variations of the isotope anomaly of NOx, HOx under several conditions prevailing in the marine boundary layer. ?17O was propagated from ozone to other species (NO, NO2, OH, HO2, RO2, NO3, N2O5, HONO, HNO3, HNO4, H2O2) according to the classical mass-balance equation applied at each time step of the model (30 seconds typically). The model confirms that diurnal variations in ?17O of NOx are well predicted by the photochemical steady-state relationship introduced by Michalski et al. (2003, GRL) during the day, but that at night a different approach must be employed (e.g. « fossilization » of the ?17O of NOx as soon as the photochemical lifetime of NOx drops below ca. 5 minutes). The model also allows to evaluate the impact on ?17O of NOx and nitrate of the frequently made simplifying assumption that ?17O(HOx)=0 permil, with and without mass-independent fractionation during the H+O2-HO2 reaction. Recommendations for the modeling of ?17O of nitrate will be given, based on the extensive model work carried out. In addition, the link between diurnal variations of the ?17O of nitrate precursors and seasonal variations of the ?17O of nitrate will be explored. Perspectives include the implementation of halogen species in this assessment, and the full incorporation of the developed framework into the CAABA-MECCA box model.

Nitrate-to-nitrite-to-nitric oxide conversion modulated by nitrate-containing {Fe(NO)2}9 dinitrosyl iron complex (DNIC).

PubMed

Tsai, Fu-Te; Lee, Yu-Ching; Chiang, Ming-Hsi; Liaw, Wen-Feng

2013-01-07

Nitrosylation of high-spin [Fe(κ(2)-O(2)NO)(4)](2-) (1) yields {Fe(NO)}(7) mononitrosyl iron complex (MNIC) [(κ(2)-O(2)NO)(κ(1)-ONO(2))(3)Fe(NO)](2-) (2) displaying an S = 3/2 axial electron paramagnetic resonance (EPR) spectrum (g(⊥) = 3.988 and g(∥) = 2.000). The thermally unstable nitrate-containing {Fe(NO)(2)}(9) dinitrosyl iron complex (DNIC) [(κ(1)-ONO(2))(2)Fe(NO)(2)](-) (3) was exclusively obtained from reaction of HNO(3) and [(OAc)(2)Fe(NO)(2)](-) and was characterized by IR, UV-vis, EPR, superconducting quantum interference device (SQUID), X-ray absorption spectroscopy (XAS), and single-crystal X-ray diffraction (XRD). In contrast to {Fe(NO)(2)}(9) DNIC [(ONO)(2)Fe(NO)(2)](-) constructed by two monodentate O-bound nitrito ligands, the weak interaction between Fe(1) and the distal oxygens O(5)/O(7) of nitrato-coordinated ligands (Fe(1)···O(5) and Fe(1)···O(7) distances of 2.582(2) and 2.583(2) Å, respectively) may play important roles in stabilizing DNIC 3. Transformation of nitrate-containing DNIC 3 into N-bound nitro {Fe(NO)}(6) [(NO)(κ(1)-NO(2))Fe(S(2)CNEt(2))(2)] (7) triggered by bis(diethylthiocarbamoyl) disulfide ((S(2)CNEt(2))(2)) implicates that nitrate-to-nitrite conversion may occur via the intramolecular association of the coordinated nitrate and the adjacent polarized NO-coordinate ligand (nitrosonium) of the proposed {Fe(NO)(2)}(7) intermediate [(NO)(2)(κ(1)-ONO(2))Fe(S(2)CNEt(2))(2)] (A) yielding {Fe(NO)}(7) [(NO)Fe(S(2)CNEt(2))(2)] (6) along with the release of N(2)O(4) (·NO(2)) and the subsequent binding of ·NO(2) to complex 6. The N-bound nitro {Fe(NO)}(6) complex 7 undergoes Me(2)S-promoted O-atom transfer facilitated by imidazole to give {Fe(NO)}(7) complex 6 accompanied by release of nitric oxide. This result demonstrates that nitrate-containing DNIC 3 acts as an active center to modulate nitrate-to-nitrite-to-nitric oxide conversion.

Increased expression of Aspergillus parasiticus aflR, encoding a sequence-specific DNA-binding protein, relieves nitrate inhibition of aflatoxin biosynthesis.

PubMed Central

Chang, P K; Ehrlich, K C; Yu, J; Bhatnagar, D; Cleveland, T E

1995-01-01

The aflR gene from Aspergillus parasiticus and Aspergillus flavus may be involved in the regulation of aflatoxin biosynthesis. The aflR gene product, AFLR, possesses a GAL4-type binuclear zinc finger DNA-binding domain. A transformant, SU1-N3 (pHSP), containing an additional copy of aflR, showed increased transcription of aflR and the aflatoxin pathway structural genes, nor-1, ver-1, and omt-1, when cells were grown in nitrate medium, which normally suppresses aflatoxin production. Electrophoretic mobility shift assays showed that the recombinant protein containing the DNA-binding domain, AFLR1, bound specifically to the palindromic sequence, TTAGGCCTAA, 120 bp upstream of the AFLR translation start site. Expression of aflR thus appears to be autoregulated. Increased expression of aflatoxin biosynthetic genes in the transformant might result from an elevated basal level of AFLR, allowing it to overcome nitrate inhibition and to bind to the aflR promotor region, thereby initiating aflatoxin biosynthesis. Results further suggest that aflR is involved in the regulation of multiple parts of the aflatoxin biosynthetic pathway. PMID:7793958

Monofluorophosphate is a selective inhibitor of respiratory sulfate-reducing microorganisms.

PubMed

Carlson, Hans K; Stoeva, Magdalena K; Justice, Nicholas B; Sczesnak, Andrew; Mullan, Mark R; Mosqueda, Lorraine A; Kuehl, Jennifer V; Deutschbauer, Adam M; Arkin, Adam P; Coates, John D

2015-03-17

Despite the environmental and economic cost of microbial sulfidogenesis in industrial operations, few compounds are known as selective inhibitors of respiratory sulfate reducing microorganisms (SRM), and no study has systematically and quantitatively evaluated the selectivity and potency of SRM inhibitors. Using general, high-throughput assays to quantitatively evaluate inhibitor potency and selectivity in a model sulfate-reducing microbial ecosystem as well as inhibitor specificity for the sulfate reduction pathway in a model SRM, we screened a panel of inorganic oxyanions. We identified several SRM selective inhibitors including selenate, selenite, tellurate, tellurite, nitrate, nitrite, perchlorate, chlorate, monofluorophosphate, vanadate, molydate, and tungstate. Monofluorophosphate (MFP) was not known previously as a selective SRM inhibitor, but has promising characteristics including low toxicity to eukaryotic organisms, high stability at circumneutral pH, utility as an abiotic corrosion inhibitor, and low cost. MFP remains a potent inhibitor of SRM growing by fermentation, and MFP is tolerated by nitrate and perchlorate reducing microorganisms. For SRM inhibition, MFP is synergistic with nitrite and chlorite, and could enhance the efficacy of nitrate or perchlorate treatments. Finally, MFP inhibition is multifaceted. Both inhibition of the central sulfate reduction pathway and release of cytoplasmic fluoride ion are implicated in the mechanism of MFP toxicity.

Organic Nitrate Therapy, Nitrate Tolerance, and Nitrate-Induced Endothelial Dysfunction: Emphasis on Redox Biology and Oxidative Stress.

PubMed

Daiber, Andreas; Münzel, Thomas

2015-10-10

Organic nitrates, such as nitroglycerin (GTN), isosorbide-5-mononitrate and isosorbide dinitrate, and pentaerithrityl tetranitrate (PETN), when given acutely, have potent vasodilator effects improving symptoms in patients with acute and chronic congestive heart failure, stable coronary artery disease, acute coronary syndromes, or arterial hypertension. The mechanisms underlying vasodilation include the release of •NO or a related compound in response to intracellular bioactivation (for GTN, the mitochondrial aldehyde dehydrogenase [ALDH-2]) and activation of the enzyme, soluble guanylyl cyclase. Increasing cyclic guanosine-3',-5'-monophosphate (cGMP) levels lead to an activation of the cGMP-dependent kinase I, thereby causing the relaxation of the vascular smooth muscle by decreasing intracellular calcium concentrations. The hemodynamic and anti-ischemic effects of organic nitrates are rapidly lost upon long-term (low-dose) administration due to the rapid development of tolerance and endothelial dysfunction, which is in most cases linked to increased intracellular oxidative stress. Enzymatic sources of reactive oxygen species under nitrate therapy include mitochondria, NADPH oxidases, and an uncoupled •NO synthase. Acute high-dose challenges with organic nitrates cause a similar loss of potency (tachyphylaxis), but with distinct pathomechanism. The differences among organic nitrates are highlighted regarding their potency to induce oxidative stress and subsequent tolerance and endothelial dysfunction. We also address pleiotropic effects of organic nitrates, for example, their capacity to stimulate antioxidant pathways like those demonstrated for PETN, all of which may prevent adverse effects in response to long-term therapy. Based on these considerations, we will discuss and present some preclinical data on how the nitrate of the future should be designed.

Organic Nitrate Therapy, Nitrate Tolerance, and Nitrate-Induced Endothelial Dysfunction: Emphasis on Redox Biology and Oxidative Stress

PubMed Central

2015-01-01

Abstract Organic nitrates, such as nitroglycerin (GTN), isosorbide-5-mononitrate and isosorbide dinitrate, and pentaerithrityl tetranitrate (PETN), when given acutely, have potent vasodilator effects improving symptoms in patients with acute and chronic congestive heart failure, stable coronary artery disease, acute coronary syndromes, or arterial hypertension. The mechanisms underlying vasodilation include the release of •NO or a related compound in response to intracellular bioactivation (for GTN, the mitochondrial aldehyde dehydrogenase [ALDH-2]) and activation of the enzyme, soluble guanylyl cyclase. Increasing cyclic guanosine-3′,-5′-monophosphate (cGMP) levels lead to an activation of the cGMP-dependent kinase I, thereby causing the relaxation of the vascular smooth muscle by decreasing intracellular calcium concentrations. The hemodynamic and anti-ischemic effects of organic nitrates are rapidly lost upon long-term (low-dose) administration due to the rapid development of tolerance and endothelial dysfunction, which is in most cases linked to increased intracellular oxidative stress. Enzymatic sources of reactive oxygen species under nitrate therapy include mitochondria, NADPH oxidases, and an uncoupled •NO synthase. Acute high-dose challenges with organic nitrates cause a similar loss of potency (tachyphylaxis), but with distinct pathomechanism. The differences among organic nitrates are highlighted regarding their potency to induce oxidative stress and subsequent tolerance and endothelial dysfunction. We also address pleiotropic effects of organic nitrates, for example, their capacity to stimulate antioxidant pathways like those demonstrated for PETN, all of which may prevent adverse effects in response to long-term therapy. Based on these considerations, we will discuss and present some preclinical data on how the nitrate of the future should be designed. Antioxid. Redox Signal. 23, 899–942. PMID:26261901

Pathways for nitrate release from an alpine watershed: Determination using δ15N and δ18O

USGS Publications Warehouse

Campbell, Donald H.; Kendall, Carol; Chang, Cecily C.Y.; Silva, Steven R.; Tonnessen, Kathy A.

2002-01-01

Snowpack, snowmelt, precipitation, surface water, and groundwater samples from the Loch Vale watershed in Colorado were analyzed for δ15N and δ18O of nitrate to determine the processes controlling the release of atmospherically deposited nitrogen from alpine and subalpine ecosystems. Although overlap was found between the δ15N(NO3) values for all water types (−4 to +6‰), the δ18O(NO3) values for surface water and groundwater (+10 to +30‰) were usually distinct from snowpack, snowmelt, and rainfall values (+40 to +70‰). During snowmelt, δ18O(NO3) indicated that about half of the nitrate in stream water was the product of microbial nitrification; at other times that amount was greater than half. Springs emerging from talus deposits had high nitrate concentrations and a seasonal pattern in δ18O(NO3) that was similar to the pattern in the streams, indicating that shallow groundwater in talus deposits is a likely source of stream water nitrate. Only a few samples of surface water and groundwater collected during early snowmelt and large summer rain events had isotopic compositions that indicated most of the nitrate came directly from atmospheric deposition with no biological assimilation and release. This study demonstrates the value of the nitrate double‐isotope technique for determining nitrogen‐cycling processes and sources of nitrate in small, undisturbed watersheds that are enriched with inorganic nitrogen.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beliav, Alex; Qiu, Dongru; Fredrickson, James K.

Shewanella putrefaciens W3-18-1 harbours two periplasmic nitrate reductase (Nap) gene clusters, NapC-associated nap-alpha (napEDABC) and CymA-dependent nap-beta (napDAGHB), for dissimilatory nitrate respiration. CymA is a member of the NapC/NirT quinol dehydrogenase family and acts as a hub to support different respiratory pathways, including those on iron [Fe(III)] and manganese [Mn(III, IV)] (hydr)oxide, nitrate, nitrite, fumarate and arsenate in Shewanella strains. However, in our analysis it was shown that another NapC/NirT family protein, NapC, was only involved in nitrate reduction, although both CymA and NapC can transfer quinol-derived electrons to a periplasmic terminal reductase or an electron acceptor. Furthermore, our resultsmore » showed that NapC could only interact specifically with the Nap-alpha nitrate reductase while CymA could interact promiscuously with Nap-alpha, Nap-beta and the NrfA nitrite reductase for nitrate and nitrite reduction. To further explore the difference in specificity, site-directed mutagenesis on both CymA and NapC was conducted and the phenotypic changes in nitrate and nitrite reduction were tested. Our analyses demonstrated that the Lys-91 residue played a key role in nitrate reduction for quinol oxidation and the Asp-166 residue might influence the maturation of CymA. The Asp-97 residue might be one of the key factors that influence the interaction of CymA with the cytochromes NapB and NrfA.« less

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

PubMed Central

Vaccaro, Brian J.; Thorgersen, Michael P.; Lancaster, W. Andrew; Price, Morgan N.; Wetmore, Kelly M.; Poole, Farris L.; Deutschbauer, Adam; Arkin, Adam P.

2015-01-01

Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library from Pseudomonas stutzeri strain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. The dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation. PMID:26452555

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaccaro, Brian J.; Thorgersen, Michael P.; Lancaster, W. Andrew

Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library fromPseudomonas stutzeristrain RCH2 was grown under denitrifying conditions, using nitrate or nitrite asmore » an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. Finally, the dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.« less

Increase in gastric pH reduces hypotensive effect of oral sodium nitrite in rats.

PubMed

Pinheiro, Lucas C; Montenegro, Marcelo F; Amaral, Jefferson H; Ferreira, Graziele C; Oliveira, Alisson M; Tanus-Santos, Jose E

2012-08-15

The new pathway nitrate-nitrite-nitric oxide (NO) has emerged as a physiological alternative to the classical enzymatic pathway for NO formation from l-arginine. Nitrate is converted to nitrite by commensal bacteria in the oral cavity and the nitrite formed is then swallowed and reduced to NO under the acidic conditions of the stomach. In this study, we tested the hypothesis that increases in gastric pH caused by omeprazole could decrease the hypotensive effect of oral sodium nitrite. We assessed the effects of omeprazole treatment on the acute hypotensive effects produced by sodium nitrite in normotensive and L-NAME-hypertensive free-moving rats. In addition, we assessed the changes in gastric pH and plasma levels of nitrite, NO(x) (nitrate+nitrite), and S-nitrosothiols caused by treatments. We found that the increases in gastric pH induced by omeprazole significantly reduced the hypotensive effects of sodium nitrite in both normotensive and L-NAME-hypertensive rats. This effect of omeprazole was associated with no significant differences in plasma nitrite, NO(x), or S-nitrosothiol levels. Our results suggest that part of the hypotensive effects of oral sodium nitrite may be due to its conversion to NO in the acidified environment of the stomach. The increase in gastric pH induced by treatment with omeprazole blunts part of the beneficial cardiovascular effects of dietary nitrate and nitrite. Copyright © 2012 Elsevier Inc. All rights reserved.

Mapping the Spatial and Temporal Distribution of N and O Isotopes in Precipitation Nitrate Across the Northeastern and Mid-Atlantic United States

NASA Astrophysics Data System (ADS)

Elliott, E. M.; Kendall, C.; Harlin, K.; Butler, T.; Carlton, R.; Wankel, S.

2004-12-01

Atmospheric deposition of N is a universally important pathway by which ecosystems receive fixed, bioavailable N. Since the 1880s, atmospheric deposition of N has become increasingly important, as NOx emissions from fossil fuel combustion have steadily increased. In particular, the Northeastern and Mid-Atlantic U.S. receive some of the highest rates of nitrate wet deposition in the country, causing a cascade of detrimental effects. In order to effectively mediate the impacts of nitrate deposition, it is critical to understand the dynamics among NOx sources, atmospheric chemical transformations and transport, and the characteristics of the nitrate that is ultimately deposited. To address this need, this research takes advantage of recent methodological improvements, coupled with national networks (NADP, AIRMoN) of archived precipitation, to characterize N and O isotopic composition of nitrate in precipitation across the Northeastern and Mid-Atlantic U.S. We investigate the critical question of whether variations in \\delta15N and \\delta18O of nitrate wet deposition are mainly a function of atmospheric processes (e.g., seasonal variations in reaction pathways) or variable NOx source contributions (e.g., power plant emissions, vehicle exhaust). Spatial and seasonal variability of \\delta15N and \\delta18O is investigated using bimonthly archived samples from 2000. Furthermore, a high resolution record of daily precipitation from a single site is used to highlight within-season isotopic variability. Potential correlations between isotopic values and major NOx sources are explored using EPA datasets for monthly county-level emissions from two major NOx sources, electric generating units and on-road vehicles. Analysis of samples for \\Delta17O is in progress. A key concern regarding analysis of archived samples is nitrate preservation. We tested the stability of nitrate concentrations, and hence potential isotopic fractionations, by reanalyzing filtered, refrigerated, archived NADP samples with a range of nitrate and ammonium concentrations. We found highly significant correlations (R2=0.9995, p<0.001, n=28) between nitrate concentrations measured in 2000 and 2003, indicating that no major alterations had occurred. With regard to spatial patterns, preliminary isotopic analyses indicate that \\delta15N of precipitation nitrate varies considerably among states. Moreover, initial data corroborate previously reported seasonal trends in both \\delta15N and \\delta18O, with higher values in the colder months. Seasonal trends in \\delta15N are remarkably consistent, with up to an 8 \\permil difference between winter and summer months. \\delta18O values of nitrate are generally higher and have a smaller range than previously reported for precipitation, with values ranging from +60 to +90 \\permil. In addition, archived daily precipitation collected during 2000 from a single AIRMoN site give insight into the seasonal and within-season variability of \\delta15N and \\delta18O of precipitation nitrate. Back-trajectory analyses are used to examine the geographic source of air masses for individual events, and seasonal frontal patterns are discussed.

Interacting TCP and NLP transcription factors control plant responses to nitrate availability.

PubMed

Guan, Peizhu; Ripoll, Juan-José; Wang, Renhou; Vuong, Lam; Bailey-Steinitz, Lindsay J; Ye, Dening; Crawford, Nigel M

2017-02-28

Plants have evolved adaptive strategies that involve transcriptional networks to cope with and survive environmental challenges. Key transcriptional regulators that mediate responses to environmental fluctuations in nitrate have been identified; however, little is known about how these regulators interact to orchestrate nitrogen (N) responses and cell-cycle regulation. Here we report that teosinte branched1/cycloidea/proliferating cell factor1-20 (TCP20) and NIN-like protein (NLP) transcription factors NLP6 and NLP7, which act as activators of nitrate assimilatory genes, bind to adjacent sites in the upstream promoter region of the nitrate reductase gene, NIA1 , and physically interact under continuous nitrate and N-starvation conditions. Regions of these proteins necessary for these interactions were found to include the type I/II Phox and Bem1p (PB1) domains of NLP6&7, a protein-interaction module conserved in animals for nutrient signaling, and the histidine- and glutamine-rich domain of TCP20, which is conserved across plant species. Under N starvation, TCP20-NLP6&7 heterodimers accumulate in the nucleus, and this coincides with TCP20 and NLP6&7-dependent up-regulation of nitrate assimilation and signaling genes and down-regulation of the G 2 /M cell-cycle marker gene, CYCB1;1 TCP20 and NLP6&7 also support root meristem growth under N starvation. These findings provide insights into how plants coordinate responses to nitrate availability, linking nitrate assimilation and signaling with cell-cycle progression.

Active secretion and protective effect of salivary nitrate against stress in human volunteers and rats

PubMed Central

Jin, Luyuan; Qin, Lizheng; Xia, Dengsheng; Liu, Xibao; Fan, Zhipeng; Zhang, Chunmei; Gu, Liankun; He, Junqi; Ambudkar, Indu S.; Deng, Dajun; Wang, Songlin

2014-01-01

Up to 25% of the circulating nitrate in blood is actively taken up, concentrated, and secreted into saliva by the salivary glands. Salivary nitrate can be reduced to nitrite by the commensal bacteria in the oral cavity or stomach and then further converted to nitric oxide (NO) in vivo, which may play a role in gastric protection. However, whether salivary nitrate is actively secreted in human beings has not yet been determined. This study was designed to determine whether salivary nitrate is actively secreted in human beings as an acute stress response and what role salivary nitrate plays in stress-induced gastric injury. To observe salivary nitrate function under stress conditions, alteration of salivary nitrate and nitrite was analyzed among 22 healthy volunteers before and after a strong stress activity, jumping down from a platform at the height of 68m. A series of stress indexes was analyzed to monitor the stress situation. We found that both the concentration and the total amount of nitrate in mixed saliva were significantly increased in the human volunteers immediately after the jump, with an additional increase 1 h later (p < 0.01). Saliva nitrite reached a maximum immediately after the jump and was maintained 1 h later. To study the biological functions of salivary nitrate and nitrite in stress protection, we further carried out a water-immersion-restraint stress (WIRS) assay in male adult rats with bilateral parotid and submandibular duct ligature (BPSDL). Intragastric nitrate, nitrite, and NO; gastric mucosal blood flow; and gastric ulcer index (UI) were monitored and nitrate was administrated in drinking water to compensate for nitrate secretion in BPSDL animals. Significantly decreased levels of intragastric nitrate, nitrite, and NO and gastricmucosal blood flow were measured in BPSDL rats during the WIRS assay compared to sham control rats (p < 0.05). Recovery was observed in the BPSDL rats upon nitrate administration. The WIRS-induced UI was significantly higher in the BPSDL animals compared to controls, and nitrate administration rescued the WIRS-induced gastric injury in BPSDL rats. In conclusion, this study suggests that stress promotes salivary nitrate secretion and nitrite formation, which may play important roles in gastric protection against stress-induced injury via the nitrate-dependent NO pathway. PMID:23277147

Nitrate Reduction to Nitrite, Nitric Oxide and Ammonia by Gut Bacteria under Physiological Conditions

PubMed Central

Tiso, Mauro; Schechter, Alan N.

2015-01-01

The biological nitrogen cycle involves step-wise reduction of nitrogen oxides to ammonium salts and oxidation of ammonia back to nitrites and nitrates by plants and bacteria. Neither process has been thought to have relevance to mammalian physiology; however in recent years the salivary bacterial reduction of nitrate to nitrite has been recognized as an important metabolic conversion in humans. Several enteric bacteria have also shown the ability of catalytic reduction of nitrate to ammonia via nitrite during dissimilatory respiration; however, the importance of this pathway in bacterial species colonizing the human intestine has been little studied. We measured nitrite, nitric oxide (NO) and ammonia formation in cultures of Escherichia coli, Lactobacillus and Bifidobacterium species grown at different sodium nitrate concentrations and oxygen levels. We found that the presence of 5 mM nitrate provided a growth benefit and induced both nitrite and ammonia generation in E.coli and L.plantarum bacteria grown at oxygen concentrations compatible with the content in the gastrointestinal tract. Nitrite and ammonia accumulated in the growth medium when at least 2.5 mM nitrate was present. Time-course curves suggest that nitrate is first converted to nitrite and subsequently to ammonia. Strains of L.rhamnosus, L.acidophilus and B.longum infantis grown with nitrate produced minor changes in nitrite or ammonia levels in the cultures. However, when supplied with exogenous nitrite, NO gas was readily produced independently of added nitrate. Bacterial production of lactic acid causes medium acidification that in turn generates NO by non-enzymatic nitrite reduction. In contrast, nitrite was converted to NO by E.coli cultures even at neutral pH. We suggest that the bacterial nitrate reduction to ammonia, as well as the related NO formation in the gut, could be an important aspect of the overall mammalian nitrate/nitrite/NO metabolism and is yet another way in which the microbiome links diet and health. PMID:25803049

Combination of Entner-Doudoroff Pathway with MEP Increases Isoprene Production in Engineered Escherichia coli

PubMed Central

Liu, Huaiwei; Sun, Yuanzhang; Ramos, Kristine Rose M.; Nisola, Grace M.; Valdehuesa, Kris Niño G.; Lee, Won–Keun; Park, Si Jae; Chung, Wook-Jin

2013-01-01

Embden-Meyerhof pathway (EMP) in tandem with 2-C-methyl-D-erythritol 4-phosphate pathway (MEP) is commonly used for isoprenoid biosynthesis in E. coli. However, this combination has limitations as EMP generates an imbalanced distribution of pyruvate and glyceraldehyde-3-phosphate (G3P). Herein, four glycolytic pathways—EMP, Entner-Doudoroff Pathway (EDP), Pentose Phosphate Pathway (PPP) and Dahms pathway were tested as MEP feeding modules for isoprene production. Results revealed the highest isoprene production from EDP containing modules, wherein pyruvate and G3P were generated simultaneously; isoprene titer and yield were more than three and six times higher than those of the EMP module, respectively. Additionally, the PPP module that generates G3P prior to pyruvate was significantly more effective than the Dahms pathway, in which pyruvate production precedes G3P. In terms of precursor generation and energy/reducing-equivalent supply, EDP+PPP was found to be the ideal feeding module for MEP. These findings may launch a new direction for the optimization of MEP-dependent isoprenoid biosynthesis pathways. PMID:24376679

Antioxidant Systems are Regulated by Nitric Oxide-Mediated Post-translational Modifications (NO-PTMs)

PubMed Central

Begara-Morales, Juan C.; Sánchez-Calvo, Beatriz; Chaki, Mounira; Valderrama, Raquel; Mata-Pérez, Capilla; Padilla, María N.; Corpas, Francisco J.; Barroso, Juan B.

2016-01-01

Nitric oxide (NO) is a biological messenger that orchestrates a plethora of plant functions, mainly through post-translational modifications (PTMs) such as S-nitrosylation or tyrosine nitration. In plants, hundreds of proteins have been identified as potential targets of these NO-PTMs under physiological and stress conditions indicating the relevance of NO in plant-signaling mechanisms. Among these NO protein targets, there are different antioxidant enzymes involved in the control of reactive oxygen species (ROS), such as H2O2, which is also a signal molecule. This highlights the close relationship between ROS/NO signaling pathways. The major plant antioxidant enzymes, including catalase, superoxide dismutases (SODs) peroxiredoxins (Prx) and all the enzymatic components of the ascorbate-glutathione (Asa-GSH) cycle, have been shown to be modulated to different degrees by NO-PTMs. This mini-review will update the recent knowledge concerning the interaction of NO with these antioxidant enzymes, with a special focus on the components of the Asa-GSH cycle and their physiological relevance. PMID:26909095

Copper control of bacterial nitrous oxide emission and its impact on vitamin B12-dependent metabolism

PubMed Central

Sullivan, Matthew J.; Gates, Andrew J.; Appia-Ayme, Corinne; Rowley, Gary; Richardson, David J.

2013-01-01

Global agricultural emissions of the greenhouse gas nitrous oxide (N2O) have increased by around 20% over the last 100 y, but regulation of these emissions and their impact on bacterial cellular metabolism are poorly understood. Denitrifying bacteria convert nitrate in soils to inert di-nitrogen gas (N2) via N2O and the biochemistry of this process has been studied extensively in Paracoccus denitrificans. Here we demonstrate that expression of the gene encoding the nitrous oxide reductase (NosZ), which converts N2O to N2, is regulated in response to the extracellular copper concentration. We show that elevated levels of N2O released as a consequence of decreased cellular NosZ activity lead to the bacterium switching from vitamin B12-dependent to vitamin B12-independent biosynthetic pathways, through the transcriptional modulation of genes controlled by vitamin B12 riboswitches. This inhibitory effect of N2O can be rescued by addition of exogenous vitamin B12. PMID:24248380

Presidential Green Chemistry Challenge: 2003 Greener Synthetic Pathways Award

EPA Pesticide Factsheets

Presidential Green Chemistry Challenge 2003 winner, Sud-Chemie, developed a synthesis for solid oxide catalysts used to make hydrogen and clean fuels. The process creates little wastewater, no nitrates, and no or little NOx.

Theoretical and Experimental Insights into the Dissociation of 2-Hydroxyethylhydrazinium Nitrate Clusters Formed via Electrospray.

PubMed

Patrick, Amanda L; Vogelhuber, Kristen M; Prince, Benjamin D; Annesley, Christopher J

2018-03-01

Ionic liquids are used for myriad applications, including as catalysts, solvents, and propellants. Specifically, 2-hydroxyethylhydrazinium nitrate (HEHN) has been developed as a chemical propellant for space applications. The gas-phase behavior of HEHN ions and clusters is important in understanding its potential as an electrospray thruster propellant. Here, the unimolecular dissociation pathways of two clusters are experimentally observed, and theoretical modeling of hydrogen bonding and dissociation pathways is used to help rationalize those observations. The cation/deprotonated cation cluster [HEH 2 - H] + , which is observed from electrospray ionization, is calculated to be considerably more stable than the complementary cation/protonated anion adduct, [HEH + HNO 3 ] + , which is not observed experimentally. Upon collisional activation, a larger cluster [(HEHN) 2 HEH] + undergoes dissociation via loss of nitric acid at lower collision energies, as predicted theoretically. At higher collision energies, additional primary and secondary loss pathways open, including deprotonated cation loss, ion-pair loss, and double-nitric-acid loss. Taken together, these experimental and theoretical results contribute to a foundational understanding of the dissociation of protic ionic liquid clusters in the gas phase.

Oxygen isotope dynamics of atmospheric nitrate over the Antarctic plateau: First combined measurements of ozone and nitrate 17O-excess (Δ17O)

NASA Astrophysics Data System (ADS)

Vicars, William; Savarino, Joël; Erbland, Joseph; Preunkert, Susanne; Jourdain, Bruno; Frey, Markus; Gil, Jaime; Legrand, Michel

2013-04-01

Variations in the isotopic composition of atmospheric nitrate (NO3-) provide novel indicators for important processes in boundary layer chemistry, often acting as source markers for reactive nitrogen (NOx = NO + NO2) and providing both qualitative and quantitative constraints on the pathways that determine its fate. Stable isotope ratios of nitrate (δ15N, δ17O, δ18O) offer direct insight into the nature and magnitude of the fluxes associated with different processes, thus providing unique information regarding phenomena that are often difficult to quantify from concentration measurements alone. The unique and distinctive 17O-excess (Δ17O = δ17O - 0.52 × δ18O ) of ozone (O3), which is transferred to NOx via oxidation reactions in the atmosphere, has been found to be a particularly useful isotopic fingerprint in studies of NOx transformations. Constraining the propagation of 17O-excess within the NOx cycle is critical in polar areas where there exists the possibility of extending atmospheric interpretations to the glacial/interglacial time scale using deep ice core records of nitrate. Here we present measurements of the comprehensive isotopic composition of atmospheric nitrate collected at Dome C, Antarctica during December 2011 to January 2012. Sampling was conducted within the framework of the OPALE (Oxidant Production over Antarctic Land and its Export) project, thus providing an opportunity to combine our isotopic observations with a wealth of meteorological and chemical data, including in-situ concentration measurements of the gas-phase precursors involved in nitrate production (NOx, O3, OH, HO2, etc.). Furthermore, nitrate isotope analysis has been combined in this study for the first time with parallel observations of the transferrable Δ17O of surface ozone, which was measured concurrently at Dome C using our recently developed analytical approach. This unique dataset has allowed for a direct comparison of observed Δ17O(NO3-) values to those that are calculated solely from local measurements and invoke no assumptions regarding the Δ17O value of ozone and its transfer in the atmosphere. The predicted Δ17O signature for nitrate formed over the Antarctic plateau during OPALE is on the order of (21 ± 2) ‰ when production is assumed to occur only through the OH + NO2 pathway, which is expected to be the dominant formation channel during the continuously sunlit summer. This predicted value is much lower than the values measured for nitrate during OPALE, with observed Δ17O(NO3-) varying in the range of 27 - 31 ‰. This discrepancy between expected and observed Δ17O(NO3-) values suggests the existence of an unexpected process that contributes significantly to the atmospheric nitrate budget over Dome C. The relative merits of different potential explanations for this puzzling result will be discussed in the context of oxidation chemistry, air mass transport, and snow/atmosphere exchange.

The Nitrate Transporter MtNPF6.8 (MtNRT1.3) Transports Abscisic Acid and Mediates Nitrate Regulation of Primary Root Growth in Medicago truncatula1[W

PubMed Central

Pellizzaro, Anthoni; Clochard, Thibault; Cukier, Caroline; Bourdin, Céline; Juchaux, Marjorie; Montrichard, Françoise; Thany, Steeve; Raymond, Valérie; Planchet, Elisabeth; Morère-Le Paven, Marie-Christine

2014-01-01

Elongation of the primary root during postgermination of Medicago truncatula seedlings is a multigenic trait that is responsive to exogenous nitrate. A quantitative genetic approach suggested the involvement of the nitrate transporter MtNPF6.8 (for Medicago truncatula NITRATE TRANSPORTER1/PEPTIDE TRANSPORTER Family6.8) in the inhibition of primary root elongation by high exogenous nitrate. In this study, the inhibitory effect of nitrate on primary root elongation, via inhibition of elongation of root cortical cells, was abolished in npf6.8 knockdown lines. Accordingly, we propose that MtNPF6.8 mediates nitrate inhibitory effects on primary root growth in M. truncatula. pMtNPF6.8:GUS promoter-reporter gene fusion in Agrobacterium rhizogenes-generated transgenic roots showed the expression of MtNPF6.8 in the pericycle region of primary roots and lateral roots, and in lateral root primordia and tips. MtNPF6.8 expression was insensitive to auxin and was stimulated by abscisic acid (ABA), which restored the inhibitory effect of nitrate in npf6.8 knockdown lines. It is then proposed that ABA acts downstream of MtNPF6.8 in this nitrate signaling pathway. Furthermore, MtNPF6.8 was shown to transport ABA in Xenopus spp. oocytes, suggesting an additional role of MtNPF6.8 in ABA root-to-shoot translocation. 15NO3−-influx experiments showed that only the inducible component of the low-affinity transport system was affected in npf6.8 knockdown lines. This indicates that MtNPF6.8 is a major contributor to the inducible component of the low-affinity transport system. The short-term induction by nitrate of the expression of Nitrate Reductase1 (NR1) and NR2 (genes that encode two nitrate reductase isoforms) was greatly reduced in the npf6.8 knockdown lines, supporting a role of MtNPF6.8 in the primary nitrate response in M. truncatula. PMID:25367858

Legacy of contaminant N sources to the NO3− signature in rivers: a combined isotopic (δ15N-NO3−, δ18O-NO3−, δ11B) and microbiological investigation

PubMed Central

Briand, Cyrielle; Sebilo, Mathieu; Louvat, Pascale; Chesnot, Thierry; Vaury, Véronique; Schneider, Maude; Plagnes, Valérie

2017-01-01

Nitrate content of surface waters results from complex mixing of multiple sources, whose signatures can be modified through N reactions occurring within the different compartments of the whole catchment. Despite this complexity, the determination of nitrate origin is the first and crucial step for water resource preservation. Here, for the first time, we combined at the catchment scale stable isotopic tracers (δ15N and δ18O of nitrate and δ11B) and fecal indicators to trace nitrate sources and pathways to the stream. We tested this approach on two rivers in an agricultural region of SW France. Boron isotopic ratios evidenced inflow from anthropogenic waters, microbiological markers revealed organic contaminations from both human and animal wastes. Nitrate δ15N and δ18O traced inputs from the surface leaching during high flow events and from the subsurface drainage in base flow regime. They also showed that denitrification occurred within the soils before reaching the rivers. Furthermore, this study highlighted the determinant role of the soil compartment in nitrate formation and recycling with important spatial heterogeneity and temporal variability. PMID:28150819

Inorganic nitrite and nitrate in cardiovascular therapy: A better alternative to organic nitrates as nitric oxide donors?

PubMed

Münzel, Thomas; Daiber, Andreas

2018-03-01

In 1867 the organic nitrite, amyl nitrite, was introduced as a therapeutic agent in the treatment of angina pectoris and was later substituted by the organic nitrate nitroglycerin (NTG). Despite having a highly potent vasodilator capacity in veins>coronary arteries>arterioles, the vasodilator effects NTG are rapidly attenuated by the development of nitrate tolerance. We and others established that NTG treatment stimulates the production of reactive oxygen species such as superoxide and peroxynitrite with subsequent marked attenuation of the NTG vasodilator potency. The nitrite anion (NO 2 - ) has more recently been characterized to possess novel pharmacotherapeutic actions such as modulation of vasodilation under hypoxic conditions, thereby providing protection in ischemia-reperfusion injury. Administration of NO 2 - /NO 3 - has also been shown to improve myocardial function in heart failure and to lower blood pressure. Despite these positive aspects there is still a great need to study inorganic nitrate and nitrite therapy in various cardiovascular diseases in prospective outcome directed studies. In case being successful, this kind of therapy would indeed represent a cheap, therefore affordable, effective cardiovascular therapy without major side effects as observed in response to therapy with organic nitrates. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Extending double modulation: combinatorial rules for identifying the modulations necessary for determining elasticities in metabolic pathways.

PubMed

Giersch, C; Cornish-Bowden, A

1996-10-07

The double modulation method for determining the elasticities of pathway enzymes, originally devised by Kacser & Burns (Biochem. Soc. Trans. 7, 1149-1160, 1979), is extended to pathways of complex topological structure, including branching and feedback loops. An explicit system of linear equations for the unknown elasticities is derived. The constraints imposed on this linear system imply that modulations of more than one enzyme are not necessarily independent. Simple combinatorial rules are described for identifying without using any algebra the set of independent modulations that allow the determination of the elasticities of any enzyme. By repeated application, the minimum numbers of modulations required to determine the elasticities of all enzymes of a given pathway can be determined. The procedure is illustrated with numerous examples.

Bio-reduction of N-nitrosodimethylamine (NDMA) using a hydrogen-based membrane biofilm reactor.

PubMed

Chung, Jinwook; Ahn, Chang-Hoon; Chen, Zhuo; Rittmann, Bruce E

2008-01-01

N-Nitrosodimethylamine (NDMA) is a disinfection by-product shown to be carcinogenic, mutagenic, and teratogenic. A feasible detoxification pathway for NDMA is a three-step bio-reduction that leads to ammonia and dimethylamine. This study examines the bio-reduction of NDMA in a H2-based membrane biofilm reactor (MBfR) that also is active in nitrate and sulfate reductions. In particular, the study investigates the effects of H2 availability and the relative loadings of NDMA, nitrate, and sulfate, which potentially are competing electron acceptors. The results demonstrate that NDMA was bio-reduced to a major extent (i.e., at least 96%) in a H2-based MBfR in which the electron-equivalent fluxes from H2 oxidation were dominated by nitrate and sulfate reductions. NDMA reduction kinetics responded to NDMA concentration, H2 pressure, and the presence of competing acceptors. The most important factor controlling NDMA-reduction kinetics was the H2 availability, controlled primarily by the H2 pressure, and secondarily by competition from nitrate reduction.

Simultaneous removal of nitrate and pentachlorophenol from simulated groundwater using a biodenitrification reactor packed with corncob.

PubMed

Wang, Xuming; Xing, Lijun; Qiu, Tianlei; Han, Meilin

2013-04-01

Both nitrate and pentachlorophenol (PCP) are familiar pollutants in aqueous environment. This research is focused on the simultaneous removal of nitrate and PCP from simulated contaminated groundwater using a laboratory-scale denitrification reactor packed with corncob as both carbon source and biofilm support. The reactor could be started up readily, and the removal efficiencies of nitrate and PCP reached up to approximately 98% and 40-45% when their initial concentrations were 50 mg N/L and 5 mg/L, respectively, after 15-day continuous operation at 10 h of hydraulic retention time (HRT) and 25 °C. Approximately 91% of PCP removal efficiency was achieved, with 2.47 mg/L of chloride ion release at 24 h of HRT. Eighty-two percent of chlorine in PCP removed was ionized. The productions of 3-chlorophenol and phenol and chloride ion release indicate that the reductive dechlorination reaction is a major degradation pathway of PCP under the experimental conditions.

Agriculture causes nitrate fertilization of remote alpine lakes

PubMed Central

Hundey, E. J.; Russell, S. D.; Longstaffe, F. J.; Moser, K. A.

2016-01-01

Humans have altered Earth's nitrogen cycle so dramatically that reactive nitrogen (Nr) has doubled. This has increased Nr in aquatic ecosystems, which can lead to reduced water quality and ecosystem health. Apportioning sources of Nr to specific ecosystems, however, continues to be challenging, despite this knowledge being critical for mitigation and protection of water resources. Here we use Δ17O, δ18O and δ15N from Uinta Mountain (Utah, USA) snow, inflow and lake nitrate in combination with a Bayesian-based stable isotope mixing model, to show that at least 70% of nitrates in aquatic systems are anthropogenic and arrive via the atmosphere. Moreover, agricultural activities, specifically nitrate- and ammonium-based fertilizer use, are contributing most (∼60%) Nr, and data from other North American alpine lakes suggest this is a widespread phenomenon. Our findings offer a pathway towards more effective mitigation, but point to challenges in balancing food production with protection of important water resources. PMID:26853267

Effective connectivity of ascending and descending frontalthalamic pathways during sustained attention: Complex brain network interactions in adolescence.

PubMed

Jagtap, Pranav; Diwadkar, Vaibhav A

2016-07-01

Frontal-thalamic interactions are crucial for bottom-up gating and top-down control, yet have not been well studied from brain network perspectives. We applied network modeling of fMRI signals [dynamic causal modeling (DCM)] to investigate frontal-thalamic interactions during an attention task with parametrically varying levels of demand. fMRI was collected while subjects participated in a sustained continuous performance task with low and high attention demands. 162 competing model architectures were employed in DCM to evaluate hypotheses on bilateral frontal-thalamic connections and their modulation by attention demand, selected at a second level using Bayesian model selection. The model architecture evinced significant contextual modulation by attention of ascending (thalamus → dPFC) and descending (dPFC → thalamus) pathways. However, modulation of these pathways was asymmetric: while positive modulation of the ascending pathway was comparable across attention demand, modulation of the descending pathway was significantly greater when attention demands were increased. Increased modulation of the (dPFC → thalamus) pathway in response to increased attention demand constitutes novel evidence of attention-related gain in the connectivity of the descending attention pathway. By comparison demand-independent modulation of the ascending (thalamus → dPFC) pathway suggests unbiased thalamic inputs to the cortex in the context of the paradigm. Hum Brain Mapp 37:2557-2570, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

NO-Rich Diet for Lifestyle-Related Diseases

PubMed Central

Kobayashi, Jun; Ohtake, Kazuo; Uchida, Hiroyuki

2015-01-01

Decreased nitric oxide (NO) availability due to obesity and endothelial dysfunction might be causally related to the development of lifestyle-related diseases such as insulin resistance, ischemic heart disease, and hypertension. In such situations, instead of impaired NO synthase (NOS)-dependent NO generation, the entero-salivary nitrate-nitrite-NO pathway might serve as a backup system for NO generation by transmitting NO activities in the various molecular forms including NO and protein S-nitrosothiols. Recently accumulated evidence has demonstrated that dietary intake of fruits and vegetables rich in nitrate/nitrite is an inexpensive and easily-practicable way to prevent insulin resistance and vascular endothelial dysfunction by increasing the NO availability; a NO-rich diet may also prevent other lifestyle-related diseases, including osteoporosis, chronic obstructive pulmonary disease (COPD), and cancer. This review provides an overview of our current knowledge of NO generation through the entero-salivary pathway and discusses its safety and preventive effects on lifestyle-related diseases. PMID:26091235

The UK Nitrate Time Bomb (Invited)

NASA Astrophysics Data System (ADS)

Ward, R.; Wang, L.; Stuart, M.; Bloomfield, J.; Gooddy, D.; Lewis, M.; McKenzie, A.

2013-12-01

The developed world has benefitted enormously from the intensification of agriculture and the increased availability and use of synthetic fertilizers during the last century. However there has also been unintended adverse impact on the natural environment (water and ecosystems) with nitrate the most significant cause of water pollution and ecosystem damage . Many countries have introduced controls on nitrate, e.g. the European Union's Water Framework and Nitrate Directives, but despite this are continuing to see a serious decline in water quality. The purpose of our research is to investigate and quantify the importance of the unsaturated (vadose) zone pathway and groundwater in contributing to the decline. Understanding nutrient behaviour in the sub-surface environment and, in particular, the time lag between action and improvement is critical to effective management and remediation of nutrient pollution. A readily-transferable process-based model has been used to predict temporal loading of nitrate at the water table across the UK. A time-varying nitrate input function has been developed based on nitrate usage since 1925. Depth to the water table has been calculated from groundwater levels based on regional-scale observations in-filled by interpolated river base levels and vertical unsaturated zone velocities estimated from hydrogeological properties and mapping. The model has been validated using the results of more than 300 unsaturated zone nitrate profiles. Results show that for about 60% of the Chalk - the principal aquifer in the UK - peak nitrate input has yet to reach the water table and concentrations will continue to rise over the next 60 years. The implications are hugely significant especially where environmental objectives must be achieved in much shorter timescales. Current environmental and regulatory management strategies rarely take lag times into account and as a result will be poorly informed, leading to inappropriate controls and conflicts between policy makers, environmentalists and industry.

Generation of Reduced Nicotinamide Adenine Dinucleotide for Nitrate Reduction in Green Leaves 1

PubMed Central

Klepper, Lowell; Flesher, Donna; Hageman, R. H.

1971-01-01

An in vivo assay of nitrate reductase activity was developed by vacuum infiltration of leaf discs or sections with a solution of 0.2 m KNO3 (with or without phosphate buffer, pH 7.5) and incubation of the infiltrated tissue and medium under essentially anaerobic conditions in the dark. Nitrite production, for computing enzyme activity, was determined on aliquots of the incubation media, removed at intervals. By adding, separately, various metabolites of the glycolytic, pentose phosphate, and citric acid pathways to the infiltrating media, it was possible to use the in vivo assay to determine the prime source of reduced nicotinamide adenine dinucleotide (NADH) required by the cytoplasmically located NADH-specific nitrate reductase. It was concluded that sugars that migrate from the chloroplast to the cytoplasm were the prime source of energy and that the oxidation of glyceraldehyde 3-phosphate was ultimately the in vivo source of NADH for nitrate reduction. This conclusion was supported by experiments that included: inhibition studies with iodoacetate; in vitro studies that established the presence and functionality of the requisite enzymes; and studies showing the effect of light (photosynthate) and exogenous carbohydrate on loss of endogenous nitrate from plant tissue. The level of nitrate reductase activity obtained with the in vitro assay is higher (2.5- to 20-fold) than with the in vivo assay for most plant species. The work done to date would indicate that the in vivo assays are proportional to the in vitro assays with respect to ranking genotypes for nitrate-reducing potential of a given species. The in vivo assay is especially useful in studying nitrate assimilation in species like giant ragweed from which only traces of active nitrate reductase can be extracted. PMID:16657841

Sulfate, nitrate and blood pressure - An EPIC interaction between sulfur and nitrogen.

PubMed

Kuhnle, Gunter G; Luben, Robert; Khaw, Kay-Tee; Feelisch, Martin

2017-08-01

Nitrate (NO 3 - )-rich foods such as green leafy vegetables are not only part of a healthy diet, but increasingly marketed for primary prevention of cardiovascular disease (CVD) and used as ergogenic aids by competitive athletes. While there is abundant evidence for mild hypotensive effects of nitrate on acute application there is limited data on chronic intake in humans, and results from animal studies suggest no long-term benefit. This is important as nitrate can also promote the formation of nitrosamines. It is therefore classified as 'probably carcinogenic to humans', although a beneficial effect on CVD risk might compensate for an increased cancer risk. Dietary nitrate requires reduction to nitrite (NO 2 - ) by oral commensal bacteria to contribute to the formation of nitric oxide (NO). The extensive crosstalk between NO and hydrogen sulfide (H 2 S) related metabolites may further affect nitrate's bioactivity. Using nitrate and nitrite concentrations of drinking water - the only dietary source continuously monitored for which detailed data exist - in conjunction with data of >14,000 participants of the EPIC-Norfolk study, we found no inverse associations with blood pressure or CVD risk. Instead, we found a strong interaction with sulfate (SO 4 2- ). At low sulfate concentrations, nitrate was inversely associated with BP (-4mmHg in top quintile) whereas this was reversed at higher concentrations (+3mmHg in top quintile). Our findings have a potentially significant impact for pharmacology, physiology and public health, redirecting our attention from the oral microbiome and mouthwash use to interaction with sulfur-containing dietary constituents. These results also indicate that nitrate bioactivation is more complex than hitherto assumed. The modulation of nitrate bioactivity by sulfate may render dietary lifestyle interventions aimed at increasing nitrate intake ineffective and even reverse potential antihypertensive effects, warranting further investigation. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Rapid auxin-induced nitric oxide accumulation and subsequent tyrosine nitration of proteins during adventitious root formation in sunflower hypocotyls

PubMed Central

Yadav, Sunita; David, Anisha; Baluška, František; Bhatla, Satish C.

2013-01-01

Using NO specific probe (MNIP-Cu), rapid nitric oxide (NO) accumulation as a response to auxin (IAA) treatment has been observed in the protoplasts from the hypocotyls of sunflower seedlings (Helianthus annuus L.). Incubation of protoplasts in presence of NPA (auxin efflux blocker) and PTIO (NO scavenger) leads to significant reduction in NO accumulation, indicating that NO signals represent an early signaling event during auxin-induced response. A surge in NO production has also been demonstrated in whole hypocotyl explants showing adventitious root (AR) development. Evidence of tyrosine nitration of cytosolic proteins as a consequence of NO accumulation has been provided by western blot analysis and immunolocalization in the sections of AR producing hypocotyl segments. Most abundant anti-nitrotyrosine labeling is evident in proteins ranging from 25–80 kDa. Tyrosine nitration of a particular protein (25 kDa) is completely absent in presence of NPA (which suppresses AR formation). Similar lack of tyrosine nitration of this protein is also evident in other conditions which do not allow AR differentiation. Immunofluorescent localization experiments have revealed that non-inductive treatments (such as PTIO) for AR develpoment from hypocotyl segments coincide with symplastic and apoplastic localization of tyrosine nitrated proteins in the xylem elements, in contrast with negligible (and mainly apoplastic) nitration of proteins in the interfascicular cells and phloem elements. Application of NPA does not affect tyrosine nitration of proteins even in the presence of an external source of NO (SNP). Tyrosine nitrated proteins are abundant around the nuclei in the actively dividing cells of the root primordium. Thus, NO-modulated rapid response to IAA treatment through differential distribution of tyrosine nitrated proteins is evident as an inherent aspect of the AR development. PMID:23299324

Hydrogeological and multi-isotopic approach to define nitrate pollution and denitrification processes in a coastal aquifer (Sardinia, Italy)

NASA Astrophysics Data System (ADS)

Pittalis, Daniele; Carrey, Raul; Da Pelo, Stefania; Carletti, Alberto; Biddau, Riccardo; Cidu, Rosa; Celico, Fulvio; Soler, Albert; Ghiglieri, Giorgio

2018-02-01

Agricultural coastal areas are frequently affected by the superimposition of various processes, with a combination of anthropogenic and natural sources, which degrade groundwater quality. In the coastal multi-aquifer system of Arborea (Italy)—a reclaimed morass area identified as a nitrate vulnerable zone, according to Nitrate Directive 91/676/EEC—intensive agricultural and livestock activities contribute to substantial nitrate contamination. For this reason, the area can be considered a bench test for tuning an appropriate methodology aiming to trace the nitrate contamination in different conditions. An approach combining environmental isotopes, water quality and hydrogeological indicators was therefore used to understand the origins and attenuation mechanisms of nitrate pollution and to define the relationship between contaminant and groundwater flow dynamics through the multi-aquifer characterized by sandy (SHU), alluvial (AHU), and volcanic hydrogeological (VHU) units. Various groundwater chemical pathways were consistent with both different nitrogen sources and groundwater dynamics. Isotope composition suggests a mixed source for nitrate (organic and synthetic fertilizer), especially for the AHU and SHU groundwater. Moreover, marked heterotrophic denitrification and sulfate reduction processes were detected; although, for the contamination related to synthetic fertilizer, the attenuation was inefficient at removing NO3 - to less than the human consumption threshold of 50 mg/L. Various factors contributed to control the distribution of the redox processes, such as the availability of carbon sources (organic fertilizer and the presence of lagoon-deposited aquitards), well depth, and groundwater flow paths. The characterization of these processes supports water-resource management plans, future actions, and regulations, particularly in nitrate vulnerable zones.

Triple oxygen isotopes indicate urbanization affects sources of nitrate in wet and dry atmospheric deposition

NASA Astrophysics Data System (ADS)

Nelson, David M.; Tsunogai, Urumu; Ding, Dong; Ohyama, Takuya; Komatsu, Daisuke D.; Nakagawa, Fumiko; Noguchi, Izumi; Yamaguchi, Takashi

2018-05-01

Atmospheric nitrate deposition resulting from anthropogenic activities negatively affects human and environmental health. Identifying deposited nitrate that is produced locally vs. that originating from long-distance transport would help inform efforts to mitigate such impacts. However, distinguishing the relative transport distances of atmospheric nitrate in urban areas remains a major challenge since it may be produced locally and/or be transported from upwind regions. To address this uncertainty we assessed spatiotemporal variation in monthly weighted-average Δ17O and δ15N values of wet and dry nitrate deposition during one year at urban and rural sites along the western coast of the northern Japanese island of Hokkaido, downwind of the East Asian continent. Δ17O values of nitrate in wet deposition at the urban site mirrored those of wet and dry deposition at the rural site, ranging between ˜ +23 and +31 ‰ with higher values during winter and lower values in summer, which suggests the greater relative importance of oxidation of NO2 by O3 during winter and OH during summer. In contrast, Δ17O values of nitrate in dry deposition at the urban site were lower (+19 - +25 ‰) and displayed less distinct seasonal variation. Furthermore, the difference between δ15N values of nitrate in wet and dry nitrate deposition was, on average, 3 ‰ greater at the urban than rural site, and Δ17O and δ15N values were correlated for both forms of deposition at both sites with the exception of dry deposition at the urban site. These results suggest that, relative to nitrate in wet and dry deposition in rural environments and wet deposition in urban environments, nitrate in dry deposition in urban environments forms from relatively greater oxidation of NO by peroxy radicals and/or oxidation of NO2 by OH. Given greater concentrations of peroxy radicals and OH in cities, these results imply that dry nitrate deposition results from local NOx emissions more so than wet deposition, which is transported longer distances. These results illustrate the value of stable isotope data for distinguishing the transport distances and reaction pathways of atmospheric nitrate pollution.

Effects of melatonin on seedling growth, mineral nutrition, and nitrogen metabolism in cucumber under nitrate stress.

PubMed

Zhang, Ruimin; Sun, Yunkuo; Liu, Zeyu; Jin, Wen; Sun, Yan

2017-05-01

In China, excessive use of nitrogen fertilizers in glasshouses leads to nitrate accumulations in soil and plants, which then limits productivity. Melatonin, an evolutionarily highly conserved molecule, has a wide range of functions in plants. We analyzed the effects of melatonin pretreatment on the growth, mineral nutrition, and nitrogen metabolism in cucumber (Cucumis sativus L. "Jin You No. 1") when seedlings were exposed to nitrate stress. An application of 0.1 mmol/L melatonin significantly improved the growth of plants and reduced their susceptibility to damage due to high nitrate levels (0.6 mol/L) during the ensuing period of stress treatment. Although excess nitrate led to an increase in the concentrations of nitrogen, potassium, and calcium, as well as a decrease in levels of phosphorus and magnesium, exogenous melatonin generally had the opposite effect except for a further rise in calcium concentrations. Pretreatment also significantly reduced the accumulations of nitrate nitrogen and ammonium nitrogen and enhanced the activities of enzymes involved in nitrogen metabolism. Expression of Cs-NR and Cs-GOGAT, two genes that function in that metabolism, was greatly down-regulated when plants were exposed to 0.6 mol/L nitrate, but was up-regulated in plants that had received the 0.1 mmol/L melatonin pretreatment. Our results are the first evidence that melatonin has an important role in modulating the composition of mineral elements and nitrogen metabolism, thereby alleviating the inhibitory effect on growth normally associated with nitrate stress. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Locating Groundwater Pathways of Anthropogenic Contaminants Using a Novel Approach in Kānéohe Watershed, Óahu, Hawaíi

NASA Astrophysics Data System (ADS)

McKenzie, T.; Dulai, H.; Popp, B. N.; Whittier, R. B.

2017-12-01

We have applied a novel approach using radon, δ15N and δ18O values of nitrate, and contaminants of emerging concern (CECs) to identify groundwater pathways of anthropogenic contaminants. This approach was applied in Kānéohe watershed, located on the windward side of Óahu, which has been subject to persistent near shore water pollution. Previous research has indicated that there are strong seasonal differences between surface runoff and groundwater discharge into Kānéohe Bay. Three sub-watersheds of varying land-use (e.g. cesspool density, agriculture, urbanization) bordering Kānéohe Bay were studied. Seasonality, as well as spatial and temporal variations of groundwater discharge into streams and the bay were captured by a series of snapshot studies using a natural isotope of radon as a tracer for groundwater inflow. δ15N and δ18O values of nitrate were used as source tracking tools to determine the potential origin (e.g. wastewater, agriculture) of nitrate. These results were paired with spatial analysis of land-use and further coupled with CEC concentrations in order to evaluate how land-use relates to stream and groundwater contaminant distribution. Previously unrecognized groundwater pathways for contaminant transport were identified using radon in conjunction with CEC and stable isotopic techniques. We present results for stream and coastal water quality, focusing on nutrient and CEC fluxes across the land-ocean interface, as well as discuss the application of CECs as novel wastewater tracers.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou Jun; Huang Kaixun, E-mail: hxxzrf@mail.hust.edu.c

Accumulating evidence suggests that peroxynitrite (ONOO{sup -}) is involved in the pathogenesis of insulin resistance. In the current study, we investigated whether insulin resistance in vivo could be mediated by nitration of proteins involved in the early steps of the insulin signal transduction pathway. Exogenous peroxynitrite donated by 3-morpholinosydnonimine hydrochloride (SIN-1) induced in vivo nitration of the insulin receptor beta subunit (IRbeta), insulin receptor substrate (IRS)-1, and protein kinase B/Akt (Akt) in skeletal muscle of mice and dramatically reduced whole-body insulin sensitivity and muscle insulin signaling. Moreover, in high-fat diet (HFD)-fed insulin-resistant mice, we observed enhanced nitration of IRbeta andmore » IRS-1 in skeletal muscle, in parallel with impaired whole-body insulin sensitivity and muscle insulin signaling. Reversal of nitration of these proteins by treatment with the peroxynitrite decomposition catalyst FeTPPS yielded an improvement in whole-body insulin sensitivity and muscle insulin signaling in HFD-fed mice. Taken together, these findings provide new mechanistic insights for the involvement of peroxynitrite in the development of insulin resistance and suggest that nitration of proteins involved in the early steps of insulin signal transduction is a novel molecular mechanism of HFD-induced muscle insulin resistance.« less

Secondary formation of nitrated phenols: insights from observations during the Uintah Basin Winter Ozone Study (UBWOS) 2014

NASA Astrophysics Data System (ADS)

Yuan, B.; Liggio, J.; Wentzell, J.; Li, S.-M.; Stark, H.; Roberts, J. M.; Gilman, J.; Lerner, B.; Warneke, C.; Li, R.; Leithead, A.; Osthoff, H. D.; Wild, R.; Brown, S. S.; de Gouw, J. A.

2015-10-01

We describe the results from online measurements of nitrated phenols using a time of flight chemical ionization mass spectrometer (ToF-CIMS) with acetate as reagent ion in an oil and gas production region in January and February of 2014. Strong diurnal profiles were observed for nitrated phenols, with concentration maxima at night. Based on known markers (CH4, NOx, CO2), primary emissions of nitrated phenols were not important in this study. A box model was used to simulate secondary formation of phenol, nitrophenol (NP) and dinitrophenols (DNP). The box model results indicate that oxidation of aromatics in the gas phase can explain the observed concentrations of NP and DNP in this study. Photolysis was the most efficient loss pathway for NP in the gas phase. We show that aqueous-phase reactions and heterogeneous reactions were minor sources of nitrated phenols in our study. This study demonstrates that the emergence of new ToF-CIMS (including PTR-TOF) techniques allows for the measurement of intermediate oxygenates at low levels and these measurements improve our understanding of the evolution of primary VOCs in the atmosphere.

Secondary formation of nitrated phenols: insights from observations during the Uintah Basin Winter Ozone Study (UBWOS) 2014

NASA Astrophysics Data System (ADS)

Yuan, Bin; Liggio, John; Wentzell, Jeremy; Li, Shao-Meng; Stark, Harald; Roberts, James M.; Gilman, Jessica; Lerner, Brian; Warneke, Carsten; Li, Rui; Leithead, Amy; Osthoff, Hans D.; Wild, Robert; Brown, Steven S.; de Gouw, Joost A.

2016-02-01

We describe the results from online measurements of nitrated phenols using a time-of-flight chemical ionization mass spectrometer (ToF-CIMS) with acetate as reagent ion in an oil and gas production region in January and February of 2014. Strong diurnal profiles were observed for nitrated phenols, with concentration maxima at night. Based on known markers (CH4, NOx, CO2), primary emissions of nitrated phenols were not important in this study. A box model was used to simulate secondary formation of phenol, nitrophenol (NP), and dinitrophenols (DNP). The box model results indicate that oxidation of aromatics in the gas phase can explain the observed concentrations of NP and DNP in this study. Photolysis was the most efficient loss pathway for NP in the gas phase. We show that aqueous-phase reactions and heterogeneous reactions were minor sources of nitrated phenols in our study. This study demonstrates that the emergence of new ToF-CIMS (including PTR-TOF) techniques allows for the measurement of intermediate oxygenates at low levels and these measurements improve our understanding on the evolution of primary VOCs in the atmosphere.

Ultrasound-assisted activation of zero-valent magnesium for nitrate denitrification: identification of reaction by-products and pathways.

PubMed

Ileri, Burcu; Ayyildiz, Onder; Apaydin, Omer

2015-07-15

Zero-valent magnesium (Mg(0)) was activated by ultrasound (US) in an aim to promote its potential use in water treatment without pH control. In this context, nitrate reduction was studied at batch conditions using various doses of magnesium powder and ultrasound power. While neither ultrasound nor zero-valent magnesium alone was effective for reducing nitrate in water, their combination removed up to 90% of 50 mg/L NO3-N within 60 min. The rate of nitrate reduction by US/Mg(0) enhanced with increasing ultrasonic power and magnesium dose. Nitrogen gas (N2) and nitrite (NO2(-)) were detected as the major reduction by-products, while magnesium hydroxide Mg(OH)2 and hydroxide ions (OH(-)) were identified as the main oxidation products. The results from SEM-EDS measurements revealed that the surface oxide level decreased significantly when the samples of Mg(0) particles were exposed to ultrasonic treatment. The surface passivation of magnesium particles was successfully minimized by mechanical forces of ultrasound, which in turn paved the way to sustain the catalyst activity toward nitrate reduction. Copyright © 2015 Elsevier B.V. All rights reserved.

Nitrate and ammonia contaminations in drinking water and the affecting factors in Hailun, northeast China.

PubMed

Zhao, Xinfeng; Chen, Liding; Zhang, Haiping

2013-03-01

Drinking water samples (N = 228) from domestic tube wells (DTWs) and seven samples from public water supply wells (PWSWs) were collected and tested in Hailun, northeast China. The percentage of samples with nitrate and ammonia concentrations above the maximum acceptable concentration of nitrate, 10 mg N/L, and the maximum ensure concentration of ammonia, 1.5 mg/L, for the DTWs were significantly higher than for the PWSWs. Of the DTWs, an important observation was that the occurrence of groundwater nitrate contamination was directly related to well tube material with different joint pathways. Nitrate in seamless-tube wells was lower statistically significantly than those in multiple-section-tube wells (p < .001). Furthermore, well depth and hydrogeological setting might have some impacts on nitrogen contamination and the major sources of inorganic nitrogen contamination may be nitrogenous chemical fertilizer. Therefore, PWSWs built for all families are the best way to ensure the drinking water safety in villages. For DTWs it is necessary to use seamless tubes and to dig deep enough according to the depth of groundwater level. Improving the efficiency of chemical fertilizer use would also reduce the risk of groundwater contamination.

Response of the ubiquitous pelagic diatom Thalassiosira weissflogii to darkness and anoxia.

PubMed

Kamp, Anja; Stief, Peter; Knappe, Jan; de Beer, Dirk

2013-01-01

Thalassiosira weissflogii, an abundant, nitrate-storing, bloom-forming diatom in the world's oceans, can use its intracellular nitrate pool for dissimilatory nitrate reduction to ammonium (DNRA) after sudden shifts to darkness and anoxia, most likely as a survival mechanism. T. weissflogii cells that stored 4 mM (15)N-nitrate consumed 1.15 (±0.25) fmol NO3 (-) cell(-1) h(-1) and simultaneously produced 1.57 (±0.21) fmol (15)NH4 (+) cell(-1) h(-1) during the first 2 hours of dark/anoxic conditions. Ammonium produced from intracellular nitrate was excreted by the cells, indicating a dissimilatory rather than assimilatory pathway. Nitrite and the greenhouse gas nitrous oxide were produced at rates 2-3 orders of magnitude lower than the ammonium production rate. While DNRA activity was restricted to the first few hours of darkness and anoxia, the subsequent degradation of photopigments took weeks to months, supporting the earlier finding that diatoms resume photosynthesis even after extended exposure to darkness and anoxia. Considering the high global abundance of T. weissflogii, its production of ammonium and nitrous oxide might be of ecological importance for oceanic oxygen minimum zones and the atmosphere, respectively.

Inhibition of Radiolytic Molecular Hydrogen Formation by Quenching of Excited State Water

DOE PAGES

Horne, Gregory P.; Pimblott, Simon M.; LaVerne, Jay A.

2017-05-11

Comparison of experimental measurements of the yield of molecular hydrogen produced in the gamma radiolysis of water and aqueous nitrate solutions with predictions of a Monte Carlo track chemistry model shows that the nitrate anion scavenging of the hydrated electron, its precursor, and hydrogen atom cannot account for the observed decrease in the yield at high nitrate anion concentrations. Inclusion of the quenching of excited states of water (formed by either direct excitation or reaction of the water radical cation with the precursor to the hydrated electron) by the nitrate anion into the reaction scheme provides excellent agreement between themore » stochastic calculations and experiment demonstrating the existence of this short-lived species and its importance in water radiolysis. Energy transfer from the excited states of water to the nitrate anion producing an excited state provides an additional pathway for the production of nitrogen containing products not accounted for in traditional radiation chemistry scenarios. Such reactions are of central importance in predicting the behavior of liquors common in the reprocessing of spent nuclear fuel and the storage of highly radioactive liquid waste prior to vitrification.« less

Implementation of agronomical and geochemical modules into a 3D groundwater code for assessing nitrate storage and transport through unconfined Chalk aquifer

NASA Astrophysics Data System (ADS)

Picot-Colbeaux, Géraldine; Devau, Nicolas; Thiéry, Dominique; Pettenati, Marie; Surdyk, Nicolas; Parmentier, Marc; Amraoui, Nadia; Crastes de Paulet, François; André, Laurent

2016-04-01

Chalk aquifer is the main water resource for domestic water supply in many parts in northern France. In same basin, groundwater is frequently affected by quality problems concerning nitrates. Often close to or above the drinking water standards, nitrate concentration in groundwater is mainly due to historical agriculture practices, combined with leakage and aquifer recharge through the vadose zone. The complexity of processes occurring into such an environment leads to take into account a lot of knowledge on agronomy, geochemistry and hydrogeology in order to understand, model and predict the spatiotemporal evolution of nitrate content and provide a decision support tool for the water producers and stakeholders. To succeed in this challenge, conceptual and numerical models representing accurately the Chalk aquifer specificity need to be developed. A multidisciplinary approach is developed to simulate storage and transport from the ground surface until groundwater. This involves a new agronomic module "NITRATE" (NItrogen TRansfer for Arable soil to groundwaTEr), a soil-crop model allowing to calculate nitrogen mass balance in arable soil, and the "PHREEQC" numerical code for geochemical calculations, both coupled with the 3D transient groundwater numerical code "MARTHE". Otherwise, new development achieved on MARTHE code allows the use of dual porosity and permeability calculations needed in the fissured Chalk aquifer context. This method concerning the integration of existing multi-disciplinary tools is a real challenge to reduce the number of parameters by selecting the relevant equations and simplifying the equations without altering the signal. The robustness and the validity of these numerical developments are tested step by step with several simulations constrained by climate forcing, land use and nitrogen inputs over several decades. In the first time, simulations are performed in a 1D vertical unsaturated soil column for representing experimental nitrates vertical soil profiles (0-30m depth experimental measurements in Somme region). In the second time, this approach is used to simulate with a 3D model a drinking water catchment area in order to compared nitrate contents time series calculated and measured in the domestic water pumping well since 1995 (field in northern France - Avre Basin region). This numerical tool will help the decision-making in all activities in relation with water uses.

Relation of pathways and transit times of recharge water to nitrate concentrations using stable isotopes

USGS Publications Warehouse

Landon, M.K.; Delin, G.N.; Komor, S.C.; Regan, C.P.

2000-01-01

Oxygen and hydrogen stable isotope values of precipitation, irrigation water, soil water, and ground water were used with soil-moisture contents and water levels to estimate transit times and pathways of recharge water in the unsaturated zone of a sand and gravel aquifer. Nitrate-nitrogen (nitrate) concentrations in ground water were also measured to assess their relation to seasonal recharge. Stable isotope values indicated that recharge water usually had a transit time through the unsaturated zone of several weeks to months. However, wetting fronts usually moved through the unsaturated zone in hours to weeks. The much slower transit of isotopic signals than that of wetting fronts indicates that recharge was predominantly composed of older soil water that was displaced downward by more recent infiltrating water. Comparison of observed and simulated isotopic values from pure-piston flow and mixing-cell water and isotope mass balance models indicates that soil water isotopic values were usually highly mixed. Thus, movement of recharge water did not occur following a pure piston-flow displacement model but rather follows a hydrid model involving displacement of mixed older soil water with new infiltration water. An exception to this model occurred in a topographic depression, where movement of water along preferential flowpaths to the water table occurred within hours to days following spring thaw as result of depression-focused infiltration of snow melt. In an adjacent upland area, recharge of snow melt occurred one to two months later. Increases in nitrate concentrations at the water table during April-May 1993 and 1994 in a topographic lowland within a corn field were related to recharge of water that had infiltrated the previous summer and was displaced from the unsaturated zone by spring infiltration. Increases in nitrate concentrations also occurred during July-August 1994 in response to recharge of water that infiltrated during May-August 1994. These results indicate that the largest ground water nitrate concentrations were associated with recharge of water that infiltrated into the soil during May-August, when most nitrogen fertilizer was applied.

Nitrating reactive nitric oxygen species transform acetaminophen to 3-nitroacetaminophen.

PubMed

Lakshmi, V M; Hsu, F F; Davis, B B; Zenser, T V

2000-09-01

Nitrating reactive nitric oxygen species (RNOS) elicit many of the deleterious effects of the inflammatory response. Their high reactivity and short half-life make RNOS analysis difficult. Reaction of acetaminophen (APAP) with RNOS generated by various conditions was evaluated by HPLC. When [(14)C]APAP was incubated at pH 7.4, the same new product (3NAP) was produced by at least three separate pathways represented by the following conditions: myeloperoxidase oxidation of NO(2)(-), NO(2)Cl, and ONOO(-) or Sin-1. Diethylamine NONO and spermine NONO did not convert APAP to 3NAP. 3NAP was stable at pH 5, 7.4, or 9, and at pH 7.4 with ONOO(-), spermine NONO, Sin-1, or H(2)O(2). HOCl transformed 3NAP, which was prevented by APAP, ascorbic acid, taurine, or NO(2)(-). ONOO(-)-derived 3NAP was identified by (1)H NMR as 3-nitroacetaminophen or 3-nitro-N-acetyl-p-aminophenol, and the product mass was verified by EI/ESI mass spectrometry. Human polymorphonuclear neutrophils incubated with [(14)C]APAP and stimulated with beta-phorbol 12-myristate 13-acetate produced 3NAP in the presence of NO(2)(-). Neutrophil 3NAP formation was verified by mass spectrometry and was consistent with myeloperoxidase oxidation of NO(2)(-). Spermine NONO supported 3NAP formation by stimulated cells in the absence of NO(2)(-). Results demonstrate that 3NAP is a product of nitrating RNOS generated by at least three separate pathways and may be a biomarker for nitrating mediators of inflammation.

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

DOE PAGES

Vaccaro, Brian J.; Thorgersen, Michael P.; Lancaster, W. Andrew; ...

2015-10-09

Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library fromPseudomonas stutzeristrain RCH2 was grown under denitrifying conditions, using nitrate or nitrite asmore » an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. Finally, the dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.« less

NO homeostasis is a key regulator of early nitrate perception and root elongation in maize*

PubMed Central

Quaggiotti, Silvia

2014-01-01

Crop plant development is strongly dependent on nitrogen availability in the soil and on the efficiency of its recruitment by roots. For this reason, the understanding of the molecular events underlying root adaptation to nitrogen fluctuations is a primary goal to develop biotechnological tools for sustainable agriculture. However, knowledge about molecular responses to nitrogen availability is derived mainly from the study of model species. Nitric oxide (NO) has been recently proposed to be implicated in plant responses to environmental stresses, but its exact role in the response of plants to nutritional stress is still under evaluation. In this work, the role of NO production by maize roots after nitrate perception was investigated by focusing on the regulation of transcription of genes involved in NO homeostasis and by measuring NO production in roots. Moreover, its involvement in the root growth response to nitrate was also investigated. The results provide evidence that NO is produced by nitrate reductase as an early response to nitrate supply and that the coordinated induction of non-symbiotic haemoglobins (nsHbs) could finely regulate the NO steady state. This mechanism seems to be implicated on the modulation of the root elongation in response to nitrate perception. Moreover, an improved agar-plate system for growing maize seedlings was developed. This system, which allows localized treatments to be performed on specific root portions, gave the opportunity to discern between localized and systemic effects of nitrate supply to roots. PMID:24220653

NO homeostasis is a key regulator of early nitrate perception and root elongation in maize.

PubMed

Manoli, Alessandro; Begheldo, Maura; Genre, Andrea; Lanfranco, Luisa; Trevisan, Sara; Quaggiotti, Silvia

2014-01-01

Crop plant development is strongly dependent on nitrogen availability in the soil and on the efficiency of its recruitment by roots. For this reason, the understanding of the molecular events underlying root adaptation to nitrogen fluctuations is a primary goal to develop biotechnological tools for sustainable agriculture. However, knowledge about molecular responses to nitrogen availability is derived mainly from the study of model species. Nitric oxide (NO) has been recently proposed to be implicated in plant responses to environmental stresses, but its exact role in the response of plants to nutritional stress is still under evaluation. In this work, the role of NO production by maize roots after nitrate perception was investigated by focusing on the regulation of transcription of genes involved in NO homeostasis and by measuring NO production in roots. Moreover, its involvement in the root growth response to nitrate was also investigated. The results provide evidence that NO is produced by nitrate reductase as an early response to nitrate supply and that the coordinated induction of non-symbiotic haemoglobins (nsHbs) could finely regulate the NO steady state. This mechanism seems to be implicated on the modulation of the root elongation in response to nitrate perception. Moreover, an improved agar-plate system for growing maize seedlings was developed. This system, which allows localized treatments to be performed on specific root portions, gave the opportunity to discern between localized and systemic effects of nitrate supply to roots.

UVA irradiation of human skin vasodilates arterial vasculature and lowers blood pressure independently of nitric oxide synthase.

PubMed

Liu, Donald; Fernandez, Bernadette O; Hamilton, Alistair; Lang, Ninian N; Gallagher, Julie M C; Newby, David E; Feelisch, Martin; Weller, Richard B

2014-07-01

The incidence of hypertension and cardiovascular disease (CVD) correlates with latitude and rises in winter. The molecular basis for this remains obscure. As nitric oxide (NO) metabolites are abundant in human skin, we hypothesized that exposure to UVA may mobilize NO bioactivity into the circulation to exert beneficial cardiovascular effects independently of vitamin D. In 24 healthy volunteers, irradiation of the skin with two standard erythemal doses of UVA lowered blood pressure (BP), with concomitant decreases in circulating nitrate and rises in nitrite concentrations. Unexpectedly, acute dietary intervention aimed at modulating systemic nitrate availability had no effect on UV-induced hemodynamic changes, indicating that cardiovascular effects were not mediated via direct utilization of circulating nitrate. UVA irradiation of the forearm caused increased blood flow independently of NO synthase (NOS) activity, suggesting involvement of pre-formed cutaneous NO stores. Confocal fluorescence microscopy studies of human skin pre-labeled with the NO-imaging probe diaminofluorescein 2 diacetate revealed that UVA-induced NO release occurs in a NOS-independent, dose-dependent manner, with the majority of the light-sensitive NO pool in the upper epidermis. Collectively, our data provide mechanistic insights into an important function of the skin in modulating systemic NO bioavailability, which may account for the latitudinal and seasonal variations of BP and CVD.

The NO+O3 reaction: a triple oxygen isotope perspective on the reaction dynamics and atmospheric implications for the transfer of the ozone isotope anomaly.

PubMed

Savarino, J; Bhattacharya, S K; Morin, S; Baroni, M; Doussin, J-F

2008-05-21

Atmospheric nitrate shows a large oxygen isotope anomaly (Delta 17 O), characterized by an excess enrichment of 17 O over 18 O, similar to the ozone molecule. Modeling and observations assign this specific isotopic composition mainly to the photochemical steady state that exists in the atmosphere between ozone and nitrate precursors, namely, the nitrogen oxides (NOx=NO+NO2). However, this transfer is poorly quantified and is built on unverified assumptions about which oxygen atoms of ozone are transferred to NO(x), greatly weakening any interpretation of the nitrate oxygen isotopic composition in terms of chemical reaction pathways and the oxidation state of the atmosphere. With the aim to improve our understanding and quantify how nitrate inherits this unusual isotopic composition, we have carried out a triple isotope study of the reaction NO+O3. Using ozone intramolecular isotope distributions available in the literature, we have found that the central atom of the ozone is abstracted by NO with a probability of (8+/-5)%(+/-2 sigma) at room temperature. This result is at least qualitatively supported by dynamical reaction experiments, the non-Arrhenius behavior of the kinetic rate of this reaction, and the kinetic isotope fractionation factor. Finally, we have established the transfer function of the isotope anomaly of O3 to NO2, which is described by the linear relationship Delta 17 O(NO2)=A x Delta 17 O(O3)+B, with A=1.18+/-0.07(+/-1 sigma) and B=(6.6+/-1.5)[per thousand](+/-1 sigma). Such a relationship can be easily incorporated into models dealing with the propagation of the ozone isotope anomaly among oxygen-bearing species in the atmosphere and should help to better interpret the oxygen isotope anomaly of atmospheric nitrate in terms of its formation reaction pathways.

Benthic metabolism and nitrogen dynamics in an urbanised tidal creek: Domination of DNRA over denitrification as a nitrate reduction pathway

NASA Astrophysics Data System (ADS)

Dunn, Ryan J. K.; Robertson, David; Teasdale, Peter R.; Waltham, Nathan J.; Welsh, David T.

2013-10-01

Benthic oxygen and nutrient fluxes and nitrate reduction rates were determined seasonally under light and dark conditions at three sites in a micro-tidal creek within an urbanised catchment (Saltwater Creek, Australia). It was hypothesized that stormwater inputs of organic matter and inorganic nitrogen would stimulate rates of benthic metabolism and nutrient recycling and preferentially stimulate dissimilatory nitrate reduction to ammonium (DNRA) over denitrification as a pathway for nitrate reduction. Stormwaters greatly influenced water column dissolved inorganic nitrogen (DIN) and suspended solids concentrations with values following a large rainfall event being 5-20-fold greater than during the preceding dry period. Seasonally, maximum and minimum water column total dissolved nitrogen (TDN) and DIN concentrations occurred in the summer (wet) and winter (dry) seasons. Creek sediments were highly heterotrophic throughout the year, and strong sinks for oxygen, and large sources of dissolved organic and inorganic nitrogen during both light and dark incubations, although micro-phytobenthos (MPB) significantly decreased oxygen consumption and N-effluxes during light incubations due to photosynthetic oxygen production and photoassimilation of nutrients. Benthic denitrification rates ranged from 3.5 to 17.7 μmol N m2 h-1, denitrification efficiencies were low (<1-15%) and denitrification was a minor process compared to DNRA, which accounted for ˜75% of total nitrate reduction. Overall, due to the low denitrification efficiencies and high rates of N-regeneration, Saltwater Creek sediments would tend to increase rather than reduce dissolved nutrient loads to the downstream Gold Coast Broadwater and Moreton Bay systems. This may be especially true during wet periods when increased inputs of particulate organic nitrogen (PON) and suspended solids could respectively enhance rates of N-regeneration and decrease light availability to MPB, reducing their capacity to ameliorate N-effluxes through photoassimilation.

Enrichment of DNRA bacteria in a continuous culture

PubMed Central

van den Berg, Eveline M; van Dongen, Udo; Abbas, Ben; van Loosdrecht, Mark CM

2015-01-01

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are competing microbial nitrate-reduction processes. The occurrence of DNRA has been shown to be effected qualitatively by various parameters in the environment. A more quantitative understanding can be obtained using enrichment cultures in a laboratory reactor, yet no successful DNRA enrichment culture has been described. We showed that a stable DNRA-dominated enrichment culture can be obtained in a chemostat system. The enrichment was based on the hypothesis that nitrate limitation is the dominant factor in selecting for DNRA. First, a conventional denitrifying culture was enriched from activated sludge, with acetate and nitrate as substrates. Next, the acetate concentration in the medium was increased to obtain nitrate-limiting conditions. As a result, conversions shifted from denitrification to DNRA. In this selection of a DNRA culture, two important factors were the nitrate limitation and a relatively low dilution rate (0.026 h−1). The culture was a highly enriched population of Deltaproteobacteria most closely related to Geobacter lovleyi, based on 16S rRNA gene sequencing (97% similarity). We established a stable and reproducible cultivation method for the enrichment of DNRA bacteria in a continuously operated reactor system. This enrichment method allows to further investigate the DNRA process and address the factors for competition between DNRA and denitrification, or other N-conversion pathways. PMID:25909972

Wnt signal transduction pathways: modules, development and evolution.

PubMed

Nayak, Losiana; Bhattacharyya, Nitai P; De, Rajat K

2016-08-01

Wnt signal transduction pathway (Wnt STP) is a crucial intracellular pathway mainly due to its participation in important biological processes, functions, and diseases, i.e., embryonic development, stem-cell management, and human cancers among others. This is why Wnt STP is one of the highest researched signal transduction pathways. Study and analysis of its origin, expansion and gradual development to the present state as found in humans is one aspect of Wnt research. The pattern of development and evolution of the Wnt STP among various species is not clear till date. A phylogenetic tree created from Wnt STPs of multiple species may address this issue. In this respect, we construct a phylogenetic tree from modules of Wnt STPs of diverse species. We term it as the 'Module Tree'. A module is nothing but a self-sufficient minimally-dependent subset of the original Wnt STP. Authenticity of the module tree is tested by comparing it with the two reference trees. The module tree performs better than an alternative phylogenetic tree constructed from pathway topology of Wnt STPs. Moreover, an evolutionary emergence pattern of the Wnt gene family is created and the module tree is tallied with it to showcase the significant resemblances.

Genome Sequences for Six Rhodanobacter Strains, Isolated from Soils and the Terrestrial Subsurface, with Variable Denitrification Capabilities

PubMed Central

Green, Stefan J.; Rishishwar, Lavanya; Prakash, Om; Katz, Lee S.; Mariño-Ramírez, Leonardo; Jordan, I. King; Munk, Christine; Ivanova, Natalia; Mikhailova, Natalia; Watson, David B.; Brown, Steven D.; Palumbo, Anthony V.; Brooks, Scott C.

2012-01-01

We report the first genome sequences for six strains of Rhodanobacter species isolated from a variety of soil and subsurface environments. Three of these strains are capable of complete denitrification and three others are not. However, all six strains contain most of the genes required for the respiration of nitrate to gaseous nitrogen. The nondenitrifying members of the genus lack only the gene for nitrate reduction, the first step in the full denitrification pathway. The data suggest that the environmental role of bacteria from the genus Rhodanobacter should be reevaluated. PMID:22843592

Combined friction force microscopy and quantum chemical investigation of the tribotronic response at the propylammonium nitrate-graphite interface.

PubMed

Li, H; Atkin, R; Page, A J

2015-06-28

The energetic origins of the variation in friction with potential at the propylammonium nitrate-graphite interface are revealed using friction force microscopy (FFM) in combination with quantum chemical simulations. For boundary layer lubrication, as the FFM tip slides energy is dissipated via (1) boundary layer ions and (2) expulsion of near-surface ion layers from the space between the surface and advancing tip. Simulations reveal how changing the surface potential changes the ion composition of the boundary and near surface layer, which controls energy dissipation through both pathways, and thus the friction.

Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi-SlPH tomato line with reduced fruit acidity and higher pH.

PubMed

Barad, Shiri; Sela, Noa; Dubey, Amit K; Kumar, Dilip; Luria, Neta; Ment, Dana; Cohen, Shahar; Schaffer, Arthur A; Prusky, Dov

2017-08-04

The destructive phytopathogen Colletotrichum gloeosporioides causes anthracnose disease in fruit. During host colonization, it secretes ammonia, which modulates environmental pH and regulates gene expression, contributing to pathogenicity. However, the effect of host pH environment on pathogen colonization has never been evaluated. Development of an isogenic tomato line with reduced expression of the gene for acidity, SlPH (Solyc10g074790.1.1), enabled this analysis. Total RNA from C. gloeosporioides colonizing wild-type (WT) and RNAi-SlPH tomato lines was sequenced and gene-expression patterns were compared. C. gloeosporioides inoculation of the RNAi-SlPH line with pH 5.96 compared to the WT line with pH 4.2 showed 30% higher colonization and reduced ammonia accumulation. Large-scale comparative transcriptome analysis of the colonized RNAi-SlPH and WT lines revealed their different mechanisms of colonization-pattern activation: whereas the WT tomato upregulated 13-LOX (lipoxygenase), jasmonic acid and glutamate biosynthesis pathways, it downregulated processes related to chlorogenic acid biosynthesis II, phenylpropanoid biosynthesis and hydroxycinnamic acid tyramine amide biosynthesis; the RNAi-SlPH line upregulated UDP-D-galacturonate biosynthesis I and free phenylpropanoid acid biosynthesis, but mainly downregulated pathways related to sugar metabolism, such as the glyoxylate cycle and L-arabinose degradation II. Comparison of C. gloeosporioides gene expression during colonization of the WT and RNAi-SlPH lines showed that the fungus upregulates ammonia and nitrogen transport and the gamma-aminobutyric acid metabolic process during colonization of the WT, while on the RNAi-SlPH tomato, it mainly upregulates the nitrate metabolic process. Modulation of tomato acidity and pH had significant phenotypic effects on C. gloeosporioides development. The fungus showed increased colonization on the neutral RNAi-SlPH fruit, and limited colonization on the WT acidic fruit. The change in environmental pH resulted in different defense responses for the two tomato lines. Interestingly, the WT line showed upregulation of jasmonate pathways and glutamate accumulation, supporting the reduced symptom development and increased ammonia accumulation, as the fungus might utilize glutamate to accumulate ammonia and increase environmental pH for better expression of pathogenicity factors. This was not found in the RNAi-SlPH line which downregulated sugar metabolism and upregulated the phenylpropanoid pathway, leading to host susceptibility.

Updated aerosol module and its application to simulate secondary organic aerosols during IMPACT campaign May 2008

NASA Astrophysics Data System (ADS)

Li, Y. P.; Elbern, H.; Lu, K. D.; Friese, E.; Kiendler-Scharr, A.; Mentel, Th. F.; Wang, X. S.; Wahner, A.; Zhang, Y. H.

2013-03-01

The formation of Secondary organic aerosol (SOA) was simulated with the Secondary ORGanic Aerosol Model (SORGAM) by a classical gas-particle partitioning concept, using the two-product model approach, which is widely used in chemical transport models. In this study, we extensively updated SORGAM including three major modifications: firstly, we derived temperature dependence functions of the SOA yields for aromatics and biogenic VOCs, based on recent chamber studies within a sophisticated mathematic optimization framework; secondly, we implemented the SOA formation pathways from photo oxidation (OH initiated) of isoprene; thirdly, we implemented the SOA formation channel from NO3-initiated oxidation of reactive biogenic hydrocarbons (isoprene and monoterpenes). The temperature dependence functions of the SOA yields were validated against available chamber experiments. Moreover, the whole updated SORGAM module was validated against ambient SOA observations represented by the summed oxygenated organic aerosol (OOA) concentrations abstracted from Aerosol Mass Spectrometer (AMS) measurements at a rural site near Rotterdam, the Netherlands, performed during the IMPACT campaign in May 2008. In this case, we embedded both the original and the updated SORGAM module into the EURopean Air pollution and Dispersion-Inverse Model (EURAD-IM), which showed general good agreements with the observed meteorological parameters and several secondary products such as O3, sulfate and nitrate. With the updated SORGAM module, the EURAD-IM model also captured the observed SOA concentrations reasonably well especially those during nighttime. In contrast, the EURAD-IM model before update underestimated the observations by a factor of up to 5. The large improvements of the modeled SOA concentrations by updated SORGAM were attributed to the mentioned three modifications. Embedding the temperature dependence functions of the SOA yields, including the new pathways from isoprene photo oxidations, and switching on the SOA formation from NO3 initiated biogenic VOCs oxidations contributed to this enhancement by 10%, 22% and 47%, respectively. However, the EURAD-IM model with updated SORGAM still clearly underestimated the afternoon SOA observations up to a factor of two. More work such as to improve the simulated OH concentrations under high VOCs and low NOx concentrations, further including the SOA formation from semi-volatile organic compounds, the correct aging process of aerosols, oligomerization process and the influence on the biogenic SOA by the anthropogenic SOA, are still required to fill the gap.

Bioinformatics analysis reveals biophysical and evolutionary insights into the 3-nitrotyrosine post-translational modification in the human proteome

PubMed Central

Ng, John Y.; Boelen, Lies; Wong, Jason W. H.

2013-01-01

Protein 3-nitrotyrosine is a post-translational modification that commonly arises from the nitration of tyrosine residues. This modification has been detected under a wide range of pathological conditions and has been shown to alter protein function. Whether 3-nitrotyrosine is important in normal cellular processes or is likely to affect specific biological pathways remains unclear. Using GPS-YNO2, a recently described 3-nitrotyrosine prediction algorithm, a set of predictions for nitrated residues in the human proteome was generated. In total, 9.27 per cent of the proteome was predicted to be nitratable (27 922/301 091). By matching the predictions against a set of curated and experimentally validated 3-nitrotyrosine sites in human proteins, it was found that GPS-YNO2 is able to predict 73.1 per cent (404/553) of these sites. Furthermore, of these sites, 42 have been shown to be nitrated endogenously, with 85.7 per cent (36/42) of these predicted to be nitrated. This demonstrates the feasibility of using the predicted dataset for a whole proteome analysis. A comprehensive bioinformatics analysis was subsequently performed on predicted and all experimentally validated nitrated tyrosine. This found mild but specific biophysical constraints that affect the susceptibility of tyrosine to nitration, and these may play a role in increasing the likelihood of 3-nitrotyrosine to affect processes, including phosphorylation and DNA binding. Furthermore, examining the evolutionary conservation of predicted 3-nitrotyrosine showed that, relative to non-nitrated tyrosine residues, 3-nitrotyrosine residues are generally less conserved. This suggests that, at least in the majority of cases, 3-nitrotyrosine is likely to have a deleterious effect on protein function and less likely to be important in normal cellular function. PMID:23389939

Synoptic Sampling to Determine Distributed Groundwater-Surface Water Nitrate Loading and Removal Potential Along a Lowland River

NASA Astrophysics Data System (ADS)

Pai, Henry; Villamizar, Sandra R.; Harmon, Thomas C.

2017-11-01

Delineating pollutant reactive transport pathways that connect local land use patterns to surface water is an important goal. This work illustrates high-resolution river mapping of salinity or specific conductance (SC) and nitrate (NO3-) as a potential part of achieving this goal. We observed longitudinal river SC and nitrate distributions using high-resolution synoptic in situ sensing along the lower Merced River (38 river km) in Central California (USA) from 2010 to 2012. We calibrated a distributed groundwater-surface water (GW-SW) discharge model for a conservative solute using 13 synoptic SC sampling events at flows ranging from 1.3 to 31.6 m3 s-1. Nitrogen loads ranged from 0.3 to 1.6 kg N d-1 and were greater following an extended high flow period during a wet winter. Applying the distributed GW-SW discharge estimates to a simplistic reactive nitrate transport model, the model reproduced observed river nitrate distribution well (RRMSE = 5-21%), with dimensionless watershed-averaged nitrate removal (kt) ranging from 0 to 0.43. Estimates were uncertain due to GW nitrate data variability, but the resulting range was consistent with prior removal estimates. At the segment scale, estimated GW-SW nitrate loading ranged from 0 to 17 g NO3- s-1 km-1. Local loading peaked near the middle of the study reach, a location that coincides with a shallow clay lens and with confined animal feed operations in close proximity to the river. Overall, the results demonstrate the potential for high-resolution synoptic monitoring to support GW-SW modeling efforts aimed at understanding and managing nonpoint source pollution.

Reverse Methanogenesis and Respiration in Methanotrophic Archaea

PubMed Central

Koehorst, Jasper J.; Jetten, Mike S. M.; Stams, Alfons J. M.

2017-01-01

Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types. PMID:28154498

Role of Oxidative Stress in the Induction of Metallothionein-2A and Heme Oxygenase-1 Gene Expression by the Antineoplastic Agent Gallium Nitrate in Human Lymphoma Cells

PubMed Central

Yang, Meiying; Chitambar, Christopher R.

2008-01-01

The mechanisms of action of gallium nitrate, an antineoplastic drug, are only partly understood. Using a DNA microarray to examine genes induced by gallium nitrate in CCRF-CEM cells, we found that gallium increased metallothionein-2A (MT2A) and heme oxygenase-1 (HO-1) gene expression and altered the levels of other stress-related genes. MT2A and HO-1 were increased after 6 and 16 h of incubation with gallium nitrate. An increase in oxidative stress, evidenced by a decrease in cellular GSH and GSH/GSSG ratio, and an increase in dichlorodihydrofluoroscein (DCF) fluorescence, was seen after 1 – 4 h incubation of cells with gallium nitrate. DCF fluorescence was blocked by the mitochondria-targeted antioxidant mitoquinone. N-acetyl-L-cysteine blocked gallium-induced MT2A and HO-1 expression and increased gallium’s cytotoxicity. Studies with a zinc-specific fluoroprobe suggested that gallium produced an expansion of an intracellular labile zinc pool, suggesting an action of gallium on zinc homeostasis. Gallium nitrate increased the phosphorylation of p38 mitogen-activated protein kinase and activated Nrf-2, a regulator of HO-1 gene transcription. Gallium-induced Nrf-2 activation and HO-1 expression were diminished by a p38 MAP kinase inhibitor. We conclude that gallium nitrate induces cellular oxidative stress as an early event which then triggers the expression of HO-1 and MT2A through different pathways. PMID:18586083

Fate and Transformation of Nitrate in the Unsaturated Zone of Two Soil Distributed Areas in the Huaihe River Basin

NASA Astrophysics Data System (ADS)

Li, R.; Ruan, X.; Liu, C. Q.

2016-12-01

Unsaturated zone (UZ) is the most important passageway for nitrogen pollutants transporting from land surface to groundwater, and can be a hotspot for nitrogen transformation due to the transitional redox conditions. Study on the fate of nitrogen in UZ has significant implication for revealing the causes of groundwater nitrate pollution. In this study, we examined two types of UZs in Fluvo-aquic soil (FAS) and lime concretion black soil (LCBS) distributed areas which account for 33.57% and 13.31% of the arable land in the Huaihe River Basin, and determined the isotopic compositions (δ15N and δ18O) of nitrate in soil water extracts of both UZs to reveal the potential nitrification and denitrification processes. The similarity of measured δ18O-NO3- values in both upper UZs to the stoichiometrically calculated δ18O-NO3- value (3.4‰, according to the known nitrification pathway) confirms that the end product of nitrification process had a major contribution to the nitrate pool. Compared to those in the UZ of FAS area, the enrichment of heavy isotopes in nitrate coincided with the decrease of NO3-/Cl- molar ratios in the lower UZ of LCBS area, indicating the occurrence of denitrification therein. Further quantitative analyses showed that as high as 90% of the total nitrate was eliminated via denitrification based upon Rayleigh equation. Our results imply that groundwater in the FAS distributed areas may be more vulnerable to nitrate pollution induced by agricultural activities.

Ookinete-induced midgut peroxidases detonate the time bomb in anopheline mosquitoes.

PubMed

Kumar, Sanjeev; Barillas-Mury, Carolina

2005-07-01

Previous analysis of the temporal-spatial relationship between ookinete migration and the cellular localization of genes mediating midgut immune defense responses suggested that, in order to survive, parasites must complete invasion before toxic chemicals ("a bomb") are generated by the invaded cell. Recent studies indicate that ookinete invasion induces tyrosine nitration as a two-step reaction, in which NOS induction is followed by a localized increase in peroxidase activity. Peroxidases utilize nitrite and hydrogen peroxide as substrates, and detonate the time bomb by generating reactive nitrogen intermediates, such as nitrogen dioxide, which mediate nitration. There is evidence that peroxidases also mediate antimicrobial responses to bacteria, fungi and parasites in a broad range of biological systems including humans and plants. Defense reactions that generate toxic chemicals are also potentially harmful to the host mounting the response and often results in apoptosis. The two-step nitration pathway is probably an ancient response, as it has also been described in vertebrate leukocytes and probably evolved as a mechanism to circumscribe the toxic products generated during defense responses involving protein nitration.

Changes in nitric oxide release in vivo in response to vasoactive substances.

PubMed Central

Nava, E.; Wiklund, N. P.; Salazar, F. J.

1996-01-01

1. Changes in the release of nitric oxide (NO) in vivo were studied in rats following the administration of endothelium-dependent and -independent vasodilators as well as the NO synthesis inhibitor, NG-nitro-L-arginine methyl ester (L-NAME). NO production was assessed by measuring variations of nitrate in plasma by capillary ion analysis. 2. Intravenous administration of the endothelium-dependent vasodilators, bradykinin (2 and 10 micrograms kg-1 min-1) or substance P (0.3-3 micrograms kg-1 min-1) caused a transient dose-dependent hypotension followed by an increase in plasma nitrate concentration (maximal increments: 33 +/- 5% and 38 +/- 6%, for bradykinin and substance P, respectively). Prior administration of L-NAME (10 mg kg-1 min-1) inhibited the hypotension and increase in plasma nitrate caused by these substances. Intravenous administration of sodium nitrate (200 micrograms kg-1) also produced a transitory elevation in plasma nitrate which was similar in magnitude as that caused by the vasodilators. A rapid and transitory increment in plasma nitrate was observed after i.v. administration of authentic NO (400 micrograms kg-1). 3. Rats receiving the endothelium-dependent vasodilators, prostacyclin (0.6 micrograms kg-1 min-1) or adenosine (3 mg kg-1 min-1) intravenously showed a drop in blood pressure paralleled by a decrease in plasma nitrate (maximal decreases: 34 +/- 5% and 24 +/- 4%, for prostacyclin and adenosine, respectively). A similar effect on the plasmatic concentration of nitrate was observed when L-NAME (10 mg kg-1 min-1, i.v.) was administered to the animals. 4. This study demonstrates that (i) changes in plasma nitrate can be detected in vivo after stimulation or inhibition of NO synthase, (ii) an increased production of NO, measured as plasma nitrate, is related to the hypotension caused by bradykinin and substance P and (iii) a diminished concentration of plasmatic nitrate is associated to the hypotension induced by adenosine or prostacyclin (endothelium-independent vasodilators), suggesting that the L-arginine: NO pathway is capable of rapid down-regulation in response to a fall in blood pressure. PMID:8937725

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater

PubMed Central

Applegate, Olin; Li, Xunde; Kliegman, Joseph I.; Langelier, Charles; Atwill, Edward R.; Harter, Thomas; DeRisi, Joseph L.

2017-01-01

Background Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. Methods On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells) and 100 m (one well) below ground surface (bgs) as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community. Results Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR), the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN) and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK) superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems. Conclusions The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite biosynthetic capacity suggest incomplete remediation and the potential for novel pharmacologically active compounds. PMID:28384184

Fractionation of Hydrogen Isotopes by Sulfate- and Nitrate-Reducing Bacteria.

PubMed

Osburn, Magdalena R; Dawson, Katherine S; Fogel, Marilyn L; Sessions, Alex L

2016-01-01

Hydrogen atoms from water and food are incorporated into biomass during cellular metabolism and biosynthesis, fractionating the isotopes of hydrogen-protium and deuterium-that are recorded in biomolecules. While these fractionations are often relatively constant in plants, large variations in the magnitude of fractionation are observed for many heterotrophic microbes utilizing different central metabolic pathways. The correlation between metabolism and lipid δ(2)H provides a potential basis for reconstructing environmental and ecological parameters, but the calibration dataset has thus far been limited mainly to aerobes. Here we report on the hydrogen isotopic fractionations of lipids produced by nitrate-respiring and sulfate-reducing bacteria. We observe only small differences in fractionation between oxygen- and nitrate-respiring growth conditions, with a typical pattern of variation between substrates that is broadly consistent with previously described trends. In contrast, fractionation by sulfate-reducing bacteria does not vary significantly between different substrates, even when autotrophic and heterotrophic growth conditions are compared. This result is in marked contrast to previously published observations and has significant implications for the interpretation of environmental hydrogen isotope data. We evaluate these trends in light of metabolic gene content of each strain, growth rate, and potential flux and reservoir-size effects of cellular hydrogen, but find no single variable that can account for the differences between nitrate- and sulfate-respiring bacteria. The emerging picture of bacterial hydrogen isotope fractionation is therefore more complex than the simple correspondence between δ(2)H and metabolic pathway previously understood from aerobes. Despite the complexity, the large signals and rich variability of observed lipid δ(2)H suggest much potential as an environmental recorder of metabolism.

Evolutionary processes and sources of high-nitrate haze episodes over Beijing, Spring.

PubMed

Yang, Ting; Sun, Yele; Zhang, Wei; Wang, Zifa; Liu, Xingang; Fu, Pingqing; Wang, Xiquan

2017-04-01

Rare and consecutive high-nitrate haze pollution episodes were observed in Beijing in spring 2012. We present detailed characterization of the sources and evolutionary mechanisms of this haze pollution, and focus on an episode that occurred between 15 and 26 April. Submicron aerosol species were found to be substantially elevated during haze episodes, and nitrates showed the largest increase and occupation (average: 32.2%) in non-refractory submicron particles (NR-PM 1 ), which did not occur in other seasons as previously reported. The haze episode (HE) was divided into three sub-episodes, HEa, HEb, and HEc. During HEa and HEc, a shallow boundary layer, stagnant meteorological conditions, and high humidity favored the formation of high-nitrate concentrations, which were mainly produced by three different processes - daytime photochemical production, gas-particle partitioning, and nighttime heterogeneous reactions - and the decline in visibility was mainly induced by NR-PM 1. However, unlike HEa and HEc, during HEb, the contribution of high nitrates was partly from the transport of haze from the southeast of Beijing - the transport pathway was observed at ~800-1000m by aerosol Lidar - and the decline in visibility during HEb was primarily caused by PM 2.5 . Our results provide useful information for air quality improvement strategies in Beijing during Spring. Copyright © 2016. Published by Elsevier B.V.

Acid-catalyzed oxidation of 2,4-dichlorophenoxyacetic acid by ammonium nitrate in aqueous solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leavitt, D.D.; Abraham, M.A.

1990-04-01

2,4-Dichlorophenoxyacetic acid (2,4-D) was oxidized to CO{sub 2} and water by homogeneous, liquid-phase reaction with ammonium nitrate at temperatures between 250 and 450{degree}F and pressures below 100 psi. N{sub 2} and N{sub 2}O were produced from the thermal decomposition of the ammonium nitrate oxidant. An unexpected maximum in conversion was observed at an intermediate reaction temperature, which was consistent with rapid thermal decomposition of the NH{sub 4}NO{sub 3} oxidant. Postulated reaction pathways consisting of simultaneous oxidation of 2,4-D and decomposition of the oxidant allowed estimation of kinetic constants from best-fit analysis of the data. The proposed reaction model provided amore » mathematical description of 2,4-D conversion, which allowed extrapolation of the results to reaction conditions and reactor configurations that were not experimentally investigated.« less

Predicting nitrate discharge dynamics in mesoscale catchments using the lumped StreamGEM model and Bayesian parameter inference

NASA Astrophysics Data System (ADS)

Woodward, Simon James Roy; Wöhling, Thomas; Rode, Michael; Stenger, Roland

2017-09-01

The common practice of infrequent (e.g., monthly) stream water quality sampling for state of the environment monitoring may, when combined with high resolution stream flow data, provide sufficient information to accurately characterise the dominant nutrient transfer pathways and predict annual catchment yields. In the proposed approach, we use the spatially lumped catchment model StreamGEM to predict daily stream flow and nitrate concentration (mg L-1 NO3-N) in four contrasting mesoscale headwater catchments based on four years of daily rainfall, potential evapotranspiration, and stream flow measurements, and monthly or daily nitrate concentrations. Posterior model parameter distributions were estimated using the Markov Chain Monte Carlo sampling code DREAMZS and a log-likelihood function assuming heteroscedastic, t-distributed residuals. Despite high uncertainty in some model parameters, the flow and nitrate calibration data was well reproduced across all catchments (Nash-Sutcliffe efficiency against Log transformed data, NSL, in the range 0.62-0.83 for daily flow and 0.17-0.88 for nitrate concentration). The slight increase in the size of the residuals for a separate validation period was considered acceptable (NSL in the range 0.60-0.89 for daily flow and 0.10-0.74 for nitrate concentration, excluding one data set with limited validation data). Proportions of flow and nitrate discharge attributed to near-surface, fast seasonal groundwater and slow deeper groundwater were consistent with expectations based on catchment geology. The results for the Weida Stream in Thuringia, Germany, using monthly as opposed to daily nitrate data were, for all intents and purposes, identical, suggesting that four years of monthly nitrate sampling provides sufficient information for calibration of the StreamGEM model and prediction of catchment dynamics. This study highlights the remarkable effectiveness of process based, spatially lumped modelling with commonly available monthly stream sample data, to elucidate high resolution catchment function, when appropriate calibration methods are used that correctly handle the inherent uncertainties.

Abiotic mechanism for the formation of atmospheric nitrous oxide from ammonium nitrate.

PubMed

Rubasinghege, Gayan; Spak, Scott N; Stanier, Charles O; Carmichael, Gregory R; Grassian, Vicki H

2011-04-01

Nitrous oxide (N2O) is an important greenhouse gas and a primary cause of stratospheric ozone destruction. Despite its importance, there remain missing sources in the N2O budget. Here we report the formation of atmospheric nitrous oxide from the decomposition of ammonium nitrate via an abiotic mechanism that is favorable in the presence of light, relative humidity and a surface. This source of N2O is not currently accounted for in the global N2O budget. Annual production of N2O from atmospheric aerosols and surface fertilizer application over the continental United States from this abiotic pathway is estimated from results of an annual chemical transport simulation with the Community Multiscale Air Quality model (CMAQ). This pathway is projected to produce 9.3(+0.7/-5.3) Gg N2O annually over North America. N2O production by this mechanism is expected globally from both megacities and agricultural areas and may become more important under future projected changes in anthropogenic emissions.

Redundancy and modularity in membrane-associated dissimilatory nitrate reduction in Bacillus

PubMed Central

Heylen, Kim; Keltjens, Jan

2012-01-01

The genomes of two phenotypically denitrifying type strains of the genus Bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed. Results suggest that denitrification proceeds in the periplasmic space and in an analogous fashion as in Gram-negative organisms, yet with the participation of proteins that tend to be membrane-bound or membrane-associated. A considerable degree of functional redundancy was observed with marked differences between B. azotoformans LMG 9581T and B. bataviensis LMG 21833T. In addition to the already characterized menaquinol/cyt c-dependent nitric oxide reductase (Suharti et al., 2001, 2004) of which the encoding genes could be identified now, evidence for another novel nitric oxide reductase (NOR) was found. Also, our analyses confirm earlier findings on branched electron transfer with both menaquinol and cytochrome c as reductants. Quite unexpectedly, both bacilli have the disposal of two parallel pathways for nitrite reduction enabling a life style as a denitrifier and as an ammonifying bacterium. PMID:23087684

Thermal decomposition pathway of undoped and doped zinc layered gallate nanohybrid with Fe 3+, Co 2+ and Ni 2+ to produce mesoporous and high pore volume carbon material

NASA Astrophysics Data System (ADS)

Ghotbi, Mohammad Yeganeh; bin Hussein, Mohd Zobir; Yahaya, Asmah Hj; Abd Rahman, Mohd Zaki

2009-12-01

A series of brucite-like materials, undoped and doped zinc layered hydroxide nitrate with 2% (molar) Fe 3+, Co 2+ and Ni 2+ were synthesized. Organic-inorganic nanohybrid material with gallate anion as a guest, and zinc hydroxide nitrate, as an inorganic layered host was prepared by the ion-exchange method. The nanohybrid materials were heat-treated at various temperatures, 400-700 °C. X-ray diffraction, thermal analysis and also Fourier transform infrared results showed that incorporation of the doping agents within the zinc layered hydroxide salt layers has enhanced the heat-resistivity of the nanohybrid materials in the thermal decomposition pathway. Porous carbon materials can be obtained from the heat-treating the nanohybrids at 600 and 700 °C. Calcination of the nanohybrids at 700 °C under nitrogen atmosphere produces mesoporous and high pore volume carbon materials.

A Multidisciplinary Self-Directed Learning Module Improves Knowledge of a Quality Improvement Instrument: The HEART Pathway.

PubMed

Hartman, Nicholas D; Harper, Erin N; Leppert, Lauren M; Browning, Brittany M; Askew, Kim; Manthey, David E; Mahler, Simon A

We created and tested an educational intervention to support implementation of an institution wide QI project (the HEART Pathway) designed to improve care for patients with acute chest pain. Although online learning modules have been shown effective in imparting knowledge regarding QI projects, it is unknown whether these modules are effective across specialties and healthcare professions. Participants, including nurses, advanced practice clinicians, house staff and attending physicians (N = 486), were enrolled into an online, self-directed learning course exploring the key concepts of the HEART Pathway. The module was completed by 97% of enrollees (469/486) and 90% passed on the first attempt (422/469). Out of 469 learners, 323 completed the pretest, learning module and posttest in the correct order. Mean test scores across learners improved significantly from 74% to 89% from the pretest to the posttest. Following the intervention, the HEART Pathway was used for 88% of patients presenting to our institution with acute chest pain. Our data demonstrate that this online, self-directed learning module can improve knowledge of the HEART Pathway across specialties-paving the way for more efficient and informed care for acute chest pain patients.

Mesophilic, Circumneutral Anaerobic Iron Oxidation as a Remediation Mechanism for Radionuclides, Nitrate and Perchlorate

NASA Astrophysics Data System (ADS)

Bose, S.; Thrash, J. C.; Coates, J. D.

2008-12-01

Iron oxidation is a novel anaerobic metabolism where microorganisms obtain reducing equivalents from the oxidization of Fe(II) and assimilate carbon from organic carbon compounds or CO2. Recent evidence indicates that in combination with the activity of dissimilatory Fe(III)-reducing bacteria, anaerobic microbial Fe(II) oxidation can also contribute to the global iron redox cycle. Studies have also proved that Fe(II)- oxidation is ubiquitous in diverse environments and produce a broad range of insoluble iron forms as end products. These biogenic Fe(III)-oxides and mixed valence Fe minerals have a very high adsorption capacity of heavy metals and radionuclides. Adsorption and immobilization by these biogenic Fe phases produced at circumneutral pH, is now considered a very effective mode of remediation of radionuclides like Uranium, especially under variable redox conditions. By coupling soluble and insoluble Fe(II) oxidation with nitrate and perchlorate as terminal electron acceptors in-situ, anaerobic Fe-oxidation can also be used for environmental cleanup of Fe through Fe-mineral precipitation, as well as nitrate and perchlorate through reduction. Coupling of Fe as the sole electron and energy source to the reduction of perchlorate or nitrate boosts the metabolism without building up biomass hence also taking care of biofouling. To understand the mechanisms by which microorganisms can grow at circumneutral pH by mesophilic, anaerobic iron oxidation and the ability of microorganisms to reduce nitrate and perchlorate coupled to iron oxidation recent work in our lab involved the physiological characterization of Dechlorospirillum strain VDY which was capable of anaerobic iron-oxidation with either nitrate or perchlorate serving as terminal electron acceptor. Under non-growth conditions, VDY oxidized 3mM Fe(II) coupled to nitrate reduction, and 2mM Fe(II) coupled to perchlorate reduction, in 24 hours. It contained a copy of the RuBisCO cbbM subunit gene which was differentially regulated. With perchlorate as the sole terminal electron acceptor, cbbM was expressed under autotrophic growth with hydrogen as the electron donor but not during heterotrophic growth on acetate, indicating a putative carbon-fixation pathway. Similarly, Ferrutens uranioxidens strain 2002 was also capable of autotrophic growth during nitrate-dependent iron oxidation, although the carbon fixation pathway has yet to be identified. Anoxic XPRD analysis of the biogenic end products of nitrate-dependent Fe(II) oxidation by Diaphorobacter sp. strain TPSY and strain 2002 indicated the gradual appearance of green rust (GR II) with cacoxenite and lepidocrocite from the precursor vivianite over 81 days. SEM and TEM showed the presence of hexagonal plate like crystals surrounding the bacterial cells whose morphology closely resembled GR II, indicating a very low redox potential and a weakly acidic to weakly basic pH. Mixotrophic growth incubations of strain TPSY with 1, 5 and 10 mM Fe(II) showed markedly different end products. The identity of the mineral phases and the reason behind this difference is currently under investigation.

Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network.

PubMed

Qin, Tingting; Matmati, Nabil; Tsoi, Lam C; Mohanty, Bidyut K; Gao, Nan; Tang, Jijun; Lawson, Andrew B; Hannun, Yusuf A; Zheng, W Jim

2014-10-01

To enhance our knowledge regarding biological pathway regulation, we took an integrated approach, using the biomedical literature, ontologies, network analyses and experimental investigation to infer novel genes that could modulate biological pathways. We first constructed a novel gene network via a pairwise comparison of all yeast genes' Ontology Fingerprints--a set of Gene Ontology terms overrepresented in the PubMed abstracts linked to a gene along with those terms' corresponding enrichment P-values. The network was further refined using a Bayesian hierarchical model to identify novel genes that could potentially influence the pathway activities. We applied this method to the sphingolipid pathway in yeast and found that many top-ranked genes indeed displayed altered sphingolipid pathway functions, initially measured by their sensitivity to myriocin, an inhibitor of de novo sphingolipid biosynthesis. Further experiments confirmed the modulation of the sphingolipid pathway by one of these genes, PFA4, encoding a palmitoyl transferase. Comparative analysis showed that few of these novel genes could be discovered by other existing methods. Our novel gene network provides a unique and comprehensive resource to study pathway modulations and systems biology in general. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network

PubMed Central

Qin, Tingting; Matmati, Nabil; Tsoi, Lam C.; Mohanty, Bidyut K.; Gao, Nan; Tang, Jijun; Lawson, Andrew B.; Hannun, Yusuf A.; Zheng, W. Jim

2014-01-01

To enhance our knowledge regarding biological pathway regulation, we took an integrated approach, using the biomedical literature, ontologies, network analyses and experimental investigation to infer novel genes that could modulate biological pathways. We first constructed a novel gene network via a pairwise comparison of all yeast genes’ Ontology Fingerprints—a set of Gene Ontology terms overrepresented in the PubMed abstracts linked to a gene along with those terms’ corresponding enrichment P-values. The network was further refined using a Bayesian hierarchical model to identify novel genes that could potentially influence the pathway activities. We applied this method to the sphingolipid pathway in yeast and found that many top-ranked genes indeed displayed altered sphingolipid pathway functions, initially measured by their sensitivity to myriocin, an inhibitor of de novo sphingolipid biosynthesis. Further experiments confirmed the modulation of the sphingolipid pathway by one of these genes, PFA4, encoding a palmitoyl transferase. Comparative analysis showed that few of these novel genes could be discovered by other existing methods. Our novel gene network provides a unique and comprehensive resource to study pathway modulations and systems biology in general. PMID:25063300

Nickel (II) nitrate hexahydrate triggered canine neutrophil extracellular traps release in vitro.

PubMed

Wei, Zhengkai; Zhang, Xu; Wang, Yanan; Wang, Jingjing; Fu, Yunhe; Yang, Zhengtao

2018-05-30

Nickel (II) nitrate hexahydrate (Ni) is a common heavy metal material in battery manufacturing, electroplating alloy parts and ceramic staining, therefore we frequently contact with Ni-related products in daily life. In this study, we aimed to investigate the effects of Ni on neutrophils extracellular traps (NETs) release by canine polymorphonuclear neutrophils (PMNs). The structure of Ni-induced NETs was observed by fluorescence confocal microscopy. Ni-triggered NETs release was quantified by Pico Green ® and fluorescence microplate reader. In addition, the inhibitors of NADPH oxidase, ERK1/2-, p38 - signaling pathways were used for preliminary inquiry into the potential mechanism of this process. The results showed that Ni markedly triggered the formation of NETs-like structures, and these structures were mainly consisted of DNA decorated with NE and MPO. Furthermore, quantification experiments showed that Ni significantly increased NETs formation compared to control groups. These results forcefully confirmed that nickel nitrate possesses the ability to induce NETs formation. However, inhibiting the NADPH oxidase, ERK1/2- and p38 MAPK-signaling pathways did not significantly change the quantitation of Ni-induced NETs release. To our knowledge, this study is the first report of Ni-triggered NETs release in vitro, which might provide an entirely new mechanism of several diseases and health issues induced by nickel overexposure. Copyright © 2018. Published by Elsevier Ltd.

Biochemical Mechanisms and Microorganisms Involved in Anaerobic Testosterone Metabolism in Estuarine Sediments

PubMed Central

Shih, Chao-Jen; Chen, Yi-Lung; Wang, Chia-Hsiang; Wei, Sean T.-S.; Lin, I-Ting; Ismail, Wael A.; Chiang, Yin-Ru

2017-01-01

Current knowledge on the biochemical mechanisms underlying microbial steroid metabolism in anaerobic ecosystems is extremely limited. Sulfate, nitrate, and iron [Fe (III)] are common electron acceptors for anaerobes in estuarine sediments. Here, we investigated anaerobic testosterone metabolism in anaerobic sediments collected from the estuary of Tamsui River, Taiwan. The anaerobic sediment samples were spiked with testosterone (1 mM) and individual electron acceptors (10 mM), including nitrate, Fe3+, and sulfate. The analysis of androgen metabolites indicated that testosterone biodegradation under denitrifying conditions proceeds through the 2,3-seco pathway, whereas testosterone biodegradation under iron-reducing conditions may proceed through an unidentified alternative pathway. Metagenomic analysis and PCR-based functional assays suggested that Thauera spp. were the major testosterone degraders in estuarine sediment samples incubated with testosterone and nitrate. Thauera sp. strain GDN1, a testosterone-degrading betaproteobacterium, was isolated from the denitrifying sediment sample. This strain tolerates a broad range of salinity (0–30 ppt). Although testosterone biodegradation did not occur under sulfate-reducing conditions, we observed the anaerobic biotransformation of testosterone to estrogens in some testosterone-spiked sediment samples. This is unprecedented since biotransformation of androgens to estrogens is known to occur only under oxic conditions. Our metagenomic analysis suggested that Clostridium spp. might play a role in this anaerobic biotransformation. These results expand our understanding of microbial metabolism of steroids under strictly anoxic conditions. PMID:28848528

Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation.

PubMed

Jamieson, James; Prommer, Henning; Kaksonen, Anna H; Sun, Jing; Siade, Adam J; Yusov, Anna; Bostick, Benjamin

2018-05-15

Microbially driven nitrate-dependent iron (Fe) oxidation (NDFO) in subsurface environments has been intensively studied. However, the extent to which Fe(II) oxidation is biologically catalyzed remains unclear because no neutrophilic iron-oxidizing and nitrate reducing autotroph has been isolated to confirm the existence of an enzymatic pathway. While mixotrophic NDFO bacteria have been isolated, understanding the process is complicated by simultaneous abiotic oxidation due to nitrite produced during denitrification. In this study, the relative contributions of biotic and abiotic processes during NDFO were quantified through the compilation and model-based interpretation of previously published experimental data. The kinetics of chemical denitrification by Fe(II) (chemodenitrification) were assessed, and compelling evidence was found for the importance of organic ligands, specifically exopolymeric substances secreted by bacteria, in enhancing abiotic oxidation of Fe(II). However, nitrite alone could not explain the observed magnitude of Fe(II) oxidation, with 60-75% of overall Fe(II) oxidation attributed to an enzymatic pathway for investigated strains: Acidovorax ( A.) strain BoFeN1, 2AN, A. ebreus strain TPSY, Paracoccus denitrificans Pd 1222, and Pseudogulbenkiania sp. strain 2002. By rigorously quantifying the intermediate processes, this study eliminated the potential for abiotic Fe(II) oxidation to be exclusively responsible for NDFO and verified the key contribution from an additional, biological Fe(II) oxidation process catalyzed by NDFO bacteria.

Heat-Storage Modules Containing LiNO3-3H2O and Graphite Foam

NASA Technical Reports Server (NTRS)

Bootle, John

2008-01-01

A heat-storage module based on a commercial open-cell graphite foam (Poco-Foam or equivalent) imbued with lithium nitrate trihydrate (LiNO3-3H2O) has been developed as a prototype of other such modules for use as short-term heat sources or heat sinks in the temperature range of approximately 28 to 30 C. In this module, the LiNO3-3H2O serves as a phase-change heat-storage material and the graphite foam as thermally conductive filler for transferring heat to or from the phase-change material. In comparison with typical prior heat-storage modules in which paraffins are the phase-change materials and aluminum fins are the thermally conductive fillers, this module has more than twice the heat-storage capacity per unit volume.

The pleiotropic transcriptional regulator NlpR contributes to the modulation of nitrogen metabolism, lipogenesis and triacylglycerol accumulation in oleaginous rhodococci.

PubMed

Hernández, Martín A; Lara, Julia; Gago, Gabriela; Gramajo, Hugo; Alvarez, Héctor M

2017-01-01

The regulatory mechanisms involved in lipogenesis and triacylglycerol (TAG) accumulation are largely unknown in oleaginous rhodococci. In this study a regulatory protein (here called NlpR: Nitrogen lipid Regulator), which contributes to the modulation of nitrogen metabolism, lipogenesis and triacylglycerol accumulation in oleaginous rhodococci was identified. Under nitrogen deprivation conditions, in which TAG accumulation is stimulated, the nlpR gene was significantly upregulated, whereas a significant decrease of its expression and TAG accumulation occurred when cerulenin was added. The nlpR disruption negatively affected the nitrate/nitrite reduction as well as lipid biosynthesis under nitrogen-limiting conditions. In contrast, its overexpression increased TAG production during cultivation of cells in nitrogen-rich media. A putative 'NlpR-binding motif' upstream of several genes related to nitrogen and lipid metabolisms was found. The nlpR disruption in RHA1 strain led to a reduced transcription of genes involved in nitrate/nitrite assimilation, as well as in fatty acid and TAG biosynthesis. Purified NlpR was able to bind to narK, nirD, fasI, plsC and atf3 promoter regions. It was suggested that NlpR acts as a pleiotropic transcriptional regulator by activating of nitrate/nitrite assimilation genes and others genes involved in fatty acid and TAG biosynthesis, in response to nitrogen deprivation. © 2016 John Wiley & Sons Ltd.

Redefining Nitric Oxide Production in Legume Nodules through Complementary Insights from Electron Paramagnetic Resonance Spectroscopy and Specific Fluorescent Probes.

PubMed

Calvo-Begueria, Laura; Rubio, Maria C; Martínez, Jesús I; Pérez-Rontomé, Carmen; Delgado, Maria J; Bedmar, Eulogio J; Becana, Manuel

2018-04-26

Nitric oxide (NO) is a signaling molecule with multiple functions in plants. Given its critical importance and reactivity as a gaseous free radical, we have examined NO production in legume nodules using electron paramagnetic resonance (EPR) spectroscopy and the specific fluorescent dye 4,5-diaminofluorescein diacetate. Also, in this context, we critically assess previous and current views of NO production and detection in nodules. EPR of intact nodules revealed that nitrosyl-leghemoglobin (Lb2+NO) was absent from bean or soybean nodules regardless of nitrate supply, but accumulated in soybean nodules treated with nitrate that were defective in nitrite or nitric oxide reductases or that were exposed to ambient temperature. Consequently, bacteroids are a major source of NO, denitrification enzymes are required for NO homeostasis, and Lb2+NO is not responsible for the inhibition of nitrogen fixation by nitrate. Further, we noted that Lb2+NO is artifactually generated in nodule extracts or in intact nodules not analyzed immediately after detachment. The fluorescent probe detected NO formation in bean and soybean nodule infected cells and in soybean nodule parenchyma. The NO signal was slightly decreased by inhibitors of nitrate reductase but not of nitric oxide synthase, which could indicate a minor contribution of plant nitrate reductase and supports the existence of nitrate- and arginine-independent pathways for NO production. Collectively, our data indicate that EPR and fluorometric methods are complementary to draw reliable conclusions about NO production in plants.

Recent advances in α-synuclein functions, advanced glycation, and toxicity: implications for Parkinson's disease.

PubMed

Guerrero, Erika; Vasudevaraju, P; Hegde, Muralidhar L; Britton, G B; Rao, K S

2013-04-01

The toxicity of α-synuclein in the neuropathology of Parkinson's disease which includes its hallmark aggregation has been studied scrupulously in the last decade. Although little is known regarding the normal functions of α-synuclein, its association with membrane phospholipids suggests its potential role in signaling pathways. Following extensive evidences for its nuclear localization, we and others recently demonstrated DNA binding activity of α-synuclein that modulates its conformation as well as aggregation properties. Furthermore, we also underscored the similarities among various amyloidogenic proteins involved in neurodegenerative diseases including amyloid beta peptides and tau. Our more recent studies show that α-synuclein is glycated and glycosylated both in vitro and in neurons, significantly affecting its folding, oligomeric, and DNA binding properties. Glycated α-synuclein causes increased genome damage both via its direct interaction with DNA and by increased generation of reactive oxygen species as glycation byproduct. In this review, we discuss the mechanisms of glycation and other posttranslational modifications of α-synuclein, including phosphorylation and nitration, and their role in neuronal death in Parkinson's disease.

Manganese nanoparticles: impact on non-nodulated plant as a potent enhancer in nitrogen metabolism and toxicity study both in vivo and in vitro.

PubMed

Pradhan, Saheli; Patra, Prasun; Mitra, Shouvik; Dey, Kushal Kumar; Jain, Sneha; Sarkar, Samapd; Roy, Shuvrodeb; Palit, Pratip; Goswami, Arunava

2014-09-03

Mung bean plants were grown under controlled conditions and supplemented with macro- and micronutrients. The objective of this study was to determine the response of manganese nanoparticles (MnNP) in nitrate uptake, assimilation, and metabolism compared with the commercially used manganese salt, manganese sulfate (MS). MnNP was modulated to affect the assimilatory process by enhancing the net flux of nitrogen assimilation through NR-NiR and GS-GOGAT pathways. This study was associated with toxicological investigation on in vitro and in vivo systems to promote MnNP as nanofertilizer and can be used as an alternative to MS. MnNP did not impart any toxicity to the mice brain mitochondria except in the partial inhibition of complex II-III activity in ETC. Therefore, mitochondrial dysfunction and neurotoxicity, which were noted by excess usage of elemental manganese, were prevented. This is the first attempt to highlight the nitrogen uptake, assimilation, and metabolism in a plant system using a nanoparticle to promote a biosafe nanomicronutrient-based crop management.

Investigating a Sulphate-Nitrate Chemical Indirect Effect over Europe from 1980-2010

NASA Astrophysics Data System (ADS)

Pearce, H.; Mann, G. W.; Arnold, S.; O'Connor, F.; Conibear, L.; Turnock, S.; Rumbold, S.; Benduhn, F.

2017-12-01

Sulphur dioxide emission reductions have been successful in reducing surface sulphate concentrations over Europe between 1980 and 2010, with positive implications for air quality and human health. However the response of nitrate aerosol concentrations to declining NOx emissions has been non-linear. Previous studies have indicated that decreasing ammonium sulphate formation, as a result of SO2 emission reduction, may be partly responsible for this non-linearity by increasing the availability of ammonia and, hence, indirectly increasing ammonium nitrate aerosol formation. We use the UM-UKCA composition-climate model, including the GLOMAP interactive aerosol microphysics module and a recently developed `hybrid' dissolution solver (HyDis), to investigate the size-resolved partitioning of ammonia and nitric acid to the particle phase over Europe in the period 1980 to 2010. Anthropogenic emissions of SO2, NOx and NH3 are included from the MACCity inventory and change by approximately -79%, -33% and +30% respectively over Europe in this time. We evaluate the UM-UKCA simulated 1980-2010 variability in nitrate, ammonium and sulphate aerosol mass concentrations and aerosol pH, with comparison to EMEP observations, and isolate the indirect influence of reduced SO2 emissions on nitrate formation. Preliminary sensitivity tests indicate that simulated nitrate aerosol concentrations over Europe were 8% higher in 2009 than they would have been if SO2 emissions had not been reduced. The implications of this change for air quality, aerosol acidity and regional climate will be presented.

Neuronal and behavioural modulations by pathway-selective optogenetic stimulation of the primate oculomotor system

PubMed Central

Inoue, Ken-ichi; Takada, Masahiko; Matsumoto, Masayuki

2015-01-01

Optogenetics enables temporally and spatially precise control of neuronal activity in vivo. One of the key advantages of optogenetics is that it can be used to control the activity of targeted neural pathways that connect specific brain regions. While such pathway-selective optogenetic control is a popular tool in rodents, attempts at modulating behaviour using pathway-selective optogenetics have not yet been successful in primates. Here we develop a methodology for pathway-selective optogenetics in macaque monkeys, focusing on the pathway from the frontal eye field (FEF) to the superior colliculus (SC), part of the complex oculomotor network. We find that the optogenetic stimulation of FEF projections to the SC modulates SC neuron activity and is sufficient to evoke saccadic eye movements towards the response field corresponding to the stimulation site. Thus, our results demonstrate the feasibility of using pathway-selective optogenetics to elucidate neural network function in primates. PMID:26387804

Neuronal and behavioural modulations by pathway-selective optogenetic stimulation of the primate oculomotor system.

PubMed

Inoue, Ken-ichi; Takada, Masahiko; Matsumoto, Masayuki

2015-09-21

Optogenetics enables temporally and spatially precise control of neuronal activity in vivo. One of the key advantages of optogenetics is that it can be used to control the activity of targeted neural pathways that connect specific brain regions. While such pathway-selective optogenetic control is a popular tool in rodents, attempts at modulating behaviour using pathway-selective optogenetics have not yet been successful in primates. Here we develop a methodology for pathway-selective optogenetics in macaque monkeys, focusing on the pathway from the frontal eye field (FEF) to the superior colliculus (SC), part of the complex oculomotor network. We find that the optogenetic stimulation of FEF projections to the SC modulates SC neuron activity and is sufficient to evoke saccadic eye movements towards the response field corresponding to the stimulation site. Thus, our results demonstrate the feasibility of using pathway-selective optogenetics to elucidate neural network function in primates.

Process-driven bacterial community dynamics are key to cured meat colour formation by coagulase-negative staphylococci via nitrate reductase or nitric oxide synthase activities.

PubMed

Sánchez Mainar, María; Leroy, Frédéric

2015-11-06

The cured colour of European raw fermented meats is usually achieved by nitrate-into-nitrite reduction by coagulase-negative staphylococci (CNS), subsequently generating nitric oxide to form the relatively stable nitrosomyoglobin pigment. The present study aimed at comparing this classical curing procedure, based on nitrate reductase activity, with a potential alternative colour formation mechanism, based on nitric oxide synthase (NOS) activity, under different acidification profiles. To this end, meat models with and without added nitrate were fermented with cultures of an acidifying strain (Lactobacillus sakei CTC 494) and either a nitrate-reducing Staphylococcus carnosus strain or a rare NOS-positive CNS strain (Staphylococcus haemolyticus G110), or by relying on the background microbiota. Satisfactory colour was obtained in the models prepared with added nitrate and S. carnosus. In the presence of nitrate but absence of added CNS, however, cured colour was only obtained when L. sakei CTC 494 was also omitted. This was ascribed to the pH dependency of the emerging CNS background microbiota, selecting for nitrate-reducing Staphylococcus equorum strains at mild acidification conditions but for Staphylococcus saprophyticus strains with poor colour formation capability when the pH decrease was more rapid. This reliance of colour formation on the composition of the background microbiota was further explored by a side experiment, demonstrating the heterogeneity in nitrate reduction of a set of 88 CNS strains from different species. Finally, in all batches prepared with S. haemolyticus G110, colour generation failed as the strain was systematically outcompeted by the background microbiota, even when imposing milder acidification profiles. Thus, when aiming at colour formation through CNS metabolism, technological processing can severely interfere with the composition and functionality of the meat-associated CNS communities, for both nitrate reductase and NOS activities. Several major bottlenecks, among which the rareness of phenotypic NOS activity in meat-compatible CNS, need to be considered, which is seriously questioning the relevance of this pathway in fermented meats. Copyright © 2015 Elsevier B.V. All rights reserved.

Source and transport controls on the movement of nitrate to public supply wells in selected principal aquifers of the United States

USGS Publications Warehouse

McMahon, P.B.; Böhlke, J.K.; Kauffman, L.J.; Kipp, K.L.; Landon, M.K.; Crandall, C.A.; Burow, K.R.; Brown, C.J.

2008-01-01

In 2003–2005, systematic studies in four contrasting hydrogeologic settings were undertaken to improve understanding of source and transport controls on nitrate movement to public supply wells (PSW) in principal aquifers of the United States. Chemical, isotopic, and age tracer data show that agricultural fertilizers and urban septic leachate were the primary sources of large nitrate concentrations in PSW capture zones at Modesto, California (Central Valley aquifer system) and York, Nebraska (High Plains aquifer). Urban septic leachate and fertilizer (possibly nonfarm) were the primary sources of large nitrate concentrations in PSW capture zones at Woodbury, Connecticut (glacial aquifer system), and Tampa, Florida (Floridan aquifer system), respectively. Nitrate fluxes to the water table were larger in agricultural settings than urban settings, indicating that it would be beneficial to reduce PSW capture zone areas in agricultural regions. Mixing calculations indicate that about 50 to 85% of the nitrate in water from the PSW could be from those modern anthropogenic sources, with the remainder coming from sources in old (>50 years) recharge or sources in young recharge in undisturbed settings such as forests. Excess N2 concentrations and age tracers showed that denitrification at Modesto occurred gradually (first‐order rate constant of 0.02/a) in a thick reaction zone following a ∼30‐year lag time after recharge. Denitrification generally was not an important nitrate sink at Woodbury. At York and Tampa, denitrification occurred rapidly (0.5 to 6/a) in thin reaction zones in fine‐grained sediments that separated the anoxic PSW producing zones from overlying oxic, high‐nitrate ground water. Particle tracking showed that a major pathway by which anthropogenic nitrate reached the York and Tampa PSW was by movement through long well screens crossing multiple hydrogeologic units (York) and by movement through karst features (Tampa), processes which reduced ground water residence times in the denitrifying zones. These results illustrate how PSW vulnerability to nitrate contamination depends on complex variations and interactions between contaminant sources, reaction rates, transit times, mixing, and perturbation of ground water flow in contrasting hydrogeologic settings.

Source and transport controls on the movement of nitrate to public supply wells in selected principal aquifers of the United States

NASA Astrophysics Data System (ADS)

McMahon, P. B.; BöHlke, J. K.; Kauffman, L. J.; Kipp, K. L.; Landon, M. K.; Crandall, C. A.; Burow, K. R.; Brown, C. J.

2008-04-01

In 2003-2005, systematic studies in four contrasting hydrogeologic settings were undertaken to improve understanding of source and transport controls on nitrate movement to public supply wells (PSW) in principal aquifers of the United States. Chemical, isotopic, and age tracer data show that agricultural fertilizers and urban septic leachate were the primary sources of large nitrate concentrations in PSW capture zones at Modesto, California (Central Valley aquifer system) and York, Nebraska (High Plains aquifer). Urban septic leachate and fertilizer (possibly nonfarm) were the primary sources of large nitrate concentrations in PSW capture zones at Woodbury, Connecticut (glacial aquifer system), and Tampa, Florida (Floridan aquifer system), respectively. Nitrate fluxes to the water table were larger in agricultural settings than urban settings, indicating that it would be beneficial to reduce PSW capture zone areas in agricultural regions. Mixing calculations indicate that about 50 to 85% of the nitrate in water from the PSW could be from those modern anthropogenic sources, with the remainder coming from sources in old (>50 years) recharge or sources in young recharge in undisturbed settings such as forests. Excess N2 concentrations and age tracers showed that denitrification at Modesto occurred gradually (first-order rate constant of 0.02/a) in a thick reaction zone following a ˜30-year lag time after recharge. Denitrification generally was not an important nitrate sink at Woodbury. At York and Tampa, denitrification occurred rapidly (0.5 to 6/a) in thin reaction zones in fine-grained sediments that separated the anoxic PSW producing zones from overlying oxic, high-nitrate ground water. Particle tracking showed that a major pathway by which anthropogenic nitrate reached the York and Tampa PSW was by movement through long well screens crossing multiple hydrogeologic units (York) and by movement through karst features (Tampa), processes which reduced ground water residence times in the denitrifying zones. These results illustrate how PSW vulnerability to nitrate contamination depends on complex variations and interactions between contaminant sources, reaction rates, transit times, mixing, and perturbation of ground water flow in contrasting hydrogeologic settings.

Numerical experiments based on a coupled physical-biochemical ocean model to study the Kuroshio-induced nutrient supply on the shelf-slope region off the southwestern coast of Japan

NASA Astrophysics Data System (ADS)

Kuroda, Hiroshi; Takasuka, Akinori; Hirota, Yuichi; Kodama, Taketoshi; Ichikawa, Tadafumi; Takahashi, Daisuke; Aoki, Kazuhiro; Setou, Takashi

2018-03-01

We developed a triply nested 1/50° ocean model coupled with a NPZD-type lower trophic level ecosystem model and used it to conduct numerical experiments to identify the major processes that supply nutrients on the shelf-slope region north of the Kuroshio. Tosa Bay, an open-type bay facing the Kuroshio, was selected for our experiment. Comparisons of numerical simulations using different grid sizes revealed that a grid size no larger than 1/50° was essential to reproduce a time-independent density structure related to the Kuroshio jet that uplifted nitrate from subsurface waters into the euphotic zone north of the Kuroshio front. The monthly mean budget of nitrate within the euphotic zone on the shelf showed that primary production was nearly balanced by physical advection and the biochemical supply of nitrate via mechanisms such as remineralization of detritus. Eddy advection of nitrate based on Reynolds decomposition, attributable primarily to submesoscale variations, had both positive and negative values within the bay, the indication being that eddy advection functioned regionally to supply or remove nitrate. Lagrangian particle-tracking experiments were performed to examine the major pathways of the nitrate used for primary production in Tosa Bay during the summer, when subsurface maxima of primary production typically appeared. The experiments revealed that when the Kuroshio took a stable nearshore path, nitrate was frequently uplifted around the Kuroshio front and horizontally transported along the front and into the bay via the counterclockwise circulation within the bay; it was sometimes further uplifted onto the shelf.

Oxygen Isotopic Composition of Nitrate and Sulfate in Fog and River water in Podocarpus National Forest, Ecuador

NASA Astrophysics Data System (ADS)

Brothers, L. A.; Fabian, P.; Thiemens, M. H.

2006-12-01

The eastern slopes of the Andean rainforests of Ecuador possess some of the highest plant biodiversity found on the planet; however, these ecosystems are in jeopardy because region is experiences one of the highest deforestation rates in South America. This rainforest characterized by high acidity and low nutrient soils and experiences natural process which are both destabilizing and stabilizing to biodiversity rendering this a unique, though sensitive environment. There is increased concern that anthropogenic activities are affecting rainforests and could lead to higher extinction rates, changes in the biodiversity and far reaching effects on the global troposphere. Measurements of nitrate and sulfate in rain and fog water have shown periods of elevated concentrations in the Podocarpus National Park near Loja, Ecuador. These high episodes contribute to annual deposition rates that are comparable to polluted central Europe. Significant anthropogenic sources near this region are lacking and it is believed that the majority of the nitrate and sulfate pollution can be attributed to biomass burning in the Amazon basin. Concentration measurements do not elucidate the source of high nitrate and sulfate pollution; however, by measuring all three stable isotopes of oxygen in nitrate and sulfate from fog and river water provides a new way to examine the impacts of biomass burning on the region. By using stable isotope techniques atmospheric nitrate and sulfate can be resolved from terrestrial sources. This provides an unique way to trace the contributions from the biomass burning and farming sources. Current research at the field station monitors sulfate and nitrate concentrations in rain and fog water by standard methods to investigate water and nutrient pathways along with data from satellite and ground based remote sensing, in-situ observations and numerical models.

Response of maize yield, nitrate leaching, and soil nitrogen to pig slurry combined with mineral nitrogen.

PubMed

Yagüe, María R; Quílez, Dolores

2010-01-01

The application of pig (Sus scrofa) slurry (PS) is a common fertilization practice that may affect nitrate concentrations and loads in drainage and receiving water bodies. To protect water resources, many agricultural areas are being designated as vulnerable to nitrate contamination, and there is a need for scientific data aiming at reducing nitrate exports from these vulnerable zones by optimizing N fertilization strategies. The objective of this work, conducted in drainage lysimeters in a 4-yr monoculture maize (Zea mays L.) crop, is to assess the effects of four fertilization strategies combining PS (30, 60, 90, and 120 t ha(-1)) and mineral N on yield, changes in soil mineral N, and concentration and mass of nitrate in drainage waters. Grain yield was not affected by treatments in the four experimental years, nor was the soil mineral N at the end of the experiment. Effects of fertilization strategies on nitrate concentration and mass in drainage waters were detected only after 3 yr of repeated PS applications. The mass of nitrate leached over the 4 yr was positively related to the total amount of N applied, either organic or mineral. In year 2003, precipitation in spring reduced N availability for the crop in treatments with rates > or = 60 t PS ha(-1). The N-budget revealed that the transport pathways for 25% of N inputs to the system are unknown. The presowing application of pig slurry at 30 t ha(-1) complemented with mineral N at side-dressing, was the most efficient from an environmental standpoint (4-yr average of 145 kg grain yield kg(-1) N leached).

The Periplasmic Nitrate Reductase Nap Is Required for Anaerobic Growth and Involved in Redox Control of Magnetite Biomineralization in Magnetospirillum gryphiswaldense

PubMed Central

Li, Yingjie; Katzmann, Emanuel; Borg, Sarah

2012-01-01

The magnetosomes of many magnetotactic bacteria consist of membrane-enveloped magnetite crystals, whose synthesis is favored by a low redox potential. However, the cellular redox processes governing the biomineralization of the mixed-valence iron oxide have remained unknown. Here, we show that in the alphaproteobacterium Magnetospirillum gryphiswaldense, magnetite biomineralization is linked to dissimilatory nitrate reduction. A complete denitrification pathway, including gene functions for nitrate (nap), nitrite (nir), nitric oxide (nor), and nitrous oxide reduction (nos), was identified. Transcriptional gusA fusions as reporters revealed that except for nap, the highest expression of the denitrification genes coincided with conditions permitting maximum magnetite synthesis. Whereas microaerobic denitrification overlapped with oxygen respiration, nitrate was the only electron acceptor supporting growth in the entire absence of oxygen, and only the deletion of nap genes, encoding a periplasmic nitrate reductase, and not deletion of nor or nos genes, abolished anaerobic growth and also delayed aerobic growth in both nitrate and ammonium media. While loss of nosZ or norCB had no or relatively weak effects on magnetosome synthesis, deletion of nap severely impaired magnetite biomineralization and resulted in fewer, smaller, and irregular crystals during denitrification and also microaerobic respiration, probably by disturbing the proper redox balance required for magnetite synthesis. In contrast to the case for the wild type, biomineralization in Δnap cells was independent of the oxidation state of carbon substrates. Altogether, our data demonstrate that in addition to its essential role in anaerobic respiration, the periplasmic nitrate reductase Nap has a further key function by participating in redox reactions required for magnetite biomineralization. PMID:22730130

Influence of nitrogen availability on the expression of genes involved in the biosynthesis of saxitoxin and analogs in Cylindrospermopsis raciborskii.

PubMed

Vico, Paula; Aubriot, Luis; Martigani, Fátima; Rigamonti, Natalia; Bonilla, Sylvia; Piccini, Claudia

2016-06-01

The development of cyanobacterial blooms in inland aquatic ecosystems is greatly promoted by nutrient availability, especially nitrogen and phosphorous. When blooms are dominated by toxigenic species the harmful effects of nutrient loading becomes particularly relevant. Among toxic species, Cylindrospermopsis raciborskii found in South American ecosystems is characterized by the production of saxitoxin and analogs (Paralytic Shellfish Poisoning, PSP), for which the factors that trigger their production have not been elucidated. In this study, the effect of nitrate availability on the relative transcript abundance of two genes (sxtU and sxtI), both involved in different steps of PSP biosynthetic pathway, was addressed in C. raciborskii MVCC19 by qPCR. The relative transcript abundance of both genes significantly increased from the beginning to the end of growth, independent of nitrate availability in the culture medium. Differences between the genes in terms of the levels of relative expression were also found, implying that during growth in nitrate-rich or nitrate-deprived conditions C. raciborskii MVCC19 has the ability to produce different kind of PSP molecules. The presence of nifH transcripts in the nitrogen-depleted treatment confirmed that in the absence of nitrate C. raciborskii fixed atmospheric N 2 . Moreover, after transferring filaments to nitrate-rich conditions the synthesis of nifH mRNA continued for few hours, suggesting that cell adjustments enabling the utilization of soluble nitrogen sources are not immediate. Our results show that biosynthesis of saxitoxin and analogs in C. raciborskii is not related to nitrate availability, but rather is linked to cyanobacteria growth rate. Copyright © 2016. Published by Elsevier B.V.

Correlation of plasma nitrite/nitrate levels and inducible nitric oxide gene expression among women with cervical abnormalities and cancer.

PubMed

Sowjanya, A Pavani; Rao, Meera; Vedantham, Haripriya; Kalpana, Basany; Poli, Usha Rani; Marks, Morgan A; Sujatha, M

2016-01-30

Cervical cancer is caused by infection with high risk human papillomavirus (HR-HPV). Inducible nitric oxide synthase (iNOS), a soluble factor involved in chronic inflammation, may modulate cervical cancer risk among HPV infected women. The aim of the study was to measure and correlate plasma nitrite/nitrate levels with tissue specific expression of iNOS mRNA among women with different grades of cervical lesions and cervical cancer. Tissue biopsy and plasma specimens were collected from 120 women with cervical neoplasia or cancer (ASCUS, LSIL, HSIL and invasive cancer) and 35 women without cervical abnormalities. Inducible nitric oxide synthase (iNOS) mRNA from biopsy and plasma nitrite/nitrate levels of the same study subjects were measured. Single nucleotide polymorphism (SNP) analysis was performed on the promoter region and Ser608Leu (rs2297518) in exon 16 of the iNOS gene. Differences in iNOS gene expression and plasma nitrite/nitrate levels were compared across disease stage using linear and logistic regression analysis. Compared to normal controls, women diagnosed with HSIL or invasive cancer had a significantly higher concentration of plasma nitrite/nitrate and a higher median fold-change in iNOS mRNA gene expression. Genotyping of the promoter region showed three different variations: A pentanucleotide repeat (CCTTT) n, -1026T > G (rs2779249) and a novel variant -1153T > A. These variants were associated with increased levels of plasma nitrite/nitrate across all disease stages. The higher expression of iNOS mRNA and plasma nitrite/nitrate among women with pre-cancerous lesions suggests a role for nitric oxide in the natural history of cervical cancer. Copyright © 2015. Published by Elsevier Inc.

Attempting to Compensate for Reduced Neuronal Nitric Oxide Synthase Protein with Nitrate Supplementation Cannot Overcome Metabolic Dysfunction but Rather Has Detrimental Effects in Dystrophin-Deficient mdx Muscle.

PubMed

Timpani, Cara A; Trewin, Adam J; Stojanovska, Vanesa; Robinson, Ainsley; Goodman, Craig A; Nurgali, Kulmira; Betik, Andrew C; Stepto, Nigel; Hayes, Alan; McConell, Glenn K; Rybalka, Emma

2017-04-01

Duchenne muscular dystrophy arises from the loss of dystrophin and is characterized by calcium dysregulation, muscular atrophy, and metabolic dysfunction. The secondary reduction of neuronal nitric oxide synthase (nNOS) from the sarcolemma reduces NO production and bioavailability. As NO modulates glucose uptake, metabolism, and mitochondrial bioenergetics, we investigated whether an 8-week nitrate supplementation regimen could overcome metabolic dysfunction in the mdx mouse. Dystrophin-positive control (C57BL/10) and dystrophin-deficient mdx mice were supplemented with sodium nitrate (85 mg/l) in drinking water. Following the supplementation period, extensor digitorum longus and soleus were excised and radioactive glucose uptake was measured at rest (basal) and during contraction. Gastrocnemius was excised and mitochondrial respiration was measured using the Oroboros Oxygraph. Tibialis anterior was analyzed immunohistochemically for the presence of dystrophin, nNOS, nitrotyrosine, IgG and CD45+ cells, and histologically to assess areas of damage and regeneration. Glucose uptake in the basal and contracting states was normal in unsupplemented mdx muscles but was reduced following nitrate supplementation in mdx muscles only. The mitochondrial utilization of substrates was also impaired in mdx gastrocnemius during phosphorylating and maximal uncoupled respiration, and nitrate could not improve respiration in mdx muscle. Although nitrate supplementation reduced mitochondrial hydrogen peroxide emission, it induced mitochondrial uncoupling in red gastrocnemius, increased muscle fiber peroxynitrite (nitrotyrosine), and promoted skeletal muscle damage. Our novel data suggest that despite lower nNOS protein expression and likely lower NO production in mdx muscle, enhancing NO production with nitrate supplementation in these mice has detrimental effects on skeletal muscle. This may have important relevance for those with DMD.

Modules for in vitro metabolic engineering: Pathway assembly for bio-based production of value-added chemicals.

PubMed

Taniguchi, Hironori; Okano, Kenji; Honda, Kohsuke

2017-06-01

Bio-based chemical production has drawn attention regarding the realization of a sustainable society. In vitro metabolic engineering is one of the methods used for the bio-based production of value-added chemicals. This method involves the reconstitution of natural or artificial metabolic pathways by assembling purified/semi-purified enzymes in vitro . Enzymes from distinct sources can be combined to construct desired reaction cascades with fewer biological constraints in one vessel, enabling easier pathway design with high modularity. Multiple modules have been designed, built, tested, and improved by different groups for different purpose. In this review, we focus on these in vitro metabolic engineering modules, especially focusing on the carbon metabolism, and present an overview of input modules, output modules, and other modules related to cofactor management.

PREDICTING IMPACTS OF REROUTING DRAINAGE WATER FROM THE PAMLICO SOUND TO RESTORED WETLANDS—A CRITICAL COMPONENT TO GALVANIZE STAKEHOLDER COOPERATION

EPA Science Inventory

Denitrification, a microbially mediated transformation of nitrate to nitrogen gas that escapes from the wetland to the atmosphere, has been identified as the primary pathway for nitrogen removal in wetlands. Requirements for denitrification, which include anoxic conditions,...

Influence of riparian seepage zones on nitrate variability in two agricultural headwater streams

USDA-ARS?s Scientific Manuscript database

Riparian seepage zones are one of the primary pathways of groundwater transport to headwater streams. While seeps have been recognized for their contributions to streamflow, there is little information on how seeps affect stream water quality. The objective of this study was to examine the influence...

Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom[OPEN

PubMed Central

Smith, Sarah R.; McCrow, John P.; Tan, Maxine; Lichtle, Christian; Goodenough, Ursula; Bowler, Chris P.; Dupont, Christopher L.

2017-01-01

The ecological prominence of diatoms in the ocean environment largely results from their superior competitive ability for dissolved nitrate (NO3−). To investigate the cellular and genetic basis of diatom NO3− assimilation, we generated a knockout in the nitrate reductase gene (NR-KO) of the model pennate diatom Phaeodactylum tricornutum. In NR-KO cells, N-assimilation was abolished although NO3− transport remained intact. Unassimilated NO3− accumulated in NR-KO cells, resulting in swelling and associated changes in biochemical composition and physiology. Elevated expression of genes encoding putative vacuolar NO3− chloride channel transporters plus electron micrographs indicating enlarged vacuoles suggested vacuolar storage of NO3−. Triacylglycerol concentrations in the NR-KO cells increased immediately following the addition of NO3−, and these increases coincided with elevated gene expression of key triacylglycerol biosynthesis components. Simultaneously, induction of transcripts encoding proteins involved in thylakoid membrane lipid recycling suggested more abrupt repartitioning of carbon resources in NR-KO cells compared with the wild type. Conversely, ribosomal structure and photosystem genes were immediately deactivated in NR-KO cells following NO3− addition, followed within hours by deactivation of genes encoding enzymes for chlorophyll biosynthesis and carbon fixation and metabolism. N-assimilation pathway genes respond uniquely, apparently induced simultaneously by both NO3− replete and deplete conditions. PMID:28765511

Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom

DOE PAGES

McCarthy, James K.; Smith, Sarah R.; McCrow, John P.; ...

2017-09-07

The ecological prominence of diatoms in the ocean environment largely results from their superior competitive ability for dissolved nitrate (NO 3 -). To investigate the cellular and genetic basis of diatom NO 3 - assimilation, in this paper we generated a knockout in the nitrate reductase gene (NR-KO) of the model pennate diatom Phaeodactylum tricornutum. In NR-KO cells, N-assimilation was abolished although NO 3 - transport remained intact. Unassimilated NO 3 - accumulated in NR-KO cells, resulting in swelling and associated changes in biochemical composition and physiology. Elevated expression of genes encoding putative vacuolar NO 3 - chloride channel transportersmore » plus electron micrographs indicating enlarged vacuoles suggested vacuolar storage of NO 3 -. Triacylglycerol concentrations in the NR-KO cells increased immediately following the addition of NO 3 -, and these increases coincided with elevated gene expression of key triacylglycerol biosynthesis components. Simultaneously, induction of transcripts encoding proteins involved in thylakoid membrane lipid recycling suggested more abrupt repartitioning of carbon resources in NR-KO cells compared with the wild type. Conversely, ribosomal structure and photosystem genes were immediately deactivated in NR-KO cells following NO 3 - addition, followed within hours by deactivation of genes encoding enzymes for chlorophyll biosynthesis and carbon fixation and metabolism. Finally, N-assimilation pathway genes respond uniquely, apparently induced simultaneously by both NO 3 - replete and deplete conditions.« less

Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCarthy, James K.; Smith, Sarah R.; McCrow, John P.

The ecological prominence of diatoms in the ocean environment largely results from their superior competitive ability for dissolved nitrate (NO 3 -). To investigate the cellular and genetic basis of diatom NO 3 - assimilation, in this paper we generated a knockout in the nitrate reductase gene (NR-KO) of the model pennate diatom Phaeodactylum tricornutum. In NR-KO cells, N-assimilation was abolished although NO 3 - transport remained intact. Unassimilated NO 3 - accumulated in NR-KO cells, resulting in swelling and associated changes in biochemical composition and physiology. Elevated expression of genes encoding putative vacuolar NO 3 - chloride channel transportersmore » plus electron micrographs indicating enlarged vacuoles suggested vacuolar storage of NO 3 -. Triacylglycerol concentrations in the NR-KO cells increased immediately following the addition of NO 3 -, and these increases coincided with elevated gene expression of key triacylglycerol biosynthesis components. Simultaneously, induction of transcripts encoding proteins involved in thylakoid membrane lipid recycling suggested more abrupt repartitioning of carbon resources in NR-KO cells compared with the wild type. Conversely, ribosomal structure and photosystem genes were immediately deactivated in NR-KO cells following NO 3 - addition, followed within hours by deactivation of genes encoding enzymes for chlorophyll biosynthesis and carbon fixation and metabolism. Finally, N-assimilation pathway genes respond uniquely, apparently induced simultaneously by both NO 3 - replete and deplete conditions.« less

Determination of timescales of nitrate contamination by groundwater age models in a complex aquifer system

NASA Astrophysics Data System (ADS)

Koh, E. H.; Lee, E.; Kaown, D.; Lee, K. K.; Green, C. T.

2017-12-01

Timing and magnitudes of nitrate contamination are determined by various factors like contaminant loading, recharge characteristics and geologic system. Information of an elapsed time since recharged water traveling to a certain outlet location, which is defined as groundwater age, can provide indirect interpretation related to the hydrologic characteristics of the aquifer system. There are three major methods (apparent ages, lumped parameter model, and numerical model) to date groundwater ages, which differently characterize groundwater mixing resulted by various groundwater flow pathways in a heterogeneous aquifer system. Therefore, in this study, we compared the three age models in a complex aquifer system by using observed age tracer data and reconstructed history of nitrate contamination by long-term source loading. The 3H-3He and CFC-12 apparent ages, which did not consider the groundwater mixing, estimated the most delayed response time and a highest period of the nitrate loading had not reached yet. However, the lumped parameter model could generate more recent loading response than the apparent ages and the peak loading period influenced the water quality. The numerical model could delineate various groundwater mixing components and its different impacts on nitrate dynamics in the complex aquifer system. The different age estimation methods lead to variations in the estimated contaminant loading history, in which the discrepancy in the age estimation was dominantly observed in the complex aquifer system.

The Increasing Importance of Deposition of Reduced Nitrogen ...

EPA Pesticide Factsheets

Rapid development of agricultural activities and fossil fuel combustion in the United States has led to a great increase in reactive nitrogen (Nr) emissions in the second half of the twentieth century. These emissions have been linked to excess nitrogen (N) deposition (i.e. deposition exceeding critical loads) in natural ecosystems through dry and wet deposition pathways. U.S. efforts to reduce nitrogen oxides (NOx) emissions since the 1970s have substantially reduced nitrate deposition, as evidenced by decreasing trends in long-term wet deposition data. These decreases in nitrate deposition along with increases in wet ammonium deposition have altered the balance between oxidized (nitrate) and reduced (ammonium) nitrogen deposition. Across most of the U.S., wet deposition has transitioned from being nitrate dominated in the 1980s to ammonium dominated in recent years. Because ammonia has not been a regulated air pollutant in the U.S., it has historically not been commonly measured. Recent measurement efforts, however, provide a more comprehensive look at ammonia concentrations across several regions of the U.S. These data, along with more routine measurements of gas phase nitric acid and fine particle ammonium and nitrate, permit new insight into the balance of oxidized and reduced nitrogen in the total (wet + dry) U.S. inorganic reactive nitrogen deposition budget. Utilizing two years of N-containing gas and fine particle observations from 37 U.S. monitoring si

Evaluation of the plant growth-promoting activity of Pseudomonas nitroreducens in Arabidopsis thaliana and Lactuca sativa.

PubMed

Trinh, Cao Son; Lee, Hyeri; Lee, Won Je; Lee, Seok Jin; Chung, Namhyun; Han, Juhyeong; Kim, Jongyun; Hong, Suk-Whan; Lee, Hojoung

2018-06-01

Pseudomonas nitroreducens: strain IHB B 13561 (PnIHB) enhances the growth of Arabidopsis thaliana and Lactuca sativa via the stimulation of cell development and nitrate absorption. Plant growth-promoting rhizobacteria (PGPR) enhance plant development through various mechanisms; they improve the uptake of soil resources by plants to greatly promote plant growth. Here, we used Arabidopsis thaliana seedlings and Lactuca sativa to screen the growth enhancement activities of a purified PGPR, Pseudomonas nitroreducens strain IHB B 13561 (PnIHB). When cocultivated with PnIHB, both species of plants exhibited notably improved growth, particularly in regard to biomass. Quantitative reverse transcription polymerase chain reaction analysis indicated high expression levels of the nitrate transporter genes, especially NRT2.1, which plays a major role in the high-affinity nitrate transport system in roots. Moreover, enhanced activity of the cyclin-B1 promoter was observed when wild-type 'Columbia-0' Arabidopsis seedlings were exposed to PnIHB, whereas upregulation of cyclin-B also occurred in the inoculated lettuce seedlings. Overall, these results suggest that PnIHB improves A. thaliana and L. sativa growth via specific pathways involved in the promotion of cell development and enhancement of nitrate uptake.

A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea

PubMed Central

Arshad, Arslan; Speth, Daan R.; de Graaf, Rob M.; Op den Camp, Huub J. M.; Jetten, Mike S. M.; Welte, Cornelia U.

2015-01-01

Methane oxidation is an important process to mitigate the emission of the greenhouse gas methane and further exacerbating of climate forcing. Both aerobic and anaerobic microorganisms have been reported to catalyze methane oxidation with only a few possible electron acceptors. Recently, new microorganisms were identified that could couple the oxidation of methane to nitrate or nitrite reduction. Here we investigated such an enrichment culture at the (meta) genomic level to establish a metabolic model of nitrate-driven anaerobic oxidation of methane (nitrate-AOM). Nitrate-AOM is catalyzed by an archaeon closely related to (reverse) methanogens that belongs to the ANME-2d clade, tentatively named Methanoperedens nitroreducens. Methane may be activated by methyl-CoM reductase and subsequently undergo full oxidation to carbon dioxide via reverse methanogenesis. All enzymes of this pathway were present and expressed in the investigated culture. The genome of the archaeal enrichment culture encoded a variety of enzymes involved in an electron transport chain similar to those found in Methanosarcina species with additional features not previously found in methane-converting archaea. Nitrate reduction to nitrite seems to be located in the pseudoperiplasm and may be catalyzed by an unusual Nar-like protein complex. A small part of the resulting nitrite is reduced to ammonium which may be catalyzed by a Nrf-type nitrite reductase. One of the key questions is how electrons from cytoplasmically located reverse methanogenesis reach the nitrate reductase in the pseudoperiplasm. Electron transport in M. nitroreducens probably involves cofactor F420 in the cytoplasm, quinones in the cytoplasmic membrane and cytochrome c in the pseudoperiplasm. The membrane-bound electron transport chain includes F420H2 dehydrogenase and an unusual Rieske/cytochrome b complex. Based on genome and transcriptome studies a tentative model of how central energy metabolism of nitrate-AOM could work is presented and discussed. PMID:26733968

Response of an algal assemblage to nutrient enrichment and shading in a Hawaiian stream

USGS Publications Warehouse

Stephens, S.H.; Brasher, A.M.D.; Smith, C.M.

2012-01-01

To investigate the effects of nitrate enrichment, phosphate enrichment, and light availability on benthic algae, nutrient-diffusing clay flowerpots were colonized with algae at two sites in a Hawaiian stream during spring and autumn 2002 using a randomized factorial design. The algal assemblage that developed under the experimental conditions was investigated by determining biomass (ash-free dry mass and chlorophyll a concentrations) and composition of the diatom assemblage. In situ pulse amplitude-modulated fluorometry was also used to model photosynthetic rate of the algal assemblage. Algal biomass and maximum photosynthetic rate were significantly higher at the unshaded site than at the shaded site. These parameters were higher at the unshaded site with either nitrate, or to a lesser degree, nitrate plus phosphate enrichment. Analysis of similarity of diatom assemblages showed significant differences between shaded and unshaded sites, as well as between spring and autumn experiments, but not between nutrient treatments. However, several individual species of diatoms responded significantly to nitrate enrichment. These results demonstrate that light availability (shaded vs. unshaded) is the primary limiting factor to algal growth in this stream, with nitrogen as a secondary limiting factor. ?? 2011 Springer Science+Business Media B.V.

Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans.

PubMed

Vanhatalo, Anni; Blackwell, Jamie R; L'Heureux, Joanna; Williams, David W; Smith, Ann; van der Giezen, Mark; Winyard, Paul G; Kelly, James; Jones, Andrew M

2018-05-25

Imbalances in the oral microbial community have been associated with reduced cardiovascular and metabolic health. A possible mechanism linking the oral microbiota to health is the nitrate (NO 3 - )-nitrite (NO 2 - )-nitric oxide (NO) pathway, which relies on oral bacteria to reduce NO 3 - to NO 2 - . NO (generated from both NO 2 - and L-arginine) regulates vascular endothelial function and therefore blood pressure (BP). By sequencing bacterial 16S rRNA genes we examined the relationships between the oral microbiome and physiological indices of NO bioavailability and possible changes in these variables following 10 days of NO 3 - (12mmol/d) and placebo supplementation in young (18-22yrs) and old (70-79yrs) normotensive humans (n=18). NO 3 - supplementation altered the salivary microbiome compared to placebo by increasing the relative abundance of Proteobacteria (+225%) and decreasing the relative abundance of Bacteroidetes (-46%; P<0.05). After NO 3 - supplementation the relative abundances of Rothia (+127%) and Neisseria (+351%) were greater, and Prevotella (-60%) and Veillonella (-65%) were lower than in the placebo condition (all P<0.05). NO 3 - supplementation increased plasma concentration of NO 2 - and reduced systemic blood pressure in old (70-79yrs), but not young (18-22yrs), participants. High abundances of Rothia and Neisseria and low abundances of Prevotella and Veillonella were correlated with greater increases in plasma [NO 2 - ] in response to NO 3 - supplementation. The current findings indicate that the oral microbiome is malleable to change with increased dietary intake of inorganic NO 3 - , and that diet-induced changes in the oral microbial community are related to indices of NO homeostasis and vascular health in vivo. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Characterizing the capacity of hyporheic sediments to attenuate groundwater nitrate loads by adsorption.

PubMed

Meghdadi, Aminreza

2018-05-02

Nitrate has been recognized as a global threat to environmental health. In this regard, the hyporheic zone (saturated media beneath and adjacent to the stream bed) plays a crucial role in attenuating groundwater nitrate, prior to discharge into surface water. While different nitrate removal pathways have been investigated over recent decades, the adsorption capacity of hyporheic sediments under natural conditions has not yet been identified. In this study, the natural attenuation capacity of the hyporheic-sediments of the Ghezel-Ozan River, located in the north-west of Iran, was determined. The sampled sediments (from 1 m below the stream bed) were characterized via XRD, FT-IR, BET, SEM, BJH, and Zeta potential. Nitrate adsorption was evaluated using a batch experiment with hyporheic pore-water from each study site. The study was performed in the hyporheic sediments of two morphologically different zones, including Z 1 located in the parafluvial zone having the clay sediment texture (57.8% clay) with smectite/Illite mixed layer clay type and Z 2 located in the river confluence area containing silty clay sediment texture (47.6% clay) with smectite/kaolinite mixed layer clay type. Data obtained from the batch experiment were subjected to pseudo-first order, pseudo-second order, intra-particle diffusion, and Elovich mass transfer kinetic models to characterize the nitrate adsorption mechanism. Furthermore, to replicate nitrate removal efficiencies of the hyporheic sediments under natural conditions, the sampled hyporheic pore-waters were applied as initial solutions to run the batch experiment. The results of the artificial nitrate solution correlated well with pseudo-second order (R 2 >95%; in both Z 1 and Z 2 ) and maximum removal efficiencies of 85.3% and 71.2% (adsorbent dosage 90 g/L, pH = 5.5, initial adsorbate concentration of 90 mg/L) were achieved in Z 1 and Z 2 , respectively. The results of the nitrate adsorption analysis revealed that the nitrate removal efficiencies varied from 17.24 ± 1.86% in Z 1 during the wet season to 28.13 ± 0.89% in Z 2 during the dry season. The results obtained by this study yielded strong evidence of the potential of hyporheic sediments to remove nitrate from an aqueous environment with great efficiency. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

Protein Tyrosine Nitration: Role in Aging.

PubMed

Chakravarti, Bulbul; Chakravarti, Deb N

2017-01-01

Aging is the inevitable fate of all living organisms, but the molecular basis of physiological aging is poorly understood. Oxidative stress is believed to play a key role in the aging process. In addition to Reactive Oxygen Species (ROS), Reactive Nitrogen Species (RNS) are generated during aerobic metabolism in living organisms. Although protein damage and functional modification by ROS have been demonstrated in details, fewer studies have been reported on protein damage by RNS and its implication in the aging process. Proteins undergoing tyrosine nitration are associated with pathophysiology of several diseases, as well as physiological aging. The purpose of the current review article is to provide a brief summary of the biochemical mechanisms of tyrosine nitration, methodologies used for the detection of these modified proteins, effect of RNS induced post translational modification on biological functions and the putative role of tyrosine nitrated proteins in the aging process. Published studies on the role of RNS in age related functional alteration of various organs/ tissues were critically reviewed and evaluated. Covalent modification of various proteins by tyrosine nitration is associated with modification of biological functions of various organs/tissues such as skeletal muscle, heart, brain and liver due to aging. This information will be helpful to further investigate the interplay of different biochemical pathways and networks involved in the tyrosine nitration of various proteins due to aging with the ultimate goal to prevent the detrimental effects of RNS on the functional activities of these proteins. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Climatic and physiographic controls on catchment-scale nitrate loss at different spatial scales: insights from a top-down model development approach

NASA Astrophysics Data System (ADS)

Shafii, Mahyar; Basu, Nandita; Schiff, Sherry; Van Cappellen, Philippe

2017-04-01

Dramatic increase in nitrogen circulating in the biosphere due to anthropogenic activities has resulted in impairment of water quality in groundwater and surface water causing eutrophication in coastal regions. Understanding the fate and transport of nitrogen from landscape to coastal areas requires exploring the drivers of nitrogen processes in both time and space, as well as the identification of appropriate flow pathways. Conceptual models can be used as diagnostic tools to provide insights into such controls. However, diagnostic evaluation of coupled hydrological-biogeochemical models is challenging. This research proposes a top-down methodology utilizing hydrochemical signatures to develop conceptual models for simulating the integrated streamflow and nitrate responses while taking into account dominant controls on nitrate variability (e.g., climate, soil water content, etc.). Our main objective is to seek appropriate model complexity that sufficiently reproduces multiple hydrological and nitrate signatures. Having developed a suitable conceptual model for a given watershed, we employ it in sensitivity studies to demonstrate the dominant process controls that contribute to the nitrate response at scales of interest. We apply the proposed approach to nitrate simulation in a range of small to large sub-watersheds in the Grand River Watershed (GRW) located in Ontario. Such multi-basin modeling experiment will enable us to address process scaling and investigate the consequences of lumping processes in terms of models' predictive capability. The proposed methodology can be applied to the development of large-scale models that can help decision-making associated with nutrients management at regional scale.

Nutrient controls on new production in the Bodega Bay, California, coastal upwelling plume

NASA Astrophysics Data System (ADS)

Dugdale, R. C.; Wilkerson, F. P.; Hogue, V. E.; Marchi, A.

2006-12-01

A theoretical framework for the time-dependent processes leading to the high rates of new production in eastern boundary upwelling systems has been assembled from a series of past upwelling studies. As part of the CoOP WEST (Wind Events and Shelf Transport) study, new production in the Bodega Bay upwelling area and it's control by ambient nitrate and ammonium concentrations and the advective wind regime are described. Data and analyses are focused primarily on the WEST 2001 cruise (May-June 2001) when the two legs differed greatly in wind regimes but not nutrient concentrations. Elevated concentrations of ammonium in upwelled water with high nitrate were observed in both legs. Nitrate uptake by phytoplankton as a function of nitrate concentration was linear rather than Michaelis-Menten-like, modulated by inhibitory levels of ammonium, yielding coefficients that enable the specific nitrate uptake element of new production to be estimated from nutrient concentrations. The range of specific nitrate uptake rates for the two legs of WEST 2001 were similar, essentially a physiological response to nutrient conditions. However, the low "realization" of new production i.e. incorporation of biomass as particulate nitrogen that occurred in this system compared to the theoretical maximum possible was determined by the strong advective and turbulent conditions that dominated the second leg of the WEST 2001 study. These data are compared with other upwelling areas using a physiological shift-up model [Dugdale, R.C., Wilkerson, F.P., Morel, A. 1990. Realization of new production in coastal upwelling areas: a means to compare relative performance. Limnology and Oceanography 35, 822-829].

Leghemoglobin green derivatives with nitrated hemes evidence production of highly reactive nitrogen species during aging of legume nodules.

PubMed

Navascués, Joaquín; Pérez-Rontomé, Carmen; Gay, Marina; Marcos, Manuel; Yang, Fei; Walker, F Ann; Desbois, Alain; Abián, Joaquín; Becana, Manuel

2012-02-14

Globins constitute a superfamily of proteins widespread in all kingdoms of life, where they fulfill multiple functions, such as efficient O(2) transport and modulation of nitric oxide bioactivity. In plants, the most abundant Hbs are the symbiotic leghemoglobins (Lbs) that scavenge O(2) and facilitate its diffusion to the N(2)-fixing bacteroids in nodules. The biosynthesis of Lbs during nodule formation has been studied in detail, whereas little is known about the green derivatives of Lbs generated during nodule senescence. Here we characterize modified forms of Lbs, termed Lba(m), Lbc(m), and Lbd(m), of soybean nodules. These green Lbs have identical globins to the parent red Lbs but their hemes are nitrated. By combining UV-visible, MS, NMR, and resonance Raman spectroscopies with reconstitution experiments of the apoprotein with protoheme or mesoheme, we show that the nitro group is on the 4-vinyl. In vitro nitration of Lba with excess nitrite produced several isomers of nitrated heme, one of which is identical to those found in vivo. The use of antioxidants, metal chelators, and heme ligands reveals that nitration is contingent upon the binding of nitrite to heme Fe, and that the reactive nitrogen species involved derives from nitrous acid and is most probably the nitronium cation. The identification of these green Lbs provides conclusive evidence that highly oxidizing and nitrating species are produced in nodules leading to nitrosative stress. These findings are consistent with a previous report showing that the modified Lbs are more abundant in senescing nodules and have aberrant O(2) binding.

Injection of Emulsified Vegetable Oil for Long-Term Bioreduction of Uranium

NASA Astrophysics Data System (ADS)

Brooks, S. C.; Watson, D. B.; Schadt, C. W.; Jardine, P. M.; Gihring, T. M.; Zhang, G.; Mehlhorn, T.; Lowe, K.; Phillips, J.; Earles, J.; Wu, W.; Criddle, C. S.; Kemner, K. M.; Boyanov, M.

2011-12-01

In situ bioremediation of a uranium and nitrate-contaminated aquifer with the slow-release electron donor, emulsified vegetable oil (EVO), was tested at the US DOE Subsurface Biogeochemical Research Program (SBR) Integrated Field Research Challenge (IFRC) site, in Oak Ridge, TN. The EVO injection took place in Area 2 of the IFRC located about 300 m downgradient of the former S-3 disposal ponds. Liquid wastes, disposed in the ponds from 1951 to 1983, were primarily composed of nitric acid, plating wastes containing various metals (Cr, Ni) radionuclides (U, Tc), inorganics (nitrate, sulfate) and organic contaminants (tetrachloroethylene, acetone). Prior pond closure in 1987, large volumes of waste fluids migrated into the subsurface, down Bear Creek Valley and into Bear Creek. Contaminants detected at Area 2 were transported through a high permeability gravelly fill that is considered a preferred transport pathway for U to Bear Creek. Groundwater in the gravelly fill is contaminated with U (1-3 mg/L), sulfate (95-130 mg/L), and nitrate (20-40 mg/L) and 500 mg/kg or higher U has been detected on the solid phase of the fill material. The objective of this study is to investigate the feasibility and long-term sustainability of U(VI) reduction and immobilization, and nitrate degradation in the high permeability, high flow gravel fill using EVO as the electron donor. A one-time EVO injection was conducted over a 2 hour period in the highly permeable gravel (hydraulic conductivity 0.08 cm/sec) in the well instrumented IFRC Area 2 field plot. Extensive monitoring of geochemical parameters, dissolved gases and microbial populations were conducted during the test. A bromide tracer test was conducted prior to the injection of the EVO to assess transport pathways and rates. Geochemical analysis of site groundwater demonstrated the sequential bioreduction of oxygen, nitrate, Mn(IV), Fe(III) and sulfate. Transient accumulation of acetate was observed as an intermediate in the oil degradation. Reduction and removal of U and nitrate from groundwater was observed in all wells in hydraulic connection to the injection wells after 2-4 weeks. U concentrations in groundwater were reduced to below 30 ppb (US EPA drinking water standard) at some well locations and nitrate was reduced to below detectable levels. Rebound of U in groundwater was observed together with the rebound of sulfate concentrations as the EVO was consumed. The flux of U and nitrate contamination from groundwater to the surface water receptor (Bear Creek) was significantly reduced by the EVO injection over a one year period. Uranium (VI) reduction to U(IV) in the field tests was confirmed by X-ray absorption near-edge spectroscopy (XANES) analysis. The reduced U(IV) was determined by X-ray absorption fine structure (XAFS) to be in an Fe-U complex, not uraninite. The activities of major Fe(III)- and sulfate-reducing bacteria with U(VI)-reducing capability as well as methanogens was stimulated after injection of the oil.

Quantitative proteomic analyses of the microbial degradation of estrone under various background nitrogen and carbon conditions.

PubMed

Du, Zhe; Chen, Yinguang; Li, Xu

2017-10-15

Microbial degradation of estrogenic compounds can be affected by the nitrogen source and background carbon in the environment. However, the underlying mechanisms are not well understood. The objective of this study was to elucidate the molecular mechanisms of estrone (E1) biodegradation at the protein level under various background nitrogen (nitrate or ammonium) and carbon conditions (no background carbon, acetic acid, or humic acid as background carbon) by a newly isolated bacterial strain. The E1 degrading bacterial strain, Hydrogenophaga atypica ZD1, was isolated from river sediments and its proteome was characterized under various experimental conditions using quantitative proteomics. Results show that the E1 degradation rate was faster when ammonium was used as the nitrogen source than with nitrate. The degradation rate was also faster when either acetic acid or humic acid was present in the background. Proteomics analyses suggested that the E1 biodegradation products enter the tyrosine metabolism pathway. Compared to nitrate, ammonium likely promoted E1 degradation by increasing the activities of the branched-chain-amino-acid aminotransferase (IlvE) and enzymes involved in the glutamine synthetase-glutamine oxoglutarate aminotransferase (GS-GOGAT) pathway. The increased E1 degradation rate with acetic acid or humic acid in the background can also be attributed to the up-regulation of IlvE. Results from this study can help predict and explain E1 biodegradation kinetics under various environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Heterotrophic nitrogen removal by Acinetobacter sp. Y1 isolated from coke plant wastewater.

PubMed

Liu, YuXiang; Hu, Tingting; Song, Yujie; Chen, Hongping; Lv, YongKang

2015-11-01

A strain of Acinetobacter sp. Y1, which exhibited an amazing ability to remove ammonium, nitrite and nitrate, was isolated from the activated sludge of a coking wastewater treatment plant. The aim of this work was to study the ability, influence factors and possible pathway of nitrogen removal by Acinetobacter sp. Y1. Results showed that maximum removal rate of NH4(+)-N by the strain was 10.28 mg-N/L/h. Carbon source had significant influence on the growth and ammonium removal efficiencies of strain Y1. Pyruvate, citrate and acetate were favourable carbon sources for the strain. Temperature, pH value and shaking speed could affect the growth and nitrogen removal ability. Nitrate or nitrite could be used as a sole nitrogen source for the growth and removed efficiently by the strain. N2 levels increased to 53.74%, 50.21% and 55.13% within 36 h when 100 mg/L NH4(+)-N, NO2(-)-N or NO3(-) -N was used as sole nitrogen source in the gas detection experiment. The activities of hydroxylamine oxidoreductase (HAO), nitrate reductase (NR) and nitrite reductase (NiR), which are key enzymes in heterotrophic nitrification and aerobic denitrification, were all detectable in the strain. Consequently, a possible pathway for ammonium removal by the strain was also suggested. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Direct observation of ClO from chlorine nitrate photolysis. [as mechanism of polar ozone depletion

NASA Technical Reports Server (NTRS)

Minton, Timothy K.; Nelson, Christine M.; Moore, Teresa A.; Okumura, Mitchio

1992-01-01

Chlorine nitrate photolysis has been investigated with the use of a molecular beam technique. Excitation at both 248 and 193 nanometers led to photodissociation by two pathways, ClONO2 yields ClO + NO2 and ClONO2 yields Cl + NO3, with comparable yields. This experiment provides a direct measurement of the ClO product channel and consequently raises the possibility of an analogous channel in ClO dimer photolysis. Photodissociation of the ClO dimer is a critical step in the catalytic cycle that is presumed to dominate polar stratospheric ozone destruction. A substantial yield of ClO would reduce the efficiency of this cycle.

Effect of Short-Circuit Pathways on Water Quality in Selected Confined Aquifers (Invited)

NASA Astrophysics Data System (ADS)

McMahon, P. B.

2010-12-01

Confined aquifers in the United States generally contain fewer anthropogenic contaminants than unconfined aquifers because confined aquifers often contain water recharged prior to substantial human development and redox conditions are more reducing, which favors degradation of common contaminants like nitrate and chlorinated solvents. Groundwater in a confined part of the High Plains aquifer near York, Nebraska had an adjusted radiocarbon age of about 2,000 years, and groundwater in a confined part of the Floridan aquifer near Tampa, Florida had apparent ages greater than 60 years on the basis of tritium measurements. Yet compounds introduced more recently into the environment (anthropogenic nitrate and volatile organic compounds) were detected in selected public-supply wells completed in both aquifers. Depth-dependent measurements of flow and chemistry in the pumping supply wells, groundwater age dating, numerical modeling of groundwater flow, and other monitoring data indicated that the confined aquifers sampled by the supply wells were connected to contaminated unconfined aquifers by short-circuit pathways. In the High Plains aquifer, the primary pathways appeared to be inactive irrigation wells screened in both the unconfined and confined aquifers. In the Floridan aquifer, the primary pathways were karst sinkholes and conduits. Heavy pumping in both confined systems exacerbated the problem by reducing the potentiometric surface and increasing groundwater velocities, thus enhancing downward gradients and reducing reaction times for processes like denitrification. From a broader perspective, several confined aquifers in the U.S. have experienced large declines in their potentiometric surfaces because of groundwater pumping and this could increase the potential for contamination in those aquifers, particularly where short-circuit pathways connect them to shallower, contaminated sources of water, such as was observed in York and Tampa.

Pathway-related modules involved in the application of sevoflurane or propofol in off-pump coronary artery bypass graft surgery.

PubMed

Bu, Xiangmei; Wang, Bo; Wang, Yaoqi; Wang, Zhigang; Gong, Chunzhi; Qi, Feng; Zhang, Caixia

2017-07-01

Off-pump coronary artery bypass graft (CABG) surgery has recently emerged as a means to avoid the sequelae of extracorporeal circulation, including the whole-body inflammatory response, coagulation disorders and multiple organ dysfunction. At present, gas anesthesia, sevoflurane and intravenous anesthesia and propofol have been widely used during the CABG. To further understand the underlying mechanisms of these anesthetics on the gene level, the present study conducted pathway-related module analysis based on a co-expression network. This was performed in order to identify significant pathways in coronary artery disease patients who had undergone off-pump CABG surgery before and after applying sevoflurane or propofol. A total of 269 and 129 differentially expressed genes were obtained in the sevoflurane and propofol groups, respectively. In total, eight and seven pathways (P<0.05) in the sevoflurane and propofol groups were separately obtained via Kyoto Encyclopedia of Genes and Genome pathway analysis. Finally, eight and seven pathway-related modules in the sevoflurane and propofol groups were obtained, respectively. Furthermore, the mean degree of complement and coagulation cascades pathway-related module in both of the groups was the highest. It was predicted that during the CABG, the anesthetics might activate the complement and coagulation systems in order to possess some cardioprotective properties.

Network analysis of genomic alteration profiles reveals co-altered functional modules and driver genes for glioblastoma.

PubMed

Gu, Yunyan; Wang, Hongwei; Qin, Yao; Zhang, Yujing; Zhao, Wenyuan; Qi, Lishuang; Zhang, Yuannv; Wang, Chenguang; Guo, Zheng

2013-03-01

The heterogeneity of genetic alterations in human cancer genomes presents a major challenge to advancing our understanding of cancer mechanisms and identifying cancer driver genes. To tackle this heterogeneity problem, many approaches have been proposed to investigate genetic alterations and predict driver genes at the individual pathway level. However, most of these approaches ignore the correlation of alteration events between pathways and miss many genes with rare alterations collectively contributing to carcinogenesis. Here, we devise a network-based approach to capture the cooperative functional modules hidden in genome-wide somatic mutation and copy number alteration profiles of glioblastoma (GBM) from The Cancer Genome Atlas (TCGA), where a module is a set of altered genes with dense interactions in the protein interaction network. We identify 7 pairs of significantly co-altered modules that involve the main pathways known to be altered in GBM (TP53, RB and RTK signaling pathways) and highlight the striking co-occurring alterations among these GBM pathways. By taking into account the non-random correlation of gene alterations, the property of co-alteration could distinguish oncogenic modules that contain driver genes involved in the progression of GBM. The collaboration among cancer pathways suggests that the redundant models and aggravating models could shed new light on the potential mechanisms during carcinogenesis and provide new indications for the design of cancer therapeutic strategies.

Toward a Mechanistic Understanding of Anaerobic Nitrate-Dependent Iron Oxidation: Balancing Electron Uptake and Detoxification

PubMed Central

Carlson, Hans K.; Clark, Iain C.; Melnyk, Ryan A.; Coates, John D.

2011-01-01

The anaerobic oxidation of Fe(II) by subsurface microorganisms is an important part of biogeochemical cycling in the environment, but the biochemical mechanisms used to couple iron oxidation to nitrate respiration are not well understood. Based on our own work and the evidence available in the literature, we propose a mechanistic model for anaerobic nitrate-dependent iron oxidation. We suggest that anaerobic iron-oxidizing microorganisms likely exist along a continuum including: (1) bacteria that inadvertently oxidize Fe(II) by abiotic or biotic reactions with enzymes or chemical intermediates in their metabolic pathways (e.g., denitrification) and suffer from toxicity or energetic penalty, (2) Fe(II) tolerant bacteria that gain little or no growth benefit from iron oxidation but can manage the toxic reactions, and (3) bacteria that efficiently accept electrons from Fe(II) to gain a growth advantage while preventing or mitigating the toxic reactions. Predictions of the proposed model are highlighted and experimental approaches are discussed. PMID:22363331

N2O and N2 production during heterotrophic nitrification by Alcaligenes faecalis strain NR.

PubMed

Zhao, Bin; An, Qiang; He, Yi Liang; Guo, Jin Song

2012-07-01

A heterotrophic nitrifier, strain NR, was isolated from a membrane bioreactor. Strain NR was identified as Alcaligenes faecalis by Auto-Microbic system and 16S rRNA gene sequence analysis. A. faecalis strain NR shows a capability of heterotrophic nitrification and N(2)O and N(2) production as well under the aerobic condition. Further tests demonstrated that neither nitrite nor nitrate could be denitrified aerobically by strain NR. However, when hydroxylamine was used as the sole nitrogen source, nitrogenous gases were detected. With an enzyme assay, a 0.063 U activity of hydroxylamine oxidase was observed, while nitrate reductase and nitrite reductase were undetectable. Thus, nitrogenous gas was speculated to be produced via hydroxylamine. Therefore, two different metabolic pathways might exist in A. faecalis NR. One is heterotrophic nitrification by oxidizing ammonium to nitrite and nitrate. The other is oxidizing ammonium to nitrogenous gas directly via hydroxylamine. Copyright © 2012 Elsevier Ltd. All rights reserved.

Nitrate assimilation pathway (NAP): role of structural (nit) and transporter (ntr1) genes in Fusarium oxysporum f.sp. lycopersici growth and pathogenicity.

PubMed

Gomez-Gil, Lucia; Camara Almiron, Jesus; Rodriguez Carrillo, Patricia Lizett; Olivares Medina, Cindy Nayely; Bravo Ruiz, Gustavo; Romo Rodriguez, Pamela; Corrales Escobosa, Alma Rosa; Gutierrez Corona, Felix; Roncero, M Isabel

2018-04-01

The tomato pathogen Fusarium oxysporum f.sp. lycopersici possesses the capability to use nitrate as the only nitrogen source under aerobic and anaerobic conditions and to activate virulence-related functions when cultivated in the presence of nitrate, but not in ammonium. The genome of F. oxysporum f.sp. lycopersici encodes three paralogs nitrate reductase (NR) genes (nit1, nit2 and nit3) and one predicted ortholog of the Aspergillus nidulans high-affinity nitrate/nitrite transporters NtrA and NtrB, named ntr1. We set out to clarify the role of nit1, nit2, nit3 and ntr1 genes in nitrate assimilation and in the virulence of F. oxysporum f.sp. lycopersici. Quantitative RT-PCR analysis revealed that only nit1, nit2 and ntr1 are expressed at significant levels during growth in nitrate as the only nitrogen source. Targeted deletion of nit1 and ntr1, but not of nit2 or nit3, severely impaired growth of F. oxysporum on nitrate as nitrogen source, indicating that Nit1 and Ntr1 proteins are involved in nitrate assimilation by the fungus; biochemical analysis of nit mutants indicated that Nit1 and Nit2 enzymes contribute to about 50 and 30% of the total NR activity, respectively. In addition, a spontaneous chlorate-resistant mutant derived from F. oxysporum 4287, denoted NitFG, was characterized, showing inability to grow in nitrate under aerobic and anaerobic conditions and low levels of NR activity, in spite of its increased transcription levels of nit1 and nit2 genes. Tomato plant infection assays showed that NitFG and ∆ntr1 mutants induced an earlier death in tomato plants, whereas the single mutants ∆nit1, ∆nit2 and ∆nit1∆nit2 double mutant showed a mortality rate similar to the wild-type strain. Taken together, these results indicate that the Nit1 and Ntr1 proteins are important for nitrate assimilation of F. oxysporum f.sp. lycopersici incubated under aerobic and anaerobic conditions and that this metabolic process is not essential for the virulence of the fungus. These observations open new questions about the role of Nit1, Nit2, and Nit3 proteins in other routes of nitrate metabolism in this pathogenic fungus and in the possible regulatory role that can be exerted by the AreA protein in these routes.

Dietary nitrate restores compensatory vasodilation and exercise capacity in response to a compromise in oxygen delivery in the noncompensator phenotype.

PubMed

Bentley, Robert F; Walsh, Jeremy J; Drouin, Patrick J; Velickovic, Aleksandra; Kitner, Sarah J; Fenuta, Alyssa M; Tschakovsky, Michael E

2017-09-01

Recently, dietary nitrate supplementation has been shown to improve exercise capacity in healthy individuals through a potential nitrate-nitrite-nitric oxide pathway. Nitric oxide has been shown to play an important role in compensatory vasodilation during exercise under hypoperfusion. Previously, we established that certain individuals lack a vasodilation response when perfusion pressure reductions compromise exercising muscle blood flow. Whether this lack of compensatory vasodilation in healthy, young individuals can be restored with dietary nitrate supplementation is unknown. Six healthy (21 ± 2 yr), recreationally active men completed a rhythmic forearm exercise. During steady-state exercise, the exercising arm was rapidly transitioned from an uncompromised (below heart) to a compromised (above heart) position, resulting in a reduction in local pressure of -31 ± 1 mmHg. Exercise was completed following 5 days of nitrate-rich (70 ml, 0.4 g nitrate) and nitrate-depleted (70 ml, ~0 g nitrate) beetroot juice consumption. Forearm blood flow (in milliliters per minute; brachial artery Doppler and echo ultrasound), mean arterial blood pressure (in millimeters of mercury; finger photoplethysmography), exercising forearm venous effluent (ante-cubital vein catheter), and plasma nitrite concentrations (chemiluminescence) revealed two distinct vasodilatory responses: nitrate supplementation increased (plasma nitrite) compared with placebo (245 ± 60 vs. 39 ± 9 nmol/l; P < 0.001), and compensatory vasodilation was present following nitrate supplementation (568 ± 117 vs. 714 ± 139 ml ⋅ min -1 ⋅ 100 mmHg -1 ; P = 0.005) but not in placebo (687 ± 166 vs. 697 ± 171 min -1 ⋅ 100 mmHg -1 ; P = 0.42). As such, peak exercise capacity was reduced to a lesser degree (-4 ± 39 vs. -39 ± 27 N; P = 0.01). In conclusion, dietary nitrate supplementation during a perfusion pressure challenge is an effective means of restoring exercise capacity and enabling compensatory vasodilation. NEW & NOTEWORTHY Previously, we identified young, healthy persons who suffer compromised exercise tolerance when exercising muscle perfusion pressure is reduced as a result of a lack of compensatory vasodilation. The ability of nitrate supplementation to restore compensatory vasodilation in such noncompensators is unknown. We demonstrated that beetroot juice supplementation led to compensatory vasodilation and restored perfusion and exercise capacity. Elevated plasma nitrite is an effective intervention for correcting the absence of compensatory vasodilation in the noncompensator phenotype. Copyright © 2017 the American Physiological Society.

Performance of dentrification beds for removing nitrate from drainage water at cold temperatures

USDA-ARS?s Scientific Manuscript database

Transport of soluble nitrogen and phosphorus to water bodies has been a concern for many years due to human health issues, and is a major contributor to the formation of oxygen deficiency in aquatic ecosystems. Agricultural subsurface drainage is one pathway for transport of excess nutrients to surf...

Identification of gene expression profiles and key genes in subchondral bone of osteoarthritis using weighted gene coexpression network analysis.

PubMed

Guo, Sheng-Min; Wang, Jian-Xiong; Li, Jin; Xu, Fang-Yuan; Wei, Quan; Wang, Hai-Ming; Huang, Hou-Qiang; Zheng, Si-Lin; Xie, Yu-Jie; Zhang, Chi

2018-06-15

Osteoarthritis (OA) significantly influences the quality life of people around the world. It is urgent to find an effective way to understand the genetic etiology of OA. We used weighted gene coexpression network analysis (WGCNA) to explore the key genes involved in the subchondral bone pathological process of OA. Fifty gene expression profiles of GSE51588 were downloaded from the Gene Expression Omnibus database. The OA-associated genes and gene ontologies were acquired from JuniorDoc. Weighted gene coexpression network analysis was used to find disease-related networks based on 21756 gene expression correlation coefficients, hub-genes with the highest connectivity in each module were selected, and the correlation between module eigengene and clinical traits was calculated. The genes in the traits-related gene coexpression modules were subject to functional annotation and pathway enrichment analysis using ClusterProfiler. A total of 73 gene modules were identified, of which, 12 modules were found with high connectivity with clinical traits. Five modules were found with enriched OA-associated genes. Moreover, 310 OA-associated genes were found, and 34 of them were among hub-genes in each module. Consequently, enrichment results indicated some key metabolic pathways, such as extracellular matrix (ECM)-receptor interaction (hsa04512), focal adhesion (hsa04510), the phosphatidylinositol 3'-kinase (PI3K)-Akt signaling pathway (PI3K-AKT) (hsa04151), transforming growth factor beta pathway, and Wnt pathway. We intended to identify some core genes, collagen (COL)6A3, COL6A1, ITGA11, BAMBI, and HCK, which could influence downstream signaling pathways once they were activated. In this study, we identified important genes within key coexpression modules, which associate with a pathological process of subchondral bone in OA. Functional analysis results could provide important information to understand the mechanism of OA. © 2018 Wiley Periodicals, Inc.

A one-stage cultivation process for lipid- and carbohydrate-rich biomass of Scenedesmus obtusiusculus based on artificial and natural water sources.

PubMed

Schulze, Christian; Reinhardt, Jakob; Wurster, Martina; Ortiz-Tena, José Guillermo; Sieber, Volker; Mundt, Sabine

2016-10-01

A one-stage cultivation process of the microalgae Scenedesmus obtusiusculus with medium based on natural water sources was developed to enhance lipids and carbohydrates. A medium based on artificial sea water, Baltic Sea water and river water with optimized nutrient concentrations compared to the standard BG-11 for nitrate (-75%), phosphate and iron (-90%) was used for cultivation. Although nitrate exhaustion over cultivation resulted in nitrate limitation, growth of the microalgae was not reduced. The lipid content increased from 6.0% to 19.9%, an increase in oleic and stearic acid was observed. The unsaponifiable matter of the lipid fraction was reduced from 19.5% to 11.4%. The carbohydrate yield rose from 45% to 50% and the protein content decreased from 32.4% to 15.9%. Using natural water sources with optimized nutrient concentrations could open the opportunity to modulate biomass composition and to reduce the cultivation costs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nitric oxide isotopic analyzer based on a compact dual-modulation Faraday rotation spectrometer.

PubMed

Zhang, Eric; Huang, Stacey; Ji, Qixing; Silvernagel, Michael; Wang, Yin; Ward, Bess; Sigman, Daniel; Wysocki, Gerard

2015-10-14

We have developed a transportable spectroscopic nitrogen isotopic analyzer. The spectrometer is based on dual-modulation Faraday rotation spectroscopy of nitric oxide isotopologues with near shot-noise limited performance and baseline-free operation. Noise analysis indicates minor isotope ((15)NO) detection sensitivity of 0.36 ppbv·Hz(-1/2), corresponding to noise-equivalent Faraday rotation angle (NEA) of 1.31 × 10(-8) rad·Hz(-1/2) and noise-equivalent absorbance (αL)min of 6.27 × 10(-8) Hz(-1/2). White-noise limited performance at 2.8× the shot-noise limit is observed up to ~1000 s, allowing reliable calibration and sample measurement within the drift-free interval of the spectrometer. Integration with wet-chemistry based on acidic vanadium(III) enables conversion of aqueous nitrate/nitrite samples to gaseous NO for total nitrogen isotope analysis. Isotopic ratiometry is accomplished via time-multiplexed measurements of two NO isotope transitions. For 5 μmol potassium nitrate samples, the instrument consistently yields ratiometric precision below 0.3‰, thus demonstrating potential as an in situ diagnostic tool for environmental nitrogen cycle studies.

Methane: Fuel or Exhaust at the Emergence of Life?

PubMed

Russell, Michael J; Nitschke, Wolfgang

2017-10-01

As many of the methanogens first encountered at hydrothermal vents were thermophilic to hyperthermophilic and comprised one of the lower roots of the evolutionary tree, it has been assumed that methanogenesis was one of the earliest, if not the earliest, pathway to life. It being well known that hydrothermal springs associated with serpentinization also bore abiotic methane, it had been further assumed that emergent biochemistry merely adopted and quickened this supposed serpentinization reaction. Yet, recent hydrothermal experiments simulating serpentinization have failed to generate methane so far, thus casting doubt on this assumption. The idea that the inverse view is worthy of debate, that is, that methanotrophy was the earlier, is stymied by the "fact" that methanotrophy itself has been termed "reverse methanogenesis," so allotting the methanogens the founding pedigree. Thus, attempting to suggest instead that methanogenesis might be termed reverse methanotrophy would require "unlearning"-a challenge to the subconscious! Here we re-examine the "impossibility" of methanotrophy predating methanogenesis as in what we have termed the "denitrifying methanotrophic acetogenic pathway." Advantages offered by such thinking are that methane would not only be a fuel but also a ready source of reduced carbon to combine with formate or carbon monoxide-available in hydrothermal fluids-to generate acetate, a target molecule of the first autotrophs. And the nitrate/nitrite required for the putative oxidation of methane with activated NO would also be a ready source of fixed nitrogen for amination reactions. Theoretical conditions for such a putative pathway would be met in a hydrothermal green rust-bearing exhalative pile and associated chimneys subject to proton and electron counter gradients. This hypothesis could be put to test in a high-pressure hydrothermal reaction chamber in which a cool carbonate/nitrate/nitrite-bearing early acidulous ocean simulant is juxtaposed across a precipitate membrane to an alkaline solution of hydrogen and methane. Key Words: Green rust-Methanotrophy-Nitrate reduction-Emergence of life. Astrobiology 17, 1053-1066.

Methane: Fuel or Exhaust at the Emergence of Life?

PubMed Central

Nitschke, Wolfgang

2017-01-01

Abstract As many of the methanogens first encountered at hydrothermal vents were thermophilic to hyperthermophilic and comprised one of the lower roots of the evolutionary tree, it has been assumed that methanogenesis was one of the earliest, if not the earliest, pathway to life. It being well known that hydrothermal springs associated with serpentinization also bore abiotic methane, it had been further assumed that emergent biochemistry merely adopted and quickened this supposed serpentinization reaction. Yet, recent hydrothermal experiments simulating serpentinization have failed to generate methane so far, thus casting doubt on this assumption. The idea that the inverse view is worthy of debate, that is, that methanotrophy was the earlier, is stymied by the “fact” that methanotrophy itself has been termed “reverse methanogenesis,” so allotting the methanogens the founding pedigree. Thus, attempting to suggest instead that methanogenesis might be termed reverse methanotrophy would require “unlearning”—a challenge to the subconscious! Here we re-examine the “impossibility” of methanotrophy predating methanogenesis as in what we have termed the “denitrifying methanotrophic acetogenic pathway.” Advantages offered by such thinking are that methane would not only be a fuel but also a ready source of reduced carbon to combine with formate or carbon monoxide—available in hydrothermal fluids—to generate acetate, a target molecule of the first autotrophs. And the nitrate/nitrite required for the putative oxidation of methane with activated NO would also be a ready source of fixed nitrogen for amination reactions. Theoretical conditions for such a putative pathway would be met in a hydrothermal green rust-bearing exhalative pile and associated chimneys subject to proton and electron counter gradients. This hypothesis could be put to test in a high-pressure hydrothermal reaction chamber in which a cool carbonate/nitrate/nitrite-bearing early acidulous ocean simulant is juxtaposed across a precipitate membrane to an alkaline solution of hydrogen and methane. Key Words: Green rust—Methanotrophy—Nitrate reduction—Emergence of life. Astrobiology 17, 1053–1066. PMID:28949766

On the Mechanisms Linking Nitrogen Oxides to Trends in Ammonium Nitrate Aerosol over the Last Decade in the San Joaquin Valley

NASA Astrophysics Data System (ADS)

Pusede, S. E.; Zhang, Q.; Parworth, C.; Kim, H.; Shusterman, A.; Saleh, A.; Duffey, K.; Wooldridge, P. J.; Valin, L. C.; Fried, A.; Nowak, J. B.; Crawford, J. H.; Cohen, R. C.

2014-12-01

Nitrogen oxide (NOx) abundances across the U.S. have fallen steadily over the last fifteen years. Patterns in anthropogenic sources result in 2-fold lower NOx on weekends than weekdays largely without co-occurring changes in other emissions. These trends taken together provide a near perfect NOx constraint on the nonlinear chemistry of ozone, on the key oxidants nitrate radical (NO3) and hydroxyl radical (OH), and on secondary aerosol formation. We use this NOx constraint to interpret trends in wintertime PM2.5 over the last decade in San Joaquin Valley, California, a location with severe aerosol pollution and where a large portion of the total aerosol mass is ammonium nitrate (NH4NO3). We combine the 12-year routine monitoring record and the air- and ground-based DISCOVER-AQ-2013 datasets to quantify the impact of NOx emission controls on the frequency of wintertime exceedances of the national PM2.5 standard. Nitrate ion (NO3-) is the oxidation product of NO2 and is formed by distinct daytime and nighttime pathways, both of which are nonlinear functions of the NO2 abundance. We present observationally derived decadal trends in both pathways and show that NOx reductions have worked to simultaneously increase daytime and decrease nighttime NH4NO3 production over the last 15 years. The net effect has been a substantial decrease in NH4NO3 via decreased NO3-radical initiated production in the nocturnal residual layer, a layer largely separated from nighttime emissions at the surface. Whereas NO3- production in the nocturnal residual layer drove NH4NO3 chemistry over the last decade, OH-initiated chemistry at the surface is poised to be the most important source of NH4NO3 in the next decade.

OH radical-initiated oxidation of (E)- and (Z)-β-ocimene in the presence of NOx: the role of light-dependent monoterpenes in organic nitrate and secondary organic aerosol formation in the above-canopy forest environment

NASA Astrophysics Data System (ADS)

Slade, J. H., Jr.; Jayarathne, T.; Morales, A. C.; Shepson, P. B.

2017-12-01

Biogenic volatile organic compound (BVOC) oxidation represents a significant pathway in the production of secondary organic aerosol (SOA). BVOC oxidation products, including organic nitrates (ON), impact both the SOA burden and the oxidative capacity of the atmosphere by sequestering NOx. A recent field study in the mixed deciduous/coniferous forest of northern Michigan showed that concentrations of multifunctional monoterpene-derived hydroxy nitrates (MTN) and SOA can be greater in the above-canopy environment during daytime, but the source of MTN is unclear as model simulations cannot replicate the higher concentrations above canopy. Light-dependent monoterpenes, including the polyolefinic species, trans-ocimene, may be one such contributor to the higher measured ON and SOA above canopy as this compound has been predicted to be an important source of monoterpene-derived ON during daytime in this environment. However, there are currently no measurements of the ON (and SOA yields) from trans-ocimene oxidation by OH in the presence of NOx, the dominant pathway for daytime ON production. Here we conduct photochemical reaction chamber studies of the OH radical-initiated oxidation of authentic (E)- and (Z)-β-ocimene isomers in the presence of NOx to examine the total (gas and particle) ON, hydroxy nitrate, and SOA yields. The effects of variable chamber relative humidity and seed particle acidity on the ON and SOA yields are examined to better understand the role of hydrolysis on SOA formation and the lifetime of ocimene-derived ON in the particles. This work underscores the importance of light-dependent monoterpenes on mediating the oxidative capacity of the near canopy forest environment and has important implications for understanding NOx cycling and the formation of SOA in forests, which are not currently included in atmospheric models.

Investigating eukaryotic fermentation as the likely source of unassigned dissolved inorganic carbon production in permeable sediments under anoxic conditions.

NASA Astrophysics Data System (ADS)

Bourke, M.; Cook, P. L. M.

2016-02-01

Experiments using flow through columns have revealed that in permeable sediments, under anoxic conditions, only 2-5% of dissolved inorganic carbon (DIC) production could be attributed to external electron acceptors including nitrate, sulphate and iron.. The remaining 95-98% of DIC production remains unassigned to any biogeochemical pathway. This possibly ubiquitous phenomenon has been observed at several sites around Port Phillip Bay in Victoria, Australia and the Danish Baltic Sea. Identifying the process by which this unassigned DIC is being generated and determining which organisms are responsible, has been the primary focus of this research. CaCO3 dissolution has been dismissed as a potential abiotic explanation for this unassigned DIC production on the basis of sample effluent analyses for alkalinity and Ca2+ and the observation that treating the sediments with HgCl2 inhibited all DIC production, suggesting a biotic source is likely. Dissimilatory nitrate reduction to ammonium using an intracellular pool of nitrate has also been dismissed as an explanation due to the concentration of nitrate in intracellular pools was determined to be negligible in relation to the DIC production. The most likely explanation appears to be fermentation, whereby, organic carbon would be used as both the electron acceptor and donor. Experiments employing the use of two broad spectrum antibiotics, amoxicillin and ciprofloxacin, have revealed that DIC production continues unaffected, whilst established bacterial processes, like denitrification, are inhibited. This suggests that the source is eukaryotic. After approximately 48 hours of anoxia, dissolved hydrogen was detected at approximately 5 µM and increased to 72 µM over a 3 day period, representing 85% of the DIC production rate on a mole per mole basis. These are the first observations of hydrogen production in permeable sediments, and support the fermentation hypothesis, as hydrogen is a typical product of fermentative pathways.

A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants

PubMed Central

Borowsky, Alexander T.

2017-01-01

Plants produce diverse specialized metabolites (SMs), but the genes responsible for their production and regulation remain largely unknown, hindering efforts to tap plant pharmacopeia. Given that genes comprising SM pathways exhibit environmentally dependent coregulation, we hypothesized that genes within a SM pathway would form tight associations (modules) with each other in coexpression networks, facilitating their identification. To evaluate this hypothesis, we used 10 global coexpression data sets, each a meta-analysis of hundreds to thousands of experiments, across eight plant species to identify hundreds of coexpressed gene modules per data set. In support of our hypothesis, 15.3 to 52.6% of modules contained two or more known SM biosynthetic genes, and module genes were enriched in SM functions. Moreover, modules recovered many experimentally validated SM pathways, including all six known to form biosynthetic gene clusters (BGCs). In contrast, bioinformatically predicted BGCs (i.e., those lacking an associated metabolite) were no more coexpressed than the null distribution for neighboring genes. These results suggest that most predicted plant BGCs are not genuine SM pathways and argue that BGCs are not a hallmark of plant specialized metabolism. We submit that global gene coexpression is a rich, largely untapped resource for discovering the genetic basis and architecture of plant natural products. PMID:28408660

Aquatic photolysis of β2-agonist salbutamol: kinetics and mechanism studies.

PubMed

Zhou, Lei; Wang, Qi; Zhang, Ya; Ji, Yuefei; Yang, Xi

2017-02-01

Salbutamol (SAL) has been widely used as medicine both in treating asthma and in animal primary production; an increasing number of reports have detected SAL in natural waters. The photolysis kinetic and pathway of SAL in aquatic system were studied, as well as the effect of several natural water constituents, such as nitrate, dissolved oxygen (DO) and ferric ions. According to our research, the direct photolysis of SAL followed pseudo-first-order reaction kinetics. Alkaline condition could promote the degradation of SAL; the increase of solution pH would simultaneously increase the fraction of the deprotonated forms of SAL (including the deprotonated and zwitterionic species), which were easier to be excited, and result in the bathochromic shift of the UV-Vis spectrum and, finally, accelerate the degradation rate of SAL. The presence of nitrate could enhance the removal rate of SAL via generation hydroxyl radical (·OH) under irradiation. In addition, the absence of oxygen in the reaction solution could decrease the photolysis. Moreover, Fe(III) was able to chelate with SAL to form an octahedral complex, which was photochemically reactive. The octahedral complex could generate ·OH to oxidize SAL itself in turn. The pathways of SAL photolysis were also investigated by means of the solid phase extraction (SPE)-LC-MS method. The major pathways of SAL photodegradation included oxidation and side-chain cleavage.

Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum

PubMed Central

Vega, Andrea; Canessa, Paulo; Hoppe, Gustavo; Retamal, Ignacio; Moyano, Tomas C.; Canales, Javier; Gutiérrez, Rodrigo A.; Rubilar, Joselyn

2015-01-01

Nitrogen (N) is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants. PMID:26583019

Transcriptomic analysis of Staphylococcus xylosus in the presence of nitrate and nitrite in meat reveals its response to nitrosative stress

PubMed Central

Vermassen, Aurore; de la Foye, Anne; Loux, Valentin; Talon, Régine; Leroy, Sabine

2014-01-01

Staphylococcus xylosus is one of the major starter cultures used for meat fermentation because of its crucial role in the reduction of nitrate to nitrite which contributes to color and flavor development. Despite longstanding use of these additives, their impact on the physiology of S. xylosus has not yet been explored. We present the first in situ global gene expression profile of S. xylosus in meat supplemented with nitrate and nitrite at the levels used in the meat industry. More than 600 genes of S. xylosus were differentially expressed at 24 or 72 h of incubation. They represent more than 20% of the total genes and let us to suppose that addition of nitrate and nitrite to meat leads to a global change in gene expression. This profile revealed that S. xylosus is subject to nitrosative stress caused by reactive nitrogen species (RNS) generated from nitrate and nitrite. To overcome this stress, S. xylosus has developed several oxidative stress resistance mechanisms, such as modulation of the expression of several genes involved in iron homeostasis and in antioxidant defense. Most of which belong to the Fur and PerR regulons, respectively. S. xylosus has also counteracted this stress by developing DNA and protein repair. Furthermore, it has adapted its metabolic response—carbon and nitrogen metabolism, energy production and cell wall biogenesis—to the alterations produced by nitrosative stress. PMID:25566208

Influence of Hydrological Flow Paths on Rates and Forms of Nitrogen Losses from Mediterranean Watersheds

NASA Astrophysics Data System (ADS)

Lohse, K. A.; Sanderman, J.; Amundson, R. G.

2005-12-01

Patterns of precipitation and runoff in California are changing and likely to influence the structure and functioning of watersheds. Studies have demonstrated that hydrologic flushing during seasonal transitions in Mediterranean ecosystems can exert a strong control on nitrogen (N) export, yet few studies have examined the influence of different hydrological flow paths on rates and forms of nitrogen (N) losses. Here we illuminate the influence of variations in precipitation and hydrological pathways on the rate and form of N export along a toposequence of a well-characterized Mediterranean catchment in northern California. As a part of a larger study examining particulate and dissolved carbon loss, we analyzed seasonal patterns of dissolved organic nitrogen (DON), nitrate and ammonium concentrations in rainfall, throughfall, matrix and preferential flow, and stream samples over the course of one water year. We also analyzed seasonal soil N dynamics along this toposequence. During the transition to the winter rain season, but prior to any soil water displacement to the stream, DON and nitrate moved through near-surface soils as preferential flow. Once hillslope soils became saturated, saturated subsurface flow flushed nitrate from the hollow resulting in high stream nitrate/DON concentrations. Between storms, stream nitrate/DON concentrations were lower and appeared to reflect deep subsurface water flow chemistry. During the transition to the wet season, rates of soil nitrate production were high in the hollow relative to the hillslope soils. In the spring, these rates systematically declined as soil moisture decreased. Results from our study suggest seasonal fluctuations in soil moisture control soil N cycling and seasonal changes in the hydrological connection between hillslope soils and streams control the seasonal production and export of hydrologic N.

Endothelial relaxation mechanisms and nitrative stress are partly restored by Vitamin D3 therapy in a rat model of polycystic ovary syndrome.

PubMed

Masszi, Gabriella; Benko, Rita; Csibi, Noemi; Horvath, Eszter M; Tokes, Anna-Maria; Novak, Agnes; Beres, Nora Judit; Tarszabo, Robert; Buday, Anna; Repas, Csaba; Bekesi, Gabor; Patocs, Attila; Nadasy, Gyorgy L; Hamar, Peter; Benyo, Zoltan; Varbiro, Szabolcs

2013-08-06

In polycystic ovary syndrome (PCOS), metabolic and cardiovascular dysfunction is related to hyperandrogenic status and insulin resistance, however, Vitamin D3 has a beneficial effect partly due to its anti-oxidant capacity. Nitrative stress is a major factor in the development of cardiovascular dysfunction and insulin resistance in various diseases. Our aim was to determine the effects of vitamin D3 in a rat model of PCOS, particularly the pathogenic role of nitrative stress. Female Wistar rats weighing 100-140g were administered vehicle (C), dihydrotestosterone (DHT) or dihydrotestosterone plus vitamin D3 (DHT+D) (n=10 per group). On the 10th week, acetylcholine (Ach) induced relaxation ability of the isolated thoracic aorta rings was determined. In order to examine the possible role of endothelial nitric oxide synthase (eNOS) and cyclooxygenase-2 (COX-2) pathways in the impaired endothelial function, immunohistochemical labeling of aortas with anti-eNOS and anti-COX-2 antibodies was performed. Leukocyte smears, aorta and ovary tissue sections were also immunostained with anti-nitrotyrosine antibody to determine nitrative stress. Relaxation ability of aorta was reduced in group DHT, and vitamin D3 partly restored Ach induced relaxation. eNOS labeling was significantly lower in DHT rats compared to the other two groups, however COX-2 staining showed an increment. Nitrative stress showed a significant increase in response to dihydrotestosterone, while vitamin D3 treatment, in case of the ovaries, was able to reverse this effect. Nitrative stress may play a role in the pathogenesis of PCOS and in the development of the therapeutic effect of vitamin D3. Copyright © 2013 Elsevier Inc. All rights reserved.

Targeting nitrative stress for attenuating cisplatin-induced downregulation of cochlear LIM domain only 4 and ototoxicity.

PubMed

Jamesdaniel, Samson; Rathinam, Rajamani; Neumann, William L

2016-12-01

Cisplatin-induced ototoxicity remains a primary dose-limiting adverse effect of this highly effective anticancer drug. The clinical utility of cisplatin could be enhanced if the signaling pathways that regulate the toxic side-effects are delineated. In previous studies, we reported cisplatin-induced nitration of cochlear proteins and provided the first evidence for nitration and downregulation of cochlear LIM domain only 4 (LMO4) in cisplatin ototoxicity. Here, we extend these findings to define the critical role of nitrative stress in cisplatin-induced downregulation of LMO4 and its consequent ototoxic effects in UBOC1 cell cultures derived from sensory epithelial cells of the inner ear and in CBA/J mice. Cisplatin treatment increased the levels of nitrotyrosine and active caspase 3 in UBOC1 cells, which was detected by immunocytochemical and flow cytometry analysis, respectively. The cisplatin-induced nitrative stress and apoptosis were attenuated by co-treatment with SRI110, a peroxynitrite decomposition catalyst (PNDC), which also attenuated the cisplatin-induced downregulation of LMO4 in a dose-dependent manner. Furthermore, transient overexpression of LMO4 in UBOC1 cells prevented cisplatin-induced cytotoxicity while repression of LMO4 exacerbated cisplatin-induced cell death, indicating a direct link between LMO4 protein levels and cisplatin ototoxicity. Finally, auditory brainstem responses (ABR) recorded from CBA/J mice indicated that co-treatment with SRI110 mitigated cisplatin-induced hearing loss. Together, these results suggest that cisplatin-induced nitrative stress leads to a decrease in the levels of LMO4, downregulation of LMO4 is a critical determinant in cisplatin-induced ototoxicity, and targeting peroxynitrite could be a promising strategy for mitigating cisplatin-induced hearing loss. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Assessing denitrification in groundwater using natural gradient tracer tests with 15N: In situ measurement of a sequential multistep reaction

USGS Publications Warehouse

Smith, Richard L.; Böhlke, John Karl; Garabedian, Stephen P.; Revesz, Kinga M.; Yoshinari, Tadashi

2004-01-01

Denitrification was measured within a nitrate‐contaminated aquifer on Cape Cod, Massachusetts, using natural gradient tracer tests with 15N nitrate. The aquifer contained zones of relatively high concentrations of nitrite (up to 77 μM) and nitrous oxide (up to 143 μM) and has been the site of previous studies examining ground water denitrification using the acetylene block technique. Small‐scale (15–24 m travel distance) tracer tests were conducted by injecting 15N nitrate and bromide as tracers into a depth interval that contained nitrate, nitrite, nitrous oxide, and excess nitrogen gas. The timing of the bromide breakthrough curves at down‐gradient wells matched peaks in 15N abundance above background for nitrate, nitrite, nitrous oxide, and nitrogen gas after more than 40 days of travel. Results were simulated with a one‐dimensional transport model using linked reaction kinetics for the individual steps of the denitrification reaction pathway. It was necessary to include within the model spatial variations in background concentrations of all nitrogen oxide species. The model indicated that nitrite production (0.036–0.047 μmol N (L aquifer)−1 d−1) was faster than the subsequent denitrification steps (0.013–0.016 μmol N (L aquifer)−1 d−1 for nitrous oxide and 0.013–0.020 μmol N (L aquifer)−1 d−1 for nitrogen gas) and that the total rate of reaction was slower than indicated by both acetylene block tracer tests and laboratory incubations. The rate of nitrate removal by denitrification was much slower than the rate of transport, indicating that nitrate would migrate several kilometers down‐gradient before being completely consumed.

Tradeoffs between Maize Silage Yield and Nitrate Leaching in a Mediterranean Nitrate-Vulnerable Zone under Current and Projected Climate Scenarios

PubMed Central

Basso, Bruno; Giola, Pietro; Dumont, Benjamin; Migliorati, Massimiliano De Antoni; Cammarano, Davide; Pruneddu, Giovanni; Giunta, Francesco

2016-01-01

Future climatic changes may have profound impacts on cropping systems and affect the agronomic and environmental sustainability of current N management practices. The objectives of this work were to i) evaluate the ability of the SALUS crop model to reproduce experimental crop yield and soil nitrate dynamics results under different N fertilizer treatments in a farmer’s field, ii) use the SALUS model to estimate the impacts of different N fertilizer treatments on NO3- leaching under future climate scenarios generated by twenty nine different global circulation models, and iii) identify the management system that best minimizes NO3- leaching and maximizes yield under projected future climate conditions. A field experiment (maize-triticale rotation) was conducted in a nitrate vulnerable zone on the west coast of Sardinia, Italy to evaluate N management strategies that include urea fertilization (NMIN), conventional fertilization with dairy slurry and urea (CONV), and no fertilization (N0). An ensemble of 29 global circulation models (GCM) was used to simulate different climate scenarios for two Representative Circulation Pathways (RCP6.0 and RCP8.5) and evaluate potential nitrate leaching and biomass production in this region over the next 50 years. Data collected from two growing seasons showed that the SALUS model adequately simulated both nitrate leaching and crop yield, with a relative error that ranged between 0.4% and 13%. Nitrate losses under RCP8.5 were lower than under RCP6.0 only for NMIN. Accordingly, levels of plant N uptake, N use efficiency and biomass production were higher under RCP8.5 than RCP6.0. Simulations under both RCP scenarios indicated that the NMIN treatment demonstrated both the highest biomass production and NO3- losses. The newly proposed best management practice (BMP), developed from crop N uptake data, was identified as the optimal N fertilizer management practice since it minimized NO3- leaching and maximized biomass production over the long term. PMID:26784113

Dissecting the effects of nitrate, sucrose and osmotic potential on Arabidopsis root and shoot system growth in laboratory assays

PubMed Central

Roycewicz, Peter; Malamy, Jocelyn E.

2012-01-01

Studying the specific effects of water and nutrients on plant development is difficult because changes in a single component can often trigger multiple response pathways. Such confounding issues are prevalent in commonly used laboratory assays. For example, increasing the nitrate concentration in growth media alters both nitrate availability and osmotic potential. In addition, it was recently shown that a change in the osmotic potential of media alters the plant's ability to take up other nutrients such as sucrose. It can also be difficult to identify the initial target tissue of a particular environmental cue because there are correlated changes in development of many organs. These growth changes may be coordinately regulated, or changes in development of one organ may trigger changes in development of another organ as a secondary effect. All these complexities make analyses of plant responses to environmental factors difficult to interpret. Here, we review the literature on the effects of nitrate, sucrose and water availability on root system growth and discuss the mechanisms underlying these effects. We then present experiments that examine the impact of nitrate, sucrose and water on root and shoot system growth in culture using an approach that holds all variables constant except the one under analysis. We found that while all three factors also alter root system size, changes in sucrose and osmotic potential also altered shoot system size. In contrast, we found that, when osmotic effects are controlled, nitrate specifically inhibits root system growth while having no effect on shoot system growth. This effectively decreases the root : shoot ratio. Alterations in root : shoot ratio have been widely observed in response to nitrogen starvation, where root growth is selectively increased, but the present results suggest that alterations in this ratio can be triggered across a wide spectrum of nitrate concentrations. PMID:22527391

Fine-tuning of root elongation by ethylene: a tool to study dynamic structure–function relationships between root architecture and nitrate absorption

PubMed Central

Le Deunff, Erwan; Lecourt, Julien; Malagoli, Philippe

2016-01-01

Background Recently developed genetic and pharmacological approaches have been used to explore NO3−/ethylene signalling interactions and how the modifications in root architecture by pharmacological modulation of ethylene biosynthesis affect nitrate uptake. Key Results Structure–function studies combined with recent approaches to chemical genomics highlight the non-specificity of commonly used inhibitors of ethylene biosynthesis such as AVG (l-aminoethoxyvinylglycine). Indeed, AVG inhibits aminotransferases such as ACC synthase (ACS) and tryptophan aminotransferase (TAA) involved in ethylene and auxin biosynthesis but also some aminotransferases implied in nitrogen (N) metabolism. In this framework, it can be assumed that the products of nitrate assimilation and hormones may interact through a hub in carbon (C) and N metabolism to drive the root morphogenetic programme (RMP). Although ethylene/auxin interactions play a major role in cell division and elongation in root meristems, shaping of the root system depends also on energetic considerations. Based on this finding, the analysis is extended to nutrient ion–hormone interactions assuming a fractal or constructal model for root development. Conclusion Therefore, the tight control of root structure–function in the RMP may explain why over-expressing nitrate transporter genes to decouple structure–function relationships and improve nitrogen use efficiency (NUE) has been unsuccessful. PMID:27411681

Inhibition of amyloidogenesis by non-steroidal anti-inflammatory drugs and their hybrid nitrates

PubMed Central

Schiefer, Isaac T.; Abdul-Hay, Samer; Wang, Huali; Vanni, Michael; Qin, Zhihui; Thatcher, Gregory R. J.

2011-01-01

Poor blood-brain barrier penetration of non-steroidal anti-inflammatory drugs (NSAIDs) has been blamed for the failure of the selective amyloid lowering agent (SALA) R-flurbiprofen in phase 3 clinical trials for Alzheimer’s disease (AD). NO-donor NSAIDs (NO-NSAIDs) provide an alternative, gastric-sparing approach to NSAID SALAs, which may improve bioavailability. NSAID analogs were studied for anti-inflammatory activity and for SALA activity in N2a neuronal cells transfected with human amyloid precursor protein (APP). Flurbiprofen (1) analogs were obtained with enhanced anti-inflammatory and anti-amyloidogenic properties compared to 1, however, esterification led to elevated Aβ1–42 levels. Hybrid nitrate prodrugs possessed superior anti-inflammatory activity and reduced toxicity relative to the parent NSAIDs, including clinical candidate, CHF5074. Although hybrid nitrates elevated Aβ1–42 at higher concentration, SALA activity was observed at low concentrations (≤ 1 µM): both Aβ1–42 and the ratio of Aβ1–42/Aβ1–40 were lowered. This biphasic SALA activity was attributed to the intact nitrate drug. For several compounds the selective modulation of amyloidogenesis was tested using an immunoprecipitation MALDI-TOF approach. These data support the development of NO-NSAIDs as an alternative approach towards a clinically useful SALA. PMID:21405086

Screening for Key Pathways Associated with the Development of Osteoporosis by Bioinformatics Analysis

PubMed Central

Liu, Yanqing; Wang, Yueqiu; Zhang, Yanxia; Liu, Zhiyong; Xiang, Hongfei; Peng, Xianbo

2017-01-01

Objectives. We aimed to find the key pathways associated with the development of osteoporosis. Methods. We downloaded expression profile data of GSE35959 and analyzed the differentially expressed genes (DEGs) in 3 comparison groups (old_op versus middle, old_op versus old, and old_op versus senescent). KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses were carried out. Besides, Venn diagram analysis and gene functional interaction (FI) network analysis were performed. Results. Totally 520 DEGs, 966 DEGs, and 709 DEGs were obtained in old_op versus middle, old_op versus old, and old_op versus senescent groups, respectively. Lysosome pathway was the significantly enriched pathways enriched by intersection genes. The pathways enriched by subnetwork modules suggested that mitotic metaphase and anaphase and signaling by Rho GTPases in module 1 had more proteins from module. Conclusions. Lysosome pathway, mitotic metaphase and anaphase, and signaling by Rho GTPases may be involved in the development of osteoporosis. Furthermore, Rho GTPases may regulate the balance of bone resorption and bone formation via controlling osteoclast and osteoblast. These 3 pathways may be regarded as the treatment targets for osteoporosis. PMID:28466021

Development of a Water-Quality Lab That Enhances Learning & Connects Students to the Land

ERIC Educational Resources Information Center

Enos-Berlage, Jodi

2012-01-01

A 3-week laboratory module was developed for an undergraduate microbiology course that would connect student learning to a real-life challenge, specifically a local water-quality project. The laboratory series included multiple field trips, sampling of soil and water, and subsequent analysis for bacteria and nitrate. Laboratory results confirmed…

Ras-sensitive IMP modulation of the Raf/MEK/ERK cascade through KSR1.

PubMed

Matheny, Sharon A; White, Michael A

2006-01-01

The E3 ubiquitin ligase IMP (impedes mitogenic signal propagation) was isolated as a novel Ras effector that negatively regulates ERK1/2 activation. Current evidence suggests that IMP limits the functional assembly of Raf/MEK complexes by inactivation of the KSR1 adaptor/scaffold protein. Interaction with Ras-GTP stimulates IMP autoubiquitination to relieve limitations on KSR function. The elevated sensitivity of IMP-depleted cells to ERK1/2 pathway activation suggests IMP acts as a signal threshold regulator by imposing reversible restrictions on the assembly of functional Raf/MEK/ERK kinase modules. These observations challenge commonly held concepts of signal transmission by Ras to the MAPK pathway and provide evidence for the role of amplitude modulation in tuning cellular responses to ERK1/2 pathway engagement. Here we describe details of the methods, including RNA interference, ubiquitin ligase assays, and protein complex analysis, that can be used to display the Ras-sensitive contribution of IMP to KSR-dependent modulation of the Raf/MEK/ERK pathway.

New methodology for the thermal characterization of thermoelectric liquids

NASA Astrophysics Data System (ADS)

Touati, Karim; Depriester, Michael; Kuriakose, Maju; Hadj Sahraoui, Abdelhak

2015-09-01

A new and accurate method for the thermal characterization of thermoelectric liquids is proposed. The experiment is based on a self-generated voltage due to the Seebeck effect. This voltage is provided by the sample when one of its two faces is thermally excited using a modulated laser. The sample used is tetradodecylammonium nitrate salt/1-octanol mixture, with high Seebeck coefficient. The thermal properties of the used sample (thermal diffusivity, effusivity, and conductivity) are found and compared to those obtained by other photothermal techniques. In addition to this, a study of the electrolyte thermal parameters with the variation of tetradodecylammonium nitrate concentration was also carried out. This new method is promising due to its accuracy and its simplicity.

Differential Effect of Lactobacillus johnsonii BFE 6128 on Expression of Genes Related to TLR Pathways and Innate Immunity in Intestinal Epithelial Cells.

PubMed

Seifert, Stephanie; Rodriguez Gómez, Manuel; Watzl, Bernhard; Holzapfel, Wilhelm H; Franz, Charles M A P; Vizoso Pinto, María G

2010-12-01

Probiotics have been shown to enhance immune defenses, but their mechanisms of action are only partially understood. We investigated the modulation of signal pathways involved in innate immunity in enterocytes by Lactobacillus johnsonii BFE 6128 isolated from 'Kule naoto', a Maasai traditional fermented milk product. This lactobacillus sensitized HT29 intestinal epithelial cells toward recognition of Salmonella enterica serovar Typhimurium by increasing the IL-8 levels released after challenge with this pathogen and by differentially modulating genes related to toll-like receptor (TLR) pathways and innate immunity. Thus, the modulation of pro-inflammatory mediators and TLR-pathway-related molecules may be an important mechanism contributing to the potential stimulation of innate immunity by lactobacilli at the intestinal epithelial level.

Implications of Green Tea and Its Constituents in the Prevention of Cancer via the Modulation of Cell Signalling Pathway

PubMed Central

Rahmani, Arshad H.; Al shabrmi, Fahad M.; Allemailem, Khaled S.; Aly, Salah M.; Khan, Masood A.

2015-01-01

Green tea is commonly used as a beverage worldwide, especially in China, Japan, Morocco, and Saudi Arabia. Green tea and its constituents have been considered very effective in the prevention and treatment of various diseases. It contains a variety of catechins, which show a pivotal role in the modulation of biological activities and also act as chemopreventive agents. Earlier studies have confirmed that green tea and its chief constituent epigallocatechin gallate (EGCG) have a potential role in the management of cancer through the modulation of cell signaling pathways. In this review, we focused on the beneficial effects of green tea and its constituents in the cancer prevention and treatment and its impact on modulation of molecular pathways. PMID:25977926

Androstenediol inhibits the trauma-hemorrhage-induced increase in caspase-3 by downregulating the inducible nitric oxide synthase pathway.

PubMed

Kiang, Juliann G; Peckham, Russell M; Duke, Leah E; Shimizu, Tomoharu; Chaudry, Irshad H; Tsokos, George C

2007-03-01

Soft tissue trauma and hemorrhage (T-H) diminishes various aspects of liver function, while it increases hepatic nitrate/nitrite, inducible nitric oxide synthase (iNOS), and endothelin-1 levels. Treatment with androstenediol (AED) inhibits the T-H-induced alterations of the above parameters. We sought to identify the molecular events underlying the beneficial effect of AED. Exposure of rats to T-H significantly increased the caspase-3 activity and protein, whereas treatment with AED significantly limited these increases. AED treatment also suppressed the T-H-induced increase in iNOS by effectively altering the levels of key transcription factors involved in the regulation of iNOS expression. Immunoprecipitation and immunoblotting analyses indicate that T-H increased apoptosome formation, and AED treatment significantly decreased it. Modulating the iNOS protein by transfecting cells with iNOS gene or small interfering RNA further confirmed the correlation between iNOS and caspase-3. Our data indicate that AED limits caspase-3 expression by suppressing the expression of transcription factors involved in the production of iNOS, resulting in decreased apoptosome. AED can potentially be a useful adjuvant for limiting liver apoptosis following T-H shock.

Npr1 Ser/Thr Protein Kinase Links Nitrogen Source Quality and Carbon Availability with the Yeast Nitrate Transporter (Ynt1) Levels*

PubMed Central

Martín, Yusé; González, Yelvis V.; Cabrera, Elisa; Rodríguez, Celia; Siverio, José M.

2011-01-01

Ynt1, the single high affinity nitrate and nitrite transporter of the yeast Hansenula polymorpha, is regulated by the quality of nitrogen sources. Preferred nitrogen sources cause Ynt1 dephosphorylation, ubiquitinylation, endocytosis, and vacuolar degradation. In contrast, under nitrogen limitation Ynt1 is phosphorylated and sorted to the plasma membrane. We show here the involvement of the Ser/Thr kinase HpNpr1 in Ynt1 phosphorylation and regulation of Ynt1 levels in response to nitrogen source quality and the availability of carbon. In Δnpr1, Ynt1 phosphorylation does not take place, although Ynt1 ubiquitin conjugates increase. As a result, in this strain Ynt1 is sorted to the vacuole, from both plasma membrane and the later biosynthetic pathway in nitrogen-free conditions and nitrate. In contrast, overexpression of NPR1 blocks down-regulation of Ynt1, increasing Ynt1 phosphorylation at Ser-244 and -246 and reducing ubiquitinylation. Furthermore, Npr1 is phosphorylated in response to the preferred nitrogen sources, and indeed it is dephosphorylated in nitrogen-free medium. Under conditions where Npr1 is phosphorylated, Ynt1 is not and vice versa. We show for the first time that carbon starvation leads to Npr1 phosphorylation, whereas Ynt1 is dephosphorylated and degraded in the vacuole. Rapamycin prevents this, indicating a possible role of the target of rapamycin signaling pathway in this process. We concluded that Npr1 plays a key role in adapting Ynt1 levels to the nitrogen quality and availability of a source of carbon. PMID:21652715

Metabolic flux analysis of Cyanothece sp. ATCC 51142 under mixotrophic conditions.

PubMed

Alagesan, Swathi; Gaudana, Sandeep B; Sinha, Avinash; Wangikar, Pramod P

2013-11-01

Cyanobacteria are a group of photosynthetic prokaryotes capable of utilizing solar energy to fix atmospheric carbon dioxide to biomass. Despite several "proof of principle" studies, low product yield is an impediment in commercialization of cyanobacteria-derived biofuels. Estimation of intracellular reaction rates by (13)C metabolic flux analysis ((13)C-MFA) would be a step toward enhancing biofuel yield via metabolic engineering. We report (13)C-MFA for Cyanothece sp. ATCC 51142, a unicellular nitrogen-fixing cyanobacterium, known for enhanced hydrogen yield under mixotrophic conditions. Rates of reactions in the central carbon metabolism under nitrogen-fixing and -non-fixing conditions were estimated by monitoring the competitive incorporation of (12)C and (13)C from unlabeled CO2 and uniformly labeled glycerol, respectively, into terminal metabolites such as amino acids. The observed labeling patterns suggest mixotrophic growth under both the conditions, with a larger fraction of unlabeled carbon in nitrate-sufficient cultures asserting a greater contribution of carbon fixation by photosynthesis and an anaplerotic pathway. Indeed, flux analysis complements the higher growth observed under nitrate-sufficient conditions. On the other hand, the flux through the oxidative pentose phosphate pathway and tricarboxylic acid cycle was greater in nitrate-deficient conditions, possibly to supply the precursors and reducing equivalents needed for nitrogen fixation. In addition, an enhanced flux through fructose-6-phosphate phosphoketolase possibly suggests the organism's preferred mode under nitrogen-fixing conditions. The (13)C-MFA results complement the reported predictions by flux balance analysis and provide quantitative insight into the organism's distinct metabolic features under nitrogen-fixing and -non-fixing conditions.

Uranyl nitrate-exposed rat alveolar macrophages cell death: Influence of superoxide anion and TNF α mediators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orona, N.S.; Tasat, D.R., E-mail: deborah.tasat@unsam.edu.ar; School of Dentistry, University of Buenos Aires, M. T. de Alvear 2142

2012-06-15

Uranium compounds are widely used in the nuclear fuel cycle, military and many other diverse industrial processes. Health risks associated with uranium exposure include nephrotoxicity, cancer, respiratory, and immune disorders. Macrophages present in body tissues are the main cell type involved in the internalization of uranium particles. To better understand the pathological effects associated with depleted uranium (DU) inhalation, we examined the metabolic activity, phagocytosis, genotoxicity and inflammation on DU-exposed rat alveolar macrophages (12.5–200 μM). Stability and dissolution of DU could differ depending on the dissolvent and in turn alter its biological action. We dissolved DU in sodium bicarbonate (NaHCO{submore » 3} 100 mM) and in what we consider a more physiological vehicle resembling human internal media: sodium chloride (NaCl 0.9%). We demonstrate that uranyl nitrate in NaCl solubilizes, enters the cell, and elicits its cytotoxic effect similarly to when it is diluted in NaHCO{sub 3}. We show that irrespective of the dissolvent employed, uranyl nitrate impairs cell metabolism, and at low doses induces both phagocytosis and generation of superoxide anion (O{sub 2}{sup −}). At high doses it provokes the secretion of TNFα and through all the range of doses tested, apoptosis. We herein suggest that at DU low doses O{sub 2}{sup −} may act as the principal mediator of DNA damage while at higher doses the signaling pathway mediated by O{sub 2}{sup −} may be blocked, prevailing damage to DNA by the TNFα route. The study of macrophage functions after uranyl nitrate treatment could provide insights into the pathophysiology of uranium‐related diseases. -- Highlights: ► Uranyl nitrate effect on cultured macrophages is linked to the doses and independent of its solubility. ► At low doses uranyl nitrate induces generation of superoxide anion. ► At high doses uranyl nitrate provokes secretion of TNFα. ► Uranyl nitrate induces apoptosis through all the range of doses tested.« less

Reversible Oxidation of a Conserved Methionine in the Nuclear Export Sequence Determines Subcellular Distribution and Activity of the Fungal Nitrate Regulator NirA.

PubMed

Gallmetzer, Andreas; Silvestrini, Lucia; Schinko, Thorsten; Gesslbauer, Bernd; Hortschansky, Peter; Dattenböck, Christoph; Muro-Pastor, María Isabel; Kungl, Andreas; Brakhage, Axel A; Scazzocchio, Claudio; Strauss, Joseph

2015-07-01

The assimilation of nitrate, a most important soil nitrogen source, is tightly regulated in microorganisms and plants. In Aspergillus nidulans, during the transcriptional activation process of nitrate assimilatory genes, the interaction between the pathway-specific transcription factor NirA and the exportin KapK/CRM1 is disrupted, and this leads to rapid nuclear accumulation and transcriptional activity of NirA. In this work by mass spectrometry, we found that in the absence of nitrate, when NirA is inactive and predominantly cytosolic, methionine 169 in the nuclear export sequence (NES) is oxidized to methionine sulfoxide (Metox169). This oxidation depends on FmoB, a flavin-containing monooxygenase which in vitro uses methionine and cysteine, but not glutathione, as oxidation substrates. The function of FmoB cannot be replaced by alternative Fmo proteins present in A. nidulans. Exposure of A. nidulans cells to nitrate led to rapid reduction of NirA-Metox169 to Met169; this reduction being independent from thioredoxin and classical methionine sulfoxide reductases. Replacement of Met169 by isoleucine, a sterically similar but not oxidizable residue, led to partial loss of NirA activity and insensitivity to FmoB-mediated nuclear export. In contrast, replacement of Met169 by alanine transformed the protein into a permanently nuclear and active transcription factor. Co-immunoprecipitation analysis of NirA-KapK interactions and subcellular localization studies of NirA mutants lacking different parts of the protein provided evidence that Met169 oxidation leads to a change in NirA conformation. Based on these results we propose that in the presence of nitrate the activation domain is exposed, but the NES is masked by a central portion of the protein (termed nitrate responsive domain, NiRD), thus restricting active NirA molecules to the nucleus. In the absence of nitrate, Met169 in the NES is oxidized by an FmoB-dependent process leading to loss of protection by the NiRD, NES exposure, and relocation of the inactive NirA to the cytosol.

NO oxidation on Zeolite Supported Cu Catalysts: Formation and Reactivity of Surface Nitrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Hai-Ying; Wei, Zhehao; Kollar, Marton

2016-04-18

The comparative activities of a small-pore Cu-CHA and a large-pore Cu-BEA catalyst for the selective catalytic reduction (SCR) of NOx with NH3, and for the oxidation of NO to NO2 and the subsequent formation of surface nitrates were investigated. Although both catalysts are highly active in SCR reactions, they exhibit very low NO oxidation activity. Furthermore, Cu-CHA is even less active than Cu-BEA in catalyzing NO oxidation but is clearly more active for SCR reactions. Temperature-programed desorption (TPD) experiments following the adsorption of (NO2 + NO + O2) with different NO2:NO ratios reveal that the poor NO oxidation activity ofmore » the two catalysts is not due to the formation of stable surface nitrates. On the contrary, NO is found to reduce and decompose the surface nitrates on both catalysts. To monitor the reaction pathways, isotope exchange experiments were conducted by using 15NO to react with 14N-nitrate covered catalyst surfaces. The evolution of FTIR spectra during the isotope exchange process demonstrates that 14N-nitrates are simply displaced with no formation of 15N-nitrates on the Cu-CHA sample, which is clearly different from that observed on the Cu-BEA sample where formation of 15N-nitrates is apparent. The results suggest that the formal oxidation state of N during the NO oxidation on Cu-CHA mainly proceeds from its original +2 to a +3 oxidation state, whereas reaching a higher oxidation state for N, such as +4 or +5, is possible on Cu-BEA. The authors at PNNL gratefully acknowledge the US Department of Energy (DOE), Energy Efficiency and Renewable Energy, Vehicle Technologies Office for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle.« less

Pan-phylum Comparison of Nematode Metabolic Potential

PubMed Central

Tyagi, Rahul; Rosa, Bruce A.; Lewis, Warren G.; Mitreva, Makedonka

2015-01-01

Nematodes are among the most important causative pathogens of neglected tropical diseases. The increased availability of genomic and transcriptomic data for many understudied nematode species provides a great opportunity to investigate different aspects of their biology. Increasingly, metabolic potential of pathogens is recognized as a critical determinant governing their development, growth and pathogenicity. Comparing metabolic potential among species with distinct trophic ecologies can provide insights on overall biology or molecular adaptations. Furthermore, ascertaining gene expression at pathway level can help in understanding metabolic dynamics over development. Comparison of biochemical pathways (or subpathways, i.e. pathway modules) among related species can also retrospectively indicate potential mistakes in gene-calling and functional annotation. We show with numerous illustrative case studies that comparisons at the level of pathway modules have the potential to uncover biological insights while remaining computationally tractable. Here, we reconstruct and compare metabolic modules found in the deduced proteomes of 13 nematodes and 10 non-nematode species (including hosts of the parasitic nematode species). We observed that the metabolic potential is, in general, concomitant with phylogenetic and/or ecological similarity. Varied metabolic strategies are required among the nematodes, with only 8 out of 51 pathway modules being completely conserved. Enzyme comparison based on topology of metabolic modules uncovered diversification between parasite and host that can potentially guide therapeutic intervention. Gene expression data from 4 nematode species were used to study metabolic dynamics over their life cycles. We report unexpected differential metabolism between immature and mature microfilariae of the human filarial parasite Brugia malayi. A set of genes potentially important for parasitism is also reported, based on an analysis of gene expression in C. elegans and the human hookworm Necator americanus. We illustrate how analyzing and comparing metabolism at the level of pathway modules can improve existing knowledge of nematode metabolic potential and can provide parasitism related insights. Our reconstruction and comparison of nematode metabolic pathways at a pan-phylum and inter-phylum level enabled determination of phylogenetic restrictions and differential expression of pathways. A visualization of our results is available at http://nematode.net and the program for identification of module completeness (modDFS) is freely available at SourceForge. The methods reported will help biologists to predict biochemical potential of any organism with available deduced proteome, to direct experiments and test hypotheses. PMID:26000881

Pseudomonads Isolated from Pristine Background Groundwater Proliferate More Effectively in Co-culture than in Monoculture Under Denitrifying Conditions

NASA Astrophysics Data System (ADS)

Aaring, A. B.; Lancaster, A.; Novichkov, P.; Adams, M. W. W.; Deutschbauer, A. M.; Chakraborty, R.

2016-12-01

As part of the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) consortium, we study the microbial community at the U.S. Department of Energy's Field Research Center (FRC) in Oak Ridge. The groundwater at this site contains plumes of nitrate with concentrations up to 14,000mg/L among other contaminants, though molybdenum concentrations are low. Because molybdenum is essential to nitrate reduction, this can be inhibitory to growth. Several strains of Pseudomonas were isolated from the same background groundwater sample. These isolates utilized diverse carbon sources ranging from acetate to glucose while growing under denitrifying conditions. The strains were also screened for nitrate tolerance and a couple of them were shown to be tolerant to 300-400 mM nitrate under anaerobic conditions. In the field site the bacteria live in consortia rather than in isolation, therefore we hypothesized that growth of these strains will be more robust in co-culture, as the denitrification pathway was segmented between the species. Three of the isolates (Pseudomonas fluorescens strains N1B4, N2E2, N2E3) were selected for in-depth analysis based on growth in pairwise co-cultures relative to monocultures, and the availability of the relevant genetic tools, such as transposon mutant libraries. Full genome sequencing showed that strain N2E3 has a truncated dentrification pathway: it lacks nitrous oxide reductase. Our results show strain N2E2 grow to maximum cell density an average of 45 hours more quickly when grown with strain N2E3 than in monoculture. Utilizing RB-TnSeq libraries of our strains, it was also found that some genes involved in nitrate reduction, sulfate permeability, molybdenum utilization, and anaerobic reduction are important for growth under these conditions. In addition, a few unexpected genes were also shown to be positively correlated to growth, such as genes homologous to genes for DNA proofreading or antibiotic production. These data help to broaden our understanding of how bacteria interact and grow in conditions that are relevant to the environment and enable us to probe the ways in which bacterial communities interact and overcome genetic deficiencies of individual strains to deal with environmental conditions.

Protein Tyrosine Nitration: Biochemical Mechanisms and Structural Basis of its Functional Effects

PubMed Central

Radi, Rafael

2012-01-01

CONSPECTUS The nitration of protein tyrosine residues to 3-nitrotyrosine represents an oxidative postranslational modification that unveils the disruption of nitric oxide (•NO) signaling and metabolism towards pro-oxidant processes. Indeed, excess levels of reactive oxygen species in the presence of •NO or •NO-derived metabolites lead to the formation of nitrating species such as peroxynitrite. Thus, protein 3-nitrotyrosine has been established as a biomarker of cell, tissue and systemic “nitroxidative stress”. Moreover, tyrosine nitration modifies key properties of the amino acid (i.e. phenol group pKa, redox potential, hydrophobicity and volume). Thus, the incorporation of a nitro group (−NO2) to protein tyrosines can lead to profound structural and functional changes, some of which contribute to altered cell and tissue homeostasis. In this Account, I describe our current efforts to define 1) biologically-relevant mechanisms of protein tyrosine nitration and 2) how this modification can cause changes in protein structure and function at the molecular level. First, the relevance of protein tyrosine nitration via free radical-mediated reactions (in both peroxynitrite-dependent or independent pathways) involving the intermediacy of tyrosyl radical (Tyr•) will be underscored. This feature of the nitration process becomes critical as Tyr• can take variable fates, including the formation of 3-nitrotyrosine. Fast kinetic techniques, electron paramagnetic resonance (EPR) studies, bioanalytical methods and kinetic simulations have altogether assisted to characterize and fingerprint the reactions of tyrosine with peroxynitrite and one-electron oxidants and its further evolution to 3-nitrotyrosine. Recent findings show that nitration of tyrosines in proteins associated to biomembranes is linked to the lipid peroxidation process via a connecting reaction that involves the one-electron oxidation of tyrosine by lipid peroxyl radicals (LOO•). Second, immunochemical and proteomic-based studies indicate that protein tyrosine nitration is a selective process in vitro and in vivo, preferentially directed to a subset of proteins, and within those proteins, typically one or two tyrosine residues are site-specifically modified. The nature and site(s) of formation of the proximal oxidizing/nitrating species, the physico-chemical characteristics of the local microenvironment and also structural features of the protein account for part of this selectivity. Then, how this relatively subtle chemical modification in one tyrosine residue can sometimes cause dramatic changes in protein activity has remained elusive. Herein, I will analyze recent structural biology data of two pure and homogenously nitrated mitochondrial proteins (i.e. cytochrome c and MnSOD) to illustrate regio-selectivity and structural effects of tyrosine nitration, and subsequent impact in protein loss- or even gain-of-function. PMID:23157446

A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants.

PubMed

Wisecaver, Jennifer H; Borowsky, Alexander T; Tzin, Vered; Jander, Georg; Kliebenstein, Daniel J; Rokas, Antonis

2017-05-01

Plants produce diverse specialized metabolites (SMs), but the genes responsible for their production and regulation remain largely unknown, hindering efforts to tap plant pharmacopeia. Given that genes comprising SM pathways exhibit environmentally dependent coregulation, we hypothesized that genes within a SM pathway would form tight associations (modules) with each other in coexpression networks, facilitating their identification. To evaluate this hypothesis, we used 10 global coexpression data sets, each a meta-analysis of hundreds to thousands of experiments, across eight plant species to identify hundreds of coexpressed gene modules per data set. In support of our hypothesis, 15.3 to 52.6% of modules contained two or more known SM biosynthetic genes, and module genes were enriched in SM functions. Moreover, modules recovered many experimentally validated SM pathways, including all six known to form biosynthetic gene clusters (BGCs). In contrast, bioinformatically predicted BGCs (i.e., those lacking an associated metabolite) were no more coexpressed than the null distribution for neighboring genes. These results suggest that most predicted plant BGCs are not genuine SM pathways and argue that BGCs are not a hallmark of plant specialized metabolism. We submit that global gene coexpression is a rich, largely untapped resource for discovering the genetic basis and architecture of plant natural products. © 2017 American Society of Plant Biologists. All rights reserved.

lncRNA co-expression network model for the prognostic analysis of acute myeloid leukemia

PubMed Central

Pan, Jia-Qi; Zhang, Yan-Qing; Wang, Jing-Hua; Xu, Ping; Wang, Wei

2017-01-01

Acute myeloid leukemia (AML) is a highly heterogeneous hematologic malignancy with great variability of prognostic behaviors. Previous studies have reported that long non-coding RNAs (lncRNAs) play an important role in AML and may thus be used as potential prognostic biomarkers. However, thus use of lncRNAs as prognostic biomarkers in AML and their detailed mechanisms of action in this disease have not yet been well characterized. For this purpose, in the present study, the expression levels of lncRNAs and mRNAs were calculated using the RNA-seq V2 data for AML, following which a lncRNA-lncRNA co-expression network (LLCN) was constructed. This revealed a total of 8 AML prognosis-related lncRNA modules were identified, which displayed a significant correlation with patient survival (p≤0.05). Subsequently, a prognosis-related lncRNA module pathway network was constructed to interpret the functional mechanism of the prognostic modules in AML. The results indicated that these prognostic modules were involved in the AML pathway, chemokine signaling pathway and WNT signaling pathway, all of which play important roles in AML. Furthermore, the investigation of lncRNAs in these prognostic modules suggested that an lncRNA (ZNF571-AS1) may be involved in AML via the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway by regulating KIT and STAT5. The results of the present study not only provide potential lncRNA modules as prognostic biomarkers, but also provide further insight into the molecular mechanisms of action of lncRNAs. PMID:28204819

Identification of miRNA-Mediated Core Gene Module for Glioma Patient Prediction by Integrating High-Throughput miRNA, mRNA Expression and Pathway Structure

PubMed Central

Han, Junwei; Shang, Desi; Zhang, Yunpeng; Zhang, Wei; Yao, Qianlan; Han, Lei; Xu, Yanjun; Yan, Wei; Bao, Zhaoshi; You, Gan; Jiang, Tao; Kang, Chunsheng; Li, Xia

2014-01-01

The prognosis of glioma patients is usually poor, especially in patients with glioblastoma (World Health Organization (WHO) grade IV). The regulatory functions of microRNA (miRNA) on genes have important implications in glioma cell survival. However, there are not many studies that have investigated glioma survival by integrating miRNAs and genes while also considering pathway structure. In this study, we performed sample-matched miRNA and mRNA expression profilings to systematically analyze glioma patient survival. During this analytical process, we developed pathway-based random walk to identify a glioma core miRNA-gene module, simultaneously considering pathway structure information and multi-level involvement of miRNAs and genes. The core miRNA-gene module we identified was comprised of four apparent sub-modules; all four sub-modules displayed a significant correlation with patient survival in the testing set (P-values≤0.001). Notably, one sub-module that consisted of 6 miRNAs and 26 genes also correlated with survival time in the high-grade subgroup (WHO grade III and IV), P-value = 0.0062. Furthermore, the 26-gene expression signature from this sub-module had robust predictive power in four independent, publicly available glioma datasets. Our findings suggested that the expression signatures, which were identified by integration of miRNA and gene level, were closely associated with overall survival among the glioma patients with various grades. PMID:24809850

Yeast nitrogen utilization in the phyllosphere during plant lifespan under regulation of autophagy

PubMed Central

Shiraishi, Kosuke; Oku, Masahide; Kawaguchi, Kosuke; Uchida, Daichi; Yurimoto, Hiroya; Sakai, Yasuyoshi

2015-01-01

Recently, microbe-plant interactions at the above-ground parts have attracted great attention. Here we describe nitrogen metabolism and regulation of autophagy in the methylotrophic yeast Candida boidinii, proliferating and surviving on the leaves of Arabidopsis thaliana. After quantitative analyses of yeast growth on the leaves of A. thaliana with the wild-type and several mutant yeast strains, we showed that on young leaves, nitrate reductase (Ynr1) was necessary for yeast proliferation, and the yeast utilized nitrate as nitrogen source. On the other hand, a newly developed methylamine sensor revealed appearance of methylamine on older leaves, and methylamine metabolism was induced in C. boidinii, and Ynr1 was subjected to degradation. Biochemical and microscopic analysis of Ynr1 in vitro during a shift of nitrogen source from nitrate to methylamine revealed that Ynr1 was transported to the vacuole being the cargo for biosynthetic cytoplasm-to-vacuole targeting (Cvt) pathway, and degraded. Our results reveal changes in the nitrogen source composition for phyllospheric yeasts during plant aging, and subsequent adaptation of the yeasts to this environmental change mediated by regulation of autophagy. PMID:25900611

Review: the environmental status and implications of the nitrate time lag in Europe and North America

NASA Astrophysics Data System (ADS)

Vero, Sara E.; Basu, Nandita B.; Van Meter, Kimberly; Richards, Karl G.; Mellander, Per-Erik; Healy, Mark G.; Fenton, Owen

2018-02-01

The efficacy of water quality policies aiming to reduce or prevent nitrate contamination of waterbodies may be constrained by the inherent delay or "time lag" of water and solute transport through unsaturated (soil) and saturated (groundwater) pathways. These delays must be quantified in order to establish realistic deadlines, thresholds and policy expectations, and to design effective best management practices. The objective of this review is to synthesise the current state of research on nitrate-related time lags in both the European and North American environmental and legislative contexts. The durations of time lags have been found to differ according to climatic, pedological, landscape and management scenarios. Elucidation of these driving factors at a watershed scale is essential where water quality is impaired or at risk. Finally, the existence of time lags is increasingly being acknowledged at a policy level and incorporated into the development of environmental legislation. However, the full impact of these time lags is not yet fully understood or appreciated, and continued outreach and education in scientific, public and policy venues is still required.

Nitrification in agricultural soils: impact, actors and mitigation.

PubMed

Beeckman, Fabian; Motte, Hans; Beeckman, Tom

2018-04-01

Nitrogen is one of the most important nutrients for plant growth and hence heavily applied in agricultural systems via fertilization. Nitrification, that is, the conversion of ammonium via nitrite to nitrate by soil microorganisms, however, leads to nitrate leaching and gaseous nitrous oxide production and as such to an up to 50% loss of nitrogen availability for the plant. Nitrate leaching also results in eutrophication of groundwater, drinking water and recreational waters, toxic algal blooms and biodiversity loss, while nitrous oxide is a greenhouse gas with a global warming potential 300× greater than carbon dioxide. Logically, inhibition of nitrification is an important strategy used in agriculture to reduce nitrogen losses, and contributes to a more environmental-friendly practice. However, recently identified and crucial players in nitrification, that is, ammonia-oxidizing archaea and comammox bacteria, seem to be under-investigated in this respect. In this review, we give an update on the different pathways in ammonia oxidation, the relevance for agriculture and the interaction with nitrification inhibitors. As such, we hope to pinpoint possible strategies to optimize the efficiency of nitrification inhibition. Copyright © 2018 Elsevier Ltd. All rights reserved.

Distinct domains within the NITROGEN LIMITATION ADAPTATION protein mediate its subcellular localization and function in the nitrate-dependent phosphate homeostasis pathway

USDA-ARS?s Scientific Manuscript database

The NITROGEN LIMITATION ADAPTATION (NLA) protein is a RING-type E3 ubiquitin ligase that plays an essential role in the regulation of nitrogen and phosphate homeostasis. NLA is localized to two distinct subcellular sites, the plasma membrane and nucleus, and contains four distinct domains: i) a RING...

Microbial denitrification dominates nitrate losses from forest ecosystems

PubMed Central

Fang, Yunting; Koba, Keisuke; Makabe, Akiko; Takahashi, Chieko; Zhu, Weixing; Hayashi, Takahiro; Hokari, Azusa A.; Urakawa, Rieko; Bai, Edith; Houlton, Benjamin Z.; Xi, Dan; Zhang, Shasha; Matsushita, Kayo; Tu, Ying; Liu, Dongwei; Zhu, Feifei; Wang, Zhenyu; Zhou, Guoyi; Chen, Dexiang; Makita, Tomoko; Toda, Hiroto; Liu, Xueyan; Chen, Quansheng; Zhang, Deqiang; Li, Yide; Yoh, Muneoki

2015-01-01

Denitrification removes fixed nitrogen (N) from the biosphere, thereby restricting the availability of this key limiting nutrient for terrestrial plant productivity. This microbially driven process has been exceedingly difficult to measure, however, given the large background of nitrogen gas (N2) in the atmosphere and vexing scaling issues associated with heterogeneous soil systems. Here, we use natural abundance of N and oxygen isotopes in nitrate (NO3−) to examine dentrification rates across six forest sites in southern China and central Japan, which span temperate to tropical climates, as well as various stand ages and N deposition regimes. Our multiple stable isotope approach across soil to watershed scales shows that traditional techniques underestimate terrestrial denitrification fluxes by up to 98%, with annual losses of 5.6–30.1 kg of N per hectare via this gaseous pathway. These N export fluxes are up to sixfold higher than NO3− leaching, pointing to widespread dominance of denitrification in removing NO3− from forest ecosystems across a range of conditions. Further, we report that the loss of NO3− to denitrification decreased in comparison to leaching pathways in sites with the highest rates of anthropogenic N deposition. PMID:25605898

Enhancement of Naringenin Biosynthesis from Tyrosine by Metabolic Engineering of Saccharomyces cerevisiae.

PubMed

Lyu, Xiaomei; Ng, Kuan Rei; Lee, Jie Lin; Mark, Rita; Chen, Wei Ning

2017-08-09

Flavonoids are an important class of plant polyphenols that possess a variety of health benefits. In this work, S. cerevisiae was metabolically engineered to produce the flavonoid naringenin, using tyrosine as the precursor. Our strategy to improve naringenin production comprised three modules. In module 1, we employed a modified GAL system to overexpress the genes of the naringenin biosynthesis pathway and investigated their synergistic action. In module 2, we simultaneously up-regulated acetyl-CoA production and down-regulated fatty acid biosynthesis in order to increase the precursor supply, malonyl-CoA. In module 3, we engineered the tyrosine biosynthetic pathway to eliminate the feedback inhibition of tyrosine and also down-regulated competing pathways. It was found that modules 1 and 3 played important roles in improving naringenin production. We succeeded in producing up to ∼90 mg/L of naringenin in our final strain, which is a 20-fold increase as compared to the parental strain.

Sources, transformations, and hydrological processes that control stream nitrate and dissolved organic matter concentrations during snowmelt in an upland forest

USGS Publications Warehouse

Sebestyen, Stephen D.; Boyer, Elizabeth W.; Shanley, James B.; Kendall, Carol; Doctor, Daniel H.; Aiken, George R.; Ohte, Nobuhito

2008-01-01

We explored catchment processes that control stream nutrient concentrations at an upland forest in northeastern Vermont, USA, where inputs of nitrogen via atmospheric deposition are among the highest in the nation and affect ecosystem functioning. We traced sources of water, nitrate, and dissolved organic matter (DOM) using stream water samples collected at high frequency during spring snowmelt. Hydrochemistry, isotopic tracers, and end‐member mixing analyses suggested the timing, sources, and source areas from which water and nutrients entered the stream. Although stream‐dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) both originated from leaching of soluble organic matter, flushing responses between these two DOM components varied because of dynamic shifts of hydrological flow paths and sources that supply the highest concentrations of DOC and DON. High concentrations of stream water nitrate originated from atmospheric sources as well as nitrified sources from catchment soils. We detected nitrification in surficial soils during late snowmelt which affected the nitrate supply that was available to be transported to streams. However, isotopic tracers showed that the majority of nitrate in upslope surficial soil waters after the onset of snowmelt originated from atmospheric sources. A fraction of the atmospheric nitrogen was directly delivered to the stream, and this finding highlights the importance of quick flow pathways during snowmelt events. These findings indicate that interactions among sources, transformations, and hydrologic transport processes must be deciphered to understand why concentrations vary over time and over space as well as to elucidate the direct effects of human activities on nutrient dynamics in upland forest streams.

FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants1

PubMed Central

Tohge, Takayuki; Klie, Sebastian; Fernie, Alisdair R.

2016-01-01

Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression networks have indicated that, not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce, and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one-third of the genes of a plant’s genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in coexpression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen- and root-specific cell wall modules that multiplied to confer tip growth in pollen tubes and root hairs, respectively. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html. PMID:26754669

Nitric Oxide Isotopic Analyzer Based on a Compact Dual-Modulation Faraday Rotation Spectrometer

PubMed Central

Zhang, Eric; Huang, Stacey; Ji, Qixing; Silvernagel, Michael; Wang, Yin; Ward, Bess; Sigman, Daniel; Wysocki, Gerard

2015-01-01

We have developed a transportable spectroscopic nitrogen isotopic analyzer. The spectrometer is based on dual-modulation Faraday rotation spectroscopy of nitric oxide isotopologues with near shot-noise limited performance and baseline-free operation. Noise analysis indicates minor isotope (15NO) detection sensitivity of 0.36 ppbv·Hz−1/2, corresponding to noise-equivalent Faraday rotation angle (NEA) of 1.31 × 10−8 rad·Hz−1/2 and noise-equivalent absorbance (αL)min of 6.27 × 10−8 Hz−1/2. White-noise limited performance at 2.8× the shot-noise limit is observed up to ~1000 s, allowing reliable calibration and sample measurement within the drift-free interval of the spectrometer. Integration with wet-chemistry based on acidic vanadium(III) enables conversion of aqueous nitrate/nitrite samples to gaseous NO for total nitrogen isotope analysis. Isotopic ratiometry is accomplished via time-multiplexed measurements of two NO isotope transitions. For 5 μmol potassium nitrate samples, the instrument consistently yields ratiometric precision below 0.3‰, thus demonstrating potential as an in situ diagnostic tool for environmental nitrogen cycle studies. PMID:26473876

Nitrate addition to groundwater impacted by ethanol-blended fuel accelerates ethanol removal and mitigates the associated metabolic flux dilution and inhibition of BTEX biodegradation

NASA Astrophysics Data System (ADS)

Corseuil, Henry Xavier; Gomez, Diego E.; Schambeck, Cássio Moraes; Ramos, Débora Toledo; Alvarez, Pedro J. J.

2015-03-01

A comparison of two controlled ethanol-blended fuel releases under monitored natural attenuation (MNA) versus nitrate biostimulation (NB) illustrates the potential benefits of augmenting the electron acceptor pool with nitrate to accelerate ethanol removal and thus mitigate its inhibitory effects on BTEX biodegradation. Groundwater concentrations of ethanol and BTEX were measured 2 m downgradient of the source zones. In both field experiments, initial source-zone BTEX concentrations represented less than 5% of the dissolved total organic carbon (TOC) associated with the release, and measurable BTEX degradation occurred only after the ethanol fraction in the multicomponent substrate mixture decreased sharply. However, ethanol removal was faster in the nitrate amended plot (1.4 years) than under natural attenuation conditions (3.0 years), which led to faster BTEX degradation. This reflects, in part, that an abundant substrate (ethanol) can dilute the metabolic flux of target pollutants (BTEX) whose biodegradation rate eventually increases with its relative abundance after ethanol is preferentially consumed. The fate and transport of ethanol and benzene were accurately simulated in both releases using RT3D with our general substrate interaction module (GSIM) that considers metabolic flux dilution. Since source zone benzene concentrations are relatively low compared to those of ethanol (or its degradation byproduct, acetate), our simulations imply that the initial focus of cleanup efforts (after free-product recovery) should be to stimulate the degradation of ethanol (e.g., by nitrate addition) to decrease its fraction in the mixture and speed up BTEX biodegradation.

Nitrate addition to groundwater impacted by ethanol-blended fuel accelerates ethanol removal and mitigates the associated metabolic flux dilution and inhibition of BTEX biodegradation.

PubMed

Corseuil, Henry Xavier; Gomez, Diego E; Schambeck, Cássio Moraes; Ramos, Débora Toledo; Alvarez, Pedro J J

2015-03-01

A comparison of two controlled ethanol-blended fuel releases under monitored natural attenuation (MNA) versus nitrate biostimulation (NB) illustrates the potential benefits of augmenting the electron acceptor pool with nitrate to accelerate ethanol removal and thus mitigate its inhibitory effects on BTEX biodegradation. Groundwater concentrations of ethanol and BTEX were measured 2 m downgradient of the source zones. In both field experiments, initial source-zone BTEX concentrations represented less than 5% of the dissolved total organic carbon (TOC) associated with the release, and measurable BTEX degradation occurred only after the ethanol fraction in the multicomponent substrate mixture decreased sharply. However, ethanol removal was faster in the nitrate amended plot (1.4 years) than under natural attenuation conditions (3.0 years), which led to faster BTEX degradation. This reflects, in part, that an abundant substrate (ethanol) can dilute the metabolic flux of target pollutants (BTEX) whose biodegradation rate eventually increases with its relative abundance after ethanol is preferentially consumed. The fate and transport of ethanol and benzene were accurately simulated in both releases using RT3D with our general substrate interaction module (GSIM) that considers metabolic flux dilution. Since source zone benzene concentrations are relatively low compared to those of ethanol (or its degradation byproduct, acetate), our simulations imply that the initial focus of cleanup efforts (after free-product recovery) should be to stimulate the degradation of ethanol (e.g., by nitrate addition) to decrease its fraction in the mixture and speed up BTEX biodegradation. Copyright © 2014 Elsevier B.V. All rights reserved.

Nitrates and Nitrites in the Treatment of Ischemic Cardiac Disease

PubMed Central

Nossaman, Vaughn E.; Nossaman, Bobby D.; Kadowitz, Philip J.

2010-01-01

The organic nitrite, amyl of nitrite, was initially used as a therapeutic agent in the treatment of angina pectoris in 1867, but was replaced over a decade later by the organic nitrate, nitroglycerin (NTG), due to the ease of administration and longer duration of action. The administration of organic nitrate esters, such as NTG, continues to be used in the treatment of angina pectoris and heart failure during the birth of modern pharmacology. The clinical effectiveness is due to vasodilator activity in large veins and arteries through an as yet unidentified method of delivering nitric oxide (NO), or a NO-like compound to vascular smooth muscle cells. The major drawback with NTG administration is the rapid development of tolerance; and with amyl of nitrite, the duration and route of administration. Although amyl of nitrite are no longer used in the treatments of hypertension or ischemic heart disease, the nitrite anion has recently been discovered to possess novel pharmacologic actions such as modulating hypoxic vasodilation and providing cytoprotection in ischemia-reperfusion injury. Although the actions of these two similar chemical classes (nitrites and organic nitrates) have often been considered to be alike, we still do not understand their mechanism of action. However, the recent discovery that the nitrite anion, derived from either sodium nitrite or an intermediate NTG form, may act as a storage form for NO and provides support for investigating the use of these agents in the treatment of ischemic cardiovascular states. We review what is presently known about the use of nitrites and nitrates, the potential uses of these agents, and their mechanisms of action. PMID:20539102

Chemical form of selenium differentially influences DNA repair pathways following exposure to lead nitrate.

PubMed

McKelvey, Shauna M; Horgan, Karina A; Murphy, Richard A

2015-01-01

Lead, an environmental toxin is known to induce a broad range of physiological and biochemical dysfunctions in humans through a number of mechanisms including the deactivation of antioxidants thus leading to generation of reactive oxygen species (ROS) and subsequent DNA damage. Selenium on the other hand has been proven to play an important role in the protection of cells from free radical damage and oxidative stress, though its effects are thought to be form and dose dependent. As the liver is the primary organ required for metabolite detoxification, HepG2 cells were chosen to assess the protective effects of various selenium compounds following exposure to the genotoxic agent lead nitrate. Initially DNA damage was quantified using a comet assay, gene expression patterns associated with DNA damage and signalling were also examined using PCR arrays and the biological pathways which were most significantly affected by selenium were identified. Interestingly, the organic type selenium compounds (selenium yeast and selenomethionine) conferred protection against lead induced DNA damage in HepG2 cells; this is evident by reduction in the quantity of DNA present in the comet tail of cells cultured in their presence with lead. This trend also followed through the gene expression changes noted in DNA damage pathways analysed. These results were in contrast with those of inorganic sodium selenite which promoted lead induced DNA damage evident in both the comet assay results and the gene expression analysis. Over all this study provided valuable insights into the effects which various selenium compounds had on the DNA damage and signalling pathway indicating the potential for using organic forms of selenium such as selenium enriched yeast to protect against DNA damaging agents. Copyright © 2014 Elsevier GmbH. All rights reserved.

PTPRS Regulates Colorectal Cancer RAS Pathway Activity by Inactivating Erk and Preventing Its Nuclear Translocation.

PubMed

Davis, Thomas B; Yang, Mingli; Schell, Michael J; Wang, Heiman; Ma, Le; Pledger, W Jack; Yeatman, Timothy J

2018-06-18

Colorectal cancer (CRC) growth and progression is frequently driven by RAS pathway activation through upstream growth factor receptor activation or through mutational activation of KRAS or BRAF. Here we describe an additional mechanism by which the RAS pathway may be modulated in CRC. PTPRS, a receptor-type protein tyrosine phosphatase, appears to regulate RAS pathway activation through ERK. PTPRS modulates ERK phosphorylation and subsequent translocation to the nucleus. Native mutations in PTPRS, present in ~10% of CRC, may reduce its phosphatase activity while increasing ERK activation and downstream transcriptional signaling.

Is resistant starch protective against colorectal cancer via modulation of the WNT signalling pathway?

PubMed

Malcomson, Fiona C; Willis, Naomi D; Mathers, John C

2015-08-01

Epidemiological and experimental evidence suggests that non-digestible carbohydrates (NDC) including resistant starch are protective against colorectal cancer. These anti-neoplastic effects are presumed to result from the production of the SCFA, butyrate, by colonic fermentation, which binds to the G-protein-coupled receptor GPR43 to regulate inflammation and other cancer-related processes. The WNT pathway is central to the maintenance of homeostasis within the large bowel through regulation of processes such as cell proliferation and migration and is frequently aberrantly hyperactivated in colorectal cancers. Abnormal WNT signalling can lead to irregular crypt cell proliferation that favours a hyperproliferative state. Butyrate has been shown to modulate the WNT pathway positively, affecting functional outcomes such as apoptosis and proliferation. Butyrate's ability to regulate gene expression results from epigenetic mechanisms, including its role as a histone deacetylase inhibitor and through modulating DNA methylation and the expression of microRNA. We conclude that genetic and epigenetic modulation of the WNT signalling pathway may be an important mechanism through which butyrate from fermentation of resistant starch and other NDC exert their chemoprotective effects.

Modulation of apoptosis sensitivity through the interplay with autophagic and proteasomal degradation pathways

PubMed Central

Delgado, M E; Dyck, L; Laussmann, M A; Rehm, M

2014-01-01

Autophagic and proteasomal degradation constitute the major cellular proteolysis pathways. Their physiological and pathophysiological adaptation and perturbation modulates the relative abundance of apoptosis-transducing proteins and thereby can positively or negatively adjust cell death susceptibility. In addition to balancing protein expression amounts, components of the autophagic and proteasomal degradation machineries directly interact with and co-regulate apoptosis signal transduction. The influence of autophagic and proteasomal activity on apoptosis susceptibility is now rapidly gaining more attention as a significant modulator of cell death signalling in the context of human health and disease. Here we present a concise and critical overview of the latest knowledge on the molecular interplay between apoptosis signalling, autophagy and proteasomal protein degradation. We highlight that these three pathways constitute an intricate signalling triangle that can govern and modulate cell fate decisions between death and survival. Owing to rapid research progress in recent years, it is now possible to provide detailed insight into the mechanisms of pathway crosstalk, common signalling nodes and the role of multi-functional proteins in co-regulating both protein degradation and cell death. PMID:24457955

The Role of the Wnt/β-catenin Signaling Pathway in Formation and Maintenance of Bone and Teeth

PubMed Central

Duan, Peipei; Bonewald, LF

2016-01-01

The Wnt signaling pathway is known as one of the important molecular cascades that regulate cell fate throughout lifespan. The Wnt signaling pathway is further separated into the canonical signaling pathway that depends on the function of β-catenin (Wnt/β-catenin pathway) and the noncanonical pathways that operate independently of β-catenin (planar cell polarity pathway and Wnt/Ca2+ pathway). The Wnt/β-catenin signaling pathway is complex and consists of numerous receptors, inhibitors, activators, modulators, phosphatases, kinases and other components. However, there is one central, critical molecule to this pathway, β-catenin. While there are at least 3 receptors, LRP 4, 5 and 6, and over twenty activators known as the wnts, and several inhibitors such as sclerostin, dickkopf and secreted frizzled-related protein, these all target β-catenin. These regulators/modulators function to target β-catenin either to the proteasome for degradation or to the nucleus to regulate gene expression. Therefore, the interaction of β-catenin with different factors and Wnt/β-catenin signaling pathway will be the subject of this review with a focus on how this pathway relates to and functions in the formation and maintenance of bone and teeth based on mainly basic and pre-clinical research. Also in this review, the role of this pathway in osteocytes, bone cells embedded in the mineralized matrix, is covered in depth. This pathway is not only important in mineralized tissue growth and development, but for modulation of the skeleton in response to loading and unloading and the viability and health of the adult and aging skeleton. PMID:27210503

Patients' and procedural characteristics of AV-block during slow pathway modulation for AVNRT-single center 10year experience.

PubMed

Wasmer, Kristina; Dechering, Dirk G; Köbe, Julia; Leitz, Patrick; Frommeyer, Gerrit; Lange, Phillip S; Kochhäuser, Simon; Reinke, Florian; Pott, Christian; Mönnig, Gerold; Breithardt, Günter; Eckardt, Lars

2017-10-01

Permanent AV-block is a recognized and feared complication of slow pathway modulation for AVNRT. We aimed to assess incidence of transient and permanent AV-block as well as consequences of transient AV-block in a large contemporary AVNRT ablation cohort. We searched our single center prospective ablation database for occurrence of transient and permanent AV-block during slow pathway modulation between January 2004 and October 2015. We analyzed patients' and procedural characteristics as well as outcome of patients in whom transient or permanent AV-block occurred. Of 9170 patients who underwent a catheter ablation at our institution between January 2004 and October 2015, 2101 patients (64% women, mean age 50±18years) underwent slow pathway modulation. In three patients, permanent AV-block occurred during RF application. Additional two patients had transient AV-block that recovered (after a few minutes and 25min), but recurred within two days of the procedure. All five patients underwent dual chamber pacemaker implantation (0.2%). Transient AV-block related to RF delivery occurred in 44 patients (2%). Transient mechanical AV-block occurred in additional 17 patients (0.8%). In 12 patients, ablation was continued despite transient AV-block. One of these patients developed permanent AV-block. Permanent AV-block following slow pathway modulation is a rare event, occurring in 0.2% of patients in a large contemporary single center cohort. Transient AV-block is more frequent (2%). Copyright © 2017 Elsevier B.V. All rights reserved.

Single-cell sequencing of Thiomargarita reveals genomic flexibility for adaptation to dynamic redox conditions

DOE PAGES

Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja; ...

2016-06-21

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiornargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of amore » chain-forming " Candidatus Thiomargarita nelsonii Thio36", and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. " Ca. T. nelsonii Thio36" is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that " Ca. T. nelsonii Thio36" can function as a chemolithoautotroph. Carbon can be fixed via the Calvin-Benson-Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO 2 fixation pathway. Surprisingly, " Ca. T. nelsonii Thio36" also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na +-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae " Ca. T. nelsonii Thio36" encodes many genes similar to those of (filamentous) cyanobacteria. In conclusion, the genome of " Ca. T. nelsonii Thio36" provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiornargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of amore » chain-forming " Candidatus Thiomargarita nelsonii Thio36", and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. " Ca. T. nelsonii Thio36" is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that " Ca. T. nelsonii Thio36" can function as a chemolithoautotroph. Carbon can be fixed via the Calvin-Benson-Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO 2 fixation pathway. Surprisingly, " Ca. T. nelsonii Thio36" also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na +-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae " Ca. T. nelsonii Thio36" encodes many genes similar to those of (filamentous) cyanobacteria. In conclusion, the genome of " Ca. T. nelsonii Thio36" provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.« less

Regulation of Transient Receptor Potential channels by the phospholipase C pathway

PubMed Central

Rohacs, Tibor

2013-01-01

Transient Receptor Potential (TRP) channels were discovered while analyzing visual mutants in drosophila. The protein encoded by the transient receptor potential (trp) gene is a Ca2+ permeable cation channel activated downstream of the phospholipase C (PLC) pathway. While searching for homologues in other organisms, a surprisingly large number of mammalian TRP channels were cloned. The regulation of TRP channels is quite diverse, but many of them are either activated downstream of the PLC pathway, or modulated by it. This review will summarize the current knowledge on regulation of TRP channels by the PLC pathway, with special focus on TRPC-s, which can be considered as effectors of the PLC pathway, and the heat and capsaicin sensitive TRPV1, which is modulated by the PLC pathway in a complex manner. PMID:23916247

Modularity of nitrogen-oxide reducing soil bacteria: linking phenotype to genotype.

PubMed

Roco, Constance A; Bergaust, Linda L; Bakken, Lars R; Yavitt, Joseph B; Shapleigh, James P

2017-06-01

Model denitrifiers convert NO3- to N 2 , but it appears that a significant fraction of natural populations are truncated, conducting only one or two steps of the pathway. To better understand the diversity of partial denitrifiers in soil and whether discrepancies arise between the presence of known N-oxide reductase genes and phenotypic features, bacteria able to reduce NO3- to NO2- were isolated from soil, N-oxide gas products were measured for eight isolates, and six were genome sequenced. Gas phase analyses revealed that two were complete denitrifiers, which genome sequencing corroborated. The remaining six accumulated NO and N 2 O to varying degrees and genome sequencing of four indicated that two isolates held genes encoding nitrate reductase as the only dissimilatory N-oxide reductase, one contained genes for both nitrate and nitric oxide reductase, and one had nitrate and nitrite reductase. The results demonstrated that N-oxide production was not always predicted by the genetic potential and suggested that partial denitrifiers could be readily isolated among soil bacteria. This supported the hypothesis that each N-oxide reductase could provide a selectable benefit on its own, and therefore, reduction of nitrate to dinitrogen may not be obligatorily linked to complete denitrifiers but instead a consequence of a functionally diverse community. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Nitrite oxidation in the Namibian oxygen minimum zone.

PubMed

Füssel, Jessika; Lam, Phyllis; Lavik, Gaute; Jensen, Marlene M; Holtappels, Moritz; Günter, Marcel; Kuypers, Marcel M M

2012-06-01

Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in (15)N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (≤372 nM NO(2)(-) d(-1)) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ~9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO(3)(-) was re-oxidized back to NO(3)(-) via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways.

Ntdin, a tobacco senescence-associated gene, is involved in molybdenum cofactor biosynthesis.

PubMed

Yang, Seung Hwan; Berberich, Thomas; Miyazaki, Atsushi; Sano, Hiroshi; Kusano, Tomonobu

2003-10-01

To date, dozens of genes have been reported to be up-regulated with senescence in higher plants. Radish din1 and its ortholog sen1 of Arabidopsis are known as such, but their function is not clear yet. Here we have isolated their counterpart cDNA from tobacco and designated it as NTDIN: Its product, Ntdin, a 185 amino acid polypeptide with 56.8% and 54.2% identity to Atsen1 and Rsdin1, respectively, is localized in chloroplasts. Transcripts of Ntdin are induced by sulfate or nitrate but not by phosphate, suggesting its involvement in sulfur and nitrogen metabolism. A database search revealed that Ntdin shows similarity with the C-terminal region of Nicotiana plumbaginifolia Cnx5, which functions in molybdenum cofactor (Moco) biosynthesis. Transgenic tobacco plants with suppressed Ntdin are more tolerant to chlorate, a substrate analog of nitrate reductase, than controls, implying low nitrate reductase activity in the transgenic plants due to a deficiency of Moco. Indeed, enzymatic activities of two molybdoenzymes, nitrate reductase and xanthine dehydrogenase, in transgenic plants are found to be significantly lower than in control plants. Direct measurement of Moco contents reveals that those transgenic plants contain about 5% Moco of those of the control plants. Abscisic acid and indole-3-acidic acid, whose biosynthetic pathways require Moco, up-regulated Ntdin expression. Taken together, it is concluded that Ntdin functions in a certain step in Moco biosynthesis.

Potential Sabotage of Host Cell Physiology by Apicomplexan Parasites for Their Survival Benefits

PubMed Central

Chakraborty, Shalini; Roy, Sonti; Mistry, Hiral Uday; Murthy, Shweta; George, Neena; Bhandari, Vasundhra; Sharma, Paresh

2017-01-01

Plasmodium, Toxoplasma, Cryptosporidium, Babesia, and Theileria are the major apicomplexan parasites affecting humans or animals worldwide. These pathogens represent an excellent example of host manipulators who can overturn host signaling pathways for their survival. They infect different types of host cells and take charge of the host machinery to gain nutrients and prevent itself from host attack. The mechanisms by which these pathogens modulate the host signaling pathways are well studied for Plasmodium, Toxoplasma, Cryptosporidium, and Theileria, except for limited studies on Babesia. Theileria is a unique pathogen taking into account the way it modulates host cell transformation, resulting in its clonal expansion. These parasites majorly modulate similar host signaling pathways, however, the disease outcome and effect is different among them. In this review, we discuss the approaches of these apicomplexan to manipulate the host–parasite clearance pathways during infection, invasion, survival, and egress. PMID:29081773

Caenorhabditis elegans as Model System in Pharmacology and Toxicology: Effects of Flavonoids on Redox-Sensitive Signalling Pathways and Ageing

PubMed Central

Koch, Karoline; Havermann, Susannah; Büchter, Christian

2014-01-01

Flavonoids are secondary plant compounds that mediate diverse biological activities, for example, by scavenging free radicals and modulating intracellular signalling pathways. It has been shown in various studies that distinct flavonoid compounds enhance stress resistance and even prolong the life span of organisms. In the last years the model organism C. elegans has gained increasing importance in pharmacological and toxicological sciences due to the availability of various genetically modified nematode strains, the simplicity of modulating genes by RNAi, and the relatively short life span. Several studies have been performed demonstrating that secondary plant compounds influence ageing, stress resistance, and distinct signalling pathways in the nematode. Here we present an overview of the modulating effects of different flavonoids on oxidative stress, redox-sensitive signalling pathways, and life span in C. elegans introducing the usability of this model system for pharmacological and toxicological research. PMID:24895670

Extracellular Protein Kinase A Modulates Intracellular Calcium/Calmodulin-Dependent Protein Kinase II, Nitric Oxide Synthase, and the Glutamate-Nitric Oxide-cGMP Pathway in Cerebellum. Differential Effects in Hyperammonemia.

PubMed

Cabrera-Pastor, Andrea; Llansola, Marta; Felipo, Vicente

2016-12-21

Extracellular protein kinases, including cAMP-dependent protein kinase (PKA), modulate neuronal functions including N-methyl-d-aspartate (NMDA) receptor-dependent long-term potentiation. NMDA receptor activation increases calcium, which binds to calmodulin and activates nitric oxide synthase (NOS), increasing nitric oxide (NO), which activates guanylate cyclase, increasing cGMP, which is released to the extracellular fluid, allowing analysis of this glutamate-NO-cGMP pathway in vivo by microdialysis. The function of this pathway is impaired in hyperammonemic rats. The aims of this work were to assess (1) whether the glutamate-NO-cGMP pathway is modulated in cerebellum in vivo by an extracellular PKA, (2) the role of phosphorylation and activity of calcium/calmodulin-dependent protein kinase II (CaMKII) and NOS in the pathway modulation by extracellular PKA, and (3) whether the effects are different in hyperammonemic and control rats. The pathway was analyzed by in vivo microdialysis. The role of extracellular PKA was analyzed by inhibiting it with a membrane-impermeable inhibitor. The mechanisms involved were analyzed in freshly isolated cerebellar slices from control and hyperammonemic rats. In control rats, inhibiting extracellular PKA reduces the glutamate-NO-cGMP pathway function in vivo. This is due to reduction of CaMKII phosphorylation and activity, which reduces NOS phosphorylation at Ser1417 and NOS activity, resulting in reduced guanylate cyclase activation and cGMP formation. In hyperammonemic rats, under basal conditions, CaMKII phosphorylation and activity are increased, increasing NOS phosphorylation at Ser847, which reduces NOS activity, guanylate cyclase activation, and cGMP. Inhibiting extracellular PKA in hyperammonemic rats normalizes CaMKII phosphorylation and activity, NOS phosphorylation, NOS activity, and cGMP, restoring normal function of the pathway.

Redox interventions to increase exercise performance

PubMed Central

2015-01-01

Abstract Skeletal muscle continually produces reactive oxygen species (ROS) and nitric oxide (NO) derivatives. Both oxidant cascades have complex effects on muscle contraction, metabolic function and tissue perfusion. Strenuous exercise increases oxidant production by muscle, limiting performance during endurance exercise tasks. Conversely, redox interventions that modulate ROS or NO activity have the potential to improve performance. Antioxidants have long been known to buffer ROS activity and lessen oxidative perturbations during exercise. The capacity to enhance human performance varies among antioxidant categories. Vitamins, provitamins and nutriceuticals often blunt oxidative changes at the biochemical level but do not enhance performance. In contrast, reduced thiol donors have been shown to delay fatigue or increase endurance under a variety of experimental conditions. Dietary nitrate supplementation has recently emerged as a second redox strategy for increasing endurance. Purified nitrate salts and nitrate‐rich foods, notably beetroot and beetroot juice, are reported to lessen the oxygen cost of exercise, increase efficiency, and enhance performance during endurance tasks. These findings are exciting but enigmatic since nitrate per se has little bioactivity and cannot be converted to NO by mammalian cells. Overall, the available data suggest exercise endurance can be augmented by redox‐active supplements, either reduced thiol donors or dietary nitrates. These findings have clear implications for athletes seeking a competitive edge. More importantly, interventions that increase endurance may benefit individuals whose physical activity is limited by illness, ageing, or frailty. PMID:26584644

Generation and esterification of electrophilic fatty acid nitroalkenes in triacylglycerides

PubMed Central

Fazzari, Marco; Khoo, Nicholas; Woodcock, Steven R.; Li, Lihua; Freeman, Bruce A.; Schopfer, Francisco J.

2015-01-01

Electrophilic fatty acid nitroalkenes (NO2-FA) are products of nitric oxide and nitrite-mediated unsaturated fatty acid nitration. These electrophilic products induce pleiotropic signaling actions that modulate metabolic and inflammatory responses in cell and animal models. The metabolism of NO2-FA includes reduction of the vinyl nitro moiety by prostaglandin reductase-1, mitochondrial β–oxidation and Michael addition with low molecular weight nucleophilic amino acids. Complex lipid reactions of fatty acid nitroalkenes are not well defined. Herein we report the detection and characterization of NO2-FA-containing triacylglycerides (NO2-FA-TAG) via mass spectrometry-based methods. In this regard, unsaturated fatty acids of dietary triacylglycerides are targets for nitration reactions during gastric acidification, where NO2-FA-TAG can be detected in rat plasma after oral administration of nitro-oleic acid (NO2-OA). Furthermore, the characterization and profiling of these species, including the generation of beta oxidation and dehydrogenation products, could be detected in NO2-OA supplemented adipocytes. These data revealed that NO2-FA-TAG, formed by either the direct nitration of esterified unsaturated fatty acids or the incorporation of nitrated free fatty acids into triacylglycerides, contribute to the systemic distribution of these reactive electrophilic mediators and may serve as a depot for subsequent mobilization by lipases to in turn impact adipocyte homeostasis and tissue signaling events. PMID:26066303

The nitrate-reduction gene cluster components exert lineage-dependent contributions to optimization of Sinorhizobium symbiosis with soybeans.

PubMed

Liu, Li Xue; Li, Qin Qin; Zhang, Yun Zeng; Hu, Yue; Jiao, Jian; Guo, Hui Juan; Zhang, Xing Xing; Zhang, Biliang; Chen, Wen Xin; Tian, Chang Fu

2017-12-01

Receiving nodulation and nitrogen fixation genes does not guarantee rhizobia an effective symbiosis with legumes. Here, variations in gene content were determined for three Sinorhizobium species showing contrasting symbiotic efficiency on soybeans. A nitrate-reduction gene cluster absent in S. sojae was found to be essential for symbiotic adaptations of S. fredii and S. sp. III. In S. fredii, the deletion mutation of the nap (nitrate reductase), instead of nir (nitrite reductase) and nor (nitric oxide reductase), led to defects in nitrogen-fixation (Fix - ). By contrast, none of these core nitrate-reduction genes were required for the symbiosis of S. sp. III. However, within the same gene cluster, the deletion of hemN1 (encoding oxygen-independent coproporphyrinogen III oxidase) in both S. fredii and S. sp. III led to the formation of nitrogen-fixing (Fix + ) but ineffective (Eff - ) nodules. These Fix + /Eff - nodules were characterized by significantly lower enzyme activity of glutamine synthetase indicating rhizobial modulation of nitrogen-assimilation by plants. A distant homologue of HemN1 from S. sojae can complement this defect in S. fredii and S. sp. III, but exhibited a more pleotropic role in symbiosis establishment. These findings highlighted the lineage-dependent optimization of symbiotic functions in different rhizobial species associated with the same host. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Exogenous trehalose improves growth under limiting nitrogen through upregulation of nitrogen metabolism.

PubMed

Lin, Yingchao; Zhang, Jie; Gao, Weichang; Chen, Yi; Li, Hongxun; Lawlor, David W; Paul, Matthew J; Pan, Wenjie

2017-12-19

The trehalose (Tre) pathway has strong effects on growth and development in plants through regulation of carbon metabolism. Altering either Tre or trehalose 6-phosphate (T6P) can improve growth and productivity of plants as observed under different water availability. As yet, there are no reports of the effects of modification of Tre orT6P on plant performance under limiting nutrition. Here we report that nitrogen (N) metabolism is positively affected by exogenous application of Tre in nitrogen-deficient growing conditions. Spraying foliage of tobacco (Nicotiana tabacum) with trehalose partially alleviated symptoms of nitrogen deficiency through upregulation of nitrate and ammonia assimilation and increasing activities of nitrate reductase (NR), glycolate oxidase (GO), glutamine synthetase (GS) and glutamine oxoglutarate aminotransferase (GOGAT) with concomitant changes in ammonium (NH 4 + ) and nitrate (NO 3 - ) concentrations, glutamine and amino acids. Chlorophyll and total nitrogen content of leaves and rates of photosynthesis were increased compared to nitrogen-deficient plants without applied Tre. Total plant biomass accumulation was also higher in Tre -fed nitrogen-deficient plants, with a smaller proportion of dry weight partitioned to roots, compared to nitrogen-deficient plants without applied Tre. Consistent with higher nitrogen assimilation and growth, Tre application reduced foliar starch. Minimal effects of Tre feeding were observed on nitrogen-sufficient plants. The data show, for the first time, significant stimulatory effects of exogenous Tre on nitrogen metabolism and growth in plants growing under deficient nitrogen. Under such adverse conditions metabolism is regulated for survival rather than productivity. Application of Tre can alter this regulation towards maintenance of productive functions under low nitrogen. This has implications for considering approaches to modifying the Tre pathway for to improve crop nitrogen-use efficiency and production.

A-Type Carrier Protein ErpA Is Essential for Formation of an Active Formate-Nitrate Respiratory Pathway in Escherichia coli K-12

PubMed Central

Pinske, Constanze

2012-01-01

A-type carrier (ATC) proteins of the Isc (iron-sulfur cluster) and Suf (sulfur mobilization) iron-sulfur ([Fe-S]) cluster biogenesis pathways are proposed to traffic preformed [Fe-S] clusters to apoprotein targets. In this study, we analyzed the roles of the ATC proteins ErpA, IscA, and SufA in the maturation of the nitrate-inducible, multisubunit anaerobic respiratory enzymes formate dehydrogenase N (Fdh-N) and nitrate reductase (Nar). Mutants lacking SufA had enhanced activities of both enzymes. While both Fdh-N and Nar activities were strongly reduced in an iscA mutant, both enzymes were inactive in an erpA mutant and in a mutant unable to synthesize the [Fe-S] cluster scaffold protein IscU. It could be shown for both Fdh-N and Nar that loss of enzyme activity correlated with absence of the [Fe-S] cluster-containing small subunit. Moreover, a slowly migrating form of the catalytic subunit FdnG of Fdh-N was observed, consistent with impeded twin arginine translocation (TAT)-dependent transport. The highly related Fdh-O enzyme was also inactive in the erpA mutant. Although the Nar enzyme has its catalytic subunit NarG localized in the cytoplasm, it also exhibited aberrant migration in an erpA iscA mutant, suggesting that these modular enzymes lack catalytic integrity due to impaired cofactor biosynthesis. Cross-complementation experiments demonstrated that multicopy IscA could partially compensate for lack of ErpA with respect to Fdh-N activity but not Nar activity. These findings suggest that ErpA and IscA have overlapping roles in assembly of these anaerobic respiratory enzymes but demonstrate that ErpA is essential for the production of active enzymes. PMID:22081393

Microbiological oxidation of antimony(III) with oxygen or nitrate by bacteria isolated from contaminated mine sediments

USGS Publications Warehouse

Terry, Lee R.; Kulp, Thomas R.; Wiatrowski, Heather A.; Miller, Laurence G.; Oremland, Ronald S.

2015-01-01

Bacterial oxidation of arsenite [As(III)] is a well-studied and important biogeochemical pathway that directly influences the mobility and toxicity of arsenic in the environment. In contrast, little is known about microbiological oxidation of the chemically similar anion antimonite [Sb(III)]. In this study, two bacterial strains, designated IDSBO-1 and IDSBO-4, which grow on tartrate compounds and oxidize Sb(III) using either oxygen or nitrate, respectively, as a terminal electron acceptor, were isolated from contaminated mine sediments. Both isolates belonged to the Comamonadaceae family and were 99% similar to previously described species. We identify these novel strains as Hydrogenophagataeniospiralis strain IDSBO-1 and Variovorax paradoxus strain IDSBO-4. Both strains possess a gene with homology to the aioA gene, which encodes an As(III)-oxidase, and both oxidize As(III) aerobically, but only IDSBO-4 oxidized Sb(III) in the presence of air, while strain IDSBO-1 could achieve this via nitrate respiration. Our results suggest that expression of aioA is not induced by Sb(III) but may be involved in Sb(III) oxidation along with an Sb(III)-specific pathway. Phylogenetic analysis of proteins encoded by the aioA genes revealed a close sequence similarity (90%) among the two isolates and other known As(III)-oxidizing bacteria, particularly Acidovorax sp. strain NO1. Both isolates were capable of chemolithoautotrophic growth using As(III) as a primary electron donor, and strain IDSBO-4 exhibited incorporation of radiolabeled [14C]bicarbonate while oxidizing Sb(III) from Sb(III)-tartrate, suggesting possible Sb(III)-dependent autotrophy. Enrichment cultures produced the Sb(V) oxide mineral mopungite and lesser amounts of Sb(III)-bearing senarmontite as precipitates.

Blood Pressure-Lowering Effect of Orally Ingested Nitrite Is Abolished by a Proton Pump Inhibitor.

PubMed

Montenegro, Marcelo F; Sundqvist, Michaela L; Larsen, Filip J; Zhuge, Zhengbing; Carlström, Mattias; Weitzberg, Eddie; Lundberg, Jon O

2017-01-01

Inorganic nitrate and nitrite from dietary and endogenous sources are metabolized to NO and other bioactive nitrogen oxides that affect blood pressure. The mechanisms for nitrite bioactivation are unclear, but recent studies in rodents suggest that gastric acidity may influence the systemic effects of this anion. In a randomized, double-blind, placebo-controlled crossover study, we tested the effects of a proton pump inhibitor on the acute cardiovascular effects of nitrite. Fifteen healthy nonsmoking, normotensive subjects, aged 19 to 39 years, were pretreated with placebo or esomeprazole (3×40 mg) before ingesting sodium nitrite (0.3 mg kg -1 ), followed by blood pressure monitoring. Nitrite reduced systolic blood pressure by a maximum of 6±1.3 mm Hg when taken after placebo, whereas pretreatment with esomeprazole blunted this effect. Peak plasma nitrite, nitrate, and nitroso species levels after nitrite ingestion were similar in both interventions. In 8 healthy volunteers, we then infused increasing doses of sodium nitrite (1, 10, and 30 nmol kg -1 min -1 ) intravenously. Interestingly, although plasma nitrite peaked at similar levels as with orally ingested nitrite (≈1.8 µmol/L), no changes in blood pressure were observed. In rodents, esomeprazole did not affect the blood pressure response to the NO donor, DEA NONOate, or vascular relaxation to nitroprusside and acetylcholine, demonstrating an intact downstream NO-signaling pathway. We conclude that the acute blood pressure-lowering effect of nitrite requires an acidic gastric environment. Future studies will reveal if the cardiovascular complications associated with the use of proton pump inhibitors are linked to interference with the nitrate-nitrite-NO pathway. © 2016 American Heart Association, Inc.

An algorithm for modularization of MAPK and calcium signaling pathways: comparative analysis among different species.

PubMed

Nayak, Losiana; De, Rajat K

2007-12-01

Signaling pathways are large complex biochemical networks. It is difficult to analyze the underlying mechanism of such networks as a whole. In the present article, we have proposed an algorithm for modularization of signal transduction pathways. Unlike studying a signaling pathway as a whole, this enables one to study the individual modules (less complex smaller units) easily and hence to study the entire pathway better. A comparative study of modules belonging to different species (for the same signaling pathway) has been made, which gives an overall idea about development of the signaling pathways over the taken set of species of calcium and MAPK signaling pathways. The superior performance, in terms of biological significance, of the proposed algorithm over an existing community finding algorithm of Newman [Newman MEJ. Modularity and community structure in networks. Proc Natl Acad Sci USA 2006;103(23):8577-82] has been demonstrated using the aforesaid pathways of H. sapiens.

Nitrite- and Nitrate-Dependent Methanotrophs - Environmental Detection and Relevance in Freshwater Ecosystems

NASA Astrophysics Data System (ADS)

Ettwig, K. F.

2014-12-01

Humans continue to have an enormous impact on global C and N cycles. While a clear stimulation of methane emissions through human activities is evident, the role of also increasingly released nitrogenous compounds as electron acceptors for microbial methane oxidation is not well constrained. We have developed diverse methods for environmental detection of nitrate(NO3-)- and - predominantly - nitrite(NO2-)-dependent methanotrophs, which have been applied to several freshwater environments. In contrast to most metabolically flexible heterotrophic denitrifiers, the microorganisms responsible for methane-dependent nitrate/nitrite reduction seem to be specialized to use methane only, grow slowly and employ pathways different from each other and from model organisms, which necessitate new approaches for the assessment of their environmental relevance. Nitrite-dependent methane oxidation is carried out by bacteria of the NC10 phylum, whereas nitrate-dependent methane oxidizers are close relatives of methanogenic archaea and sulfate-dependent anaerobic methanotrophs (ANME-2). Laboratory enrichment cultures of the nitrite-reducing methanotroph Methylomirabilis oxyfera (NC10 phylum) have formed the basis for its genetic and physiological characterization and the development of several independent methods for its sensitive detection. M. oxyfera differs from all known microorganisms by encoding an incomplete denitrification pathway, in which the last 2 steps, the reduction of NO via N2O to N2, apparently is replaced by the dismutation of NO to N2 and O2. The intracellularly produced O2 is used for methane oxidation via a methane monooxygenase, analogously to the phylogenetically unrelated proteobacterial methanotrophs. But unlike in proteobacteria, C is not assimilated from methane, but rather CO2, with important consequences for the interpretation of environmental isotope labelling studies. In addition, M. oxyfera is characterized by a distinct PLFA profile, including methylated lipids so far not found in any other organism. Case studies using specific primers together with lipid profiles and 13C-labelling in peatlands and other freshwater environments illustrate that the newly developed approaches and biomarkers enable the demonstration of M. oxyfera's role as a methane sink.

Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

NASA Astrophysics Data System (ADS)

Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

2014-12-01

Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine oxidoreductase (HAO) were abundant and more similar to known anammox HAO genes than those used in aerobic ammonia oxidation. The elevated levels of anammox transcripts suggest that anammox may play a significant role in nitrogen cycling within groundwater systems.

Assessing and Modulating Kynurenine Pathway Dynamics in Huntington's Disease: Focus on Kynurenine 3-Monooxygenase.

PubMed

Sathyasaikumar, Korrapati V; Breda, Carlo; Schwarcz, Robert; Giorgini, Flaviano

2018-01-01

The link between disturbances in kynurenine pathway (KP) metabolism and Huntington's disease (HD) pathogenesis has been explored for a number of years. Several novel genetic and pharmacological tools have recently been developed to modulate key regulatory steps in the KP such as the reaction catalyzed by the enzyme kynurenine 3-monooxygenase (KMO). This insight has offered new options for exploring the mechanistic link between this metabolic pathway and HD, and provided novel opportunities for the development of candidate drug-like compounds. Here, we present an overview of the field, focusing on some novel approaches for interrogating the pathway experimentally.

A statistical framework for biomedical literature mining.

PubMed

Chung, Dongjun; Lawson, Andrew; Zheng, W Jim

2017-09-30

In systems biology, it is of great interest to identify new genes that were not previously reported to be associated with biological pathways related to various functions and diseases. Identification of these new pathway-modulating genes does not only promote understanding of pathway regulation mechanisms but also allow identification of novel targets for therapeutics. Recently, biomedical literature has been considered as a valuable resource to investigate pathway-modulating genes. While the majority of currently available approaches are based on the co-occurrence of genes within an abstract, it has been reported that these approaches show only sub-optimal performances because 70% of abstracts contain information only for a single gene. To overcome such limitation, we propose a novel statistical framework based on the concept of ontology fingerprint that uses gene ontology to extract information from large biomedical literature data. The proposed framework simultaneously identifies pathway-modulating genes and facilitates interpreting functions of these new genes. We also propose a computationally efficient posterior inference procedure based on Metropolis-Hastings within Gibbs sampler for parameter updates and the poor man's reversible jump Markov chain Monte Carlo approach for model selection. We evaluate the proposed statistical framework with simulation studies, experimental validation, and an application to studies of pathway-modulating genes in yeast. The R implementation of the proposed model is currently available at https://dongjunchung.github.io/bayesGO/. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Integrins as Modulators of Transforming Growth Factor Beta Signaling in Dermal Fibroblasts During Skin Regeneration After Injury.

PubMed

Boo, Stellar; Dagnino, Lina

2013-06-01

Abnormal wound repair results from disorders in granulation tissue remodeling, and can lead to hypertrophic scarring and fibrosis. Excessive scarring can compromise tissue function and decrease tissue resistance to additional injuries. The development of potential therapies to minimize scarring is, thus, necessary to address an important clinical problem. It has been clearly established that multiple cytokines and growth factors participate in the regulation of cutaneous wound healing. More recently, it has become apparent that these factors do not necessarily activate isolated signaling pathways. Rather, in some cases, there is cross-modulation of several cellular pathways involved in this process. Two of the key pathways that modulate each other during wound healing are activated by transforming growth factor-β and by extracellular matrix proteins acting through integrins. The pathogenesis of excessive scarring upon wound healing is not fully understood, as a result of the complexity of this process. However, the fact that many pathways combine to produce fibrosis provides multiple potential therapeutic targets. Some of them have been identified, such as focal adhesion kinase and integrin-linked kinase. Currently, a major challenge is to develop pharmacological inhibitors of these proteins with therapeutic value to promote efficient wound repair. The ability to better understand how different pathways crosstalk during wound repair and to identify and pharmacologically modulate key factors that contribute to the regulation of multiple wound-healing pathways could potentially provide effective therapeutic targets to decrease or prevent excessive scar formation and/or development of fibrosis.

Nitrate and Nitrogen Oxides: Sources, Health Effects and Their Remediation.

PubMed

Hakeem, Khalid Rehman; Sabir, Muhammad; Ozturk, Munir; Akhtar, Mohd Sayeed; Ibrahim, Faridah Hanum

Increased use of nitrogenous (N) fertilizers in agriculture has significantly altered the global N-cycle because they release nitrogenous gases of environmental concerns. The emission of nitrous oxide (N 2 O) contributes to the global greenhouse gas accumulation and the stratospheric ozone depletion. In addition, it causes nitrate leaching problem deteriorating ground water quality. The nitrate toxicity has been reported in a number of studies showing the health hazards like methemoglobinemia in infants and is a potent cause of cancer. Despite these evident negative environmental as well as health impacts, consumption of N fertilizer cannot be reduced in view of the food security for the teeming growing world population. Various agronomic and genetic modifications have been practiced to tackle this problem. Some agronomic techniques adopted include split application of N, use of slow-release fertilizers, nitrification inhibitors and encouraging the use of organic manure over chemical fertilizers. As a matter of fact, the use of chemical means to remediate nitrate from the environment is very difficult and costly. Particularly, removal of nitrate from water is difficult task because it is chemically non-reactive in dilute aqueous solutions. Hence, the use of biological means for nitrate remediation offers a promising strategy to minimize the ill effects of nitrates and nitrites. One of the important goals to reduce N-fertilizer application can be effectively achieved by choosing N-efficient genotypes. This will ensure the optimum uptake of applied N in a balanced manner and exploring the molecular mechanisms for their uptake as well as metabolism in assimilatory pathways. The objectives of this paper are to evaluate the interrelations which exist in the terrestrial ecosystems between the plant type and characteristics of nutrient uptake and analyze the global consumption and demand for fertilizer nitrogen in relation to cereal production, evaluate the various methods used to determine nitrogen use efficincy (NUE), determine NUE for the major cereals grown across large agroclimatic regions, determine the key factors that control NUE, and finally analyze various strategies available to improve the use efficiency of fertilizer nitrogen.

Nitrogen and Martian Habitability: Insights from Five Years of Curiosity Measurements

NASA Astrophysics Data System (ADS)

Stern, J. C.; Sutter, B.; Navarro-Gonzalez, R.; McKay, C.; Ming, D. W.; Mahaffy, P. R.; Archer, D., Jr.; Franz, H. B.; Freissinet, C.; Jackson, W. A.; Conrad, P. G.; Glavin, D. P.; Trainer, M. G.; Malespin, C.; McAdam, A.; Eigenbrode, J. L.; Teinturier, S.; Manning, C.

2017-12-01

The detection of "fixed" N on Mars in the form of nitrate by the Sample Analysis at Mars (SAM) instrument suite on the Mars Science Laboratory (MSL) Curiosity Rover [1] has major implications for martian habitability. "Follow the nitrogen" has been proposed as a strategy in the search for both extant and extinct life on Mars [e.g., 2]. Nitrogen is so crucial to life on Earth that life developed metabolic pathways to break the triple bond of N2 and "fix" atmospheric nitrogen to more biologically available molecules for use in proteins and informational polymers. Sequestration of nitrate in regolith has long been predicted to contribute to the removal of N from the martian atmosphere [e.g., 3], and our detections confirm that nitrogen fixation was occurring on ancient Mars. Detections of fixed nitrogen, particularly within the context of the habitable environment in Yellowknife Bay characterized by the MSL payload, are an important tool to assess whether life ever could have existed on ancient Mars. We present 5 years of analyses and interpretation of nitrate in solid martian drilled and scooped samples by SAM on MSL. Nitrate abundance reported by SAM in situ measurements ranges from non-detection to 681 ± 304 mg/kg [1,4] in the samples examined to date. The measured abundances are consistent with nitrogen fixation via impact generated thermal shock on ancient Mars and/or dry deposition from photochemistry of thermospheric NO. We review the integration of SAM data with terrestrial Mars analog work in order to better understand the timing of nitrogen fixation and mobility of nitrogen on Mars, and thus its availability to putative biology. In particular, the relationship between nitrate and other soluble salts, such as perchlorate, may help reveal the timing of nitrogen fixation and post-depositional behavior of nitrate on Mars [4]. Finally, we present a comparison of isotopic composition (δ15N) of nitrate with δ15N of atmospheric nitrogen (δ15N ≈ 574‰, [5]), which can be used to constrain atmospheric loss of N2 and model the evolution of the atmosphere on Mars.

Heart Failure, Left Ventricular Remodeling, and Circulating Nitric Oxide Metabolites.

PubMed

Chirinos, Julio A; Akers, Scott R; Trieu, Lien; Ischiropoulos, Harry; Doulias, Paschalis-Thomas; Tariq, Ali; Vassim, Izzah; Koppula, Maheswara R; Syed, Amer Ahmed; Soto-Calderon, Haideliza; Townsend, Raymond R; Cappola, Thomas P; Margulies, Kenneth B; Zamani, Payman

2016-10-14

Stable plasma nitric oxide (NO) metabolites (NO M ), composed predominantly of nitrate and nitrite, are attractive biomarkers of NO bioavailability. NO M levels integrate the influence of NO-synthase-derived NO production/metabolism, dietary intake of inorganic nitrate/nitrite, and clearance of NO M . Furthermore, nitrate and nitrite, the most abundant NO M , can be reduced to NO via the nitrate-nitrite-NO pathway. We compared serum NO M among subjects without heart failure (n=126), subjects with heart failure and preserved ejection fraction (HFpEF; n=43), and subjects with heart failure and reduced ejection fraction (HFrEF; n=32). LV mass and extracellular volume fraction were measured with cardiac MRI. Plasma NO M levels were measured after reduction to NO via reaction with vanadium (III)/hydrochloric acid. Subjects with HFpEF demonstrated significantly lower unadjusted levels of NO M (8.0 μmol/L; 95% CI 6.2-10.4 μmol/L; ANOVA P=0.013) than subjects without HF (12.0 μmol/L; 95% CI 10.4-13.9 μmol/L) or those with HFrEF (13.5 μmol/L; 95% CI 9.7-18.9 μmol/L). There were no significant differences in NO M between subjects with HFrEF and subjects without HF. In a multivariable model that adjusted for age, sex, race, diabetes mellitus, body mass index, current smoking, systolic blood pressure, and glomerular filtration rate, HFpEF remained a predictor of lower NO M (β=-0.43; P=0.013). NO M did not correlate with LV mass, or LV diffuse fibrosis. HFpEF, but not HFrEF, is associated with reduced plasma NO M , suggesting greater endothelial dysfunction, enhanced clearance, or deficient dietary ingestion of inorganic nitrate. Our findings may underlie the salutary effects of inorganic nitrate supplementation demonstrated in recent clinical trials in HFpEF. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Influence of aerosol chemical composition on N2O5 uptake: airborne regional measurements in northwestern Europe

NASA Astrophysics Data System (ADS)

Morgan, W. T.; Ouyang, B.; Allan, J. D.; Aruffo, E.; Di Carlo, P.; Kennedy, O. J.; Lowe, D.; Flynn, M. J.; Rosenberg, P. D.; Williams, P. I.; Jones, R.; McFiggans, G. B.; Coe, H.

2015-01-01

Aerosol chemical composition was found to influence nighttime atmospheric chemistry during a series of airborne measurements in northwestern Europe in summer conditions, which has implications for regional air quality and climate. The uptake of dinitrogen pentoxide, γ (N2O5), to particle surfaces was found to be modulated by the amount of water content and ammonium nitrate present in the aerosol. The conditions prevalent in this study suggest that the net uptake rate of N2O5 to atmospheric aerosols was relatively efficient compared to previous studies, with γ (N2O5) values in the range 0.01-0.03. This is likely a consequence of the elevated relative humidity in the region, which promotes greater aerosol water content. Increased nitrate concentrations relative to particulate water were found to suppress N2O5 uptake. The results presented here contrast with previous ambient studies of N2O5 uptake, which have generally taken place in low-nitrate environments in the USA. Comparison of the N2O5 uptake derived from the measurements with a parameterised scheme that is based on the ratio of particulate water to nitrate yielded reasonably good agreement in terms of the magnitude and variation in uptake, provided the effect of chloride was neglected. An additional suppression of the parameterised uptake is likely required to fully capture the variation in N2O5 uptake, which could be achieved via the known suppression by organic aerosol. However, existing parameterisations representing the suppression by organic aerosol were unable to fully represent the variation in N2O5 uptake. These results provide important ambient measurement constraint on our ability to predict N2O5 uptake in regional and global aerosol models. N2O5 uptake is a potentially important source of nitrate aerosol and a sink of the nitrate radical, which is the main nocturnal oxidant in the atmosphere. The results further highlight the importance of ammonium nitrate in northwestern Europe as a key component of atmospheric composition in the region.

Influence of aerosol chemical composition on N2O5 uptake: airborne regional measurements in North-Western Europe

NASA Astrophysics Data System (ADS)

Morgan, W. T.; Ouyang, B.; Allan, J. D.; Aruffo, E.; Di Carlo, P.; Kennedy, O. J.; Lowe, D.; Flynn, M. J.; Rosenberg, P. D.; Williams, P. I.; Jones, R.; McFiggans, G. B.; Coe, H.

2014-07-01

Aerosol chemical composition was found to influence nighttime atmospheric chemistry during a series of airborne measurements in North-Western Europe in summer conditions, which has implications for regional air quality and climate. The uptake of dinitrogen pentoxide, γ (N2O5), to particle surfaces was found to be modulated by the amount of water content and ammonium nitrate present in the aerosol. The conditions prevalent in this study suggest that the net uptake rate of N2O5 to atmospheric aerosols was relatively efficient compared to previous studies, with γ (N2O5) values in the range 0.01-0.03. This is likely a consequence of the elevated relative humidity in the region, which promotes greater aerosol water content. Increased nitrate concentrations relative to particulate water were found to suppress N2O5 uptake. The results presented here contrast with previous ambient studies of N2O5 uptake, which have generally taken place in low-nitrate environments in the USA. Comparison of the N2O5 uptake derived from the measurements with a parameterised scheme that is based on the ratio of particulate water to nitrate yielded reasonably good agreement in terms of the magnitude and variation in uptake, provided the effect of chloride was neglected. An additional suppression of the parameterised uptake is likely required to fully capture the variation in N2O5 uptake, which could be achieved via the known suppression by organic aerosol. However, existing parameterisations representing the suppression by organic aerosol were unable to fully represent the variation in N2O5 uptake. These results provide important ambient measurement constraint on our ability to predict N2O5 uptake in regional and global aerosol models. N2O5 uptake is a potentially important source of nitrate aerosol and a sink of the nitrate radical, which is the main nocturnal oxidant in the atmosphere. The results further highlight the importance of ammonium nitrate in North-Western Europe as a key component of atmospheric composition in the region.

Comparative analyses of hydrological responses of two adjacent watersheds to climate variability and change using the SWAT model

NASA Astrophysics Data System (ADS)

Lee, Sangchul; Yeo, In-Young; Sadeghi, Ali M.; McCarty, Gregory W.; Hively, Wells D.; Lang, Megan W.; Sharifi, Amir

2018-01-01

Water quality problems in the Chesapeake Bay Watershed (CBW) are expected to be exacerbated by climate variability and change. However, climate impacts on agricultural lands and resultant nutrient loads into surface water resources are largely unknown. This study evaluated the impacts of climate variability and change on two adjacent watersheds in the Coastal Plain of the CBW, using the Soil and Water Assessment Tool (SWAT) model. We prepared six climate sensitivity scenarios to assess the individual impacts of variations in CO2 concentration (590 and 850 ppm), precipitation increase (11 and 21 %), and temperature increase (2.9 and 5.0 °C), based on regional general circulation model (GCM) projections. Further, we considered the ensemble of five GCM projections (2085-2098) under the Representative Concentration Pathway (RCP) 8.5 scenario to evaluate simultaneous changes in CO2, precipitation, and temperature. Using SWAT model simulations from 2001 to 2014 as a baseline scenario, predicted hydrologic outputs (water and nitrate budgets) and crop growth were analyzed. Compared to the baseline scenario, a precipitation increase of 21 % and elevated CO2 concentration of 850 ppm significantly increased streamflow and nitrate loads by 50 and 52 %, respectively, while a temperature increase of 5.0 °C reduced streamflow and nitrate loads by 12 and 13 %, respectively. Crop biomass increased with elevated CO2 concentrations due to enhanced radiation- and water-use efficiency, while it decreased with precipitation and temperature increases. Over the GCM ensemble mean, annual streamflow and nitrate loads showed an increase of ˜ 70 % relative to the baseline scenario, due to elevated CO2 concentrations and precipitation increase. Different hydrological responses to climate change were observed from the two watersheds, due to contrasting land use and soil characteristics. The watershed with a larger percent of croplands demonstrated a greater increased rate of 5.2 kg N ha-1 in nitrate yield relative to the watershed with a lower percent of croplands as a result of increased export of nitrate derived from fertilizer. The watershed dominated by poorly drained soils showed increased nitrate removal due do enhanced denitrification compared to the watershed dominated by well-drained soils. Our findings suggest that increased implementation of conservation practices would be necessary for this region to mitigate increased nitrate loads associated with predicted changes in future climate.

Using Multi-Isotope Tracer Methods to Understand the Sources of Nitrate in Aerosols, Fog and River Water in Podocarpus National Forest, Ecuador

NASA Astrophysics Data System (ADS)

Brothers, L. A.; Dominguez, G.; Fabian, P.; Thiemens, M. H.

2008-12-01

The eastern slopes of the Andean rainforests of Ecuador possess some of the highest plant biodiversity found on the planet; however, these ecosystems are in jeopardy because region is experiences one of the highest deforestation rates in South America. This rainforest characterized by high acidity and low nutrient soils and experiences natural process which are both destabilizing and stabilizing to biodiversity rendering this a unique, though sensitive environment. There is increased concern that anthropogenic activities especially biomass burning are affecting the rainforests and could lead to higher extinction rates, changes in the biodiversity and far reaching effects on the global troposphere. Measurements of nitrate and sulfate in rain and fog water have shown periods of elevated concentrations in the Podocarpus National Park near Loja, Ecuador. These high episodes contribute to annual deposition rates that are comparable to polluted regions of North America and Europe. Significant anthropogenic sources such as large scale industry or a major city, near this forest are lacking. It is believed that the majority of the nitrate and sulfate pollution is due to the large amount of biomass burning during the dry season in the Amazon Basin. In recent years it has been shown that large amount of dust is transported across the Atlantic from Africa which reaches South America. Concentration measurements do not elucidate the source of high nitrate and sulfate pollution; however, by measuring all three stable isotopes of oxygen in nitrate and sulfate from fog and river water provides a new way to examine the impacts of biomass burning on the region. By using stable isotope techniques atmospheric nitrate and sulfate can be resolved from terrestrial sources. This provides a unique way to trace the contributions from the biomass burning and farming sources. Current research at the field station, Estación Científica San Francisco in the Podocarpus National Forest monitors sulfate and nitrate concentrations in rain and fog water by standard methods to investigate water and nutrient pathways along with data from satellite and ground based remote sensing, observations and numerical models. We hope to pair this with a multi-isotope tracer method and NOAA Hysplit Back trajectories, and satellite imagery for information about the number of fires burning in the region to help identify sources of the high nitrate deposition.

The Search for Nitrates on Mars by the Sample Analysis at Mars (SAM) Instrument

NASA Technical Reports Server (NTRS)

Navarro-Gonzalez, Rafael; Stern, Jennifer C.; Freissinet, Caroline; McKay, Chirstopher P.; Sutter, Brad; Archer, P. Douglas, Jr.; McAdam, Amy; Franz, Heather; Coll, Partice J.; Glavin, Daniel Patrick;

NO2 uptake under practically relevant conditions on BaO/Pt(111)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mudiyanselage, Kumudu; Szanyi, János

2012-02-01

The formation of nitrites and nitrates (Ba(NOx)2) under practically relevant conditions (PNO2 up to 1.0 Torr and T = 500 K) and their thermal decomposition on BaO (>20 monolayer equivalent (MLE))/Pt(1 1 1) were studied using temperature programmed desorption (TPD), infrared reflection absorption (IRA), and Xray photoelectron (XP) spectroscopies. The exposure of BaO to 1.0 × 10-8 Torr NO2 at 500 K leads to the formation of a Ba(NOx)2 layer with small, disordered crystalline nitrate clusters. Under these conditions (PNO2 = 1.0 × 10-8 Torr and T = 500 K) only the top portion of the BaO layer converts tomore » Ba(NOx)2 and the nitrites in this Ba(NOx)2 layer stay without converting completely to nitrates even after 100 min of NO2 exposure. In the thermal decomposition of Ba(NOx)2, first nitrites decompose, releasing NO and then the decomposition of nitrates occurs via two pathways releasing NO2 and NO + O2. At 500 K and PNO2 ≥ 1.0 × 10-7 Torr, first NO2 reacts with BaO to form small disordered crystalline Ba(NO3)2 particles and then these particles agglomerate to form large, well-ordered (bulk-like) crystalline nitrates as the NO2 exposure increases. The thermal decomposition of these well-ordered, bulk-like crystalline nitrate aggregates occurs in two steps releasing NO2 and NO + O2 in each step in two different temperature regions. NO2 pressure ≥1.0 × 10-5 Torr is required for the complete oxidation of initially formed nitrites to nitrates and the full nitration of the BaO layer at 500 K sample temperature. We gratefully acknowledge the US Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle Memorial Institute under contract number DE-AC05-76RL01830.« less

The two faces of Hippo: targeting the Hippo pathway for regenerative medicine and cancer treatment

PubMed Central

Johnson, Randy; Halder, Georg

2014-01-01

The Hippo signaling pathway is an emerging growth control and tumor suppressor pathway that regulates cell proliferation and stem cell functions. Defects in Hippo signaling and hyperactivation of its downstream effectors YAP and TAZ contribute to the development of cancer, suggesting that pharmacological inhibition of YAP and TAZ activity may be an effective anticancer strategy. Conversely, YAP and TAZ can also play beneficial roles in stimulating tissue repair and regeneration following injury, therefore activation of YAP and TAZ may be useful in these contexts. Recently, a complex network of intracellular and extracellular signaling pathways that modulate YAP and TAZ activities have been identified. Here we review the regulation of the Hippo signaling pathway, its functions in normal homeostasis and disease, and recent progress in the identification of small molecule pathway modulators. PMID:24336504

MASM, a Matrine Derivative, Offers Radioprotection by Modulating Lethal Total-Body Irradiation-Induced Multiple Signaling Pathways in Wistar Rats.

PubMed

Li, Jianzhong; Xu, Jing; Lu, Yiming; Qiu, Lei; Xu, Weiheng; Lu, Bin; Hu, Zhenlin; Chu, Zhiyong; Chai, Yifeng; Zhang, Junping

2016-05-17

Matrine is an alkaloid extracted from Sophora flavescens Ait and has many biological activities, such as anti-inflammatory, antitumor, anti-fibrosis, and immunosuppressive properties. In our previous studies, the matrine derivative MASM was synthesized and exhibited potent inhibitory activity against liver fibrosis. In this study, we mainly investigated its protection against lethal total-body irradiation (TBI) in rats. Administration of MASM reduced the radiation sickness characteristics and increased the 30-day survival of rats before or after lethal TBI. Ultrastructural observation illustrated that pretreatment of rats with MASM significantly attenuated the TBI-induced morphological changes in the different organs of irradiated rats. Gene expression profiles revealed that pretreatment with MASM had a dramatic effect on gene expression changes caused by TBI. Pretreatment with MASM prevented differential expression of 53% (765 genes) of 1445 differentially expressed genes induced by TBI. Pathway enrichment analysis indicated that these genes were mainly involved in a total of 21 pathways, such as metabolic pathways, pathways in cancer, and mitogen-activated protein kinase (MAPK) pathways. Our data indicated that pretreatment of rats with MASM modulated these pathways induced by TBI, suggesting that the pretreatment with MASM might provide the protective effects on lethal TBI mainly or partially through the modulation of these pathways, such as multiple MAPK pathways. Therefore, MASM has the potential to be used as an effective therapeutic or radioprotective agent to minimize irradiation damages and in combination with radiotherapy to improve the efficacy of cancer therapy.

Ripening of pepper (Capsicum annuum) fruit is characterized by an enhancement of protein tyrosine nitration.

PubMed

Chaki, Mounira; Álvarez de Morales, Paz; Ruiz, Carmelo; Begara-Morales, Juan C; Barroso, Juan B; Corpas, Francisco J; Palma, José M

2015-09-01

Pepper (Capsicum annuum, Solanaceae) fruits are consumed worldwide and are of great economic importance. In most species ripening is characterized by important visual and metabolic changes, the latter including emission of volatile organic compounds associated with respiration, destruction of chlorophylls, synthesis of new pigments (red/yellow carotenoids plus xanthophylls and anthocyanins), formation of pectins and protein synthesis. The involvement of nitric oxide (NO) in fruit ripening has been established, but more work is needed to detail the metabolic networks involving NO and other reactive nitrogen species (RNS) in the process. It has been reported that RNS can mediate post-translational modifications of proteins, which can modulate physiological processes through mechanisms of cellular signalling. This study therefore examined the potential role of NO in nitration of tyrosine during the ripening of California sweet pepper. The NO content of green and red pepper fruit was determined spectrofluorometrically. Fruits at the breaking point between green and red coloration were incubated in the presence of NO for 1 h and then left to ripen for 3 d. Profiles of nitrated proteins were determined using an antibody against nitro-tyrosine (NO2-Tyr), and profiles of nitrosothiols were determined by confocal laser scanning microscopy. Nitrated proteins were identified by 2-D electrophoresis and MALDI-TOF/TOF analysis. Treatment with NO delayed the ripening of fruit. An enhancement of nitrosothiols and nitroproteins was observed in fruit during ripening, and this was reversed by the addition of exogenous NO gas. Six nitrated proteins were identified and were characterized as being involved in redox, protein, carbohydrate and oxidative metabolism, and in glutamate biosynthesis. Catalase was the most abundant nitrated protein found in both green and red fruit. The RNS profile reported here indicates that ripening of pepper fruit is characterized by an enhancement of S-nitrosothiols and protein tyrosine nitration. The nitrated proteins identified have important functions in photosynthesis, generation of NADPH, proteolysis, amino acid biosynthesis and oxidative metabolism. The decrease of catalase in red fruit implies a lower capacity to scavenge H2O2, which would promote lipid peroxidation, as has already been reported in ripe pepper fruit. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Ripening of pepper (Capsicum annuum) fruit is characterized by an enhancement of protein tyrosine nitration

PubMed Central

Chaki, Mounira; Álvarez de Morales, Paz; Ruiz, Carmelo; Begara-Morales, Juan C.; Barroso, Juan B.; Corpas, Francisco J.; Palma, José M.

2015-01-01

Background and Aims Pepper (Capsicum annuum, Solanaceae) fruits are consumed worldwide and are of great economic importance. In most species ripening is characterized by important visual and metabolic changes, the latter including emission of volatile organic compounds associated with respiration, destruction of chlorophylls, synthesis of new pigments (red/yellow carotenoids plus xanthophylls and anthocyanins), formation of pectins and protein synthesis. The involvement of nitric oxide (NO) in fruit ripening has been established, but more work is needed to detail the metabolic networks involving NO and other reactive nitrogen species (RNS) in the process. It has been reported that RNS can mediate post-translational modifications of proteins, which can modulate physiological processes through mechanisms of cellular signalling. This study therefore examined the potential role of NO in nitration of tyrosine during the ripening of California sweet pepper. Methods The NO content of green and red pepper fruit was determined spectrofluorometrically. Fruits at the breaking point between green and red coloration were incubated in the presence of NO for 1 h and then left to ripen for 3 d. Profiles of nitrated proteins were determined using an antibody against nitro-tyrosine (NO2-Tyr), and profiles of nitrosothiols were determined by confocal laser scanning microscopy. Nitrated proteins were identified by 2-D electrophoresis and MALDI-TOF/TOF analysis. Key Results Treatment with NO delayed the ripening of fruit. An enhancement of nitrosothiols and nitroproteins was observed in fruit during ripening, and this was reversed by the addition of exogenous NO gas. Six nitrated proteins were identified and were characterized as being involved in redox, protein, carbohydrate and oxidative metabolism, and in glutamate biosynthesis. Catalase was the most abundant nitrated protein found in both green and red fruit. Conclusions The RNS profile reported here indicates that ripening of pepper fruit is characterized by an enhancement of S-nitrosothiols and protein tyrosine nitration. The nitrated proteins identified have important functions in photosynthesis, generation of NADPH, proteolysis, amino acid biosynthesis and oxidative metabolism. The decrease of catalase in red fruit implies a lower capacity to scavenge H2O2, which would promote lipid peroxidation, as has already been reported in ripe pepper fruit. PMID:25814060

Modulation of the Isoprenoid/Cholesterol Biosynthetic Pathway During Neuronal Differentiation In Vitro.

PubMed

Cartocci, Veronica; Segatto, Marco; Di Tunno, Ilenia; Leone, Stefano; Pfrieger, Frank W; Pallottini, Valentina

2016-09-01

During differentiation, neurons acquire their typical shape and functional properties. At present, it is unclear, whether this important developmental step involves metabolic changes. Here, we studied the contribution of the mevalonate (MVA) pathway to neuronal differentiation using the mouse neuroblastoma cell line N1E-115 as experimental model. Our results show that during differentiation, the activity of 3-hydroxy 3-methylglutaryl Coenzyme A reductase (HMGR), a key enzyme of MVA pathway, and the level of Low Density Lipoprotein receptor (LDLr) decrease, whereas the level of LDLr-related protein-1 (LRP1) and the dimerization of Scavanger Receptor B1 (SRB-1) rise. Pharmacologic inhibition of HMGR by simvastatin accelerated neuronal differentiation by modulating geranylated proteins. Collectively, our data suggest that during neuronal differentiation, the activity of the MVA pathway decreases and we postulate that any interference with this process impacts neuronal morphology and function. Therefore, the MVA pathway appears as an attractive pharmacological target to modulate neurological and metabolic symptoms of developmental neuropathologies. J. Cell. Biochem. 117: 2036-2044, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

PyPathway: Python Package for Biological Network Analysis and Visualization.

PubMed

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

Predicting Redox Conditions in Groundwater Using Statistical Techniques: Implications for Nitrate Transport in Groundwater and Streams

NASA Astrophysics Data System (ADS)

Tesoriero, A. J.; Terziotti, S.

2014-12-01

Nitrate trends in streams often do not match expectations based on recent nitrogen source loadings to the land surface. Groundwater discharge with long travel times has been suggested as the likely cause for these observations. The fate of nitrate in groundwater depends to a large extent on the occurrence of denitrification along flow paths. Because denitrification in groundwater is inhibited when dissolved oxygen (DO) concentrations are high, defining the oxic-suboxic interface has been critical in determining pathways for nitrate transport in groundwater and to streams at the local scale. Predicting redox conditions on a regional scale is complicated by the spatial variability of reaction rates. In this study, logistic regression and boosted classification tree analysis were used to predict the probability of oxic water in groundwater in the Chesapeake Bay watershed. The probability of oxic water (DO > 2 mg/L) was predicted by relating DO concentrations in over 3,000 groundwater samples to indicators of residence time and/or electron donor availability. Variables that describe position in the flow system (e.g., depth to top of the open interval), soil drainage and surficial geology were the most important predictors of oxic water. Logistic regression and boosted classification tree analysis correctly predicted the presence or absence of oxic conditions in over 75 % of the samples in both training and validation data sets. Predictions of the percentages of oxic wells in deciles of risk were very accurate (r2>0.9) in both the training and validation data sets. Depth to the bottom of the oxic layer was predicted and is being used to estimate the effect that groundwater denitrification has on stream nitrate concentrations and the time lag between the application of nitrogen at the land surface and its effect on streams.

Acute dietary nitrate supplementation enhances compensatory vasodilation during hypoxic exercise in older adults.

PubMed

Casey, Darren P; Treichler, David P; Ganger, Charles T; Schneider, Aaron C; Ueda, Kenichi

2015-01-15

We have previously demonstrated that aging reduces the compensatory vasodilator response during hypoxic exercise due to blunted nitric oxide (NO) signaling. Recent evidence suggests that NO bioavailability can be augmented by dietary nitrate through the nitrate-nitrite pathway. Thus we tested the hypothesis that acute dietary nitrate supplementation increases the compensatory vasodilator response to hypoxic exercise, particularly in older adults. Thirteen young (25 ± 1 yr) and 12 older (64 ± 2 yr) adults performed rhythmic forearm exercise at 20% of maximum voluntary contraction during normoxia and hypoxia (∼80% O2 saturation); both before (control) and 3 h after beetroot juice (BR) consumption. Forearm vascular conductance (FVC; ml·min(-1)·100 mmHg(-1)) was calculated from forearm blood flow (ml/min) and blood pressure (mmHg). Compensatory vasodilation was defined as the relative increase in FVC due to hypoxic exercise (i.e., % increase compared with respective normoxic exercise trial). Plasma nitrite was determined from venous blood samples obtained before the control trials and each of the exercise trials (normoxia and hypoxia) after BR. Consumption of BR increased plasma nitrite in both young and older adults (P < 0.001). During the control condition, the compensatory vasodilator response to hypoxic exercise was attenuated in older compared with young adults (3.8 ± 1.7% vs. 14.2 ± 1.2%, P < 0.001). Following BR consumption, compensatory vasodilation did not change in young (13.7 ± 3.3%, P = 0.81) adults but was substantially augmented in older adults (11.4 ± 2.1%, P < 0.01). Our data suggest that acute dietary nitrate supplementation increases the compensatory vasodilator response to hypoxic exercise in older but not young adults. Copyright © 2015 the American Physiological Society.

Dietary nitrate supplementation improves team sport-specific intense intermittent exercise performance.

PubMed

Wylie, Lee J; Mohr, Magni; Krustrup, Peter; Jackman, Sarah R; Ermιdis, Georgios; Kelly, James; Black, Matthew I; Bailey, Stephen J; Vanhatalo, Anni; Jones, Andrew M

2013-07-01

Recent studies have suggested that dietary inorganic nitrate (NO₃(-)) supplementation may improve muscle efficiency and endurance exercise tolerance but possible effects during team sport-specific intense intermittent exercise have not been examined. We hypothesized that NO₃(-) supplementation would enhance high-intensity intermittent exercise performance. Fourteen male recreational team-sport players were assigned in a double-blind, randomized, crossover design to consume 490 mL of concentrated, nitrate-rich beetroot juice (BR) and nitrate-depleted placebo juice (PL) over ~30 h preceding the completion of a Yo-Yo intermittent recovery level 1 test (Yo-Yo IR1). Resting plasma nitrite concentration ([NO₂(-)]) was ~400% greater in BR compared to PL. Plasma [NO₂(-)] declined by 20% in PL (P < 0.05) and by 54 % in BR (P < 0.05) from pre-exercise to end-exercise. Performance in the Yo-Yo IR1 was 4.2% greater (P < 0.05) with BR (1,704 ± 304 m) compared to PL (1,636 ± 288 m). Blood [lactate] was not different between BR and PL, but the mean blood [glucose] was lower (3.8 ± 0.8 vs. 4.2 ± 1.1 mM, P < 0.05) and the rise in plasma [K(+)] tended to be reduced in BR compared to PL (P = 0.08). These findings suggest that NO₃(-) supplementation may promote NO production via the nitrate-nitrite-NO pathway and enhance Yo-Yo IR1 test performance, perhaps by facilitating greater muscle glucose uptake or by better maintaining muscle excitability. Dietary NO₃(-) supplementation improves performance during intense intermittent exercise and may be a useful ergogenic aid for team sports players.

Spatial and Temporal Comparison of DNRA Communities in New River Estuary, USA

NASA Astrophysics Data System (ADS)

Song, B.; Lisa, J.; Tobias, C. R.

2016-02-01

Dissimilatory nitrate reduction to ammonium (DNRA) is an important nitrate respiring pathway, competing with denitrification, in various ecosystems. Studies examining the diversity and composition of DNRA communities are limited and their link to DNRA activity is unknown. We conducted a multidisciplinary investigation of sediment communities in the upper reaches of a eutrophic estuary to examine spatial and temporal variation of DNRA community structures and determine their linkage to activities. Sediment samples were collected seasonally from two study sites (AA2 and JAX) in the New River Estuary, North Carolina, USA. 15N-nitrate tracer experiments were conducted to measure potential DNRA rates while abundance of DNRA communities was measured using quantitative PCR of cytochrome C nitrite reductase genes (nrfA). Composition and diversity of DNRA communities were also examined based on next generation sequencing (NGS) of nrfA genes using an Ion Torrent PGM. Bioinformatic analysis was conducted using the FunGene pipeline and Mothur program. Higher DNRA activities were measured at JAX and associated with higher abundance of nrfA genes. Seasonal variation in DNRA rates and nrfA gene abundance was more evident at JAX than AA2. Nitrate concentration and dissolved oxygen in bottom water were significantly and positively correlated with activities and abundance of DNRA communities. The nrfA NGS analysis revealed that spatial variation of DNRA communities was much greater than temporal variation with salinity, dissolved organic carbon, and nitrate as the most important environmental variables affecting these communities. Diversity of DNRA communities was negative correlated with the DNRA rates and nrfA gene abundance, which suggests that dominant members of the DNRA community are responsible for higher rates. Thus, our multidisciplinary study clearly demonstrates the linkage between structure and activities of DNRA communities in the upper reaches of New River Estuary.

Flurbiprofen benzyl nitrate (NBS-242) inhibits the growth of A-431 human epidermoid carcinoma cells and targets β-catenin.

PubMed

Nath, Niharika; Liu, Xiaoping; Jacobs, Lloydine; Kashfi, Khosrow

2013-01-01

The Wnt/β-catenin/T cell factor (TCF) signaling pathway is important in the development of nonmelanoma skin cancers (NMSCs). Nitric-oxide-releasing nonsteroidal anti-inflammatory drugs (NO-NSAIDs) are chemopreventive agents consisting of a traditional NSAID attached to an NO-releasing moiety through a chemical spacer. Previously we showed that an aromatic spacer enhanced the potency of a particular NO-NSAID compared to an aliphatic spacer. We synthesized an NO-releasing NSAID with an aromatic spacer (flurbiprofen benzyl nitrate, NBS-242), and using the human skin cancer cell line A-431, we evaluated its effects on cell kinetics, Wnt/β-catenin, cyclin D1, and caspase-3. NBS-242 inhibited the growth of A-431 cancer cells, being ~15-fold more potent than flurbiprofen and up to 5-fold more potent than NO-flurbiprofen with an aliphatic spacer, the half maximal inhibitory concentrations (IC50) for growth inhibition being 60 ± 4 μM, 320 ± 20 μM, and 880 ± 65 μM for NBS-242, NO-flurbiprofen, and flurbiprofen, respectively. This effect was associated with inhibition of proliferation, accumulation of cells in the G0/G1 phase of the cell cycle, and an increase in apoptotic cell population. NBS-242 cleaved β-catenin both in the cytoplasm and the nucleus of A-431 cells. NBS-242 activated caspase-3 whose activation was reflected in the cleavage of procaspase-3. To test the functional consequence of β-catenin cleavage, we determined the expression of cyclin D1, a Wnt-response gene. NBS-242 reduced cyclin D1 levels in a concentration dependent manner. These findings establish a strong inhibitory effect of NBS-242 in A-431 human epidermoid carcinoma cells. NBS-242 modulates parameters that are important in determining cellular mass.

Understanding the hydrologic control of N cycle: Effect of water filled pore space on heterotrophic nitrification, denitrification and dissimilatory nitrate reduction to ammonium mechanisms in unsaturated soils

NASA Astrophysics Data System (ADS)

Mekala, C.; Nambi, Indumathi M.

2017-07-01

Irrigation practice will be effective if it supplies optimal water and nutrients to crops and act as a filter for contaminants leaching to ground water. There is always a scope for improving the fertilizer use efficiency and scheduling of wastewater irrigation if the fate and transport of nutrients particularly nitrogenous compounds in the soil are well understood. In the present study, nitrogen transport experiments for two different agricultural soils are performed under varying saturation 33, 57, 78% water filled pore space for sandy soil 1 and 52, 81 and 96% for loam soil 2. A HYDRUS 2D model with constructed wetland (CW2D) module could simulate aerobic nitrification and anoxic denitrification well for both soils and estimated the reaction kinetics. A hot spot of Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway has been observed at 81% moisture content for a loamy sand soil. The presence of high organic content and reductive soil environment (5.53 C/NO3- ratio; ORP = - 125 mV) results in ammonium accumulation of 16.85 mg in the soil. The overall observation from this study is nitrification occurs in a wide range of saturations 33-78% with highest at 57% whereas denitrification is significant at higher water saturations 57-78% for sandy soil texture. For a loamy sand soil, denitrification is dominant at 96% saturation with least nitrification at all saturation studies. The greatest nitrogen losses (> 90%) was observed for soil 2 while 30-70% for soil1. The slow dispersive subsurface transport with varying oxygen dynamics enhanced nitrogen losses from soil2 due to lesser soil permeability. This in turn, prevents NO3- leaching and groundwater contamination. This type of modeling study should be used before planning field experiments for designing optimal irrigation and fertigation schedules.

Understanding the response of Desulfovibrio desulfuricans ATCC 27774 to the electron acceptors nitrate and sulfate - biosynthetic costs modulate substrate selection.

PubMed

Sousa, Joana R; Silveira, Célia M; Fontes, Pedro; Roma-Rodrigues, Catarina; Fernandes, Alexandra R; Van Driessche, Gonzalez; Devreese, Bart; Moura, Isabel; Moura, José J G; Almeida, M Gabriela

2017-11-01

Sulfate-reducing bacteria (SRB) are a diverse group of anaerobic microorganisms that obtain their energy from dissimilatory sulfate reduction. Some SRB species have high respiratory versatility due to the possible use of alternative electron acceptors. A good example is Desulfovibrio desulfuricans ATCC 27774, which grows in the presence of nitrate (end product: ammonium) with higher rates and yields to those observed in sulfate containing medium (end product: sulfide). In this work, the mechanisms supporting the respiratory versatility of D. desulfuricans were unraveled through the analysis of the proteome of the bacterium under different experimental conditions. The most remarkable difference in the two-dimensional gel electrophoresis maps is the high number of spots exclusively represented in the nitrate medium. Most of the proteins with increase abundance are involved in the energy metabolism and the biosynthesis of amino acids (or proteins), especially those participating in ammonium assimilation processes. qPCR analysis performed during different stages of the bacterium's growth showed that the genes involved in nitrate and nitrite reduction (napA and nrfA, respectively) have different expressions profiles: while napA did not vary significantly, nrfA was highly expressed at a 6h time point. Nitrite levels measured along the growth curve revealed a peak at 3h. Thus, the initial consumption of nitrate and concomitant production of nitrite must induce nrfA expression. The activation of alternative mechanisms for energy production, aside several N-assimilation metabolisms and detoxification processes, solves potential survival problems in adapting to different environments and contributes to higher bacterial growth rates. Copyright © 2017 Elsevier B.V. All rights reserved.

Allostery in a disordered protein: Oxidative modifications to α-Synuclein act distally to regulate membrane binding

PubMed Central

Sevcsik, Eva; Trexler, Adam J.; Dunn, Joanna M.; Rhoades, Elizabeth

2011-01-01

Both oxidative stress and aggregation of the protein α-synuclein (aS) have been implicated as key factors in the etiology of Parkinson’s disease. Specifically, oxidative modifications to aS disrupt its binding to lipid membranes, an interaction considered critical to its native function. Here we seek to provide a mechanistic explanation for this phenomenon by investigating the effects of oxidative nitration of tyrosine residues on the structure of aS and its interaction with lipid membranes. Membrane binding is mediated by the first ~95 residues of aS. We find that nitration of the single tyrosine (Y39) in this domain disrupts binding due to electrostatic repulsion. Moreover, we observe that nitration of the three tyrosines (Y125/133/136) in the C-terminal domain is equally effective in perturbing binding, an intriguing result given that the C-terminus is not thought to interact directly with membranes. Our investigations show that tyrosine nitration results in a change of the conformational states populated by aS in solution, with the most prominent changes occurring in the C-terminal region. These results lead us to suggest that nitration of Y125/133/136 reduces the membrane binding affinity of aS through allosteric coupling by altering the ensemble of conformational states and depopulating those capable of membrane binding. While allostery is a well-established concept for structured proteins, it has only recently been discussed in the context of disordered proteins. We propose that allosteric regulation through modification of specific residues in, or ligand binding to, the C-terminus may even be a general mechanism for modulating aS function. PMID:21491910

Assessment of the first indirect radiative effect of ammonium-sulfate-nitrate aerosols in East Asia

NASA Astrophysics Data System (ADS)

Han, Xiao; Zhang, Meigen; Skorokhod, Andrei

2017-11-01

A physically based cloud nucleation parameterization was introduced into an optical properties/radiative transfer module incorporated with the off-line air quality modeling system Regional Atmospheric Modeling System (RAMS)-Models-3 Community Multi Scale Air Quality (CMAQ) to investigate the distribution features of the first indirect radiative effects of sulfate, nitrate, and ammonium-sulfate-nitrate (ASN) over East Asia for the years of 2005, 2010, and 2013. The relationship between aerosol particles and cloud droplet number concentration could be properly described by this parameterization because the simulated cloud fraction and cloud liquid water path were generally reliable compared with Moderate Resolution Imaging Spectroradiometer (MODIS) retrieved data. Simulation results showed that the strong effect of indirect forcing was mainly concentrated in Southeast China, the East China Sea, the Yellow Sea, and the Sea of Japan. The highest indirect radiative forcing of ASN reached -3.47 W m-2 over Southeast China and was obviously larger than the global mean of the indirect forcing of all anthropogenic aerosols. In addition, sulfate provided about half of the contribution to the ASN indirect forcing effect. However, the effect caused by nitrate was weak because the mass burden of nitrate was very low during summer, whereas the cloud fraction was the highest. The analysis indicated that even though the interannual variation of indirect forcing magnitude generally followed the trend of aerosol mass burden from 2005 to 2013, the cloud fraction was an important factor that determined the distribution pattern of indirect forcing. The heaviest aerosol loading in North China did not cause a strong radiative effect because of the low cloud fraction over this region.

[Modulating expression of key genes within β-carotene synthetic pathway in recombinant Escherichia coli with RBS library to improve β-carotene production].

PubMed

Dai, Guanping; Sun, Tao; Miao, Liangtian; Li, Qingyan; Xiao, Dongguang; Zhang, Xueli

2014-08-01

β-carotene belongs to carotenoids family, widely applied in pharmaceuticals, neutraceuticals, cosmetics and food industries. In this study, three key genes (dxs, idi, and crt operon) within β-carotene synthetic pathway in recombinant Escherichia coli strain CAR005 were modulated with RBS Library to improve β-carotene production. There were 7%, 11% and 17% increase of β-carotene yield respectively after modulating dxs, idi and crt operon genes with RBS Library, demonstrating that modulating gene expression with regulatory parts libraries would have more opportunities to obtain optimal production of target compound. Combined modulation of crt operon, dxs and idi genes led to 35% increase of β-carotene yield compared to parent strain CAR005. The optimal gene expression strength identified in single gene modulation would not be the optimal strength when used in combined modulation. Our study provides a new strategy for improving production of target compound through modulation of gene expression.

Co-expression analysis reveals key gene modules and pathway of human coronary heart disease.

PubMed

Tang, Yu; Ke, Zun-Ping; Peng, Yi-Gen; Cai, Ping-Tai

2018-02-01

Coronary heart disease is a kind of disease which causes great injury to people world-widely. Although gene expression analyses had been performed previously, to our best knowledge, systemic co-expression analysis for this disease is still lacking to date. Microarray data of coronary heart disease was downloaded from NCBI with the accession number of GSE20681. Co-expression modules were constructed by WGCNA. Besides, the connectivity degree of eigengenes was analyzed. Furthermore, GO and KEGG enrichment analysis was performed on these eigengenes in these constructed modules. A total of 11 co-expression modules were constructed by the 3000 up-regulated genes from the 99 samples with coronary heart disease. The average number of genes in these modules was 270. The interaction analysis indicated the relative independence of gene expression in these modules. The functional enrichment analysis showed that there was a significant difference in the enriched terms and degree among these 11 modules. The results showed that modules 9 and 10 played critical roles in the occurrence of coronary disease. Pathways of hsa00190 (oxidative phosphorylation) and (hsa01130: biosynthesis of antibiotics) were thought to be closely related to the occurrence and development of coronary heart disease. Our result demonstrated that modules 9 and 10 were the most critical modules in the occurrence of coronary heart disease. Pathways as hsa00190 (oxidative phosphorylation) and (hsa01130: biosynthesis of antibiotics) had the potential to serve as the prognostic and predictive marker of coronary heart disease. © 2017 Wiley Periodicals, Inc.

Modulation of the Kynurenine Pathway for the Potential Treatment of Neurodegenerative Diseases

NASA Astrophysics Data System (ADS)

Courtney, Stephen; Scheel, Andreas

Modulation of tryptophan metabolism and in particular the kynurenine pathway is of considerable interest in the discovery of potential new treatments for neurodegenerative diseases. A number of small molecule inhibitors of the kynurenine metabolic pathway enzymes have been identified over recent years; a summary of these and their utility has been reviewed in this chapter. In particular, inhibitors of kynurenine monooxygenase represent an opportunity to develop a therapy for Huntington's disease; progress in the optimization of small molecule inhibitors of this enzyme is also described.

Rational modular design of metabolic network for efficient production of plant polyphenol pinosylvin.

PubMed

Wu, Junjun; Zhang, Xia; Zhu, Yingjie; Tan, Qinyu; He, Jiacheng; Dong, Mingsheng

2017-05-03

Efficient biosynthesis of the plant polyphenol pinosylvin, which has numerous applications in nutraceuticals and pharmaceuticals, is necessary to make biological production economically viable. To this end, an efficient Escherichia coli platform for pinosylvin production was developed via a rational modular design approach. Initially, different candidate pathway enzymes were screened to construct de novo pinosylvin pathway directly from D-glucose. A comparative analysis of pathway intermediate pools identified that this initial construct led to the intermediate cinnamic acid accumulation. The pinosylvin synthetic pathway was then divided into two new modules separated at cinnamic acid. Combinatorial optimization of transcriptional and translational levels of these two modules resulted in a 16-fold increase in pinosylvin titer. To further improve the concentration of the limiting precursor malonyl-CoA, the malonyl-CoA synthesis module based on clustered regularly interspaced short palindromic repeats interference was assembled and optimized with other two modules. The final pinosylvin titer was improved to 281 mg/L, which was the highest pinosylvin titer even directly from D-glucose without any additional precursor supplementation. The rational modular design approach described here could bolster our capabilities in synthetic biology for value-added chemical production.

Elastic and Photoelastic Properties of M(NO3)2, MO (M = Mg, Ca, Sr, Ba)

NASA Astrophysics Data System (ADS)

Zhuravlev, Yu. N.; Korabel'nikov, D. V.

2017-05-01

The paper deals with ab initio investigations of elastic and photoelastic properties of oxides and nitrates of alkaline-earth metals. In gradient approximation of the density functional theory (DFT), these properties are studied with the use of the linear combination of the atomic orbital technique. DFT calculations are done with the CRYSTAL 14 software package. The paper introduces the elastic and photoelastic constants, anisotropy parameters for single-crystalline phases and the elastic modules, hardness, Poisson ratio for polycrystalline phases. Such parameters as sonic speed, Debye temperature, thermal conductivity, and Gruneisen parameter are estimated herein. For the fist time, mechanical stability, anisotropy of elastic and photoelastic properties and their dependences are investigated ab initio in this paper. Experimental results on elastic and photoelastic properties of oxides and nitrates are in good agreement with theoretical calculations.

A new network representation of the metabolism to detect chemical transformation modules.

PubMed

Sorokina, Maria; Medigue, Claudine; Vallenet, David

2015-11-14

Metabolism is generally modeled by directed networks where nodes represent reactions and/or metabolites. In order to explore metabolic pathway conservation and divergence among organisms, previous studies were based on graph alignment to find similar pathways. Few years ago, the concept of chemical transformation modules, also called reaction modules, was introduced and correspond to sequences of chemical transformations which are conserved in metabolism. We propose here a novel graph representation of the metabolic network where reactions sharing a same chemical transformation type are grouped in Reaction Molecular Signatures (RMS). RMS were automatically computed for all reactions and encode changes in atoms and bonds. A reaction network containing all available metabolic knowledge was then reduced by an aggregation of reaction nodes and edges to obtain a RMS network. Paths in this network were explored and a substantial number of conserved chemical transformation modules was detected. Furthermore, this graph-based formalism allows us to define several path scores reflecting different biological conservation meanings. These scores are significantly higher for paths corresponding to known metabolic pathways and were used conjointly to build association rules that should predict metabolic pathway types like biosynthesis or degradation. This representation of metabolism in a RMS network offers new insights to capture relevant metabolic contexts. Furthermore, along with genomic context methods, it should improve the detection of gene clusters corresponding to new metabolic pathways.

Chemical genetic screen identifies lithocholic acid as an anti-aging compound that extends yeast chronological life span in a TOR-independent manner, by modulating housekeeping longevity assurance processes.

PubMed

Goldberg, Alexander A; Richard, Vincent R; Kyryakov, Pavlo; Bourque, Simon D; Beach, Adam; Burstein, Michelle T; Glebov, Anastasia; Koupaki, Olivia; Boukh-Viner, Tatiana; Gregg, Christopher; Juneau, Mylène; English, Ann M; Thomas, David Y; Titorenko, Vladimir I

2010-07-01

In chronologically aging yeast, longevity can be extended by administering a caloric restriction (CR) diet or some small molecules. These life-extending interventions target the adaptable target of rapamycin (TOR) and cAMP/protein kinase A (cAMP/PKA) signaling pathways that are under the stringent control of calorie availability. We designed a chemical genetic screen for small molecules that increase the chronological life span of yeast under CR by targeting lipid metabolism and modulating housekeeping longevity pathways that regulate longevity irrespective of the number of available calories. Our screen identifies lithocholic acid (LCA) as one of such molecules. We reveal two mechanisms underlying the life-extending effect of LCA in chronologically aging yeast. One mechanism operates in a calorie availability-independent fashion and involves the LCA-governed modulation of housekeeping longevity assurance pathways that do not overlap with the adaptable TOR and cAMP/PKA pathways. The other mechanism extends yeast longevity under non-CR conditions and consists in LCA-driven unmasking of the previously unknown anti-aging potential of PKA. We provide evidence that LCA modulates housekeeping longevity assurance pathways by suppressing lipid-induced necrosis, attenuating mitochondrial fragmentation, altering oxidation-reduction processes in mitochondria, enhancing resistance to oxidative and thermal stresses, suppressing mitochondria-controlled apoptosis, and enhancing stability of nuclear and mitochondrial DNA.

Metabolism as a Target for Modulation in Autoimmune Diseases.

PubMed

Huang, Nick; Perl, Andras

2018-05-05

Metabolic pathways are now well recognized as important regulators of immune differentiation and activation, and thus influence the development of autoimmune diseases such as systemic lupus erythematosus (SLE). The mechanistic target of rapamycin (mTOR) has emerged as a key sensor of metabolic stress and an important mediator of proinflammatory lineage specification. Metabolic pathways control the production of mitochondrial reactive oxygen species (ROS), which promote mTOR activation and also modulate the antigenicity of proteins, lipids, and DNA, thus placing ROS at the heart of metabolic disturbances during pathogenesis of SLE. Therefore, we review here the pathways that control ROS production and mTOR activation and identify targets for safe therapeutic modulation of the signaling network that underlies autoimmune diseases, focusing on SLE. Copyright © 2018. Published by Elsevier Ltd.

Genetic Polymorphism in Extracellular Regulators of Wnt Signaling Pathway

PubMed Central

Sharma, Ashish Ranjan; Seo, Eun-Min; Nam, Ju-Suk

2015-01-01

The Wnt signaling pathway is mediated by a family of secreted glycoproteins through canonical and noncanonical mechanism. The signaling pathways are regulated by various modulators, which are classified into two classes on the basis of their interaction with either Wnt or its receptors. Secreted frizzled-related proteins (sFRPs) are the member of class that binds to Wnt protein and antagonizes Wnt signaling pathway. The other class consists of Dickkopf (DKK) proteins family that binds to Wnt receptor complex. The present review discusses the disease related association of various polymorphisms in Wnt signaling modulators. Furthermore, this review also highlights that some of the sFRPs and DKKs are unable to act as an antagonist for Wnt signaling pathway and thus their function needs to be explored more extensively. PMID:25945348

Fine-scale in situ measurement of riverbed nitrate production and consumption in an armored permeable riverbed.

PubMed

Lansdown, Katrina; Heppell, Catherine M; Dossena, Matteo; Ullah, Sami; Heathwaite, A Louise; Binley, Andrew; Zhang, Hao; Trimmer, Mark

2014-04-15

Alteration of the global nitrogen cycle by man has increased nitrogen loading in waterways considerably, often with harmful consequences for aquatic ecosystems. Dynamic redox conditions within riverbeds support a variety of nitrogen transformations, some of which can attenuate this burden. In reality, however, assessing the importance of processes besides perhaps denitrification is difficult, due to a sparseness of data, especially in situ, where sediment structure and hydrologic pathways are intact. Here we show in situ within a permeable riverbed, through injections of (15)N-labeled substrates, that nitrate can be either consumed through denitrification or produced through nitrification, at a previously unresolved fine (centimeter) scale. Nitrification and denitrification occupy different niches in the riverbed, with denitrification occurring across a broad chemical gradient while nitrification is restricted to more oxic sediments. The narrow niche width for nitrification is in effect a break point, with the switch from activity "on" to activity "off" regulated by interactions between subsurface chemistry and hydrology. Although maxima for denitrification and nitrification occur at opposing ends of a chemical gradient, high potentials for both nitrate production and consumption can overlap when groundwater upwelling is strong.

In situ generation, metabolism and immunomodulatory signaling actions of nitro-conjugated linoleic acid in a murine model of inflammation.

PubMed

Villacorta, Luis; Minarrieta, Lucia; Salvatore, Sonia R; Khoo, Nicholas K; Rom, Oren; Gao, Zhen; Berman, Rebecca C; Jobbagy, Soma; Li, Lihua; Woodcock, Steven R; Chen, Y Eugene; Freeman, Bruce A; Ferreira, Ana M; Schopfer, Francisco J; Vitturi, Dario A

2018-05-01

Conjugated linoleic acid (CLA) is a prime substrate for intra-gastric nitration giving rise to the formation of nitro-conjugated linoleic acid (NO 2 -CLA). Herein, NO 2 -CLA generation is demonstrated within the context of acute inflammatory responses both in vitro and in vivo. Macrophage activation resulted in dose- and time-dependent CLA nitration and also in the production of secondary electrophilic and non-electrophilic derivatives. Both exogenous NO 2 -CLA as well as that generated in situ, attenuated NF-κB-dependent gene expression, decreased pro-inflammatory cytokine production and up-regulated Nrf2-regulated proteins. Importantly, both CLA nitration and the corresponding downstream anti-inflammatory actions of NO 2 -CLA were recapitulated in a mouse peritonitis model where NO 2 -CLA administration decreased pro-inflammatory cytokines and inhibited leukocyte recruitment. Taken together, our results demonstrate that the formation of NO 2 -CLA has the potential to function as an adaptive response capable of not only modulating inflammation amplitude but also protecting neighboring tissues via the expression of Nrf2-dependent genes. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Antiproliferative effect of a novel nitro-oxy derivative of celecoxib in human colon cancer cells: role of COX-2 and nitric oxide.

PubMed

Bocca, Claudia; Bozzo, Francesca; Bassignana, Andrea; Miglietta, Antonella

2010-07-01

It has been shown previously that a novel nitrooxy derivative of celecoxib exerts antiproliferative and pro-apoptotic effects in human colon cancer cells. The aim of this study was to elucidate whether these biological properties depend on COX-2 inhibition and/or NO release. Therefore, the derivative was decomposed into the parent compound celecoxib and the NO donor benzyl nitrate and the biological role of each was tested in COX-2-positive (HT-29) and -negative (SW-480) colon cancer cells. The main findings were that the nitro-oxy derivative behaved like celecoxib in HT-29 cells in terms of COX-2 and ERK/MAPK inhibition, as well as induction of apoptosis, while the benzyl nitrate had no such effects. Interestingly, the beta-catenin system was activated by the nitro-oxy derivative as well as by benzyl nitrate alone more potently than by the parent compound celecoxib, suggesting a possible regulatory role for NO. In SW480 cells, these activities were substantially less pronounced, suggesting the presence of COX-2-dependent mechanisms in the modulation of these parameters.

Isolation of the Chlamydomonas Regulatory Gene Nit2 by Transposon Tagging

PubMed Central

Schnell, R. A.; Lefebvre, P. A.

1993-01-01

Genetic evidence suggests that the NIT2 gene of Chlamydomonas reinhardtii encodes a positive regulator of the nitrate-assimilation pathway. To learn more about the function of the NIT2 gene product, we isolated the gene using a transposon-tagging strategy. A nit2 mutation caused by the insertion of a transposon was identified by testing spontaneous nit2 mutants for the presence of new copies of Gulliver or TOC1, transposable elements that have been identified in Chlamydomonas. In 2 of the 14 different mutants that were analyzed, a Gulliver element was found to be genetically and phenotypically associated with the nit2 mutation. Using the Gulliver element as a probe, one of the transposon-induced nit2 alleles was isolated, and a sequence adjoining the transposon was used to isolate the corresponding wild-type locus. The NIT2 gene was delimited by mapping DNA rearrangements associated with nit2 mutations and mutant rescue by genetic transformation. The NIT2 gene encodes a 6-kb transcript that was not detected in cells grown in the presence of ammonium. Likewise, NIT2-dependent genes are repressed in ammonium-grown cells. These results suggest that repression of the NIT2 gene may mediate metabolite repression of the nitrate assimilation pathway in Chlamydomonas. PMID:8394263

Nitric oxide induced by polyamines involves antioxidant systems against chilling stress in tomato (Lycopersicon esculentum Mill.) seedling.

PubMed

Diao, Qian-Nan; Song, Yong-Jun; Shi, Dong-Mei; Qi, Hong-Yan

Polyamines (PAs) and nitric oxide (NO) are vital signals in modulating plant response to abiotic stress. However, to our knowledge, studies on the relationship between NO and PAs in response to cold stress in tomato are limited. Accordingly, in this study, we investigated the effects of putrescine (Put) and spermidine (Spd) on NO generation and the function of Spd-induced NO in the tolerance of tomato seedling under chilling stress. Spd increased NO release via the nitric oxide synthase (NOS)-like and nitrate reductase (NR) enzymatic pathways in the seedlings, whereas Put had no such effect. Moreover, H 2 O 2 might act as an upstream signal to stimulate NO production. Both exogenous NO donor (sodium nitroprusside (SNP)) and Spd enhanced chilling tolerance in tomato, thereby protecting the photosynthetic system from damage. Compared to chilling treatment alone, Spd enhanced the gene expressions of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), and their enzyme activities in tomato leaves. However, a scavenger or inhibitor of NO abolished Spd-induced chilling tolerance and blocked the increased expression and activity due to Spd of these antioxidant enzymes in tomato leaves under chilling stress. The results showed that NO induced by Spd plays a crucial role in tomato's response to chilling stress.

Nitric oxide induced by polyamines involves antioxidant systems against chilling stress in tomato (Lycopersicon esculentum Mill.) seedling*#

PubMed Central

Diao, Qian-Nan; Song, Yong-Jun; Shi, Dong-Mei; Qi, Hong-Yan

2016-01-01

Polyamines (PAs) and nitric oxide (NO) are vital signals in modulating plant response to abiotic stress. However, to our knowledge, studies on the relationship between NO and PAs in response to cold stress in tomato are limited. Accordingly, in this study, we investigated the effects of putrescine (Put) and spermidine (Spd) on NO generation and the function of Spd-induced NO in the tolerance of tomato seedling under chilling stress. Spd increased NO release via the nitric oxide synthase (NOS)-like and nitrate reductase (NR) enzymatic pathways in the seedlings, whereas Put had no such effect. Moreover, H2O2 might act as an upstream signal to stimulate NO production. Both exogenous NO donor (sodium nitroprusside (SNP)) and Spd enhanced chilling tolerance in tomato, thereby protecting the photosynthetic system from damage. Compared to chilling treatment alone, Spd enhanced the gene expressions of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), and their enzyme activities in tomato leaves. However, a scavenger or inhibitor of NO abolished Spd-induced chilling tolerance and blocked the increased expression and activity due to Spd of these antioxidant enzymes in tomato leaves under chilling stress. The results showed that NO induced by Spd plays a crucial role in tomato’s response to chilling stress. PMID:27921397

Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit

PubMed Central

Gupta, Apoorv; Brockman Reizman, Irene M.; Reisch, Christopher R.; Prather, Kristala L. J.

2017-01-01

Metabolic engineering of microorganisms to produce desirable products on an industrial scale can result in unbalanced cellular metabolic networks that reduce productivity and yield. Metabolic fluxes can be rebalanced using dynamic pathway regulation, but few broadly applicable tools are available to achieve this. We present a pathway-independent genetic control module that can be used to dynamically regulate the expression of target genes. We applied our module to identify the optimal point to redirect glycolytic flux into heterologous engineered pathways in Escherichia coli, resulting in 5.5-fold increased titres of myo-inositol and titers of glucaric acid that improved from unmeasurable quantities to >0.8 g/L. Scaled-up production in benchtop bioreactors resulted in almost 10-fold and 5-fold increases in titers of myo-inositol and glucaric acid. We also used our module to control flux into aromatic amino acid biosynthesis to increase titers of shikimate in E. coli from unmeasurable quantities to >100 mg/L. PMID:28191902

Pharmacological modulators of autophagy activate a parallel noncanonical pathway driving unconventional LC3 lipidation.

PubMed

Jacquin, Elise; Leclerc-Mercier, Stéphanie; Judon, Celine; Blanchard, Emmanuelle; Fraitag, Sylvie; Florey, Oliver

2017-05-04

The modulation of canonical macroautophagy/autophagy for therapeutic benefit is an emerging strategy of medical and pharmaceutical interest. Many drugs act to inhibit autophagic flux by targeting lysosome function, while others were developed to activate the pathway. Here, we report the surprising finding that many therapeutically relevant autophagy modulators with lysosomotropic and ionophore properties, classified as inhibitors of canonical autophagy, are also capable of activating a parallel noncanonical autophagy pathway that drives MAP1LC3/LC3 lipidation on endolysosomal membranes. Further, we provide the first evidence supporting drug-induced noncanonical autophagy in vivo using the local anesthetic lidocaine and human skin biopsies. In addition, we find that several published inducers of autophagy and mitophagy are also potent activators of noncanonical autophagy. Together, our data raise important issues regarding the interpretation of LC3 lipidation data and the use of autophagy modulators, and highlight the need for a greater understanding of the functional consequences of noncanonical autophagy.

Relative association of Rubisco with manganese and magnesium as a regulatory mechanism in plants.

PubMed

Bloom, Arnold J; Kameritsch, Petra

2017-12-01

Rubisco, the enzyme that constitutes as much as half of the protein in a leaf, initiates either the photorespiratory pathway that supplies reductant for the assimilation of nitrate into amino acids or the C3 carbon fixation pathway that generates carbohydrates. The relative rates of these two pathways depend both on the relative extent to which O 2 and CO 2 occupies the active site of Rubisco and on whether manganese or magnesium is bound to the enzyme. This study quantified the activities of manganese and magnesium in isolated tobacco chloroplasts and the thermodynamics of binding of these metals to Rubisco purified from tobacco or a bacterium. In tobacco chloroplasts, manganese was less active than magnesium, but Rubisco purified from tobacco had a higher affinity for manganese. The activity of each metal in the chloroplast was similar in magnitude to the affinity of tobacco Rubisco for each. This indicates that, in tobacco chloroplasts, Rubisco associates almost equally with both metals and rapidly exchanges one metal for the other. Binding of magnesium was similar in Rubisco from tobacco and a bacterium, whereas binding of manganese differed greatly between the Rubisco from these species. Moreover, the ratio of leaf manganese to magnesium in C3 plants increased as atmospheric CO 2 increased. These results suggest that Rubisco has evolved to improve the energy transfers between photorespiration and nitrate assimilation and that plants regulate manganese and magnesium activities in the chloroplast to mitigate detrimental changes in their nitrogen/carbon balance as atmospheric CO 2 varies. © 2017 Scandinavian Plant Physiology Society.

Carbamylated low-density lipoprotein attenuates glucose uptake via a nitric oxide-mediated pathway in rat L6 skeletal muscle cells.

PubMed

Choi, Hye-Jung; Lee, Kyoung Jae; Hwang, Eun Ah; Mun, Kyo-Cheol; Ha, Eunyoung

2015-07-01

Carbamylation is a cyanate-mediated posttranslational modification. We previously reported that carbamylated low-density lipoprotein (cLDL) increases reactive oxygen species and apoptosis via a lectin-like oxidized LDL receptor mediated pathway in human umbilical vein endothelial cells. A recent study reported an association between cLDL and type 2 diabetes mellitus (T2DM). In the current study, the effects of cLDL on glucose transport were explored in skeletal muscle cells. The effect of cLDL on glucose uptake, glucose transporter 4 (GLUT4) translocation, and signaling pathway were examined in cultured rat L6 muscle cells using 2-deoxyglucose uptake, immunofluorescence staining and western blot analysis. The quantity of nitric oxide (NO) was evaluated by the Griess reaction. The effect of native LDL (nLDL) from patients with chronic renal failure (CRF-nLDL) on glucose uptake was also determined. It was observed that cLDL significantly attenuated glucose uptake and GLUT4 translocation to the membrane, which was mediated via the increase in inducible nitric oxide synthase (iNOS)-induced NO production. Tyrosine nitration of the insulin receptor substrate-1 (IRS‑1) was increased. It was demonstrated that CRF-nLDL markedly reduced glucose uptake compared with nLDL from healthy subjects. Collectively, these findings indicate that cLDL, alone, attenuates glucose uptake via NO-mediated tyrosine nitration of IRS‑1 in L6 rat muscle cells and suggests the possibility that cLDL is involved in the pathogenesis of T2DM.

Worming our way to novel drug discovery with the Caenorhabditis elegans proteostasis network, stress response and insulin-signaling pathways.

PubMed

O'Reilly, Linda P; Benson, Joshua A; Cummings, Erin E; Perlmutter, David H; Silverman, Gary A; Pak, Stephen C

2014-09-01

Many human diseases result from a failure of a single protein to achieve the correct folding and tertiary conformation. These so-called 'conformational diseases' involve diverse proteins and distinctive cellular pathologies. They all engage the proteostasis network (PN), to varying degrees in an attempt to mange cellular stress and restore protein homeostasis. The insulin/insulin-like growth factor signaling (IIS) pathway is a master regulator of cellular stress response, which is implicated in regulating components of the PN. This review focuses on novel approaches to target conformational diseases. The authors discuss the evidence supporting the involvement of the IIS pathway in modulating the PN and regulating proteostasis in Caenorhabditis elegans. Furthermore, they review previous PN and IIS drug screens and explore the possibility of using C. elegans for whole organism-based drug discovery for modulators of IIS-proteostasis pathways. An alternative approach to develop individualized therapy for each conformational disease is to modulate the global PN. The involvement of the IIS pathway in regulating longevity and response to a variety of stresses is well documented. Increasing data now provide evidence for the close association between the IIS and the PN pathways. The authors believe that high-throughput screening campaigns, which target the C. elegans IIS pathway, may identify drugs that are efficacious in treating numerous conformational diseases.

Integrins as Modulators of Transforming Growth Factor Beta Signaling in Dermal Fibroblasts During Skin Regeneration After Injury

PubMed Central

Boo, Stellar; Dagnino, Lina

2013-01-01

Significance Abnormal wound repair results from disorders in granulation tissue remodeling, and can lead to hypertrophic scarring and fibrosis. Excessive scarring can compromise tissue function and decrease tissue resistance to additional injuries. The development of potential therapies to minimize scarring is, thus, necessary to address an important clinical problem. Recent Advances It has been clearly established that multiple cytokines and growth factors participate in the regulation of cutaneous wound healing. More recently, it has become apparent that these factors do not necessarily activate isolated signaling pathways. Rather, in some cases, there is cross-modulation of several cellular pathways involved in this process. Two of the key pathways that modulate each other during wound healing are activated by transforming growth factor-β and by extracellular matrix proteins acting through integrins. Critical Issues The pathogenesis of excessive scarring upon wound healing is not fully understood, as a result of the complexity of this process. However, the fact that many pathways combine to produce fibrosis provides multiple potential therapeutic targets. Some of them have been identified, such as focal adhesion kinase and integrin-linked kinase. Currently, a major challenge is to develop pharmacological inhibitors of these proteins with therapeutic value to promote efficient wound repair. Future Directions The ability to better understand how different pathways crosstalk during wound repair and to identify and pharmacologically modulate key factors that contribute to the regulation of multiple wound-healing pathways could potentially provide effective therapeutic targets to decrease or prevent excessive scar formation and/or development of fibrosis. PMID:24527345

A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer.

PubMed

Yang, Mary Qu; Li, Dan; Yang, William; Zhang, Yifan; Liu, Jun; Tong, Weida

2017-01-01

Clear cell renal cell carcinoma (ccRCC) is the most common and most aggressive form of renal cell cancer (RCC). The incidence of RCC has increased steadily in recent years. The pathogenesis of renal cell cancer remains poorly understood. Many of the tumor suppressor genes, oncogenes, and dysregulated pathways in ccRCC need to be revealed for improvement of the overall clinical outlook of the disease. Here, we developed a systems biology approach to prioritize the somatic mutated genes that lead to dysregulation of pathways in ccRCC. The method integrated multi-layer information to infer causative mutations and disease genes. First, we identified differential gene modules in ccRCC by coupling transcriptome and protein-protein interactions. Each of these modules consisted of interacting genes that were involved in similar biological processes and their combined expression alterations were significantly associated with disease type. Then, subsequent gene module-based eQTL analysis revealed somatic mutated genes that had driven the expression alterations of differential gene modules. Our study yielded a list of candidate disease genes, including several known ccRCC causative genes such as BAP1 and PBRM1 , as well as novel genes such as NOD2, RRM1, CSRNP1, SLC4A2, TTLL1 and CNTN1. The differential gene modules and their driver genes revealed by our study provided a new perspective for understanding the molecular mechanisms underlying the disease. Moreover, we validated the results in independent ccRCC patient datasets. Our study provided a new method for prioritizing disease genes and pathways.

Co-expression analysis and identification of fecundity-related long non-coding RNAs in sheep ovaries

PubMed Central

Miao, Xiangyang; Luo, Qingmiao; Zhao, Huijing; Qin, Xiaoyu

2016-01-01

Small Tail Han sheep, including the FecBBFecBB (Han BB) and FecB+ FecB+ (Han++) genotypes, and Dorset sheep exhibit different fecundities. To identify novel long non-coding RNAs (lncRNAs) associated with sheep fecundity to better understand their molecular mechanisms, a genome-wide analysis of mRNAs and lncRNAs from Han BB, Han++ and Dorset sheep was performed. After the identification of differentially expressed mRNAs and lncRNAs, 16 significant modules were explored by using weighted gene coexpression network analysis (WGCNA) followed by functional enrichment analysis of the genes and lncRNAs in significant modules. Among these selected modules, the yellow and brown modules were significantly related to sheep fecundity. lncRNAs (e.g., NR0B1, XLOC_041882, and MYH15) in the yellow module were mainly involved in the TGF-β signalling pathway, and NYAP1 and BCORL1 were significantly associated with the oxytocin signalling pathway, which regulates several genes in the coexpression network of the brown module. Overall, we identified several gene modules associated with sheep fecundity, as well as networks consisting of hub genes and lncRNAs that may contribute to sheep prolificacy by regulating the target mRNAs related to the TGF-β and oxytocin signalling pathways. This study provides an alternative strategy for the identification of potential candidate regulatory lncRNAs. PMID:27982099

Co-expression analysis and identification of fecundity-related long non-coding RNAs in sheep ovaries.

PubMed

Miao, Xiangyang; Luo, Qingmiao; Zhao, Huijing; Qin, Xiaoyu

2016-12-16

Small Tail Han sheep, including the FecB B FecB B (Han BB) and FecB + FecB + (Han++) genotypes, and Dorset sheep exhibit different fecundities. To identify novel long non-coding RNAs (lncRNAs) associated with sheep fecundity to better understand their molecular mechanisms, a genome-wide analysis of mRNAs and lncRNAs from Han BB, Han++ and Dorset sheep was performed. After the identification of differentially expressed mRNAs and lncRNAs, 16 significant modules were explored by using weighted gene coexpression network analysis (WGCNA) followed by functional enrichment analysis of the genes and lncRNAs in significant modules. Among these selected modules, the yellow and brown modules were significantly related to sheep fecundity. lncRNAs (e.g., NR0B1, XLOC_041882, and MYH15) in the yellow module were mainly involved in the TGF-β signalling pathway, and NYAP1 and BCORL1 were significantly associated with the oxytocin signalling pathway, which regulates several genes in the coexpression network of the brown module. Overall, we identified several gene modules associated with sheep fecundity, as well as networks consisting of hub genes and lncRNAs that may contribute to sheep prolificacy by regulating the target mRNAs related to the TGF-β and oxytocin signalling pathways. This study provides an alternative strategy for the identification of potential candidate regulatory lncRNAs.

Innovative Water Management Technology to Reduce Environmental Impacts of Produced Water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castle, James; Rodgers, John; Alley, Bethany

2013-05-15

Clemson University with Chevron as an industry partner developed and applied treatment technology using constructed wetland systems to decrease targeted constituents in simulated and actual produced waters to achieve reuse criteria and discharge limits. Pilot-scale and demonstration constructed wetland treatment system (CWTS) experiments led to design strategies for treating a variety of constituents of concern (COCs) in produced waters including divalent metals, metalloids, oil and grease, and ammonia. Targeted biogeochemical pathways for treatment of COCs in pilot-scale CWTS experiments included divalent metal sulfide precipitation through dissimilatory sulfate reduction, metal precipitation through oxidation, reduction of selenite to insoluble elemental selenium, aerobicmore » biodegradation of oil, nitrification of ammonia to nitrate, denitrification of nitrate to nitrogen gas, separation of oil using an oilwater separator, and sorption of ammonia to zeolite. Treatment performance results indicated that CWTSs can be designed and built to promote specific environmental and geochemical conditions in order for targeted biogeochemical pathways to operate. The demonstration system successfully achieved consistent removal extents even while inflow concentrations of COCs in the produced water differed by orders of magnitude. Design strategies used in the pilot-scale and demonstration CWTSs to promote specific conditions that can be applied to designing full-scale CWTSs include plant and soil selection, water-depth selection, addition of amendments, and hydraulic retention time (HRT). These strategies allow conditions within a CWTS to be modified to achieve ranges necessary for the preferred biogeochemical treatment pathways. In the case of renovating a produced water containing COCs that require different biogeochemical pathways for treatment, a CWTS can be designed with sequential cells that promote different conditions. For example, the pilot-scale CWTS for post-reverse osmosis produced water was designed to promote oxidizing conditions within the first wetland cell for nitrification of ammonia, and the subsequent three cells were designed to promote reducing conditions for denitrification of nitrate. By incorporating multiple wetland cells in a CWTS, the conditions within each cell can be modified for removal of specific COCs. In addition, a CWTS designed with multiple cells allows for convenient sample collection points so that biogeochemical conditions of individual cells can be monitored and performance evaluated. Removal rate coefficients determined from the pilot-scale CWTS experiments and confirmed by the demonstration system can be used to calculate HRTs required to treat COCs in full-scale CWTSs. The calculated HRTs can then be used to determine the surface area or ?footprint? of a full-size CWTS for a given inflow rate of produced water.« less

Innovative Water Management Technology to Reduce Environment Impacts of Produced Water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castle, James W.; Rodgers, John H.; Alley, Bethany

2013-08-08

Clemson University with Chevron as an industry partner developed and applied treatment technology using constructed wetland systems to decrease targeted constituents in simulated and actual produced waters to achieve reuse criteria and discharge limits. Pilot-scale and demonstration constructed wetland treatment system (CWTS) experiments led to design strategies for treating a variety of constituents of concern (COCs) in produced waters including divalent metals, metalloids, oil and grease, and ammonia. Targeted biogeochemical pathways for treatment of COCs in pilot-scale CWTS experiments included divalent metal sulfide precipitation through dissimilatory sulfate reduction, metal precipitation through oxidation, reduction of selenite to insoluble elemental selenium, aerobicmore » biodegradation of oil, nitrification of ammonia to nitrate, denitrification of nitrate to nitrogen gas, separation of oil using an oilwater separator, and sorption of ammonia to zeolite. Treatment performance results indicated that CWTSs can be designed and built to promote specific environmental and geochemical conditions in order for targeted biogeochemical pathways to operate. The demonstration system successfully achieved consistent removal extents even while inflow concentrations of COCs in the produced water differed by orders of magnitude. Design strategies used in the pilot-scale and demonstration CWTSs to promote specific conditions that can be applied to designing full-scale CWTSs include plant and soil selection, water-depth selection, addition of amendments, and hydraulic retention time (HRT). These strategies allow conditions within a CWTS to be modified to achieve ranges necessary for the preferred biogeochemical treatment pathways. In the case of renovating a produced water containing COCs that require different biogeochemical pathways for treatment, a CWTS can be designed with sequential cells that promote different conditions. For example, the pilot-scale CWTS for post-reverse osmosis produced water was designed to promote oxidizing conditions within the first wetland cell for nitrification of ammonia, and the subsequent three cells were designed to promote reducing conditions for denitrification of nitrate. By incorporating multiple wetland cells in a CWTS, the conditions within each cell can be modified for removal of specific COCs. In addition, a CWTS designed with multiple cells allows for convenient sample collection points so that biogeochemical conditions of individual cells can be monitored and performance evaluated. Removal rate coefficients determined from the pilot-scale CWTS experiments and confirmed by the demonstration system can be used to calculate HRTs required to treat COCs in full-scale CWTSs. The calculated HRTs can then be used to determine the surface area or footprint of a full-size CWTS for a given inflow rate of produced water.« less

Innovative Water Management Technology to Reduce Environment Impacts of Produced Water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castle, James; Rodgers, John; Alley, Bethany

2013-05-15

Clemson University with Chevron as an industry partner developed and applied treatment technology using constructed wetland systems to decrease targeted constituents in simulated and actual produced waters to achieve reuse criteria and discharge limits. Pilot-scale and demonstration constructed wetland treatment system (CWTS) experiments led to design strategies for treating a variety of constituents of concern (COCs) in produced waters including divalent metals, metalloids, oil and grease, and ammonia. Targeted biogeochemical pathways for treatment of COCs in pilot-scale CWTS experiments included divalent metal sulfide precipitation through dissimilatory sulfate reduction, metal precipitation through oxidation, reduction of selenite to insoluble elemental selenium, aerobicmore » biodegradation of oil, nitrification of ammonia to nitrate, denitrification of nitrate to nitrogen gas, separation of oil using an oilwater separator, and sorption of ammonia to zeolite. Treatment performance results indicated that CWTSs can be designed and built to promote specific environmental and geochemical conditions in order for targeted biogeochemical pathways to operate. The demonstration system successfully achieved consistent removal extents even while inflow concentrations of COCs in the produced water differed by orders of magnitude. Design strategies used in the pilot-scale and demonstration CWTSs to promote specific conditions that can be applied to designing full-scale CWTSs include plant and soil selection, water-depth selection, addition of amendments, and hydraulic retention time (HRT). These strategies allow conditions within a CWTS to be modified to achieve ranges necessary for the preferred biogeochemical treatment pathways. In the case of renovating a produced water containing COCs that require different biogeochemical pathways for treatment, a CWTS can be designed with sequential cells that promote different conditions. For example, the pilot-scale CWTS for post-reverse osmosis produced water was designed to promote oxidizing conditions within the first wetland cell for nitrification of ammonia, and the subsequent three cells were designed to promote reducing conditions for denitrification of nitrate. By incorporating multiple wetland cells in a CWTS, the conditions within each cell can be modified for removal of specific COCs. In addition, a CWTS designed with multiple cells allows for convenient sample collection points so that biogeochemical conditions of individual cells can be monitored and performance evaluated. Removal rate coefficients determined from the pilot-scale CWTS experiments and confirmed by the demonstration system can be used to calculate HRTs required to treat COCs in full-scale CWTSs. The calculated HRTs can then be used to determine the surface area or footprint of a full-size CWTS for a given inflow rate of produced water.« less

Cannabidiol protects against hepatic ischemia/reperfusion injury by attenuating inflammatory signaling and response, oxidative/nitrative stress, and cell death

PubMed Central

Mukhopadhyay, Partha; Rajesh, Mohanraj; Horváth, Béla; Bátkai, Sándor; Park, Ogyi; Tanashian, Galin; Gao, Rachel Y; Patel, Vivek; Wink, David A.; Liaudet, Lucas; Haskó, György; Mechoulam, Raphael; Pacher, Pál

2011-01-01

Ischemia-reperfusion (I/R) is a pivotal mechanism of liver damage following liver transplantation or hepatic surgery. We have investigated the effects of cannabidiol(CBD), the non-psychotropic constituent of marijuana, in a mouse model of hepatic I/R injury. I/R triggered time-dependent increases/changes in markers of liver injury (serum transaminases), hepatic oxidative/nitrative stress (4-hydroxy-2-nonenal, nitrotyrosine content/staining, gp91phox and inducible nitric oxide synthase mRNA), mitochondrial dysfunction (decreased complex I activity), inflammation (tumor necrosis factor alpha (TNF-α), cyclooxygenase 2, macrophage inflammatory protein-1α/2, inter-cellular adhesion molecule 1 mRNA levels, tissue neutrophil infiltration, nuclear factor kappa B (NF-KB) activation), stress signaling (p38MAPK and JNK) and cell death (DNA fragmentation, PARP activity, and TUNEL). CBD significantly reduced the extent of liver inflammation, oxidative/nitrative stress and cell death, and also attenuated the bacterial endotoxin-triggered NF-KB activation and TNF-α production in isolated Kupffer cells, likewise the adhesion molecules expression in primary human liver sinusoidal endothelial cells stimulated with TNF-α, and attachment of human neutrophils to the activated endothelium. These protective effects were preserved in CB2 knockout mice and were not prevented by CB1/2 antagonists in vitro. Thus, CBD may represent a novel, protective strategy against I/R injury by attenuating key inflammatory pathways and oxidative/nitrative tissue injury, independent from classical CB1/2 receptors. PMID:21362471

Nitrite oxidation in the Namibian oxygen minimum zone

PubMed Central

Füssel, Jessika; Lam, Phyllis; Lavik, Gaute; Jensen, Marlene M; Holtappels, Moritz; Günter, Marcel; Kuypers, Marcel MM

2012-01-01

Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in 15N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (⩽372 nM NO2− d−1) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ∼9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO3− was re-oxidized back to NO3− via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways. PMID:22170426

Linear ion-trap mass spectrometric characterization of human pituitary nitrotyrosine-containing proteins

NASA Astrophysics Data System (ADS)

Zhan, Xianquan; Desiderio, Dominic M.

2007-01-01

The nitric oxide-mediated Tyr-nitration of endogenous proteins is associated with several pathological and physiological processes. In order to investigate the presence - and potential roles - of Tyr-nitration in the human pituitary, a large-format two-dimensional gel separation plus a Western blot against a specific anti-3-nitrotyrosine antibody were used to separate and detect nitroproteins from a human pituitary proteome. The nitroproteins were subjected to in-gel trypsin digestion, and high-sensitivity vacuum matrix-assisted laser desorption/ionization (vMALDI) linear ion-trap tandem mass spectrometry was used to analyze the tryptic peptides. Those MS/MS data were used to determine the amino acid sequence and the specific nitration site of each tryptic nitropeptide, and were matched to corresponding proteins with Bioworks TuboSEQUEST software. Compared to our previous study, 16 new nitrotyrosine-immunoreactive positive Western blot spots were found within the area pI 3.0-10 and Mr 10-100 kDa. Four new nitroproteins were discovered: the stanniocalcin 1 precursor--involved in calcium and phosphate metabolism; mitochondrial co-chaperone protein HscB, which might act as a co-chaperone in iron-sulfur cluster assembly in mitochrondria; progestin and adipoQ receptor family member III--a seven-transmembrane receptor; proteasome subunit alpha type 2--involved in an ATP/ubiquitin-dependent non-lysosomal proteolytic pathway. Those data demonstrate that nitric oxide-mediated Tyr-nitration might participate in various biochemical, metabolic, and pathological processes in the human pituitary.

The mitochondrial fatty acid synthesis (mtFASII) pathway is capable of mediating nuclear-mitochondrial cross talk through the PPAR system of transcriptional activation

PubMed Central

Parl, Angelika; Mitchell, Sabrina L.; Clay, Hayley B.; Reiss, Sara; Li, Zhen; Murdock, Deborah G.

2013-01-01

Mammalian cells contain two fatty acid synthesis pathways, the cytosolic FASI pathway, and the mitochondrial FASII pathway. The selection behind the conservation of the mitochondrial pathway is not completely understood, given the presence of the cytosolic FAS pathway. In this study, we show through heterologous gene reporter systems and PCR based arrays that overexpression of MECR, the last step in the mtFASII pathway, causes modulation of gene expression through the PPAR pathway. Electromobility shift assays (EMSAs) demonstrate that overexpression of MECR causes increased binding of PPARs to DNA, while cell fractionation and imaging studies show that MECR remains localized to the mitochondria. Interestingly, knock down of the mtFASII pathway lessens the effect of MECR on this transcriptional modulation. Our data are most consistent with MECR-mediated transcriptional activation through products of the mtFASII pathway, although we cannot rule out MECR acting as a coactivator. Further investigation into the physiological relevance of this communication will be necessary to better understand some of the phenotypic consequences of deficits in this pathway observed in animal models and human disease. PMID:24161390

Nitric Oxide Mediates the Hormonal Control of Crassulacean Acid Metabolism Expression in Young Pineapple Plants1[W][OA

PubMed Central

Freschi, Luciano; Rodrigues, Maria Aurineide; Domingues, Douglas Silva; Purgatto, Eduardo; Van Sluys, Marie-Anne; Magalhaes, Jose Ronaldo; Kaiser, Werner M.; Mercier, Helenice

2010-01-01

Genotypic, developmental, and environmental factors converge to determine the degree of Crassulacean acid metabolism (CAM) expression. To characterize the signaling events controlling CAM expression in young pineapple (Ananas comosus) plants, this photosynthetic pathway was modulated through manipulations in water availability. Rapid, intense, and completely reversible up-regulation in CAM expression was triggered by water deficit, as indicated by the rise in nocturnal malate accumulation and in the expression and activity of important CAM enzymes. During both up- and down-regulation of CAM, the degree of CAM expression was positively and negatively correlated with the endogenous levels of abscisic acid (ABA) and cytokinins, respectively. When exogenously applied, ABA stimulated and cytokinins repressed the expression of CAM. However, inhibition of water deficit-induced ABA accumulation did not block the up-regulation of CAM, suggesting that a parallel, non-ABA-dependent signaling route was also operating. Moreover, strong evidence revealed that nitric oxide (NO) may fulfill an important role during CAM signaling. Up-regulation of CAM was clearly observed in NO-treated plants, and a conspicuous temporal and spatial correlation was also evident between NO production and CAM expression. Removal of NO from the tissues either by adding NO scavenger or by inhibiting NO production significantly impaired ABA-induced up-regulation of CAM, indicating that NO likely acts as a key downstream component in the ABA-dependent signaling pathway. Finally, tungstate or glutamine inhibition of the NO-generating enzyme nitrate reductase completely blocked NO production during ABA-induced up-regulation of CAM, characterizing this enzyme as responsible for NO synthesis during CAM signaling in pineapple plants. PMID:20147491

[Exploration of common biological pathways for attention deficit hyperactivity disorder and low birth weight].

PubMed

Xiang, Bo; Yu, Minglan; Liang, Xuemei; Lei, Wei; Huang, Chaohua; Chen, Jing; He, Wenying; Zhang, Tao; Li, Tao; Liu, Kezhi

2017-12-10

To explore common biological pathways for attention deficit hyperactivity disorder (ADHD) and low birth weight (LBW). Thei-Gsea4GwasV2 software was used to analyze the result of genome-wide association analysis (GWAS) for LBW (pathways were derived from Reactome), and nominally significant (P< 0.05, FDR< 0.25) pathways were tested for replication in ADHD.Significant pathways were analyzed with DAPPLE and Reatome FI software to identify genes involved in such pathways, with each cluster enriched with the gene ontology (GO). The Centiscape2.0 software was used to calculate the degree of genetic networks and the betweenness value to explore the core node (gene). Weighed gene co-expression network analysis (WGCNA) was then used to explore the co-expression of genes in these pathways.With gene expression data derived from BrainSpan, GO enrichment was carried out for each gene module. Eleven significant biological pathways was identified in association with LBW, among which two (Selenoamino acid metabolism and Diseases associated with glycosaminoglycan metabolism) were replicated during subsequent ADHD analysis. Network analysis of 130 genes in these pathways revealed that some of the sub-networksare related with morphology of cerebellum, development of hippocampus, and plasticity of synaptic structure. Upon co-expression network analysis, 120 genes passed the quality control and were found to express in 3 gene modules. These modules are mainly related to the regulation of synaptic structure and activity regulation. ADHD and LBW share some biological regulation processes. Anomalies of such proces sesmay predispose to ADHD.

Insights into significant pathways and gene interaction networks underlying breast cancer cell line MCF-7 treated with 17β-estradiol (E2).

PubMed

Huan, Jinliang; Wang, Lishan; Xing, Li; Qin, Xianju; Feng, Lingbin; Pan, Xiaofeng; Zhu, Ling

2014-01-01

Estrogens are known to regulate the proliferation of breast cancer cells and to alter their cytoarchitectural and phenotypic properties, but the gene networks and pathways by which estrogenic hormones regulate these events are only partially understood. We used global gene expression profiling by Affymetrix GeneChip microarray analysis, with KEGG pathway enrichment, PPI network construction, module analysis and text mining methods to identify patterns and time courses of genes that are either stimulated or inhibited by estradiol (E2) in estrogen receptor (ER)-positive MCF-7 human breast cancer cells. Of the genes queried on the Affymetrix Human Genome U133 plus 2.0 microarray, we identified 628 (12h), 852 (24h) and 880 (48 h) differentially expressed genes (DEGs) that showed a robust pattern of regulation by E2. From pathway enrichment analysis, we found out the changes of metabolic pathways of E2 treated samples at each time point. At 12h time point, the changes of metabolic pathways were mainly focused on pathways in cancer, focal adhesion, and chemokine signaling pathway. At 24h time point, the changes were mainly enriched in neuroactive ligand-receptor interaction, cytokine-cytokine receptor interaction and calcium signaling pathway. At 48 h time point, the significant pathways were pathways in cancer, regulation of actin cytoskeleton, cell adhesion molecules (CAMs), axon guidance and ErbB signaling pathway. Of interest, our PPI network analysis and module analysis found that E2 treatment induced enhancement of PRSS23 at the three time points and PRSS23 was in the central position of each module. Text mining results showed that the important genes of DEGs have relationship with signal pathways, such as ERbB pathway (AREG), Wnt pathway (NDP), MAPK pathway (NTRK3, TH), IP3 pathway (TRA@) and some transcript factors (TCF4, MAF). Our studies highlight the diverse gene networks and metabolic and cell regulatory pathways through which E2 operates to achieve its widespread effects on breast cancer cells. © 2013 Elsevier B.V. All rights reserved.

Role of antecedent conditions on nitrogen and phosphorus mobilisation observed in a lowland arable catchment in eastern England: insights from high-frequency monitoring

NASA Astrophysics Data System (ADS)

Outram, Faye; Hiscock, Kevin; Dugdale, Stephen; Lovett, Andrew

2015-04-01

In order to reduce annual riverine loadings of nutrients which are responsible for degradation of ecosystems downstream and in near coastal areas, it is important to first understand the mobilisation and pathways responsible for transporting them from source to river and how these pathways vary in space and time. The Blackwater tributary of the River Wensum in Norfolk, England, has been equipped with a sensor network as part of the Demonstration Test Catchments project, which has the aim of reducing pollution from agriculture to river systems whilst maintaining food security by the trial of mitigation measures on working farms at the sub-catchment level. The River Wensum is a lowland chalk catchment with intensive arable agriculture and high occurrence of tile drainage on heavier soils. Three hydrological years of high-frequency data have been gathered in the Blackwater since October 2011, including rainfall, half hourly measurements of discharge and groundwater level coupled with hydrochemical parameters including nitrate, total phosphorus (TP) and total reactive phosphorus (TRP). In the three years of data collection, there were distinct departures from long-term rainfall averages as the winter of 2011-12 was extremely dry following a drought from the previous hydrological year, followed by a summer which was unseasonably wet, which continued into the following winter. The relationship between rainfall, storage and discharge was found to be complex, which in turn had an impact on the dominant controls transporting nutrients from the landscape to the river network. Thirty three storms occurred throughout the three year period which have been analysed in the context of the range of hydrometeorological conditions observed throughout the dataset. Discharge-concentration hysteretic responses of nitrogen, TP and TRP have been used alongside statistical analysis of storm characteristics including antecedent hydrological conditions. The nitrate storm response showed distinct seasonal patterns which were greatly impacted by the activation of tile drain flow throughout the winter period and during the fertiliser application window between March-May, with the dry winter in 2011-12 standing apart from the more 'typical' years. Four different storm response categories were identified for nitrate according to dominant flow pathways. The phosphorus response was far less uniform throughout the study period, showing patterns of exhaustion with successive events. Both nitrate and phosphorus loads were disproportionate to flow volume in storm events which occurred after significant dry periods. The data show the importance of antecedent conditions in the storage, mobilisation and transport of nitrogen and phosphorus in agricultural catchments which has important implications for the conceptual understanding of catchment functioning and environmental management.

River-groundwater connectivity and nutrient dynamics in a mesoscale catchment

NASA Astrophysics Data System (ADS)

Fleckenstein, Jan H.; Musolff, Andreas; Gilfedder, Benjamin; Frei, Sven; Wankmüller, Fabian; Trauth, Nico

2017-04-01

Diffuse solute exports from catchments are governed by many interrelated factors such as land use, climate, geological-/ hydrogeological setup and morphology. Those factors create spatial variations in solute concentrations and turnover rates in the subsurface as well as in the stream network. River-groundwater connectivity is a crucial control in this context: On the one hand groundwater is a main pathway for nitrate inputs to the stream. On the other hand, groundwater connectivity with the stream affects the magnitude of hyporheic exchange of stream water with the stream bed. We present results of a longitudinal sampling campaign along the Selke river, a 67 km long third-order stream in the Harz mountains in central Germany. Water quality at the catchment outlet is strongly impacted by agriculture with high concentrations of nitrate and a chemostatic nitrate export regime. However, the specific nitrate pathways to the stream are not fully understood as there is arable land distributed throughout the catchment. While the sparsely distributed arable land in the mountainous upper catchment receives much higher amounts of precipitation, the downstream alluvial plains are drier, but more intensively used. The three-day campaign was conducted in June 2016 under constant low flow conditions. Stream water samples were taken every 2 km along the main stem of the river and at its major tributaries. Samples were analyzed for field parameters, major cations and anions, N-O isotopes, nutrients and Radon-222 (Rn) concentrations. Additionally, at each sampling location, river discharge was manually measured using current meters. Groundwater influxes to each sampled river section were quantified from the Rn measurements using the code FINIFLUX, (Frei and Gilfedder 2015). Rn and ion concentrations showed an increase from the spring to the mouth, indicating a growing impact of groundwater flux to the river. However, increases in groundwater gains were not gradual. The strongest gains were observed downstream of where the Selke River leaves the Harz Mountains and enters the alluvial plains. At this location, land use, hydrogeological setup and river slope as well as average slope of the contributing catchment area change significantly. Downstream of this point 15N isotope values were also significantly higher, suggesting higher denitrification activity in the deeper aquifers of lower catchment. While specific discharge (discharge per catchment area) was 3 times higher in the upper catchment, nitrate mass flux per area was more than 3 times higher in lower catchment compared to the respective other part of the catchment. We conclude that catchment morphology, (hydro)geology and hydrology control river-groundwater connectivity while the interplay with land use controls in stream nitrate concentrations. Repeated sampling campaigns will allow assessing seasonal changes in solute inputs and turnover. References Frei, S. & Gilfedder, B.S. (2015): FINIFLUX: An implicit finite element model for quantification of groundwater fluxes and hyporheic exchange in streams and rivers using radon. Water Resources Research, DOI: 10.1002/2015WR017212.

A novel method to identify hub pathways of rheumatoid arthritis based on differential pathway networks.

PubMed

Wei, Shi-Tong; Sun, Yong-Hua; Zong, Shi-Hua

2017-09-01

The aim of the current study was to identify hub pathways of rheumatoid arthritis (RA) using a novel method based on differential pathway network (DPN) analysis. The present study proposed a DPN where protein‑protein interaction (PPI) network was integrated with pathway‑pathway interactions. Pathway data was obtained from background PPI network and the Reactome pathway database. Subsequently, pathway interactions were extracted from the pathway data by building randomized gene‑gene interactions and a weight value was assigned to each pathway interaction using Spearman correlation coefficient (SCC) to identify differential pathway interactions. Differential pathway interactions were visualized using Cytoscape to construct a DPN. Topological analysis was conducted to identify hub pathways that possessed the top 5% degree distribution of DPN. Modules of DPN were mined according to ClusterONE. A total of 855 pathways were selected to build pathway interactions. By filtrating pathway interactions of weight values >0.7, a DPN with 312 nodes and 791 edges was obtained. Topological degree analysis revealed 15 hub pathways, such as heparan sulfate/heparin‑glycosaminoglycan (HS‑GAG) degradation, HS‑GAG metabolism and keratan sulfate degradation for RA based on DPN. Furthermore, hub pathways were also important in modules, which validated the significance of hub pathways. In conclusion, the proposed method is a computationally efficient way to identify hub pathways of RA, which identified 15 hub pathways that may be potential biomarkers and provide insight to future investigation and treatment of RA.

Nitrogen and Triple Oxygen Isotopic Analyses of Atmospheric Particulate Nitrate over the Pacific Ocean

NASA Astrophysics Data System (ADS)

Kamezaki, Kazuki; Hattori, Shohei; Iwamoto, Yoko; Ishino, Sakiko; Furutani, Hiroshi; Miki, Yusuke; Miura, Kazuhiko; Uematsu, Mitsuo; Yoshida, Naohiro

2017-04-01

Nitrate plays a significant role in the biogeochemical cycle. Atmospheric nitrate (NO3- and HNO3) are produced by reaction precursor as NOx (NO and NO2) emitted by combustion, biomass burning, lightning, and soil emission, with atmospheric oxidants like ozone (O3), hydroxyl radical (OH), peroxy radical and halogen oxides. Recently, industrial activity lead to increases in the concentrations of nitrogen species (NOx and NHy) throughout the environment. Because of the increase of the amount of atmospheric nitrogen deposition, the oceanic biogeochemical cycle are changed (Galloway et al., 2004; Kim et al., 2011). However, the sources and formation pathways of atmospheric nitrate are still uncertain over the Pacific Ocean because the long-term observation is limited. Stable isotope analysis is useful tool to gain information of sources, sinks and formation pathways. The nitrogen stable isotopic composition (δ15N) of atmospheric particulate NO3- can be used to posses information of its nitrogen sources (Elliott et al., 2007). Triple oxygen isotopic compositions (Δ17O = δ17O - 0.52 ×δ18O) of atmospheric particulate NO3- can be used as tracer of the relative importance of mass-independent oxygen bearing species (e.g. O3, BrO; Δ17O ≠ 0 ‰) and mass-dependent oxygen bearing species (e.g. OH radical; Δ17O ≈ 0 ‰) through the formation processes from NOx to NO3- in the atmosphere (Michalski et al., 2003; Thiemens, 2006). Here, we present the isotopic compositions of atmospheric particulate NO3- samples collected over the Pacific Ocean from 40˚ S to 68˚ N. We observed significantly low δ15N values for atmospheric particulate NO3- on equatorial Pacific Ocean during both cruises. Although the data is limited, combination analysis of δ15N and Δ17O values for atmospheric particulate NO3- showed the possibility of the main nitrogen source of atmospheric particulate NO3- on equatorial Pacific Ocean is ammonia oxidation in troposphere. Furthermore, the Δ17O values for atmospheric particulate NO3- originated from Central North Pacific Ocean showed the possibility of atmospheric particulate NO3- formation pathway is reaction NO2 with halogen oxides. At the presentation, we discuss the sources and formation pathways of atmospheric particulate NO3- by using stable isotopic analyses for each region. References J. N. Galloway, A. R. Townsend, J. Willem Erisman, M. Bekunda, Z. Cai, J. R. Freney, L. A. Martinelli, S. P. Seitzinger, M. A. Sutton, Biogeochemistry, 70, 153-226, 2004 T. W. Kim, K. Lee, R. G. Najjar, H.D. Jeong, H. J. Jeong, Science 334, 505-509, 2011 E. M. Elliott, C. Kendall, S. D. Wankel, D. A. Burns, E. W. Boyer, K. Harlin, D. J. Bain, and T. J. Butler, Environ. Sci. Technol., 41, 7661-7667, 2007 G. Michalski, Z. Scott, M. Kabiling, and M. H. Thiemens, Geophys. Res. Lett., 30, 1870, 2003 M. H. Thiemens, Annu. Rev. Earth Planet. Sc., 34, 217-262, 2006

Autophagy modulation as a potential therapeutic target for diverse diseases

PubMed Central

Rubinsztein, David C.; Codogno, Patrice; Levine, Beth

2012-01-01

Autophagy is an essential, conserved lysosomal degradation pathway that controls the quality of the cytoplasm by eliminating protein aggregates and damaged organelles. It begins when double-membraned autophagosomes engulf portions of the cytoplasm, which is followed by fusion of these vesicles with lysosomes and degradation of the autophagic contents. In addition to its vital homeostatic role, this degradation pathway is involved in various human disorders, including metabolic conditions, neurodegenerative diseases, cancers and infectious diseases. This article provides an overview of the mechanisms and regulation of autophagy, the role of this pathway in disease and strategies for therapeutic modulation. PMID:22935804

Expanding the Interactome of TES by Exploiting TES Modules with Different Subcellular Localizations.

PubMed

Sala, Stefano; Van Troys, Marleen; Medves, Sandrine; Catillon, Marie; Timmerman, Evy; Staes, An; Schaffner-Reckinger, Elisabeth; Gevaert, Kris; Ampe, Christophe

2017-05-05

The multimodular nature of many eukaryotic proteins underlies their temporal or spatial engagement in a range of protein cocomplexes. Using the multimodule protein testin (TES), we here report a proteomics approach to increase insight in cocomplex diversity. The LIM-domain containing and tumor suppressor protein TES is present at different actin cytoskeleton adhesion structures in cells and influences cell migration, adhesion and spreading. TES module accessibility has been proposed to vary due to conformational switching and variants of TES lacking specific domains target to different subcellular locations. By applying iMixPro AP-MS ("intelligent Mixing of Proteomes"-affinity purification-mass spectrometry) to a set of tagged-TES modular variants, we identified proteins residing in module-specific cocomplexes. The obtained distinct module-specific interactomes combine to a global TES interactome that becomes more extensive and richer in information. Applying pathway analysis to the module interactomes revealed expected actin-related canonical pathways and also less expected pathways. We validated two new TES cocomplex partners: TGFB1I1 and a short form of the glucocorticoid receptor. TES and TGFB1I1 are shown to oppositely affect cell spreading providing biological validity for their copresence in complexes since they act in similar processes.

Curcumin mediates anticancer effects by modulating multiple cell signaling pathways.

PubMed

Kunnumakkara, Ajaikumar B; Bordoloi, Devivasha; Harsha, Choudhary; Banik, Kishore; Gupta, Subash C; Aggarwal, Bharat B

2017-08-01

Curcumin, a component of a spice native to India, was first isolated in 1815 by Vogel and Pelletier from the rhizomes of Curcuma longa (turmeric) and, subsequently, the chemical structure of curcumin as diferuloylmethane was reported by Milobedzka et al. [(1910) 43., 2163-2170]. Since then, this polyphenol has been shown to exhibit antioxidant, anti-inflammatory, anticancer, antiviral, antibacterial, and antifungal activities. The current review primarily focuses on the anticancer potential of curcumin through the modulation of multiple cell signaling pathways. Curcumin modulates diverse transcription factors, inflammatory cytokines, enzymes, kinases, growth factors, receptors, and various other proteins with an affinity ranging from the pM to the mM range. Furthermore, curcumin effectively regulates tumor cell growth via modulation of numerous cell signaling pathways and potentiates the effect of chemotherapeutic agents and radiation against cancer. Curcumin can interact with most of the targets that are modulated by FDA-approved drugs for cancer therapy. The focus of this review is to discuss the molecular basis for the anticancer activities of curcumin based on preclinical and clinical findings. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

SEEPLUS: A SIMPLE ONLINE CLIMATE MODEL

NASA Astrophysics Data System (ADS)

Tsutsui, Junichi

A web application for a simple climate model - SEEPLUS (a Simple climate model to Examine Emission Pathways Leading to Updated Scenarios) - has been developed. SEEPLUS consists of carbon-cycle and climate-change modules, through which it provides the information infrastructure required to perform climate-change experiments, even on a millennial-timescale. The main objective of this application is to share the latest scientific knowledge acquired from climate modeling studies among the different stakeholders involved in climate-change issues. Both the carbon-cycle and climate-change modules employ impulse response functions (IRFs) for their key processes, thereby enabling the model to integrate the outcome from an ensemble of complex climate models. The current IRF parameters and forcing manipulation are basically consistent with, or within an uncertainty range of, the understanding of certain key aspects such as the equivalent climate sensitivity and ocean CO2 uptake data documented in representative literature. The carbon-cycle module enables inverse calculation to determine the emission pathway required in order to attain a given concentration pathway, thereby providing a flexible way to compare the module with more advanced modeling studies. The module also enables analytical evaluation of its equilibrium states, thereby facilitating the long-term planning of global warming mitigation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parl, Angelika; Mitchell, Sabrina L.; Clay, Hayley B.

Highlights: •The function of the mitochondria fatty acid synthesis pathway is partially unknown. •Overexpression of the pathway causes transcriptional activation through PPARs. •Knock down of the pathway attenuates that activation. •The last enzyme in the pathway regulates its own transcription. •Products of the mtFASII pathway are able to drive nuclear transcription. -- Abstract: Mammalian cells contain two fatty acid synthesis pathways, the cytosolic FASI pathway, and the mitochondrial FASII pathway. The selection behind the conservation of the mitochondrial pathway is not completely understood, given the presence of the cytosolic FAS pathway. In this study, we show through heterologous gene reportermore » systems and PCR-based arrays that overexpression of MECR, the last step in the mtFASII pathway, causes modulation of gene expression through the PPAR pathway. Electromobility shift assays (EMSAs) demonstrate that overexpression of MECR causes increased binding of PPARs to DNA, while cell fractionation and imaging studies show that MECR remains localized to the mitochondria. Interestingly, knock down of the mtFASII pathway lessens the effect of MECR on this transcriptional modulation. Our data are most consistent with MECR-mediated transcriptional activation through products of the mtFASII pathway, although we cannot rule out MECR acting as a coactivator. Further investigation into the physiological relevance of this communication will be necessary to better understand some of the phenotypic consequences of deficits in this pathway observed in animal models and human disease.« less

Prefrontal-Hippocampal Pathways Underlying Inhibitory Control Over Memory

PubMed Central

Anderson, Michael C.; Bunce, Jamie G.; Barbas, Helen

2016-01-01

A key function of the prefrontal cortex is to support inhibitory control over behavior. It is widely believed that this function extends to stopping cognitive processes as well. Consistent with this, mounting evidence establishes the role of the right lateral prefrontal cortex in a clear case of cognitive control: retrieval suppression. Retrieval suppression refers to the ability to intentionally stop the retrieval process that arises when a reminder to a memory appears. Functional imaging data indicates that retrieval suppression involves top-down modulation of hippocampal activity by the dorsolateral prefrontal cortex, but the anatomical pathways supporting this inhibitory modulation remain unclear. Here we bridge this gap by integrating key findings about retrieval suppression observed through functional imaging with a detailed consideration of relevant anatomical pathways observed in non-human primates. Focusing selectively on the potential role of the anterior cingulate cortex, we develop two hypotheses about the pathways mediating interactions between lateral prefrontal cortex and the medial temporal lobes during suppression, and their cellular targets: the entorhinal gating hypothesis, and thalamo-hippocampal modulation via the nucleus reuniens. We hypothesize that whereas entorhinal gating is well situated to stop retrieval proactively, thalamo-hippocampal modulation may interrupt an ongoing act of retrieval reactively. Isolating the pathways that underlie retrieval suppression holds the potential to advance our understanding of a range of psychiatric disorders characterized by persistent intrusive thoughts. More broadly, an anatomical account of retrieval suppression would provide a key model system for understanding inhibitory control over cognition. PMID:26642918

Quantifying manganese and nitrogen cycle coupling in manganese-rich, organic carbon-starved marine sediments: Examples from the Clarion-Clipperton fracture zone

NASA Astrophysics Data System (ADS)

Mogollón, José M.; Mewes, Konstantin; Kasten, Sabine

2016-07-01

Extensive deep-sea sedimentary areas are characterized by low organic carbon contents and thus harbor suboxic sedimentary environments where secondary (autotrophic) redox cycling becomes important for microbial metabolic processes. Simulation results for three stations in the Eastern Equatorial Pacific with low organic carbon content (<0.5 dry wt %) and low sedimentation rates (10-1-100 mm ky-1) show that ammonium generated during organic matter degradation may act as a reducing agent for manganese oxides below the oxic zone. Likewise, at these sedimentary depths, dissolved reduced manganese may act as a reducing agent for oxidized nitrogen species. These manganese-coupled transformations provide a suboxic conversion pathway of ammonium and nitrate to dinitrogen. These manganese-nitrogen interactions further explain the presence and production of dissolved reduced manganese (up to tens of μM concentration) in sediments with high nitrate (>20 μM) concentrations.

Catalytic Decomposition of Hydroxylammonium Nitrate Ionic Liquid: Enhancement of NO Formation.

PubMed

Chambreau, Steven D; Popolan-Vaida, Denisia M; Vaghjiani, Ghanshyam L; Leone, Stephen R

2017-05-18

Hydroxylammonium nitrate (HAN) is a promising candidate to replace highly toxic hydrazine in monopropellant thruster space applications. The reactivity of HAN aerosols on heated copper and iridium targets was investigated using tunable vacuum ultraviolet photoionization time-of-flight aerosol mass spectrometry. The reaction products were identified by their mass-to-charge ratios and their ionization energies. Products include NH 3 , H 2 O, NO, hydroxylamine (HA), HNO 3 , and a small amount of NO 2 at high temperature. No N 2 O was detected under these experimental conditions, despite the fact that N 2 O is one of the expected products according to the generally accepted thermal decomposition mechanism of HAN. Upon introduction of iridium catalyst, a significant enhancement of the NO/HA ratio was observed. This observation indicates that the formation of NO via decomposition of HA is an important pathway in the catalytic decomposition of HAN.

Complete nitrification by Nitrospira bacteria

PubMed Central

Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra; Han, Ping; Herbold, Craig; Albertsen, Mads; Jehmlich, Nico; Palatinszky, Marton; Vierheilig, Julia; Bulaev, Alexandr; Kirkegaard, Rasmus H.; von Bergen, Martin; Rattei, Thomas; Bendinger, Bernd; Nielsen, Per H.; Wagner, Michael

2016-01-01

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered as a two-step process catalyzed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes both the pathways for ammonia and nitrite oxidation, which are concomitantly expressed during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities. PMID:26610024

Analyzing the genes related to Alzheimer's disease via a network and pathway-based approach.

PubMed

Hu, Yan-Shi; Xin, Juncai; Hu, Ying; Zhang, Lei; Wang, Ju

2017-04-27

Our understanding of the molecular mechanisms underlying Alzheimer's disease (AD) remains incomplete. Previous studies have revealed that genetic factors provide a significant contribution to the pathogenesis and development of AD. In the past years, numerous genes implicated in this disease have been identified via genetic association studies on candidate genes or at the genome-wide level. However, in many cases, the roles of these genes and their interactions in AD are still unclear. A comprehensive and systematic analysis focusing on the biological function and interactions of these genes in the context of AD will therefore provide valuable insights to understand the molecular features of the disease. In this study, we collected genes potentially associated with AD by screening publications on genetic association studies deposited in PubMed. The major biological themes linked with these genes were then revealed by function and biochemical pathway enrichment analysis, and the relation between the pathways was explored by pathway crosstalk analysis. Furthermore, the network features of these AD-related genes were analyzed in the context of human interactome and an AD-specific network was inferred using the Steiner minimal tree algorithm. We compiled 430 human genes reported to be associated with AD from 823 publications. Biological theme analysis indicated that the biological processes and biochemical pathways related to neurodevelopment, metabolism, cell growth and/or survival, and immunology were enriched in these genes. Pathway crosstalk analysis then revealed that the significantly enriched pathways could be grouped into three interlinked modules-neuronal and metabolic module, cell growth/survival and neuroendocrine pathway module, and immune response-related module-indicating an AD-specific immune-endocrine-neuronal regulatory network. Furthermore, an AD-specific protein network was inferred and novel genes potentially associated with AD were identified. By means of network and pathway-based methodology, we explored the pathogenetic mechanism underlying AD at a systems biology level. Results from our work could provide valuable clues for understanding the molecular mechanism underlying AD. In addition, the framework proposed in this study could be used to investigate the pathological molecular network and genes relevant to other complex diseases or phenotypes.

Apollo 16 Mission Anomaly Report No. 1: Oxidizer Deservicing Tank Failure

NASA Technical Reports Server (NTRS)

1972-01-01

The command module reaction control system is emptied of all remaining propellant using ground support equipment designed to provide an acid/base neutralization of the propellant in both the liquid and gaseous phases so that it may be disposed of safely. During the deactivation operation of the oxidizer from the Apollo 16 command module on 7 May 1972, the scrubber tank of the decontamination unit exploded, destroying the ground support equipment unit and damaging the building that housed the operation. Only minor injuries were received by the personnel in the area and the command module was not damaged. Test results show that the failure was caused by an insufficient quantity of neutralizer for the quantity of oxidizer. This insufficiency lead to exothermic nitration-type reactions which produced large quantities of gas at a very high rate and failed the decontamination tank.

Genome-Wide Analysis of Host Responses to Four Different Types of Microorganisms in Bombyx Mori (Lepidoptera: Bombycidae).

PubMed

Cheng, Tingcai; Lin, Ping; Huang, Lulin; Wu, Yuqian; Jin, Shengkai; Liu, Chun; Xia, Qingyou

2016-01-01

Several pathogenic microorganisms have been used to investigate the genome-wide transcriptional responses of Bombyx mori to infection. However, studies have so far each focused on one microorganism, and systematic genome-wide comparison of transcriptional responses to different pathogenic microorganisms has not been undertaken. Here, we surveyed transcriptional responses of B. mori to its natural bacterial, viral, and fungal pathogens, Bacillus bombyseptieus, B. mori nucleopolyhedrovirus (BmNPV), and Beauveria bassiana, respectively, and to nonpathogenic Escherichia coli, by microarray analysis. In total, the expression of 2,436, 1,804, 1,743, and 912 B. mori genes was modulated by infection with B. bombyseptieus, BmNPV, B. bassiana, and E. coli, respectively. Notably, the expression of 620, 400, 177, or 165 of these genes was only modulated by infection with B. bombyseptieus, BmNPV, B. bassiana, or E. coli, respectively. In contrast to the expression of genes related to juvenile hormone synthesis and metabolism, that of genes encoding juvenile hormone binding proteins was microorganism-specific. Three basal metabolic pathways were modulated by infection with any of the four microorganisms, and 3, 14, 5, and 2 metabolic pathways were specifically modulated by infection with B. bombyseptieus, BmNPV, B. bassiana, and E. coli, respectively. Interestingly, BmNPV infection modulated the JAK/STAT signaling pathway, whereas both the Imd and Toll signaling pathways were modulated by infection with B. bombyseptieus, B. bassiana, or E. coli These results elucidate potential molecular mechanisms of the host response to different microorganisms, and provide a foundation for further work on host-pathogen interaction. © The Author 2016. Published by Oxford University Press on behalf of the Entomological Society of America.

Comparative analyses of hydrological responses of two adjacent watersheds to climate variability and change using the SWAT model

USGS Publications Warehouse

Lee, Sangchul; Yeo, In-Young; Sadeghi, Ali M.; McCarty, Gregory W.; Hively, Wells; Lang, Megan W.; Sharifi, Amir

2018-01-01

Water quality problems in the Chesapeake Bay Watershed (CBW) are expected to be exacerbated by climate variability and change. However, climate impacts on agricultural lands and resultant nutrient loads into surface water resources are largely unknown. This study evaluated the impacts of climate variability and change on two adjacent watersheds in the Coastal Plain of the CBW, using the Soil and Water Assessment Tool (SWAT) model. We prepared six climate sensitivity scenarios to assess the individual impacts of variations in CO2concentration (590 and 850 ppm), precipitation increase (11 and 21 %), and temperature increase (2.9 and 5.0 °C), based on regional general circulation model (GCM) projections. Further, we considered the ensemble of five GCM projections (2085–2098) under the Representative Concentration Pathway (RCP) 8.5 scenario to evaluate simultaneous changes in CO2, precipitation, and temperature. Using SWAT model simulations from 2001 to 2014 as a baseline scenario, predicted hydrologic outputs (water and nitrate budgets) and crop growth were analyzed. Compared to the baseline scenario, a precipitation increase of 21 % and elevated CO2 concentration of 850 ppm significantly increased streamflow and nitrate loads by 50 and 52 %, respectively, while a temperature increase of 5.0 °C reduced streamflow and nitrate loads by 12 and 13 %, respectively. Crop biomass increased with elevated CO2 concentrations due to enhanced radiation- and water-use efficiency, while it decreased with precipitation and temperature increases. Over the GCM ensemble mean, annual streamflow and nitrate loads showed an increase of  ∼  70 % relative to the baseline scenario, due to elevated CO2 concentrations and precipitation increase. Different hydrological responses to climate change were observed from the two watersheds, due to contrasting land use and soil characteristics. The watershed with a larger percent of croplands demonstrated a greater increased rate of 5.2 kg N ha−1 in nitrate yield relative to the watershed with a lower percent of croplands as a result of increased export of nitrate derived from fertilizer. The watershed dominated by poorly drained soils showed increased nitrate removal due do enhanced denitrification compared to the watershed dominated by well-drained soils. Our findings suggest that increased implementation of conservation practices would be necessary for this region to mitigate increased nitrate loads associated with predicted changes in future climate.

A high throughput screening for TLR3-IRF3 signaling pathway modulators identifies several antipsychotic drugs as TLR inhibitors1

PubMed Central

Zhu, Jianzhong; Smith, Kevin; Hsieh, Paishiun N.; Mburu, Yvonne K.; Chattopadhyay, Saurabh; Sen, Ganes C.; Sarkar, Saumendra N.

2010-01-01

Toll-like Receptor 3 (TLR3) is one of the major innate immune sensors of double stranded RNA (dsRNA). The signal transduction pathway activated by TLR3, upon binding to dsRNA, leads to the activation of two major transcription factors: NF-κB and IRF3. In an effort to identify specific chemical modulators of TLR3-IRF3 signal transduction pathway we developed a cell-based read out system. Using the interferon stimulated gene 56 (ISG56) promoter driven firefly luciferase gene stably integrated in a TLR3 expressing HEK293 cell line, we were able to generate a cell line where treatment with dsRNA resulted in a dose dependent induction of luciferase activity. A screen of two pharmacologically active compound libraries using this system, identified a number of TLR3-IRF3 signaling pathway modulators. Among them we focused on a subset of inhibitors and characterized their mode of action. Several antipsychotic drugs, such as Sertraline, Trifluoperazine and Fluphenazine were found to be direct inhibitors of the innate immune signaling pathway. These inhibitors also showed the ability to inhibit ISG56 induction mediated by TLR4 and TLR7/8 pathways. Interestingly, they did not show significant effect on TLR3, TLR7 and TLR8 mediated NF-κB activation. Detailed analysis of the signaling pathway indicated that these drugs may be exerting their inhibitory effects on IRF3 via PI3K signaling pathway. The data presented here provides mechanistic explanation of possible anti-inflammatory roles of some antipsychotic drugs. PMID:20382888

Systematic analysis of microarray datasets to identify Parkinson's disease‑associated pathways and genes.

PubMed

Feng, Yinling; Wang, Xuefeng

2017-03-01

In order to investigate commonly disturbed genes and pathways in various brain regions of patients with Parkinson's disease (PD), microarray datasets from previous studies were collected and systematically analyzed. Different normalization methods were applied to microarray datasets from different platforms. A strategy combining gene co‑expression networks and clinical information was adopted, using weighted gene co‑expression network analysis (WGCNA) to screen for commonly disturbed genes in different brain regions of patients with PD. Functional enrichment analysis of commonly disturbed genes was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Co‑pathway relationships were identified with Pearson's correlation coefficient tests and a hypergeometric distribution‑based test. Common genes in pathway pairs were selected out and regarded as risk genes. A total of 17 microarray datasets from 7 platforms were retained for further analysis. Five gene coexpression modules were identified, containing 9,745, 736, 233, 101 and 93 genes, respectively. One module was significantly correlated with PD samples and thus the 736 genes it contained were considered to be candidate PD‑associated genes. Functional enrichment analysis demonstrated that these genes were implicated in oxidative phosphorylation and PD. A total of 44 pathway pairs and 52 risk genes were revealed, and a risk gene pathway relationship network was constructed. Eight modules were identified and were revealed to be associated with PD, cancers and metabolism. A number of disturbed pathways and risk genes were unveiled in PD, and these findings may help advance understanding of PD pathogenesis.

Automated system measuring triple oxygen and nitrogen isotope ratios in nitrate using the bacterial method and N2 O decomposition by microwave discharge.

PubMed

Hattori, Shohei; Savarino, Joel; Kamezaki, Kazuki; Ishino, Sakiko; Dyckmans, Jens; Fujinawa, Tamaki; Caillon, Nicolas; Barbero, Albane; Mukotaka, Arata; Toyoda, Sakae; Well, Reinhard; Yoshida, Naohiro

2016-12-30

Triple oxygen and nitrogen isotope ratios in nitrate are powerful tools for assessing atmospheric nitrate formation pathways and their contribution to ecosystems. N 2 O decomposition using microwave-induced plasma (MIP) has been used only for measurements of oxygen isotopes to date, but it is also possible to measure nitrogen isotopes during the same analytical run. The main improvements to a previous system are (i) an automated distribution system of nitrate to the bacterial medium, (ii) N 2 O separation by gas chromatography before N 2 O decomposition using the MIP, (iii) use of a corundum tube for microwave discharge, and (iv) development of an automated system for isotopic measurements. Three nitrate standards with sample sizes of 60, 80, 100, and 120 nmol were measured to investigate the sample size dependence of the isotope measurements. The δ 17 O, δ 18 O, and Δ 17 O values increased with increasing sample size, although the δ 15 N value showed no significant size dependency. Different calibration slopes and intercepts were obtained with different sample amounts. The slopes and intercepts for the regression lines in different sample amounts were dependent on sample size, indicating that the extent of oxygen exchange is also dependent on sample size. The sample-size-dependent slopes and intercepts were fitted using natural log (ln) regression curves, and the slopes and intercepts can be estimated to apply to any sample size corrections. When using 100 nmol samples, the standard deviations of residuals from the regression lines for this system were 0.5‰, 0.3‰, and 0.1‰, respectively, for the δ 18 O, Δ 17 O, and δ 15 N values, results that are not inferior to those from other systems using gold tube or gold wire. An automated system was developed to measure triple oxygen and nitrogen isotopes in nitrate using N 2 O decomposition by MIP. This system enables us to measure both triple oxygen and nitrogen isotopes in nitrate with comparable precision and sample throughput (23 min per sample on average), and minimal manual treatment. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Tight Junction–Associated Signaling Pathways Modulate Cell Proliferation in Uveal Melanoma

PubMed Central

Jayagopal, Ashwath; Yang, Jin-Long; Haselton, Frederick R.; Chang, Min S.

2011-01-01

Purpose. To investigate the role of tight junction (TJ)–associated signaling pathways in the proliferation of uveal melanoma. Methods. Human uveal melanoma cell lines overexpressing the TJ molecule blood vessel epicardial substance (Bves) were generated. The effects of Bves overexpression on TJ protein expression, cell proliferation, and cell cycle distribution were quantified. In addition, localization and transcription activity of the TJ-associated protein ZO-1–associated nucleic acid binding protein (ZONAB) were evaluated using immunofluorescence and bioluminescence reporter assays to study the involvement of Bves signaling in cell proliferation-associated pathways. Results. Bves overexpression in uveal melanoma cell lines resulted in increased expression of the TJ proteins occludin and ZO-1, reduced cell proliferation, and increased sequestration of ZONAB at TJs and reduced ZONAB transcriptional activity. Conclusions. TJ proteins are present in uveal melanoma, and TJ-associated signaling pathways modulate cell signaling pathways relevant to proliferation in uveal melanoma. PMID:20861479

Wise retained in the endoplasmic reticulum inhibits Wnt signaling by reducing cell surface LRP6.

PubMed

Guidato, Sonia; Itasaki, Nobue

2007-10-15

The Wnt signaling pathway is tightly regulated by extracellular and intracellular modulators. Wise was isolated as a secreted protein capable of interacting with the Wnt co-receptor LRP6. Studies in Xenopus embryos revealed that Wise either enhances or inhibits the Wnt pathway depending on the cellular context. Here we show that the cellular localization of Wise has distinct effects on the Wnt pathway readout. While secreted Wise either synergizes or inhibits the Wnt signals depending on the partner ligand, ER-retained Wise consistently blocks the Wnt pathway. ER-retained Wise reduces LRP6 on the cell surface, making cells less susceptible to the Wnt signal. This study provides a cellular mechanism for the action of Wise and introduces the modulation of cellular susceptibility to Wnt signals as a novel mechanism of the regulation of the Wnt pathway.

Cell Survival Signaling in Neuroblastoma

PubMed Central

Megison, Michael L.; Gillory, Lauren A.; Beierle, Elizabeth A.

2013-01-01

Neuroblastoma is the most common extracranial solid tumor of childhood and is responsible for over 15% of pediatric cancer deaths. Neuroblastoma tumorigenesis and malignant transformation is driven by overexpression and dominance of cell survival pathways and a lack of normal cellular senescence or apoptosis. Therefore, manipulation of cell survival pathways may decrease the malignant potential of these tumors and provide avenues for the development of novel therapeutics. This review focuses on several facets of cell survival pathways including protein kinases (PI3K, AKT, ALK, and FAK), transcription factors (NF-κB, MYCN and p53), and growth factors (IGF, EGF, PDGF, and VEGF). Modulation of each of these factors decreases the growth or otherwise hinders the malignant potential of neuroblastoma, and many therapeutics targeting these pathways are already in the clinical trial phase of development. Continued research and discovery of effective modulators of these pathways will revolutionize the treatment of neuroblastoma. PMID:22934706

Reconstruction of the genome-scale co-expression network for the Hippo signaling pathway in colorectal cancer.

PubMed

Dehghanian, Fariba; Hojati, Zohreh; Hosseinkhan, Nazanin; Mousavian, Zaynab; Masoudi-Nejad, Ali

2018-05-26

The Hippo signaling pathway (HSP) has been identified as an essential and complex signaling pathway for tumor suppression that coordinates proliferation, differentiation, cell death, cell growth and stemness. In the present study, we conducted a genome-scale co-expression analysis to reconstruct the HSP in colorectal cancer (CRC). Five key modules were detected through network clustering, and a detailed discussion of two modules containing respectively 18 and 13 over and down-regulated members of HSP was provided. Our results suggest new potential regulatory factors in the HSP. The detected modules also suggest novel genes contributing to CRC. Moreover, differential expression analysis confirmed the differential expression pattern of HSP members and new suggested regulatory factors between tumor and normal samples. These findings can further reveal the importance of HSP in CRC. Copyright © 2018 Elsevier Ltd. All rights reserved.

Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans

PubMed Central

Meisel, Joshua D.; Panda, Oishika; Mahanti, Parag; Schroeder, Frank C.; Kim, Dennis H.

2014-01-01

Summary Discrimination among pathogenic and beneficial microbes is essential for host organism immunity and homeostasis. Here, we show that chemosensory detection of two secondary metabolites produced by Pseudomonas aeruginosa modulates a neuroendocrine signaling pathway that promotes avoidance behavior in the simple animal host Caenorhabditis elegans. Secondary metabolites phenazine-1-carboxamide and pyochelin activate a G protein-signaling pathway in the ASJ chemosensory neuron pair that induces expression of the neuromodulator DAF-7/TGF-β. DAF-7, in turn, activates a canonical TGF-β signaling pathway in adjacent interneurons to modulate aerotaxis behavior and promote avoidance of pathogenic P. aeruginosa. Our data provide a chemical, genetic, and neuronal basis for how the behavior and physiology of a simple animal host can be modified by the microbial environment, and suggest that secondary metabolites produced by microbes may provide environmental cues that contribute to pathogen recognition and host survival. PMID:25303524

Multidimensional heuristic process for high-yield production of astaxanthin and fragrance molecules in Escherichia coli.

PubMed

Zhang, Congqiang; Seow, Vui Yin; Chen, Xixian; Too, Heng-Phon

2018-05-11

Optimization of metabolic pathways consisting of large number of genes is challenging. Multivariate modular methods (MMMs) are currently available solutions, in which reduced regulatory complexities are achieved by grouping multiple genes into modules. However, these methods work well for balancing the inter-modules but not intra-modules. In addition, application of MMMs to the 15-step heterologous route of astaxanthin biosynthesis has met with limited success. Here, we expand the solution space of MMMs and develop a multidimensional heuristic process (MHP). MHP can simultaneously balance different modules by varying promoter strength and coordinating intra-module activities by using ribosome binding sites (RBSs) and enzyme variants. Consequently, MHP increases enantiopure 3S,3'S-astaxanthin production to 184 mg l -1 day -1 or 320 mg l -1 . Similarly, MHP improves the yields of nerolidol and linalool. MHP may be useful for optimizing other complex biochemical pathways.

Flavonoid-rich apples and nitrate-rich spinach augment nitric oxide status and improve endothelial function in healthy men and women: a randomized controlled trial.

PubMed

Bondonno, Catherine P; Yang, Xingbin; Croft, Kevin D; Considine, Michael J; Ward, Natalie C; Rich, Lisa; Puddey, Ian B; Swinny, Ewald; Mubarak, Aidilla; Hodgson, Jonathan M

2012-01-01

Flavonoids and nitrates in fruits and vegetables may protect against cardiovascular disease. Dietary flavonoids and nitrates can augment nitric oxide status via distinct pathways, which may improve endothelial function and lower blood pressure. Recent studies suggest that the combination of flavonoids and nitrates can enhance nitric oxide production in the stomach. Their combined effect in the circulation is unclear. Here, our objective was to investigate the independent and additive effects of flavonoid-rich apples and nitrate-rich spinach on nitric oxide status, endothelial function, and blood pressure. A randomized, controlled, crossover trial with healthy men and women (n=30) was conducted. The acute effects of four energy-matched treatments (control, apple, spinach, and apple+spinach), administered in random order, were compared. Measurements included plasma nitric oxide status, assessed by measuring S-nitrosothiols+other nitrosylated species (RXNO) and nitrite, blood pressure, and endothelial function, measured as flow-mediated dilatation of the brachial artery. Results are means and 95% CI. Relative to control, all treatments resulted in higher RXNO (control, 33 nmol/L, 26, 42; apple, 51 nmol/L, 40, 65; spinach, 86 nmol/L, 68, 110; apple+spinach, 69 nmol/L, 54, 88; P<0.01) and higher nitrite (control, 35 nmol/L, 27, 46; apple, 69 nmol/L, 53, 90; spinach, 99 nmol/L, 76, 129; apple+spinach, 80 nmol/L, 61, 104; P<0.01). Compared to control, all treatments resulted in higher flow-mediated dilatation (P<0.05) and lower pulse pressure (P<0.05), and apple and spinach resulted in lower systolic blood pressure (P<0.05). No significant effect was observed on diastolic blood pressure. The combination of apple and spinach did not result in additive effects on nitric oxide status, endothelial function, or blood pressure. In conclusion, flavonoid-rich apples and nitrate-rich spinach can independently augment nitric oxide status, enhance endothelial function, and lower blood pressure acutely, outcomes that may benefit cardiovascular health. Copyright © 2011 Elsevier Inc. All rights reserved.

Natural attenuation processes of nitrate in a saline lake-aquifer system: Pétrola Basin (Central Spain)

NASA Astrophysics Data System (ADS)

Valiente, Nicolas; Menchen, Alfonso; Jirsa, Franz; Hein, Thomas; Wanek, Wolfgang; Gomez-Alday, Juan Jose

2016-04-01

Saline wetlands associated with intense agricultural activities in semi-arid to arid climates are among the most vulnerable environments to NO3- pollution. The endorheic Pétrola Basin (High Segura River Basin, Central Spain) was declared vulnerable to NO3- pollution by the Regional Government of Castilla-La Mancha in 1998. The hypersaline lake was classified as a heavily modified waterbody, due to the inputs of pollutants from agricultural sources and urban waste waters, the latest are discharged directly into the lake without proper treatment. Previous studies showed that the aquifer system has two main flow components: regional groundwater flow from recharge areas into the lake, and a density-driven flow from the lake to the underlying aquifer. The NO3- inputs derived from agriculture originate from nitrification of synthetic ammonium fertilizers, and afterwards, NO3- is expected to be attenuated by denitrification (up to 60%) in the saltwater-freshwater interface around the lake. However, the spatial and temporal pattern of nitrate reduction in lake sediments is not known. In this study, an isotope pairing technique was used in order to clarify the main pathways for the NO3- attenuation linked to the sediment-water interface. For that purpose mesocosm experiments were performed: organic-rich lake sediment (up to 23% organic carbon content) was incubated for 96 hours with the addition of 15N nitrate tracer. During the experiments two factors were modified: light and oxic conditions. Analyzing inorganic N-species (n=20) over time (72 hours) showed that NO3- attenuation was coupled with an increment in the NH4+ concentration (from 0.8 mg/L up to 5.3 mg/L) and a decrease in redox values (from 135.1 mV up to -422 mV) in the water column. The main outcome of this study was to elucidate the importance of different microbial pathways denitrification, dissimilatory nitrate reduction to ammonium (DNRA) and anaerobic ammonium oxidation (Anammox), in controlling the fate of NO3- in Pétrola Lake. The complete attenuation of 250 μmol of NO3- occurred during the first 30 hours of incubation under all the treatments, coupled to a temporal increase in the NO2- concentration. The results will support the understanding how hypersaline lakes are able to respond to elevated nutrient loads.

Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS

PubMed Central

Tominski, Claudia; Kappler, Andreas; Behrens, Sebastian

2016-01-01

Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458–1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae, and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochrome c system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp., and findings of other putative genes involving cytochrome c and multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration. PMID:26896135

Myeloperoxidase-generated reactive nitrogen species convert LDL into an atherogenic form in vitro

PubMed Central

Podrez, Eugene A.; Schmitt, David; Hoff, Henry F.; Hazen, Stanley L.

1999-01-01

Oxidized LDL is implicated in atherosclerosis; however, the pathways that convert LDL into an atherogenic form in vivo are not established. Production of reactive nitrogen species may be one important pathway, since LDL recovered from human atherosclerotic aorta is enriched in nitrotyrosine. We now report that reactive nitrogen species generated by the MPO-H2O2-NO2– system of monocytes convert LDL into a form (NO2-LDL) that is avidly taken up and degraded by macrophages, leading to massive cholesterol deposition and foam cell formation, essential steps in lesion development. Incubation of LDL with isolated MPO, an H2O2-generating system, and nitrite (NO2–)— a major end-product of NO metabolism—resulted in nitration of apolipoprotein B 100 tyrosyl residues and initiation of LDL lipid peroxidation. The time course of LDL protein nitration and lipid peroxidation paralleled the acquisition of high-affinity, concentration-dependent, and saturable binding of NO2-LDL to human monocyte–derived macrophages and mouse peritoneal macrophages. LDL modification and conversion into a high-uptake form occurred in the absence of free metal ions, required NO2–, occurred at physiological levels of Cl–, and was inhibited by heme poisons, catalase, and BHT. Macrophage binding of NO2-LDL was specific and mediated by neither the LDL receptor nor the scavenger receptor class A type I. Exposure of macrophages to NO2-LDL promoted cholesteryl ester synthesis, intracellular cholesterol and cholesteryl ester accumulation, and foam cell formation. Collectively, these results identify MPO-generated reactive nitrogen species as a physiologically plausible pathway for converting LDL into an atherogenic form. PMID:10359564

Characterization of nitrite degradation by Lactobacillus casei subsp. rhamnosus LCR 6013.

PubMed

Liu, Dong-mei; Wang, Pan; Zhang, Xin-yue; Xu, Xi-lin; Wu, Hui; Li, Li

2014-01-01

Nitrites are potential carcinogens. Therefore, limiting nitrites in food is critically important for food safety. The nitrite degradation capacity of Lactobacillus casei subsp. rhamnosus LCR 6013 was investigated in pickle fermentation. After LCR 6013 fermentation for 120 h at 37°C, the nitrite concentration in the fermentation system was significantly lower than that in the control sample without the LCR 6013 strain. The effects of NaCl and Vc on nitrite degradation by LCR 6013 in the De Man, Rogosa and Sharpe (MRS) medium were also investigated. The highest nitrite degradations, 9.29 mg/L and 9.89 mg/L, were observed when NaCl and Vc concentrations were 0.75% and 0.02%, respectively in the MRS medium, which was significantly higher than the control group (p ≤ 0.01). Electron capture/gas chromatography and indophenol blue staining were used to study the nitrite degradation pathway of LCR 6013. The nitrite degradation products contained N2O, but no NH4(+). The LCR 6013 strain completely degraded all NaNO2 (50.00 mg/L) after 16 h of fermentation. The enzyme activity of NiR in the periplasmic space was 2.5 times of that in the cytoplasm. Our results demonstrated that L. casei subsp. rhamnosus LCR 6013 can effectively degrade nitrites in both the pickle fermentation system and in MRS medium by NiR. Nitrites are degraded by the LCR 6013 strain, likely via the nitrate respiration pathway (NO2(-)>NO->N2O->N2), rather than the aammonium formation pathway (dissimilatory nitrate reduction to ammonium, DNRA), because the degradation products contain N2O, but not NH4(+).

Understanding the Spatio-Temporal Dynamics of Denitrification in an Oregon Salt Marsh

NASA Astrophysics Data System (ADS)

Moon, J. B.; Stecher, H. A.; DeWitt, T.; Nahlik, A.; Fennessy, M. S.; Michael, L.; Regutti, R.; Mckane, R.; Marois, D.; Naithani, K. J.

2016-12-01

Salt marshes are highly susceptible to a range of climate change effects (e.g., sea-level rise, salinity changes, storm severity, shifts in vegetation across watershed). It is unclear how these effects will alter the spatial and temporal dynamics of denitrification, a potential pathway of nitrogen interception and removal from adjacent estuaries. Our overall objective is to determine whether salt marshes in the Pacific Northwest act as sources or sinks of nitrogen to estuaries, and to be able to predict changes in these dynamics under future climate scenarios. We have built a probabilistic denitrification model based on observations from a salt marsh in the Yaquina Estuary (Newport, Oregon). We observed a non-linear relationship between denitrification rates and distance to the marsh-upland interface and soil nitrate concentrations, which are indicators of nitrate delivery flow paths from upslope red alder. We also modeled spatial variability in oxygen availability as a function of elevation, which affects inundation period, and distance to channel, which affects the saturation period through the dewatering rate. Simulations suggest denitrification "hot spots" occur in mid-marsh locations, where both nitrate availability and inundation periods are maximized. Once marsh accretion is outpaced, sea level rise will likely reduce salt marsh area due to steep adjacent uplands that limit marsh retreat, and increase inundation duration near the marsh-upland interface. Expansion of red alder cover is concurrently expected to increase nitrate availability to downslope ecosystems. Taking these effects together, our future scenario simulations suggest a movement of "hot-spots" towards the marsh-upland boundary.

Landscape hydrology and scaling of nitrate 15N and 18O isotope composition in a semi-arid agroecosystem

NASA Astrophysics Data System (ADS)

Kelley, C. J.; Martin, R. A.; Keller, C. K.; Orr, C. H.; Huggins, D. R.; Evans, R. D.

2014-12-01

Understanding how pore- to hillslope-scale processes combine to control nutrient export at larger scales is a fundamental challenge in today's agroecosystems as the carbon and contamination footprints of production agriculture come under increasing scrutiny. At the Cook Agronomy Farm (CAF) Long-Term Agricultural Research (LTAR) station near Pullman, WA we are using in-field observations to track how local-scale hydrological routing and biogeochemical processing interact to control landscape-scale water and nutrient exports. Previous research at the CAF has shown that conservative tracers and reactive nutrient quantities (NO3-,and DOC concentrations, DOM quality) in landscape-scale drainage can be explained by straightforward mixing of waters from variably contributing areas. Nitrate stable isotope composition in subsurface drain effluent indicate that most leached nitrate originates from reduced nitrogen fertilizer applied to the CAF in the autumn, which undergoes nitrification and subsequent leaching. This occurs over a timespan of weeks to months. However, water samples from contributing areas exhibit nitrate d15N and d18O significantly greater than subsurface drain effluent at all locations, and time-series consistent with the occurrence of denitrification at some locations. Possible explanations include pore-scale processing of nitrogen that does not affect the other tracers (like EC, DOM quality, and DOC concentration), and landscape-scale transport pathways that bypass our field instruments. Through this work we are contributing to a broader understand of how global change and local factors and management practices interact to affect the fate of fertilizer N, which is a cross-cutting research theme of the national LTAR network.

Nitric oxide and iron modulate heme oxygenase activity as a long distance signaling response to salt stress in sunflower seedling cotyledons.

PubMed

Singh, Neha; Bhatla, Satish C

2016-02-29

Nitric oxide is a significant component of iron signaling in plants. Heme is one of the iron sensors in plants. Free heme is highly toxic and can cause cell damage as it catalyzes the formation of reactive oxygen species (ROS). Its catabolism is carried out by heme oxygenase (HOs; EC 1.14.99.3) which uses heme both as a prosthetic group and as a substrate. Two significant events, which accompany adaptation to salt stress in sunflower seedlings, are accumulation of ROS and enhanced production of nitric oxide (NO) in roots and cotyledons. Present investigations on the immunolocalization of heme oxygenase distribution in sunflower seedling cotyledons by confocal laser scanning microscopic (CLSM) imaging provide new information on the differential spatial distribution of the inducible form of HO (HO-1) as a long distance in response to NaCl stress. The enzyme is abundantly distributed in the specialized cells around the secretory canals (SCs) in seedling cotyledons. Abundance of tyrosine nitrated proteins has also been observed in the specialized cells around the secretory canals in cotyledons derived from salt stressed seedlings. The spatial distribution of tyrosine nitrated proteins and HO-1 expression further correlates with the abundance of mitochondria in these cells. Present findings, thus, highlight a link among distribution of HO-1 expression, abundance of tyrosine nitrated proteins and mitochondria in specialized cells around the secretory canal as a long distance mechanism of salt stress tolerance in sunflower seedlings. Enhanced spatial distribution of HO-1 in response to NaCl stress in seedling cotyledons is in congruence with the observed increase in specific activity of HO-1 in NaCl stressed conditions. The enzyme activity is further enhanced by hemin (HO-1 inducer) both in the absence or presence of NaCl stress and inhibited by zinc protoporphyrin. Western blot analysis of cotyledon homogenates using anti-HO-1 polyclonal antibody shows one major band (29 kDa) of HO-1. NaCl-modulated HO-1 activity correlates with endogenous NO content in the cotyledons. Increased NO accumulation by hemin treatment also correlates with enhanced activity of HO-1 in both control and NaCl stress conditions. Present work indicates that NO positively modulates HO-1 activity in sunflower seedling cotyledons. NaCl stress tends to antagonize NO action on HO-1 activity. NO (from sodium nitroprusside; SNP) is probably positively modulating HO-1 activity by way of its interaction/binding with heme group. Present work also shows enhanced NO accumulation in seedling cotyledons both in the absence or presence of iron in the growth medium, in response to NaCl stress. Thus, a probable link between endogenous NO, NaCl stress and iron-homeostasis by way of modulation of HO-1 activity at early stage of sunflower seedling growth has been proposed. Copyright © 2016 Elsevier Inc. All rights reserved.

Assimilation of Nitrogen from Nitrite and Trinitrotoluene in Pseudomonas putida JLR11

PubMed Central

Caballero, Antonio; Esteve-Núñez, Abraham; Zylstra, Gerben J.; Ramos, Juan L.

2005-01-01

Pseudomonas putida JLR11 releases nitrogen from the 2,4,6-trinitrotoluene (TNT) ring as nitrite or ammonium. These processes can occur simultaneously, as shown by the observation that a nasB mutant impaired in the reduction of nitrite to ammonium grew at a slower rate than the parental strain. Nitrogen from TNT is assimilated via the glutamine syntethase-glutamate synthase (GS-GOGAT) pathway, as evidenced by the inability of GOGAT mutants to use TNT. This pathway is also used to assimilate ammonium from reduced nitrate and nitrite. Three mutants that had insertions in ntrC, nasT, and cnmA, which encode regulatory proteins, failed to grow on nitrite but grew on TNT, although slower than the wild type. PMID:15601726

Impact of constitutional copy number variants on biological pathway evolution.

PubMed

Poptsova, Maria; Banerjee, Samprit; Gokcumen, Omer; Rubin, Mark A; Demichelis, Francesca

2013-01-23

Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations. To trace potential evolutionary changes of well-described biological pathways, we jointly queried the genomes and the transcriptomes of a collection of individuals with Caucasian, Asian or Yoruban descent combining high-resolution array and sequencing data. We implemented an enrichment analysis of pathways accounting for CNVs and genes sizes and detected significant enrichment not only in signal transduction and extracellular biological processes, but also in metabolism pathways. Upon the estimation of CNV population differentiation (CNVs with different polymorphism frequencies across populations), we evaluated that 22% of the pathways contain at least one gene that is proximal to a CNV (CNV-gene pair) that shows significant population differentiation. The majority of these CNV-gene pairs belong to signal transduction pathways and 6% of the CNV-gene pairs show statistical association between the copy number states and the transcript levels. The analysis suggested possible examples of positive selection within individual populations including NF-kB, MAPK signaling pathways, and Alu/L1 retrotransposition factors. Altogether, our results suggest that constitutional CNVs may modulate subtle pathway changes through specific pathway enzymes, which may become fixed in some populations.

Impact of constitutional copy number variants on biological pathway evolution

PubMed Central

2013-01-01

Background Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations. To trace potential evolutionary changes of well-described biological pathways, we jointly queried the genomes and the transcriptomes of a collection of individuals with Caucasian, Asian or Yoruban descent combining high-resolution array and sequencing data. Results We implemented an enrichment analysis of pathways accounting for CNVs and genes sizes and detected significant enrichment not only in signal transduction and extracellular biological processes, but also in metabolism pathways. Upon the estimation of CNV population differentiation (CNVs with different polymorphism frequencies across populations), we evaluated that 22% of the pathways contain at least one gene that is proximal to a CNV (CNV-gene pair) that shows significant population differentiation. The majority of these CNV-gene pairs belong to signal transduction pathways and 6% of the CNV-gene pairs show statistical association between the copy number states and the transcript levels. Conclusions The analysis suggested possible examples of positive selection within individual populations including NF-kB, MAPK signaling pathways, and Alu/L1 retrotransposition factors. Altogether, our results suggest that constitutional CNVs may modulate subtle pathway changes through specific pathway enzymes, which may become fixed in some populations. PMID:23342974

Enzymes involved in the anaerobic degradation of ortho-phthalate by the nitrate-reducing bacterium Azoarcus sp. strain PA01.

PubMed

Junghare, Madan; Spiteller, Dieter; Schink, Bernhard

2016-09-01

The pathway of anaerobic degradation of o-phthalate was studied in the nitrate-reducing bacterium Azoarcus sp. strain PA01. Differential two-dimensional protein gel profiling allowed the identification of specifically induced proteins in o-phthalate-grown compared to benzoate-grown cells. The genes encoding o-phthalate-induced proteins were found in a 9.9 kb gene cluster in the genome of Azoarcus sp. strain PA01. The o-phthalate-induced gene cluster codes for proteins homologous to a dicarboxylic acid transporter, putative CoA-transferases and a UbiD-like decarboxylase that were assigned to be specifically involved in the initial steps of anaerobic o-phthalate degradation. We propose that o-phthalate is first activated to o-phthalyl-CoA by a putative succinyl-CoA-dependent succinyl-CoA:o-phthalate CoA-transferase, and o-phthalyl-CoA is subsequently decarboxylated to benzoyl-CoA by a putative o-phthalyl-CoA decarboxylase. Results from in vitro enzyme assays with cell-free extracts of o-phthalate-grown cells demonstrated the formation of o-phthalyl-CoA from o-phthalate and succinyl-CoA as CoA donor, and its subsequent decarboxylation to benzoyl-CoA. The putative succinyl-CoA:o-phthalate CoA-transferase showed high substrate specificity for o-phthalate and did not accept isophthalate, terephthalate or 3-fluoro-o-phthalate whereas the putative o-phthalyl-CoA decarboxylase converted fluoro-o-phthalyl-CoA to fluoro-benzoyl-CoA. No decarboxylase activity was observed with isophthalyl-CoA or terephthalyl-CoA. Both enzyme activities were oxygen-insensitive and inducible only after growth with o-phthalate. Further degradation of benzoyl-CoA proceeds analogous to the well-established anaerobic benzoyl-CoA degradation pathway of nitrate-reducing bacteria. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Nitric Oxide Affects Rice Root Growth by Regulating Auxin Transport Under Nitrate Supply

PubMed Central

Sun, Huwei; Feng, Fan; Liu, Juan; Zhao, Quanzhi

2018-01-01

Nitrogen (N) is a major essential nutrient for plant growth, and rice is an important food crop globally. Although ammonium (NH4+) is the main N source for rice, nitrate (NO3-) is also absorbed and utilized. Rice responds to NO3- supply by changing root morphology. However, the mechanisms of rice root growth and formation under NO3- supply are unclear. Nitric oxide (NO) and auxin are important regulators of root growth and development under NO3- supply. How the interactions between NO and auxin in regulating root growth in response to NO3- are unknown. In this study, the levels of indole-3-acetic acid (IAA) and NO in roots, and the responses of lateral roots (LRs) and seminal roots (SRs) to NH4+ and NO3-, were investigated using wild-type (WT) rice, as well as osnia2 and ospin1b mutants. NO3- supply promoted LR formation and SR elongation. The effects of NO donor and NO inhibitor/scavenger supply on NO levels and the root morphology of WT and nia2 mutants under NH4+ or NO3- suggest that NO3--induced NO is generated by the nitrate reductase (NR) pathway rather than the NO synthase (NOS)-like pathway. IAA levels, [3H] IAA transport, and PIN gene expression in roots were enhanced under NO3- relative to NH4+ supply. These results suggest that NO3- regulates auxin transport in roots. Application of SNP under NH4+ supply, or of cPTIO under NO3- supply, resulted in auxin levels in roots similar to those under NO3- and NH4+ supply, respectively. Compared to WT, the roots of the ospin1b mutant had lower auxin levels, fewer LRs, and shorter SRs. Thus, NO affects root growth by regulating auxin transport in response to NO3-. Overall, our findings suggest that NO3- influences LR formation and SR elongation by regulating auxin transport via a mechanism involving NO. PMID:29875779

A Module Analysis Approach to Investigate Molecular Mechanism of TCM Formula: A Trial on Shu-feng-jie-du Formula

PubMed Central

Zhang, Fangbo; Tang, Shihuan; Liu, Xi; Gao, Yibo; Wang, Yanping

2013-01-01

At the molecular level, it is acknowledged that a TCM formula is often a complex system, which challenges researchers to fully understand its underlying pharmacological action. However, module detection technique developed from complex network provides new insight into systematic investigation of the mode of action of a TCM formula from the molecule perspective. We here proposed a computational approach integrating the module detection technique into a 2-class heterogeneous network (2-HN) which models the complex pharmacological system of a TCM formula. This approach takes three steps: construction of a 2-HN, identification of primary pharmacological units, and pathway analysis. We employed this approach to study Shu-feng-jie-du (SHU) formula, which aimed at discovering its molecular mechanism in defending against influenza infection. Actually, four primary pharmacological units were identified from the 2-HN for SHU formula and further analysis revealed numbers of biological pathways modulated by the four pharmacological units. 24 out of 40 enriched pathways that were ranked in top 10 corresponding to each of the four pharmacological units were found to be involved in the process of influenza infection. Therefore, this approach is capable of uncovering the mode of action underlying a TCM formula via module analysis. PMID:24376467

Transintestinal transport of the anti-inflammatory drug 4F and the modulation of transintestinal cholesterol efflux[S

PubMed Central

Meriwether, David; Sulaiman, Dawoud; Wagner, Alan; Grijalva, Victor; Kaji, Izumi; Williams, Kevin J.; Yu, Liqing; Fogelman, Spencer; Volpe, Carmen; Bensinger, Steven J.; Anantharamaiah, G. M.; Shechter, Ishaiahu; Fogelman, Alan M.; Reddy, Srinivasa T.

2016-01-01

The site and mechanism of action of the apoA-I mimetic peptide 4F are incompletely understood. Transintestinal cholesterol efflux (TICE) is a process involved in the clearance of excess cholesterol from the body. While TICE is responsible for at least 30% of the clearance of neutral sterols from the circulation into the intestinal lumen, few pharmacological agents have been identified that modulate this pathway. We show first that circulating 4F selectively targets the small intestine (SI) and that it is predominantly transported into the intestinal lumen. This transport of 4F into the SI lumen is transintestinal in nature, and it is modulated by TICE. We also show that circulating 4F increases reverse cholesterol transport from macrophages and cholesterol efflux from lipoproteins via the TICE pathway. We identify the cause of this modulation of TICE either as 4F being a cholesterol acceptor with respect to enterocytes, from which 4F enhances cholesterol efflux, or as 4F being an intestinal chaperone with respect to TICE. Our results assign a novel role for 4F as a modulator of the TICE pathway and suggest that the anti-inflammatory functions of 4F may be a partial consequence of the codependent intestinal transport of both 4F and cholesterol. PMID:27199144

Genome-wide identification, classification and transcriptional analysis of nitrate and ammonium transporters in Coffea

PubMed Central

dos Santos, Tiago Benedito; Lima, Joni Esrom; Felicio, Mariane Silva; Soares, João Danillo Moura; Domingues, Douglas Silva

2017-01-01

Abstract Nitrogen (N) is quantitatively the main nutrient required by coffee plants, with acquisition mainly by the roots and mostly exported to coffee beans. Nitrate (NO3 –) and ammonium (NH4 +) are the most important inorganic sources for N uptake. Several N transporters encoded by different gene families mediate the uptake of these compounds. They have an important role in source preference for N uptake in the root system. In this study, we performed a genome-wide analysis, including in silico expression and phylogenetic analyses of AMT1, AMT2, NRT1/PTR, and NRT2 transporters in the recently sequenced Coffea canephora genome. We analyzed the expression of six selected transporters in Coffea arabica roots submitted to N deficiency. N source preference was also analyzed in C. arabica using isotopes. C. canephora N transporters follow the patterns observed for most eudicots, where each member of the AMT and NRT families has a particular role in N mobilization, and where some of these are modulated by N deficiency. Despite the prevalence of putative nitrate transporters in the Coffea genome, ammonium was the preferential inorganic N source for N-starved C. arabica roots. This data provides an important basis for fundamental and applied studies to depict molecular mechanisms involved in N uptake in coffee trees. PMID:28399192

Combustion synthesis of LaFeO{sub 3} sensing nanomaterial

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaza, F., E-mail: fabio.zaza@enea.it; Serra, E.; Pallozzi, V.

2015-06-23

Since industrial revolution, human activities drive towards unsustainable global economy due to the overexploitation of natural resources and the unacceptable emissions of pollution and greenhouse gases. In order to address that issue, engineering research has been focusing on gas sensors development for monitoring gas emissions and controlling the combustion process sustainability. Semiconductors metal oxides sensors are attractive technology because they require simple design and fabrication, involving high accessibility, small size and low cost. Perovskite oxides are the most promising sensing materials because sensitivity, selectivity, stability and speed-response can be modulated and optimized by changing the chemical composition. One of themore » most convenient synthesis process of perovskite is the citrate-nitrate auto-combustion method, in which nitrate is the oxidizing agent and citrate is the fuel and the chelating argent in the same time. Since the sensibility of perovskite oxides depends on the defective crystallographic structure and the nanomorphology, the experimental was designed in order to study the dependence of powder properties on the synthesis conditions, such as the solution acidity and the relative amount of metals, nitrates and citric acid. Crystalline structure was studied in depth for defining the effects of synthesis conditions on size, morphology and crystallographic structure of nanopowders of LaFeO{sub 3}.« less

Combustion synthesis of LaFeO3 sensing nanomaterial

NASA Astrophysics Data System (ADS)

Zaza, F.; Pallozzi, V.; Serra, E.; Pasquali, M.

2015-06-01

Since industrial revolution, human activities drive towards unsustainable global economy due to the overexploitation of natural resources and the unacceptable emissions of pollution and greenhouse gases. In order to address that issue, engineering research has been focusing on gas sensors development for monitoring gas emissions and controlling the combustion process sustainability. Semiconductors metal oxides sensors are attractive technology because they require simple design and fabrication, involving high accessibility, small size and low cost. Perovskite oxides are the most promising sensing materials because sensitivity, selectivity, stability and speed-response can be modulated and optimized by changing the chemical composition. One of the most convenient synthesis process of perovskite is the citrate-nitrate auto-combustion method, in which nitrate is the oxidizing agent and citrate is the fuel and the chelating argent in the same time. Since the sensibility of perovskite oxides depends on the defective crystallographic structure and the nanomorphology, the experimental was designed in order to study the dependence of powder properties on the synthesis conditions, such as the solution acidity and the relative amount of metals, nitrates and citric acid. Crystalline structure was studied in depth for defining the effects of synthesis conditions on size, morphology and crystallographic structure of nanopowders of LaFeO3.

Biodegradation of 3-Nitrotyrosine by Burkholderia sp. Strain JS165 and Variovorax paradoxus JS171

DTIC Science & Technology

2006-02-01

Bukhalid, D. M. Gibson, B. R. Crane, and R. Loria. 2004. Nitration of a peptide phytotoxin by bacterial nitric oxide synthase. Nature 429:79–82. 15...The facile isolation and the specific, regulated pathway for 3-nitrotyrosine degradation in natural ecosystems suggest that there is a significant...mechanisms have been established (19). No information is available on the biodegradation of natural nitro- aromatic compounds, such as 3NTyr. We

The differential role of motor cortex in the stretch reflex modulation induced by changes in environmental mechanics and verbal instruction

PubMed Central

Shemmell, Jonathan; An, Je Hi; Perreault, Eric J.

2009-01-01

The motor cortex assumes an increasingly important role in higher mammals relative to that in lower mammals. This is true to such an extent that the human motor cortex is deeply involved in reflex regulation and it is common to speak of “transcortical reflex loops”. Such loops appear to add flexibility to the human stretch reflex, once considered to be immutable, allowing it to adapt across a range of functional tasks. However, the purpose of this adaptation remains unclear. A common proposal is that stretch reflexes contribute to the regulation of limb stability; increased reflex sensitivity during tasks performed in unstable environments supports this hypothesis. Alternatively, prior to movement onset, stretch reflexes can assist an imposed stretch, opposite to what would be expected from a stabilizing response. Here we show that stretch reflex modulation in tasks that require changes in limb stability is mediated by motor cortical pathways, and that these differ from pathways contributing to reflex modulation that depends on how the subject is instructed to react to an imposed perturbation. By timing muscle stretches such that the modulated portion of the reflex occurred within a cortical silent period induced by transcranial magnetic stimulation, we abolished the increase in reflex sensitivity observed when individuals stabilized arm posture within a compliant environment. Conversely, reflex modulation caused by altered task instruction was unaffected by cortical silence. These results demonstrate that task-dependent changes in reflex function can be mediated through multiple neural pathways and that these pathways have task specific roles. PMID:19846713

The differential role of motor cortex in stretch reflex modulation induced by changes in environmental mechanics and verbal instruction.

PubMed

Shemmell, Jonathan; An, Je Hi; Perreault, Eric J

2009-10-21

The motor cortex assumes an increasingly important role in higher mammals relative to that in lower mammals. This is true to such an extent that the human motor cortex is deeply involved in reflex regulation and it is common to speak of "transcortical reflex loops." Such loops appear to add flexibility to the human stretch reflex, once considered to be immutable, allowing it to adapt across a range of functional tasks. However, the purpose of this adaptation remains unclear. A common proposal is that stretch reflexes contribute to the regulation of limb stability; increased reflex sensitivity during tasks performed in unstable environments supports this hypothesis. Alternatively, before movement onset, stretch reflexes can assist an imposed stretch, opposite to what would be expected from a stabilizing response. Here we show that stretch reflex modulation in tasks that require changes in limb stability is mediated by motor cortical pathways, and that these differ from pathways contributing to reflex modulation that depend on how the subject is instructed to react to an imposed perturbation. By timing muscle stretches such that the modulated portion of the reflex occurred within a cortical silent period induced by transcranial magnetic stimulation, we abolished the increase in reflex sensitivity observed when individuals stabilized arm posture within a compliant environment. Conversely, reflex modulation caused by altered task instruction was unaffected by cortical silence. These results demonstrate that task-dependent changes in reflex function can be mediated through multiple neural pathways and that these pathways have task-specific roles.

Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress

PubMed Central

Levitan, Orly; Dinamarca, Jorge; Zelzion, Ehud; Lun, Desmond S.; Guerra, L. Tiago; Kim, Min Kyung; Kim, Joomi; Van Mooy, Benjamin A. S.; Bhattacharya, Debashish; Falkowski, Paul G.

2015-01-01

Diatoms are unicellular algae that accumulate significant amounts of triacylglycerols as storage lipids when their growth is limited by nutrients. Using biochemical, physiological, bioinformatics, and reverse genetic approaches, we analyzed how the flux of carbon into lipids is influenced by nitrogen stress in a model diatom, Phaeodactylum tricornutum. Our results reveal that the accumulation of lipids is a consequence of remodeling of intermediate metabolism, especially reactions in the tricarboxylic acid and the urea cycles. Specifically, approximately one-half of the cellular proteins are cannibalized; whereas the nitrogen is scavenged by the urea and glutamine synthetase/glutamine 2-oxoglutarate aminotransferase pathways and redirected to the de novo synthesis of nitrogen assimilation machinery, simultaneously, the photobiological flux of carbon and reductants is used to synthesize lipids. To further examine how nitrogen stress triggers the remodeling process, we knocked down the gene encoding for nitrate reductase, a key enzyme required for the assimilation of nitrate. The strain exhibits 40–50% of the mRNA copy numbers, protein content, and enzymatic activity of the wild type, concomitant with a 43% increase in cellular lipid content. We suggest a negative feedback sensor that couples photosynthetic carbon fixation to lipid biosynthesis and is regulated by the nitrogen assimilation pathway. This metabolic feedback enables diatoms to rapidly respond to fluctuations in environmental nitrogen availability. PMID:25548193

Integrative response of plant mitochondrial electron transport chain to nitrogen source.

PubMed

Hachiya, Takushi; Noguchi, Ko

2011-02-01

Nitrogen (N) availability is widely known as a determinant of plant growth and respiration rate. However, less attention has been paid to the effect of the type of N source (nitrate, nitrite or ammonium) on the respiratory system. This review summarizes the latest findings on this topic, with an emphasis on the effect of ammonium and nitric oxide (NO) on the respiratory system, and the physiological role of alternative oxidase (AOX). First, concentrated ammonium has been found to increase plant respiration rate (ammonium-dependent respiratory increase, ARI). We will introduce two hypotheses to explain ARI, futile ammonium cycling and excess reducing equivalents, and verify the validity of each hypothesis. We suggest that these two hypotheses are not necessarily mutually exclusive. Second, gene expression of AOX is suppressed when N is predominately available as nitrate instead of ammonium. We will discuss possible signaling pathways leading to this expression pattern. Third, while AOX expression is induced by NO, AOX activity itself is insensitive to NO. In contrast, activity of cytochrome c oxidase (COX) is sensitive to NO. We outline the NO production pathway, focusing on nitrite-dependent NO production, and discuss the physiological significance of the fact that AOX activity is insensitive to NO. Finally, this review aims to build an integrated scheme of the respiratory response to the type of N source, considering leaves in high light conditions or hypoxic roots.