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Sample records for active site aromatic

  1. Flexibility of active-site gorge aromatic residues and non-gorge aromatic residues in acetylcholinesterase

    SciTech Connect

    Ghattyvenkatakrishna, Pavan K; Uberbacher, Edward C

    2013-01-01

    The presence of an unusually large number of aromatic residues in the active site gorge of acetylcholinesterase has been a topic of great interest. Flexibility of these residues has been suspected to be a key player in controlling ligand traversal in the gorge. This raises the question of whether the over representation of aromatic residues in the gorge implies higher than normal flexibility of those residues. The current study suggests that it does not. Large changes in the hydrophobic cross sectional area due to dihedral oscillations are probably the reason behind their presence in the gorge.

  2. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth.

  3. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth. PMID:26940877

  4. Subway construction activity influence on polycyclic aromatic hydrocarbons in fine particles: Comparison with a background mountainous site

    NASA Astrophysics Data System (ADS)

    Kong, Shaofei; Li, Xuxu; Li, Qi; Yin, Yan; Li, Li; Chen, Kui; Liu, Dantong; Yuan, Liang; Pang, Xiaobing

    2015-07-01

    Intensive construction activities worsened the surrounding atmospheric environment in China. Eighteen polycyclic aromatic hydrocarbons (PAHs) in fine particles (PM2.5) were collected at a subway construction site (SC) of Nanjing and compared with a regional background mountainous site (BM) to examine the influence of anthropogenic activities on concentrations, sources and health risks of PAHs. Average PAH concentrations at SC were higher than BM at a factor of about 5.9. All PAH species at SC were higher than BM, with the SC/BM ratios ranging from 1.3 (NaP) to 10.3 (BaP). PAH profiles differed for the two sites. The SC site had higher mass fractions of PAHs from coal combustion and vehicle emission, while the BM site held higher mass percentages of PAHs from long-range transported wood combustion and industrial activities. Lower temperature at BM may lead to the higher mass percentages of low ring PAHs. Coal combustion, traffic emissions and biomass burning were the common sources for PAHs at both SC and BM. Construction workers were exposed to higher BaPeq concentrations, nearly ten times of the background site and their lifetime cancer risk reached to 0.6 per 1,000,000 exposed worker, owing to the influence of coal combustion, vehicle emission and industrial activities at the surroundings of SC.

  5. Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12

    PubMed Central

    Zhang, Xiaomei; Wang, Shuai; Wu, Xiuyun; Liu, Shijia; Li, Dandan; Xu, Hao; Gao, Peiji; Chen, Guanjun; Wang, Lushan

    2015-01-01

    The active site architecture of glycoside hydrolase (GH) is a contiguous subregion of the enzyme constituted by residues clustered in the three-dimensional space, recognizing the monomeric unit of ligand through hydrogen bonds and hydrophobic interactions. Mutations of the key residues in the active site architecture of the GH12 family exerted different impacts on catalytic efficiency. Binding affinities between the aromatic amino acids and carbohydrate rings were quantitatively determined by isothermal titration calorimetry (ITC) and the quantum mechanical (QM) method, showing that the binding capacity order of Tyr>Trp>His (and Phe) was determined by their side-chain properties. The results also revealed that the binding constant of a certain residue remained unchanged when altering its location, while the catalytic efficiency changed dramatically. Increased binding affinity at a relatively distant subsite, such as the mutant of W7Y at the −4 subsite, resulted in a marked increase in the intermediate product of cellotetraose and enhanced the reactivity of endoglucanase by 144%; while tighter binding near the catalytic center, i.e. W22Y at the −2 subsite, enabled the enzyme to bind and hydrolyze smaller oligosaccharides. Clarification of the specific roles of the aromatics at different subsites may pave the way for a more rational design of GHs. PMID:26670009

  6. Site-directed mutagenesis of tobacco anionic peroxidase: Effect of additional aromatic amino acids on stability and activity.

    PubMed

    Poloznikov, A A; Zakharova, G S; Chubar, T A; Hushpulian, D M; Tishkov, V I; Gazaryan, I G

    2015-08-01

    Tobacco anionic peroxidase (TOP) is known to effectively catalyze luminol oxidation without enhancers, in contrast to horseradish peroxidase (HRP). To pursue structure-activity relationship studies for TOP, two amino acids have been chosen for mutation, namely Thr151, close to the heme plane, and Phe140 at the entrance to the active site pocket. Three mutant forms TOP F140Y, T151W and F140Y/T151W have been expressed in Escherichia coli, and reactivated to yield active enzymes. Single-point mutations introducing additional aromatic amino acid residues at the surface of TOP exhibit a significant effect on the enzyme catalytic activity and stability as judged by the results of steady-state and transient kinetics studies. TOP T151W is up to 4-fold more active towards a number of aromatic substrates including luminol, whereas TOP F140Y is 2-fold more stable against thermal inactivation and 8-fold more stable in the reaction course. These steady-state observations have been rationalized with the help of transient kinetic studies on the enzyme reaction with hydrogen peroxide in a single turnover regime. The stopped-flow data reveal (a) an increased stability of F140Y Compound I towards hydrogen peroxide, and thus, a higher operational stability as compared to the wild-type enzyme, and (b) a lesser leakage of oxidative equivalents from TOP T151W Compound I resulting in the increased catalytic activity. The results obtained show that TOP unique properties can be further improved for practical applications by site-directed mutagenesis.

  7. Aromatic site description of soot particles

    SciTech Connect

    Celnik, Matthew; Raj, Abhijeet; West, Richard; Patterson, Robert; Kraft, Markus

    2008-10-15

    A new, advanced soot particle model is developed that describes soot particles by their aromatic structure, including functional site descriptions and a detailed surface chemistry mechanism. A methodology is presented for the description of polyaromatic hydrocarbon (PAH) structures by their functional sites. The model is based on statistics that describe aromatic structural information in the form of easily computed correlations, which were generated using a kinetic Monte Carlo algorithm to study the growth of single PAH molecules. A comprehensive surface reaction mechanism is presented to describe the growth and desorption of aromatic rings on PAHs. The model is capable of simulating whole particle ensembles which allows bulk properties such as soot volume fraction and number density to be found, as well as joint particle size and surface area distributions. The model is compared to the literature-standard soot model [J. Appel, H. Bockhorn, M. Frenklach, Combust. Flame 121 (2000) 122-136] in a plug-flow reactor and is shown to predict well the experimental results of soot mass, average particle size, and particle size distributions at different flow times. Finally, the carbon/hydrogen ratio and the distribution of average PAH sizes in the ensemble, as predicted by the model, are discussed. (author)

  8. Metabolic activation of aromatic amines and azo dyes.

    PubMed

    Bartsch, H

    1981-01-01

    Aromatic amines, amides and nitro compounds are a class of chemicals that produce tumors in a wide variety of tissues in experimental animals, including liver, urinary bladder, forestomach, small intestine, Zymbal's gland, subcutaneous tissue or skin. In man, exposure to some aromatic amines is associated with tumours of the urinary bladder and carcinoma of the renal pelvis. Their biological activity as carcinogens or genotoxic agents is, in all the cases that have been studied in detail, dependent on metabolic activation in vivo, occurring by multiple pathways. Differences in these metabolic pathways may largely account for the differences in tissues and species susceptibilities to cancer induction. Carcinogenicity of aromatic amines or amides is dependent on their oxidation to N-hydroxy derivatives, whilst the carcinogenicity of aromatic nitro compounds is linked to their reduction to hydroxylamines. Further conversion of the N-hydroxylamine or N-hydroxyamide to reactive intermediates can occur in several ways, which include (i) esterification of the N-hydroxy group, (ii) non-enzymic protonation of the nitrogen of the hydroxylamine and (iii) oxidation to a free radical of arylhydroxamic acids. Following generation of such reactive electrophilic intermediates in tissues or cells, macromolecular binding has been observed to nucleic acids and proteins. In many cases, arylamidated and arylaminated products are formed with nucleic acid bases; in the case of the well-studied 2-acetylaminofluorene, nucleophilic atoms of guanine are the predominant site of reaction. Relatively little is known of the structure and biological consequences of DNA adducts formed from other aromatic amines, amides or nitro compounds; more research in these directions is warranted.

  9. Evaluation of antibacterial activity of synthetic aliphatic and aromatic monoacylglycerols.

    PubMed

    Batovska, Daniela; Todorova, Iva; Parushev, Stoyan; Tsvetkova, Iva; Najdenski, Hristo; Ubukata, Makoto

    2008-01-01

    The antibacterial activity of synthetic aliphatic and aromatic monoacylglycerols (MAGs) was studied against two human pathogens: Staphylococcus aureus and Escherichia coli. The active compounds inhibited selectively S. aureus. The most active compounds amongst them were those with medium size aliphatic chain and aromatic MAGs with electron withdrawing substituents at the aryl ring. The introduction of one or two-carbon spacer between the aryl ring and the carboxylic function did not influence antibacterial effectiveness. PMID:19004249

  10. Structure-Activity Relationships in Nitro-Aromatic Compounds

    NASA Astrophysics Data System (ADS)

    Vogt, R. A.; Rahman, S.; Crespo-Hernández, C. E.

    Many nitro-aromatic compounds show mutagenic and carcinogenic properties, posing a potential human health risk. Despite this potential health hazard, nitro-aromatic compounds continue to be emitted into ambient air from municipal incinerators, motor vehicles, and industrial power plants. As a result, understanding the structural and electronic factors that influence mutagenicity in nitro-aromatic compounds has been a long standing objective. Progress toward this goal has accelerated over the years, in large part due to the synergistic efforts among toxicology, computational chemistry, and statistical modeling of toxicological data. The concerted influence of several structural and electronic factors in nitro-aromatic compounds makes the development of structure-activity relationships (SARs) a paramount challenge. Mathematical models that include a regression analysis show promise in predicting the mutagenic activity of nitro-aromatic compounds as well as in prioritizing compounds for which experimental data should be pursued. A major challenge of the structure-activity models developed thus far is their failure to apply beyond a subset of nitro-aromatic compounds. Most quantitative structure-activity relationship papers point to statistics as the most important confirmation of the validity of a model. However, the experimental evidence shows the importance of the chemical knowledge in the process of generating models with reasonable applicability. This chapter will concisely summarize the structural and electronic factors that influence the mutagenicity in nitro-aromatic compounds and the recent efforts to use quantitative structure-activity relationships to predict those physicochemical properties.

  11. [Inhibition of aromatics on ammonia-oxidizing activity of sediment].

    PubMed

    Dong, Chun-hong; Hu, Hong-ying; Wei, Dong-bin; Huang, Xia; Qian, Yi

    2004-03-01

    The inhibition of 24 aromatics on ammonia-oxidizing activity of nitrifying bacteria in sediment was measured. The effects of the kind, number and position of substituted groups on ammonia-oxidizing activity of nitrifying bacteria were discussed. The inhibition of mono-substituted benzenes on ammonia-oxidizing activity of nitrifying bacteria were in order of -OH > -NO2 > -NH2 > -Cl > -CH3 > -H. The position of substituted groups of di-substituted benzenes also affected the inhibition, and the inhibitions of dimethylbenzenes(xylene) were in order of meta-> ortho-> para-. The increase in number of substituted group on benzene-ring enhanced the inhibition of aromatics studied in this study on nitrifying bacteria. There was a linear relationship between inhibition (IC50, mumol.L-1) of aromatics on ammonia-oxidizing activity and total electronegativity (sigma E) of aromatics: lgIC50 = 14.72 - 0.91 sigma E.

  12. Palladium-catalyzed regioselective intramolecular coupling of o-carborane with aromatics via direct cage B-H activation.

    PubMed

    Quan, Yangjian; Xie, Zuowei

    2015-03-18

    Palladium-catalyzed intramolecular coupling of o-carborane with aromatics via direct cage B-H bond activation has been achieved, leading to the synthesis of a series of o-carborane-functionalized aromatics in high yields with excellent regioselectivity. In addition, the site selectivity can also be tuned by the substituents on cage carbon atom.

  13. Synthesis and anti-inflammatory activity of aromatic glucosinolates.

    PubMed

    Vo, Quan V; Trenerry, Craige; Rochfort, Simone; Wadeson, Jenny; Leyton, Carolina; Hughes, Andrew B

    2013-10-01

    Aromatic GLs are important members of the glucosinolate family of compounds because of their potential biological activity and medicinal properties. This study has shown success in the high yielding synthesis of some important aromatic GLs as well as the results of testing for anti-inflammatory properties of the synthetic GLs. 3,4-Dimethoxyphenylglucosinolate was found to be the most active anti-inflammatory of the seven glucosinolates assayed. PMID:23978357

  14. Probing the aromatic-donor-binding site of horseradish peroxidase using site-directed mutagenesis and the suicide substrate phenylhydrazine.

    PubMed

    Gilfoyle, D J; Rodriguez-Lopez, J N; Smith, A T

    1996-03-01

    The haem groups from two classes of site-directed mutants of horseradish peroxidase isoenzyme C (HRP-C) (distal haem pocket mutants, [H42L]HRP-C* and [R38K]-HRP-C* and peripheral-haem-access-channel mutants, [F142A]HRP-C* and [F143A]HRP-C*) were extracted and analysed by reverse-phase HPLC after phenylhydrazine-induced suicide inactivation. The relative abundance of the two covalently modified haems, C20-phenyl (delta-meso phenyl) and C18-hydroxymethyl haem, provided a sensitive topological probe for changes induced in the protein architecture in the vicinity of the haem active site and substrate-access channel. Although differing considerably in their efficiency as peroxidases ([H42L]HRP-C* exhibited only approximately 0.03% of the peroxidase activity of wild type), the variants studied gave rise to a modification pattern typical of an exposed haem edge thereby strengthening the argument that it is the overall protein topology rather than the intrinsic catalytic activity of the active site that determines the sites of covalent haem modification. Mutants which showed impaired ability to bind the aromatic donor benzhydroxamic acid were less readily modified by the phenyl radical at the haem C18-methyl position although the level of arylation at the haem C20 position remained remarkable constant. Our findings suggest that the overall efficacy of haem modification catalysed by HRP-C during turnover with phenylhydrazine and its vulnerability towards inactivation are related to its general ability to bind aromatic donor molecules. Results from phenylhydrazine treatment of HRP-C wild-type and mutant variants were compared with those obtained for Coprinus cinereus peroxidase, an enzyme which from its structure is known to have a remarkably open access channel to the haem edge. We show evidence that C. cinereus peroxidase is able to bind benzhydroxamic acid, albeit with a relatively high Kd (Kd 3.7 mM), a probe for aromatic-donor binding. We suggest reasons why

  15. Synthesis and antibacterial activity of pyridinium-tailored aromatic amphiphiles.

    PubMed

    Wang, Peiyi; Gao, Manni; Zhou, Lei; Wu, Zhibing; Hu, Deyu; Hu, Jun; Yang, Song

    2016-02-15

    In this Letter, the antibacterial activities of pyridinium-tailored aromatic amphiphiles were evaluated by turbidimeter tests in vitro. The bioassays revealed that most of the target compounds exhibit appreciable inhibition activities against the plant pathogenic bacteria Xanthomonas oryzae pv. oryzae, Ralstonia solanacearum, and Xanthomonas axonopodis pv. citri. The half-maximal effective concentrations (EC50) of 2-NP-10, 9-AP-10, and 9-AP-7 against these three bacteria were relatively high, which may be ascribed to the favourable hydrophobicity/hydrophilicity balance in these compounds. Our results suggest that pyridinium-tailored aromatic amphiphiles are promising bactericide candidates against plant bacterial diseases. PMID:26832217

  16. Synthesis and antibacterial activity of pyridinium-tailored aromatic amphiphiles.

    PubMed

    Wang, Peiyi; Gao, Manni; Zhou, Lei; Wu, Zhibing; Hu, Deyu; Hu, Jun; Yang, Song

    2016-02-15

    In this Letter, the antibacterial activities of pyridinium-tailored aromatic amphiphiles were evaluated by turbidimeter tests in vitro. The bioassays revealed that most of the target compounds exhibit appreciable inhibition activities against the plant pathogenic bacteria Xanthomonas oryzae pv. oryzae, Ralstonia solanacearum, and Xanthomonas axonopodis pv. citri. The half-maximal effective concentrations (EC50) of 2-NP-10, 9-AP-10, and 9-AP-7 against these three bacteria were relatively high, which may be ascribed to the favourable hydrophobicity/hydrophilicity balance in these compounds. Our results suggest that pyridinium-tailored aromatic amphiphiles are promising bactericide candidates against plant bacterial diseases.

  17. Impact of dietary aromatic amino acids on osteoclastic activity.

    PubMed

    Refaey, Mona El; Zhong, Qing; Ding, Ke-Hong; Shi, Xing-Ming; Xu, Jianrui; Bollag, Wendy B; Hill, William D; Chutkan, Norman; Robbins, Richard; Nadeau, Hugh; Johnson, Maribeth; Hamrick, Mark W; Isales, Carlos M

    2014-08-01

    We had shown that aromatic amino acid (phenylalanine, tyrosine, and tryptophan) supplementation prevented bone loss in an aging C57BL/6 mice model. In vivo results from the markers of bone breakdown suggested an inhibition of osteoclastic activity or differentiation. To assess osteoclastic differentiation, we examined the effects of aromatic amino acids on early /structural markers as vitronectin receptor, calcitonin receptor, and carbonic anhydrase II as well as, late/functional differentiation markers; cathepsin K and matrix metalloproteinase 9 (MMP-9). Our data demonstrate that the aromatic amino acids down-regulated early and late osteoclastic differentiation markers as measured by real time PCR. Our data also suggest a link between the vitronectin receptor and the secreted cathepsin K that both showed consistent effects to the aromatic amino acid treatment. However, the non-attachment related proteins, calcitonin receptor, and carbonic anhydrase II, demonstrated less consistent effects in response to treatment. Our data are consistent with aromatic amino acids down-regulating osteoclastic differentiation by suppressing remodeling gene expression thus contributing initially to the net increase in bone mass seen in vivo.

  18. Enumeration of aromatic oxygenase genes to evaluate monitored natural attenuation at gasoline-contaminated sites.

    PubMed

    Baldwin, Brett R; Nakatsu, Cindy H; Nies, Loring

    2008-02-01

    Monitoring groundwater benzene, toluene, ethylbenzene, and xylene (BTEX) concentrations is the typical method to assess monitored natural attenuation (MNA) and bioremediation as corrective actions at gasoline-contaminated sites. Conclusive demonstration of bioremediation, however, relies on converging lines of chemical and biological evidence to support a decision. In this study, real-time PCR quantification of aromatic oxygenase genes was used to evaluate the feasibility of MNA at two gasoline-impacted sites. Phenol hydroxylase (PHE), ring-hydroxylating toluene monooxygenase (RMO), naphthalene dioxygenase (NAH), toluene monooxygenase (TOL), toluene dioxygenase (TOD), and biphenyl dioxygenase (BPH4) genes were routinely detected in BTEX-impacted wells. Aromatic oxygenase genes were not detected in sentinel wells outside the plume indicating that elevated levels of oxygenase genes corresponded to petroleum hydrocarbon contamination. Total aromatic oxygenase gene copy numbers detected in impacted wells were on the order of 10(6)-10(9)copies L(-1). PHE, RMO, NAH, TOD, and BPH4 gene copies positively correlated to total BTEX concentration. Mann-Kendall analysis of benzene concentrations was used to evaluate the status of the dissolved BTEX plume. The combination of trend analysis of contaminant concentrations with quantification of aromatic oxygenase genes was used to assess the feasibility of MNA as corrective measures at both sites.

  19. Lactoperoxidase-catalyzed activation of carcinogenic aromatic and heterocyclic amines.

    PubMed

    Gorlewska-Roberts, Katarzyna M; Teitel, Candee H; Lay, Jackson O; Roberts, Dean W; Kadlubar, Fred F

    2004-12-01

    Lactoperoxidase, an enzyme secreted from the human mammary gland, plays a host defensive role through antimicrobial activity. It has been implicated in mutagenic and carcinogenic activation in the human mammary gland. The potential role of heterocyclic and aromatic amines in the etiology of breast cancer led us to examination of the lactoperoxidase-catalyzed activation of the most commonly studied arylamine carcinogens: 2-amino-1-methyl-6-phenylimidazo[4,5-b]-pyridine (PhIP), benzidine, 4-aminobiphenyl (ABP), 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), and 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx). In vitro activation was performed with lactoperoxidase (partially purified from bovine milk or human milk) in the presence of hydrogen peroxide and calf thymus DNA. Products formed during enzymatic activation were monitored by HPLC with ultraviolet and radiometric detection. Two of these products were characterized as hydrazo and azo derivatives by means of mass spectrometry. The DNA binding level of 3H- and 14C-radiolabeled amines after peroxidase-catalyzed activation was dependent on the hydrogen peroxide concentration, and the highest levels of carcinogen binding to DNA were observed at 100 microM H2O2. Carcinogen activation and the level of binding to DNA were in the order of benzidine > ABP > IQ > MeIQx > PhIP. One of the ABP adducts was identified, and the level at which it is formed was estimated to be six adducts/10(5) nucleotides. The susceptibility of aromatic and heterocyclic amines for lactoperoxidase-catalyzed activation and the binding levels of activated products to DNA suggest a potential role of lactoperoxidase-catalyzed activation of carcinogens in the etiology of breast cancer.

  20. Effects of ozonation on mutagenic activity of polycyclic aromatic hydrocarbons

    SciTech Connect

    Fouillet, B.; Chambon, P.; Chambon, R. ); Castegnaro, M. ); Weill, N. )

    1991-07-01

    In this study, four polycyclic aromatic hydrocarbons were tested. Benzo(a)pyrene (B(a)P), Chrysene (CH), 7,12-dimethylbenzo(a)-anthracene (DMBA) and 3-methylcholanthrene (MCA) in hexane were treated with ozone to determine the effectiveness of degradation and to evaluate the genetic properties of ozone byproducts. Two types of ozonation were carried out: partial ozonation and total ozonation. The disappearance of parent compounds and the appearance of ozone byproducts were measured by high performance liquid chromatography (HPLC) coupled with spectrofluorimetry and U.V. spectrophotometry. Plate incorporation mutagenicity assay, using a Salmonella typhimurium strain, was used to test the ozone byproducts with and without metabolic activation.

  1. ANSID: a Solid-Phase Proteomic Approach for Identification and Relative Quantification of Aromatic Nitration Sites

    NASA Astrophysics Data System (ADS)

    Nuriel, Tal; Whitehouse, Julia; Ma, Yuliang; Mercer, Emily; Brown, Neil; Gross, Steven

    2015-12-01

    Nitration of tyrosine and other aromatic amino acid residues in proteins occurs in the setting of inflammatory, neurodegenerative and cardiovascular diseases – importantly, this modification has been implicated in the pathogenesis of diverse diseases and the physiological process of tissue aging. To understand the biological consequences of aromatic nitration in both health and disease, it is critical to molecularly identify the proteins that undergo nitration, specify their cognate modification sites and quantify their extent of nitration. To date, unbiased identification of nitrated proteins has painstakingly employed 2D-gel electrophoresis followed by Western Blotting with an anti-nitrotyrosine antibody for detection. Apart from being relatively slow and laborious, this method suffers from limited coverage, the potential for false-positive identifications and failure to reveal specific amino acid modification sites. To overcome these shortcomings, we have developed a solid-phase, chemical-capture approach for unbiased and high-throughput discovery of nitrotyrosine and nitrotryptophan sites in proteins. Utilizing this method, we have successfully identified several endogenously nitrated proteins in rat brain and a total of 244 nitrated peptides from 145 proteins following in vitro exposure of rat brain homogenates to the nitrating agent peroxynitrite (1 mM). As expected, Tyr residues constituted the great majority of peroxynitrite-mediated protein nitration sites; however, we were surprised to discover several brain proteins that contain nitrated Trp residues. By incorporating a stable-isotope labeling step, this new Aromatic Nitrtion Site IDentification (ANSID) method was also adapted for relative quantification of nitration site abundances in proteins. Application of the quantitative ANSID method offers great potential to advance our understanding of the role of protein nitration in disease pathogenesis and normal physiology.

  2. ANSID: a Solid-Phase Proteomic Approach for Identification and Relative Quantification of Aromatic Nitration Sites

    NASA Astrophysics Data System (ADS)

    Nuriel, Tal; Whitehouse, Julia; Ma, Yuliang; Mercer, Emily; Brown, Neil; Gross, Steven

    2015-12-01

    Nitration of tyrosine and other aromatic amino acid residues in proteins occurs in the setting of inflammatory, neurodegenerative and cardiovascular diseases - importantly, this modification has been implicated in the pathogenesis of diverse diseases and the physiological process of tissue aging. To understand the biological consequences of aromatic nitration in both health and disease, it is critical to molecularly identify the proteins that undergo nitration, specify their cognate modification sites and quantify their extent of nitration. To date, unbiased identification of nitrated proteins has painstakingly employed 2D-gel electrophoresis followed by Western Blotting with an anti-nitrotyrosine antibody for detection. Apart from being relatively slow and laborious, this method suffers from limited coverage, the potential for false-positive identifications and failure to reveal specific amino acid modification sites. To overcome these shortcomings, we have developed a solid-phase, chemical-capture approach for unbiased and high-throughput discovery of nitrotyrosine and nitrotryptophan sites in proteins. Utilizing this method, we have successfully identified several endogenously nitrated proteins in rat brain and a total of 244 nitrated peptides from 145 proteins following in vitro exposure of rat brain homogenates to the nitrating agent peroxynitrite (1 mM). As expected, Tyr residues constituted the great majority of peroxynitrite-mediated protein nitration sites; however, we were surprised to discover several brain proteins that contain nitrated Trp residues. By incorporating a stable-isotope labeling step, this new Aromatic Nitrtion Site IDentification (ANSID) method was also adapted for relative quantification of nitration site abundances in proteins. Application of the quantitative ANSID method offers great potential to advance our understanding of the role of protein nitration in disease pathogenesis and normal physiology.

  3. The synergic effect between Mo species and acid sites in Mo/HMCM-22 catalysts for methane aromatization.

    PubMed

    Ma, Ding; Zhu, Qingjun; Wu, Zili; Zhou, Danhong; Shu, Yuying; Xin, Qin; Xu, Yide; Bao, Xinhe

    2005-08-21

    The acid properties of Mo/HMCM-22 catalyst, which is the precursor form of the working catalyst for methane aromatization reaction, and the synergic effect between Mo species and acid sites were studied and characterized by various characterization techniques. It is concluded that Brønsted and Lewis acidities of HMCM-22 are modified due to the introduction of molybdenum. We suggest a monomer of Mo species is formed by the exchange of Mo species with the Brønsted acid sites. On the other hand, coordinate unsaturated sites (CUS) are suggested to be responsible for the formation of newly detected Lewis acid sites. Computer modelling is established and coupling with experimental results, it is then speculated that the effective activation of methane is properly accomplished on Mo species accommodated in the 12 MR supercages of MCM-22 zeolite whereas the Brønsted acid sites in the same channel system play a key role for the formation of benzene. A much more pronounced volcano-typed reactivity curve of the Mo/HMCM-22 catalysts, as compared with that of the Mo/HZSM-5, with respect to Mo loading is found and this can be well understood due to the unique channel structure of MCM-22 zeolite and synergic effect between Mo species and acid sites.

  4. Sources, fate, and toxic hazards of oxygenated polycyclic aromatic hydrocarbons (PAHs) at PAH-contaminated sites.

    PubMed

    Lundstedt, Staffan; White, Paul A; Lemieux, Christine L; Lynes, Krista D; Lambert, Iain B; Oberg, Lars; Haglund, Peter; Tysklind, Mats

    2007-09-01

    In this paper we show that oxygenated polycyclic aromatic hydrocarbons (oxy-PAHs) are important cocontaminants that should be taken into account during risk assessment and remediation of sites with high levels of PAHs. The presented data, which have been collected both from our own research and the published literature, demonstrate that oxy-PAHs are abundant but neglected contaminants at these sites. The oxy-PAHs show relatively high persistency and because they are formed through transformation of PAHs, their concentrations in the environment may even increase as the sites are remediated by methods that promote PAH degradation. Furthermore, we show that oxy-PAHs are toxic to both humans and the environment, although the toxicity seems to be manifested through other effects than those known to be important for polycyclic aromatic compounds in general, that is, mutagenicity and carcinogenicity. Finally, we present data that support the hypothesis that oxy-PAHs are more mobile in the environment than PAHs, due to their polarity, and thus have a higher tendency to spread from contaminated sites via surface water and groundwater. We believe that oxy-PAHs should be included in monitoring programs at PAH-contaminated sites, even if a number of other toxicologically relevant compounds that may also be present, such as nitro-PAHs and azaarenes, are not monitored. This is because oxy-PAH levels are difficult to predict from the PAH levels, because their environmental behavior differs substantially from that of PAHs, and oxy-PAHs may be formed as PAHs are degraded.

  5. An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin.

    PubMed

    Karpowich, Nathan K; Song, Jinmei; Wang, Da-Neng

    2016-07-31

    ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA'). We have characterized the structural basis of substrate binding by the EcfS subunit for riboflavin from Thermotoga maritima, TmRibU. TmRibU binds riboflavin with high affinity, and the protein-substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound TmRibU reveals an electronegative binding pocket at the extracellular surface in which the substrate is completely buried. Analysis of the intermolecular contacts indicates that nearly every available substrate hydrogen bond is satisfied. A conserved aromatic residue at the extracellular end of TM5, Tyr130, caps the binding site to generate a substrate-bound, occluded state, and non-conservative mutation of Tyr130 reduces the stability of this conformation. Using a novel fluorescence binding assay, we find that an aromatic residue at this position is essential for high-affinity substrate binding. Comparison with other S subunit structures suggests that TM5 and Loop5-6 contain a dynamic, conserved motif that plays a key role in gating substrate entry and release by S subunits of ECF transporters. PMID:27312125

  6. Probing the role of aromatic residues at the secondary saccharide binding sites of human salivary α-amylase in substrate hydrolysis and bacterial binding

    PubMed Central

    Ragunath, Chandran; Manuel, Suba G.A.; Venkataraman, Venkat; Sait, Hameetha B.R.; Kasinathan, Chinnasamy; Ramasubbu, Narayanan

    2008-01-01

    SUMMARY Human salivary α-amylase (HSAmy) has three distinct functions relevant to oral health: 1) hydrolysis of starch; 2) binding to hydroxyapatite; and 3) binding to bacteria (e.g. viridans streptococci). Although the active site of HSAmy for starch hydrolysis is well characterized, the regions responsible for the bacterial binding are yet to be defined. Since HSAmy possesses several secondary saccharide-binding sites in which aromatic residues are prominently located, we hypothesized that one or more of the secondary saccharide binding sites harboring the aromatic residues may play an important role in bacterial binding. To test this hypothesis, the aromatic residues at five secondary binding sites were mutated to alanine to generate six mutants representing either single (W203A, Y276A and W284A), double (Y276A/W284A and W316A/W388A) or multiple (HSAmy-ar; W134A/W203A/Y276A/W284A/W316A/W388A) mutations. The crystal structure of HSAmy-ar was determined at a resolution of 1.5 Å as an acarbose complex and compared with the existing wild type acarbose complex. The wild type and the mutant enzymes were characterized for their abilities to exhibit enzyme activity, starch binding, hydroxyapatite and bacterial binding activities. Our results clearly showed that 1) mutation of aromatic residues does not alter the overall conformation of the molecule; 2) the single or double mutants showed either moderate or minimal changes in both starch and bacterial binding activities activity whereas the HSAmy-ar showed significant reduction in these activities; 3) the starch hydrolytic activity was reduced 10-fold in HSAmy-ar; 4) oligosaccharide hydrolytic activity was reduced in all the mutants but the action pattern was similar to that of the wild type enzyme; and 5) the hydroxyaptite binding was unaffected in HSAmy-ar. These results clearly show that the aromatic residues at the secondary saccharide binding sites in HSAmy play a critical role in bacterial binding and starch

  7. Antibacterial activity of phenolic compounds and aromatic alcohols.

    PubMed

    Lucchini, J J; Corre, J; Cremieux, A

    1990-05-01

    The antibacterial properties of phenolic compounds and aromatic alcohols (growth inhibition, lethal effect and cytological damage) were investigated. The role of protein and RNA synthesis in the bactericidal action was also determined. All compounds tested demonstrated lethal properties and the ability to alter membranes, especially in Gram-negative bacteria. Efficacious concentrations, however, varied greatly among the compounds. These data corroborate previous findings which suggest that the mechanism of action of these compounds is related to their lipophilia. Moreover, since it was demonstrated that the lethal effect of two aromatic alcohols (phenethyl alcohol and benzyl alcohol) stops when protein synthesis is inhibited, it is likely that both possess specific mechanisms of action.

  8. Polycyclic aromatic hydrocarbons (PAHs) in atmospheric urban area: monitoring on various types of sites.

    PubMed

    Dejean, Solène; Raynaud, Christine; Meybeck, Mariam; Della Massa, Jean-Pierre; Simon, Valérie

    2009-01-01

    The air quality over the Toulouse urban area (France) is recorded daily by the regional "Midi-Pyrénées" atmospheric pollution measurements network (ORAMIP). Relevant data is collected from about 100 analysers spread over more than thirty stations. The regulations covering major indicators of atmospheric pollution (ozone, nitrogen dioxide, sulphur dioxide) have been updated in recent years to include additional compounds like polycyclic aromatic hydrocarbons (PAHs). The ORAMIP, in partnership with the ENSIACET has undertaken background PAH average concentration measurements over the urban agglomeration of Toulouse during spring 2006 for various types of sites (traffic, urban, industrial). The sampling was performed using a low volume air sampler equipped with quartz fiber filters and polyurethane foams For the two urban sites, total atmospheric concentrations between 12 and 20 ng/m(3) have been obtained, whereas for the industrial site the values averaged 22 ng/m(3). In addition, and regardless of site, the average concentrations of benzo[a]pyrene, at present the only regulated PAH, were always less than the 1 ng/m(3) limit.

  9. Temporal variability of Polycyclic Aromatic Hydrocarbons in a receptor site of Puebla -Tlaxcala Valley.

    NASA Astrophysics Data System (ADS)

    Padilla Barrera, Zuhelen; Torres Jardón, Ricardo; Gerardo Ruiz, Luis; Castro, Telma

    2015-04-01

    The Puebla-Tlaxcala Valley is a region with high population scattered over two states, where emissions from combustion of a variety of materials and fuels represent a major problem in the deterioration of air quality. Polycyclic aromatic hydrocarbons (PAHs) are a class of semi-volatile organic compounds that are formed during combustion. PAH are present in large amounts in the particulate matter comes from the combustion and no combustion. The particle-bound PAHs are formed by accumulation and condensation mechanisms in the particle. In its condensed form are mainly associated with fine particles (< 0.10 um). The major emission sources of PAHs are open burning, industrial boilers and emission from cars and trucks. Emission rates of PAHs vary significantly depending on vehicle use: fuel type, engine type and catalytic converter, and once emitted into the atmosphere, particulate PAHs may undergo transformation by photo-oxidation. The measurements were made with a photoelectric aerosol sensor (PAS 2000 CE) and a diffusion charger (DC 2000 CE), the first determines the concentration of PAHs, while the second determines the active surface of particles. The use of these two sensors in parallel is a useful tool to identify quantitatively the greatest source of emission, describe the physical and chemical characteristics of the particles. Correlations between PAHs with the active surface (DC), NOy and CO, together with an analysis of weather atmospheric transport to approximate the possible origin of these particles. The coefficient PAHs / DC associated with the backward trajectory analysis is a tool to identify potential areas of emission. The correlation between PAHs and NOx reflects emissions associated with diesel combustion, while the correlation between PAHs and CO, combustion of gasoline. Concentration patterns were recorded over 24 hours in both PAHs and DC. The average concentration of PAHs was 4.9 ng/m3 and the maximum of 81.9 ng/m3 , while the average active

  10. Gaseous and particulate polycyclic aromatic hydrocarbons at the Gosan background site in East Asia

    NASA Astrophysics Data System (ADS)

    Kim, J. Y.; Lee, J. Y.; Choi, S.-D.; Kim, Y. P.; Ghim, Y. S.

    2012-03-01

    The seasonal intensive field measurements of gaseous and particulate polycyclic aromatic hydrocarbons (PAHs) were carried out at the Gosan international background site from November 2001 to August 2003. The annual average concentrations of gaseous and particulate PAHs are 1.4 ng m-3 and 2.9 ng m-3 (∑14PAH), respectively. Distinct seasonal variations exist with the highest concentration in winter and the lowest concentration in summer. In comparison with other places in Korea and other countries, the most distinguishing features at Gosan are the significantly low concentrations of low-molecular weight gaseous PAHs. In addition, noticeably high particulate PAH concentrations measured at urban and background areas in Korea could represent the regional characteristics of East Asia under the influence of high emission from China. The BaP equivalent concentrations (BaPeq) at Gosan, which are based on the US EPA's toxicity equivalency factors for carcinogenic PAHs, are much higher than those at coastal or background sites in USA and Europe, and even comparable with that at urban sites in Europe. The possibility of more aged PAHs in the atmosphere associated with the long range transport of PAHs during winter period was suggested. It was found that larger fraction of non-exchangeable PAHs had strong influence to the gas/particle partitioning of PAHs at Gosan.

  11. Annulation of aromatic imines via directed C-H bond activation.

    PubMed

    Thalji, Reema K; Ahrendt, Kateri A; Bergman, Robert G; Ellman, Jonathan A

    2005-08-19

    A directed C-H bond activation approach to the synthesis of indans, tetralins, dihydrofurans, dihydroindoles, and other polycyclic aromatic compounds is presented. Cyclization of aromatic ketimines and aldimines containing alkenyl groups tethered at the meta position relative to the imine directing group has been achieved using (PPh3)3RhCl (Wilkinson's catalyst). The cyclization of a range of aromatic ketimines and aldimines provides bi- and tricyclic ring systems with good regioselectivity. Different ring sizes and substitution patterns can be accessed through the coupling of monosubstituted, 1,1- or 1,2-disubstituted, and trisubstituted alkenes bearing both electron-rich and electron-deficient functionality.

  12. Seawater Polluted with Highly Concentrated Polycyclic Aromatic Hydrocarbons Suppresses Osteoblastic Activity in the Scales of Goldfish, Carassius auratus.

    PubMed

    Suzuki, Nobuo; Sato, Masayuki; Nassar, Hossam F; Abdel-Gawad, Fagr Kh; Bassem, Samah M; Yachiguchi, Koji; Tabuchi, Yoshiaki; Endo, Masato; Sekiguchi, Toshio; Urata, Makoto; Hattori, Atsuhiko; Mishima, Hiroyuki; Shimasaki, Youhei; Oshima, Yuji; Hong, Chun-Sang; Makino, Fumiya; Tang, Ning; Toriba, Akira; Hayakawa, Kazuichi

    2016-08-01

    We have developed an original in vitro bioassay using teleost scale, that has osteoclasts, osteoblasts, and bone matrix as each marker: alkaline phosphatase (ALP) for osteoblasts and tartrate-resistant acid phosphatase (TRAP) for osteoclasts. Using this scale in vitro bioassay, we examined the effects of seawater polluted with highly concentrated polycyclic aromatic hydrocarbons (PAHs) and nitro-polycyclic aromatic hydrocarbons (NPAHs) on osteoblastic and osteoclastic activities in the present study. Polluted seawater was collected from two sites (the Alexandria site on the Mediterranean Sea and the Suez Canal site on the Red Sea). Total levels of PAHs in the seawater from the Alexandria and Suez Canal sites were 1364.59 and 992.56 ng/l, respectively. We were able to detect NPAHs in both seawater samples. Total levels of NPAHs were detected in the seawater of the Alexandria site (12.749 ng/l) and the Suez Canal site (3.914 ng/l). Each sample of polluted seawater was added to culture medium at dilution rates of 50, 100, and 500, and incubated with the goldfish scales for 6 hrs. Thereafter, ALP and TRAP activities were measured. ALP activity was significantly suppressed by both polluted seawater samples diluted at least 500 times, but TRAP activity did not change. In addition, mRNA expressions of osteoblastic markers (ALP, osteocalcin, and the receptor activator of the NF-κB ligand) decreased significantly, as did the ALP enzyme activity. In fact, ALP activity decreased on treatment with PAHs and NPAHs. We conclude that seawater polluted with highly concentrated PAHs and NPAHs influences bone metabolism in teleosts. PMID:27498800

  13. PHOTOACTIVATED TOXICITY IN AMPHIPODS COLLECTED FROM POLYCYCLIC AROMATIC HYDROCARBON-CONTAMINATED SITES

    EPA Science Inventory

    The risk of photo-activated PAH toxicity in contaminated aquatic systems has not been well characterized. To better indicate this potential, amphipods (Gammarus spp.) were collected from two PAH contaminated sites (Hog Island and USX), as well as a reference site (Chipmunk Cove)...

  14. DEPENDENCY OF POLYCHLORINATED BIPHENYL AND POLYCYCLIC AROMATIC HYDROCARBON BIOACCUMULATION IN MYA ARENARIA ON BOTH WATER COLUMN AND SEDIMENT BED CHEMICAL ACTIVITIES

    EPA Science Inventory

    The bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) by the filter-feeding soft-shell clam Mya arenaria was evaluated at three sites near Boston (MA, USA) by assessing the chemical activities of those hydrophobic organic compounds (H...

  15. The gas/particle partitioning of polycyclic aromatic hydrocarbons collected at a sub-Arctic site in Canada

    NASA Astrophysics Data System (ADS)

    Sofowote, Uwayemi M.; Hung, Hayley; Rastogi, Ankit K.; Westgate, John N.; Su, Yushan; Sverko, Ed; D'Sa, Ivy; Roach, Pat; Fellin, Phil; McCarry, Brian E.

    2010-12-01

    Polycyclic aromatic hydrocarbons (PAH) were measured in air samples at a remote air monitoring site established in the Yukon Territory, Canada as part of a global project (International Polar Year; IPY) to study the potential for atmospheric long-range transport of anthropogenic pollutants to the Arctic. Gas- and particle-phase PAH were collected in polyurethane foam plugs and on glass fibre filters respectively from August 2007 to October 2009. PAH concentrations were found to be highest in the winter months and lowest in summer. The gas/particle partitioning coefficients of 3-5 ringed PAH were computed and seasonal averages were compared. In the summer time, lower molecular mass PAH exhibited relatively higher partitioning into the particle-phase. This particle-phase partitioning led to the shallowest slopes being recorded during summer for the log-log correlation plots between the PAH partition coefficients and their sub-cooled vapour pressures. Air mass back trajectories suggest that local impacts may be more important during the summer time which is marked by increased camping activities at camping sites in the proximity of the sampling station. In conclusion, both summer and wintertime variations in PAH concentrations and gas/particle partitioning are considered to be source- and phototransformation-dependent rather than dependent on temperature-driven shifts in equilibrium partitioning.

  16. Thiolates Chemically Induce Redox Activation of BTZ043 and Related Potent Nitro Aromatic Anti-Tuberculosis Agents

    PubMed Central

    Tiwari, Rohit; Moraski, Garrett C.; Krchňák, Viktor; Miller, Patricia A.; Colon-Martinez, Mariangelli; Herrero, Eliza; Oliver, Allen G.; Miller, Marvin J.

    2013-01-01

    The development of multidrug resistant (MDR) and extensively drug resistant (XDR) forms of tuberculosis (TB) has stimulated research efforts globally to expand the new drug pipeline. Nitro aromatic compounds, including 1, 3-Benzothiazin-4-ones (BTZs) and related agents, are a promising new class for the treatment of TB. Research has shown that the nitroso intermediates of BTZs that are generated in vivo cause suicide inhibition of decaprenylphosphoryl-β-D-ribose 2′ oxidase (DprE1), which is responsible for cell wall arabinogalactan biosynthesis. We have designed and synthesized novel anti-TB agents inspired from BTZs and other nitroaromatic compounds. Computational studies indicated that the unsubstituted aromatic carbons of BTZ043 and related nitroaromatic compounds are the most electron deficient and might be prone to nucleophilic attack. Our chemical studies on BTZ043 and the additional nitro aromatic compounds synthesized by us and the others confirmed the postulated reactivity. The results indicate that nucleophiles such as thiolates, cyanide and hydride induce non-enzymatic reduction of the nitro groups present in these compounds to the corresponding nitroso intermediates by addition at the unsubstituted electron deficient aromatic carbon present in these compounds. Furthermore we demonstrate here that these compounds are good candidates for the classical von Richter reaction. These chemical studies offer an alternate hypotheses for the mechanism of action of nitro aromatic anti-TB agents in that the cysteine thiol(ate) or a hydride source at the active site of DprE1 may trigger the reduction of the nitro groups in a manner similar to the von Richter reaction to the nitroso intermediates, to initiate the inhibition of DprE1. PMID:23402278

  17. Toxicity of N-substituted aromatics to acetoclastic methanogenic activity in granular sludge.

    PubMed Central

    Donlon, B A; Razo-Flores, E; Field, J A; Lettinga, G

    1995-01-01

    N-substituted aromatics are important priority pollutants entering the environment primarily through anthropogenic activities associated with the industrial production of dyes, explosives, pesticides, and pharmaceuticals. Anaerobic treatment of wastewaters discharged by these industries could potentially be problematical as a result of the high toxicity of N-substituted aromatics. The objective of this study was to examine the structure-toxicity relationships of N-substituted aromatic compounds to acetoclastic methanogenic bacteria. The toxicity was assayed in serum flasks by measuring methane production in granular sludge. Unacclimated cultures were used to minimize the biotransformation of the toxic organic chemicals during the test. The nature and the degree of the aromatic substitution were observed to have a profound effect on the toxicity of the test compound. Nitroaromatic compounds were, on the average, over 500-fold more toxic than their corresponding aromatic amines. Considering the facile reduction of nitro groups by anaerobic microorganisms, a dramatic detoxification of nitroaromatics towards methanogens can be expected to occur during anaerobic wastewater treatment. While the toxicity exerted by the N-substituted aromatic compounds was closely correlated with compound apolarity (log P), it was observed that at any given log P, N-substituted phenols had a toxicity that was 2 orders of magnitude higher than that of chlorophenols and alkylphenols. This indicates that toxicity due to the chemical reactivity of nitroaromatics is much more important than partitioning effects in bacterial membranes. PMID:8526501

  18. Salt site performance assessment activities

    SciTech Connect

    Kircher, J.F.; Gupta, S.K.

    1983-01-01

    During this year the first selection of the tools (codes) for performance assessments of potential salt sites have been tentatively selected and documented; the emphasis has shifted from code development to applications. During this period prior to detailed characterization of a salt site, the focus is on bounding calculations, sensitivity and with the data available. The development and application of improved methods for sensitivity and uncertainty analysis is a focus for the coming years activities and the subject of a following paper in these proceedings. Although the assessments to date are preliminary and based on admittedly scant data, the results indicate that suitable salt sites can be identified and repository subsystems designed which will meet the established criteria for protecting the health and safety of the public. 36 references, 5 figures, 2 tables.

  19. Risk Assessment Related to Atmospheric Polycyclic Aromatic Hydrocarbons in Gas and Particle Phases near Industrial Sites

    PubMed Central

    Ramírez, Noelia; Cuadras, Anna; Marcé, Rosa Maria

    2011-01-01

    Background: Inhalation is one of the main means of human exposure to polycyclic aromatic hydrocarbons (PAHs) because of their ubiquitous presence in the atmosphere. However, most studies have considered only PAHs found in the particle phase and have omitted the contribution of the gas-phase PAHs to the risk. Objective: We estimated the lifetime lung cancer risk from PAH exposure by inhalation in people living next to the largest chemical site in Southern Europe and the Mediterranean area. Methods: We determined 18 PAHs in the atmospheric gas and particle phase. We monitored the PAHs for 1 year in three locations near the chemical site in different seasons. We used toxic equivalence factors to calculate benzo[a]pyrene (BaP) equivalents (BaP-eq) for individual PAHs and applied the World Health Organization unit risk (UR) for BaP (UR = 8.7 × 10–5) to estimate lifetime cancer risks due to PAH exposures. Results: We observed some spatial and seasonal variability in PAH concentrations. The contribution of gas-phase PAHs to the total BaP-eq value was between 34% and 86%. The total estimated average lifetime lung cancer risk due to PAH exposure in the study area was 1.2 × 10–4. Conclusions: The estimated risk was higher than values recommended by the World Health Organization and U.S. Environmental Protection Agency but lower than the threshold value of 10–3 that is considered an indication of definite risk according to similar risk studies. The results also showed that risk may be underestimated if the contributions of gas-phase PAHs are not considered. PMID:21478082

  20. Antihyperlipidemic morpholine derivatives with antioxidant activity: An investigation of the aromatic substitution.

    PubMed

    Ladopoulou, Eleni M; Matralis, Alexios N; Nikitakis, Anastasios; Kourounakis, Angeliki P

    2015-11-01

    Drugs affecting more than one target could result in a more efficient treatment of multifactorial diseases as well as fewer safety concerns, compared to a one-drug one-target approach. Within our continued efforts towards the design of multifunctional molecules against atherosclerosis, we hereby report the synthesis of 17 new morpholine derivatives which structurally vary in terms of the aromatic substitution on the morpholine ring. These derivatives simultaneously suppress cholesterol biosynthesis through SQS inhibition (IC50 values of the most active compounds are between 0.7 and 5.5 μM) while exhibiting a significant protection of hepatic microsomal membranes against lipid peroxidation (with IC50 values for the most active compounds being between 73 and 200 μM). Further evaluation of these compounds was accomplished in vivo in an animal model of acute experimental hyperlipidemia, where it was observed that compounds reduced the examined lipidemic parameters (TC, TG and LDL) by 15-80%. In order to examine the mode of binding of these molecules in the active catalytic site of SQS, we also performed docking simulation studies. Our results indicate that some of the new compounds can be considered interesting structures in the search for new multifunctional agents of potential application in atherosclerosis.

  1. Heterolytic Activation of Hydrogen Promoted by Ruthenium Nanoparticles immobilized on Basic Supports and Hydrogenation of Aromatic Compounds

    NASA Astrophysics Data System (ADS)

    Fang, Minfeng

    Despite the aggressive development and deployment of new renewable and nuclear technologies, petroleum-derived transportation fuels---gasoline, diesel and jet fuels---will continue to dominate the markets for decades. Environmental legislation imposes severe limits on the tolerable proportion of aromatics, sulfur and nitrogen contents in transportation fuels, which is difficult to achieve with current refining technologies. Catalytic hydrogenation plays an important role in the production of cleaner fuels, both as a direct means to reduce the aromatics and as a key step in the hydrodenitrogenation (HDN) and hydrodesulfurization (HDS) processes. However, conventional catalysts require drastic conditions and/or are easily poisoned by S or N aromatics. Therefore, there is still a need for new efficient catalysts for hydrogenation reactions relevant to the production of cleaner fossil fuels. Our catalyst design involves metallic nanoparticles intimately associated with a basic support, with the aim of creating a nanostructure capable of promoting the heterolytic activation of hydrogen and ionic hydrogenation mechanisms, as a strategy to avoid catalyst poisoning and enhance catalytic activity. We have designed and prepared a new nanostructured catalytic material composed of RuNPs immobilized on the basic polymer P4VPy. We have demonstrated that the Ru/P4VPy catalyst can promote heterolytic hydrogen activation and a unique surface ionic hydrogenation mechanism for the efficient hydrogenation of N-aromatics. This is the first time these ionic hydrogenation pathways have been demonstrated on solid surfaces. For the RuNPs surfaces without basic sites in close proximity, the conventional homolytic H2 splitting is otherwise involved. Using the mechanistic concepts from Ru/P4VPy, we have designed and prepared the Ru/MgO catalyst, with the aim to improve the catalytic efficiency for the hydrogenation of heteroatom aromatics operating by the ionic hydrogenation mechanism. The Ru

  2. Trypanocidal activity and selectivity in vitro of aromatic amidine compounds upon bloodstream and intracellular forms of Trypanosoma cruzi.

    PubMed

    De Souza, E M; da Silva, P B; Nefertiti, A S G; Ismail, M A; Arafa, R K; Tao, B; Nixon-Smith, C K; Boykin, D W; Soeiro, M N C

    2011-02-01

    Trypanosoma cruzi is the etiological agent of Chagas disease, an important neglected illness affecting about 12-14 million people in endemic areas of Latin America. The chemotherapy of Chagas disease is quite unsatisfactory mainly due to its poor efficacy especially during the later chronic phase and the considerable well-known side effects. These facts emphasize the need to search for find new drugs. Diamidines and related compounds are minor groove binders of DNA at AT-rich sites and present excellent anti-trypanosomal activity. In the present study, six novel aromatic amidine compounds (arylimidamides and diamidines) were tested in vitro to determine activity against the infective and intracellular stages of T. cruzi, which are responsible for sustaining the infection in the mammalian hosts. In addition, their selectivity and toxicity towards primary cultures of cardiomyocyte were evaluated since these cells represent important targets of infection and inflammation in vivo. The aromatic amidines were active against T. cruzi in vitro, the arylimidamide DB1470 was the most effective compound presenting a submicromolar LD(50) values, good selectivity index, and good activity at 4 °C in the presence of blood constituents. Our results further justify trypanocidal screening assays with these classes of compounds both in vitro and in vivo in experimental models of T. cruzi infection.

  3. Spatiotemporal patterns and source implications of aromatic hydrocarbons at six rural sites across China's developed coastal regions

    NASA Astrophysics Data System (ADS)

    Zhang, Zhou; Zhang, Yanli; Wang, Xinming; Lü, Sujun; Huang, Zhonghui; Huang, Xinyu; Yang, Weiqiang; Wang, Yuesi; Zhang, Qiang

    2016-06-01

    Aromatic hydrocarbons are important anthropogenic precursors of tropospheric ozone and secondary organic aerosols. Here we measured ambient aromatic hydrocarbons from March 2012 to February 2014 at six rural sites in China's developed coastal regions. On average, benzene (B) comprised > 50% of total benzene (B), toluene (T), ethylbenzene (E), and xylenes (X) (BTEX) at sites in the Northeast China Plain (NECP) or in the North China Plain (NCP), whereas T, E, and X accounted for > 77% of total BTEX at sites in the Yangtze River Delta (YRD) and the Pearl River Delta in the south. BTEX at the northern sites was significantly correlated (p < 0.01) with combustion tracer-carbon monoxide (CO) but weakly correlated with traffic marker-methyl tert-butyl ether (MTBE), suggesting that their main sources were coal and biofuel/biomass burning with substantially elevated B levels during the winter heating period. In contrast, BTEX at the southern sites originated mainly from traffic-related and/or industrial emission sources, as indicated by the poor correlations with CO but highly significant (p < 0.01) correlations with MTBE and tetrachloroethylene, an industrial emission tracer. The B/CO emission ratios from measurement agreed within a factor of 2 with that of a previous widely used emission inventory of China, but the T/CO ratio at the NECP site and the o-X/CO ratio at the NCP site were 29% and 38% of that in the inventory, respectively; the E/CO and X/CO ratios at the YRD site were 3.2-3.5 fold that in the emission inventory.

  4. Antifungal activities of selected aromatic plants growing wild in Greece.

    PubMed

    Soković, M; Tzakou, O; Pitarokili, D; Couladis, M

    2002-10-01

    Essential oils of Origanum onites, Satureja thymbra, Salvia fruticosa (Greek sage), and Salvia pomifera subsp. calycina plants growing wild in Greece and their components carvacrol, camphor, and 1,8-cineole, were assayed for antifungal activity against 13 fungal species. Among the fungi tested were food poisoning, plant, animals and human pathogenic species. The oils presented various degrees of inhibition against all the fungi investigated. The highest and broadest activity was shown by the carvacrol content oils (O. onites and S. thymbra), while the oil of sage was the least effective. Carvacrol exhibited the highest and 1,8-cineole the lowest level of antifungal activity among the components tested. PMID:12428445

  5. Identification of primary aromatic amines in mutagenically active subfractions from coal liquefaction materials.

    PubMed

    Wilson, B W; Pelroy, R; Cresto, J T

    1980-11-01

    Gas-chromatographic mass spectral (GCMS) analyses were performed on mutagenically active components from the basic, basic tar and neutral tar subfractions of a coal-derived liquid heavy distillate. The latter material is a component fraction of an experimental oil produced in a solvent refined coal process (SRC II) pilot plant. Mutagenicity was determined with the Ames/Salmonella assay system. Thin-layer chromatography (TLC) was used to separate mutagenically active components of the basic, basic tar and neutral tar fractions from some of the other compounds contained in these complex materials. For the 3 fractions tested, mutagenic activity was localized in approx. the same TLC regions, with relative mobilities (Rf) ranging from 0.1 to 0.3. GCMS analysis of the TLC regions showed that the concentrations of primary aromatic amines, as obtained by measuring peak areas for the (M + 1)+ ion as formed in the chemical ionization mode, followed essentially the same distribution as the mutagenic activity. Primary aromatic amines identified in the active regions included aminonaphthalenes, aminoanthracenes, aminophenanthrenes, aminopyrenes and aminochrysenes. With the exception of small amounts of aminonaphthalene, primary aromatic amines were not found in TLC regions that lacked mutagenic activity.

  6. Atmospheric behaviors of polycyclic aromatic hydrocarbons at a Japanese remote background site, Noto peninsula, from 2004 to 2014

    NASA Astrophysics Data System (ADS)

    Tang, Ning; Hakamata, Mariko; Sato, Kousuke; Okada, Yumi; Yang, Xiaoyang; Tatematsu, Michiya; Toriba, Akira; Kameda, Takayuki; Hayakawa, Kazuichi

    2015-11-01

    Total suspended particulates were collected at a Japanese remote background site (Noto Air Monitoring Station; NAMS) on the Noto Peninsula from September 2004 to June 2014. Nine polycyclic aromatic hydrocarbons (PAHs) in the particulates (fluoranthene, pyrene, benz[a]anthracene, chrysene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[a]pyrene, benzo[ghi]perylene and indeno[1,2,3-cd]pyrene) were determined by HPLC with fluorescence detection. The mean total concentrations of the nine PAHs in the cold season (November to May for the years 2004-2014) was 670 pg m-3 (range 37-4100 pg m-3). The mean total concentration in the warm season (June to October for the same period) was 170 pg m-3 (range 31-960 pg m-3). The atmospheric PAH level at NAMS decreased in recent years, although no significant change was found in the warm season. An analysis of meteorological conditions showed that the atmospheric PAHs at NAMS were long range transported from Northeast China in the cold seasons and were contributed to by Japanese domestic sources in the warm seasons. Lower concentration ratios of reactive PAHs to their isomers at NAMS also supported these results. Activities associated with the Beijing Olympic and Paralympic Games in 2008 and reconstruction after the 2007 Noto Hanto earthquake may have contributed to the yearly variations of atmospheric PAH levels at NAMS during the period 2007-2009. Source control measures implemented by the Chinese and Japanese governments appear to have been effective in decreasing the atmospheric PAH levels at NAMS in recent years.

  7. Quantitative structure-activity relationship for toxicity of ionic liquids to Daphnia magna: aromaticity vs. lipophilicity.

    PubMed

    Roy, Kunal; Das, Rudra Narayan; Popelier, Paul L A

    2014-10-01

    Water solubility of ionic liquids (ILs) allows their dispersion into aquatic systems and raises concerns on their pollutant potential. Again, lipophilicity can contribute to the toxicity of ILs due to increased ability of the compounds to cross lipoidal bio-membranes. In the present work, we have performed statistical model development for toxicity of a set of ionic liquids to Daphnia magna, a widely accepted model organism for toxicity testing, using computed lipophilicity, atom-type fragment, quantum topological molecular similarity (QTMS) and extended topochemical atom (ETA) descriptors. The models have been developed and validated in accordance with the Organization for Economic Co-operation and Development (OECD) guidelines for quantitative structure-activity relationships (QSARs). The best partial least squares (PLS) model outperforms the previously reported multiple linear regression (MLR) model in statistical quality and predictive ability (R(2)=0.955, Q(2)=0.917, Rpred(2)=0.848). In this work, the ETA descriptors show importance of branching and aromaticity while the QTMS descriptor ellipticity efficiently shows which compounds are influential in the data set, with reference to the model. While obvious importance of lipophilicity is evident from the models, the best model clearly shows the importance of aromaticity suggesting that more lipophilic ILs with less toxicity may be designed by avoiding aromaticity, nitrogen atoms and increasing branching in the cationic structure. The developed quantitative models are in consonance with the recent hypothesis of importance of aromaticity for toxicity of ILs.

  8. Estrogenic Activity of Mineral Oil Aromatic Hydrocarbons Used in Printing Inks

    PubMed Central

    Tarnow, Patrick; Hutzler, Christoph; Grabiger, Stefan; Schön, Karsten; Tralau, Tewes; Luch, Andreas

    2016-01-01

    The majority of printing inks are based on mineral oils (MOs) which contain complex mixtures of saturated and aromatic hydrocarbons. Consumer exposure to these oils occurs either through direct skin contacts or, more frequently, as a result of MO migration into the contents of food packaging that was made from recycled newspaper. Despite this ubiquitous and frequent exposure little is known about the potential toxicological effects, particularly with regard to the aromatic MO fractions. From a toxicological point of view the huge amount of alkylated and unsubstituted compounds therein is reason for concern as they can harbor genotoxicants as well as potential endocrine disruptors. The aim of this study was to assess both the genotoxic and estrogenic potential of MOs used in printing inks. Mineral oils with various aromatic hydrocarbon contents were tested using a battery of in vitro assays selected to address various endpoints such as estrogen-dependent cell proliferation, activation of estrogen receptor α or transcriptional induction of estrogenic target genes. In addition, the comet assay has been applied to test for genotoxicity. Out of 15 MOs tested, 10 were found to potentially act as xenoestrogens. For most of the oils the effects were clearly triggered by constituents of the aromatic hydrocarbon fraction. From 5 oils tested in the comet assay, 2 showed slight genotoxicity. Altogether it appears that MOs used in printing inks are potential endocrine disruptors and should thus be assessed carefully to what extent they might contribute to the total estrogenic burden in humans. PMID:26771904

  9. Structure-Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide.

    PubMed

    Salter-Blanc, Alexandra J; Bylaska, Eric J; Lyon, Molly A; Ness, Stuart C; Tratnyek, Paul G

    2016-05-17

    New energetic compounds are designed to minimize their potential environmental impacts, which includes their transformation and the fate and effects of their transformation products. The nitro groups of energetic compounds are readily reduced to amines, and the resulting aromatic amines are subject to oxidation and coupling reactions. Manganese dioxide (MnO2) is a common environmental oxidant and model system for kinetic studies of aromatic amine oxidation. In this study, a training set of new and previously reported kinetic data for the oxidation of model and energetic-derived aromatic amines was assembled and subjected to correlation analysis against descriptor variables that ranged from general purpose [Hammett σ constants (σ(-)), pKas of the amines, and energies of the highest occupied molecular orbital (EHOMO)] to specific for the likely rate-limiting step [one-electron oxidation potentials (Eox)]. The selection of calculated descriptors (pKa, EHOMO, and Eox) was based on validation with experimental data. All of the correlations gave satisfactory quantitative structure-activity relationships (QSARs), but they improved with the specificity of the descriptor. The scope of correlation analysis was extended beyond MnO2 to include literature data on aromatic amine oxidation by other environmentally relevant oxidants (ozone, chlorine dioxide, and phosphate and carbonate radicals) by correlating relative rate constants (normalized to 4-chloroaniline) to EHOMO (calculated with a modest level of theory). PMID:27074054

  10. Activity of nitro-polynuclear aromatic hydrocarbons in the sister chromatid exchange assay with and without metabolic activation.

    PubMed

    Nachtman, J P; Wolff, S

    1982-01-01

    Nitro-polynuclear aromatic hydrocarbons are found in diesel particulates. These compounds are potent mutagens in the Ames test. To determine whether nitro-polynuclear aromatic hydrocarbons are active in a mammalian cell assay, 1-nitropyrene, 1,8-dinitropyrene, 2-nitrofluorene, and 4-nitrobiphenyl were incubated with cultures of Chinese hamster ovary cells. The frequency of sister chromatid exchange (SCE) was measured in the presence and absence of rat liver S-9 mix. The addition of S-9 mix resulted in a large increase in the SCEs induced by all four compounds. PMID:7067667

  11. Activity of nitro-polynuclear aromatic hydrocarbons in the sister chromatid exchange assay with and without metabolic activation. [Hamsters

    SciTech Connect

    Nachtman, J.P.; Wolff, S.

    1982-01-01

    Nitro-polynuclear aromatic hydrocarbons are found in diesel particulates.These compounds are potent mutagens in the Ames test. To determine whether nitro-polynuclear aromatic hydrocarbons are active in a mammalian cell assay, 1-nitropyrene, 1,8-dinitropyrene, 2-nitrofluorene, and 4-nitrobiphenyl were incubated with cultures of Chinese hamster ovary cells. The frequency of sister chromatic exchange (SCE) was measured in the presence and absence of rat liver S-9 mix. The addition of S-9 mix resulted in a large increase in the SCEs induced by all four compounds.

  12. Polycyclic aromatic hydrocarbons, aliphatic hydrocarbons, trace elements, and monooxygenase activity in birds nesting on the North Platte River, Casper, Wyoming, USA.

    PubMed

    Custer, T W; Custer, C M; Dickerson, K; Allen, K; Melancon, M J; Schmidt, L J

    2001-03-01

    Tree swallow (Tachycineta bicolor) and house wren (Troglodytes aedon) eggs and chicks were collected near a refinery site on the North Platte River, Casper. Wyoming, USA and at a reference site 10 km upstream. Total polycyclic aromatic hydrocarbon (PAH) concentrations in swallow and wren chicks were higher at the refinery site than at the reference site. Polycyclic aromatic hydrocarbon concentrations in sediment and chick dietary samples were consistent with these findings. The general lack of methylated PAHs in sediment, diet, and bird carcasses suggested that the PAHs were derived from combustion and not from petroleum. The predominance of odd-numbered aliphatic hydrocarbons and the low ratios (< or =0.25) of pristane:n-C17 and phytane:n-C18 in chick and diet samples also suggested that swallow and wren chicks were not being chronically exposed to petroleum. Mean ethoxyresorufin-O-dealkylase and benzyloxyresorufin-O-dealkylase activities in tree swallow livers averaged nine times higher at the refinery site than at the reference site and were probably induced by exposure to PAHs. Trace element concentrations in eggs and livers of swallows and wrens were similar or greater at the reference site than at the refinery site. Selenium, strontium, and boron concentrations were elevated in eggs and livers of swallows and wrens at both the refinery and reference sites. PMID:11349865

  13. Polycyclic aromatic hydrocarbons, aliphatic hydrocarbons, trace elements and monooxygenase activity in birds nesting on the North Platte River, Casper, Wyoming, USA

    USGS Publications Warehouse

    Custer, T.W.; Custer, Christine M.; Dickerson, K.; Allen, K.; Melancon, M.J.; Schmidt, L.J.

    2001-01-01

    Tree swallow (Tachycineta bicolor) and house wren (Troglodytes aedon) eggs and chicks were collected near a refinery site on the North Platte River, Casper, Wyoming, USA and at a reference site 10 km upstream. Total polycylic aromatic hydrocarbon (PAH) concentrations in swallow and wren chicks were higher at the refinery site than at the reference site. Polycylic aromatic hydrocarbon concentrations in sediment and chick dietary samples were consistent with these findings. The general lack of methylated PAHs in sediment, diet, and bird carcasses suggested that the PAHs were derived from combustion and not from petroleum. The predominance of odd numbered aliphatic hydrocarbons and the low ratios (≤ 0.25) of pristane: n-C17 and phytane: n-C18 in chick and diet samples also suggested that swallow and wren chicks were not being chronically exposed to petroleum. Mean ethoxyresorufin-O-dealkylase and benzyloxyresorufin-O-dealkylase activities in tree swallow livers averaged nine times higher at the refinery site than at the reference site and were probably induced by exposure to PAHs. Trace element concentrations in eggs and livers of swallows and wrens were similar or greater at the reference site than at the refinery site. Selenium, strontium, and boron concentrations were elevated in eggs and livers of swallows and wrens at both the refinery and reference sites.

  14. Asymmetric Intramolecular Alkylation of Chiral Aromatic Imines via Catalytic C-H Bond Activation

    SciTech Connect

    Watzke, Anja; Wilson, Rebecca; O'Malley, Steven; Bergman, Robert; Ellman, Jonathan

    2007-04-16

    The asymmetric intramolecular alkylation of chiral aromatic aldimines, in which differentially substituted alkenes are tethered meta to the imine, was investigated. High enantioselectivities were obtained for imines prepared from aminoindane derivatives, which function as directing groups for the rhodium-catalyzed C-H bond activation. Initial demonstration of catalytic asymmetric intramolecular alkylation also was achieved by employing a sterically hindered achiral imine substrate and catalytic amounts of a chiral amine.

  15. Activation of group IVC phospholipase A(2) by polycyclic aromatic hydrocarbons induces apoptosis of human coronary artery endothelial cells.

    PubMed

    Tithof, Patricia K; Richards, Sean M; Elgayyar, Mona A; Menn, Fu-Minn; Vulava, Vijay M; McKay, Larry; Sanseverino, John; Sayler, Gary; Tucker, Dawn E; Leslie, Christina C; Lu, Kim P; Ramos, Kenneth S

    2011-06-01

    Exposure to environmental pollutants, such as polycyclic aromatic hydrocarbons (PAHs) found in coal tar mixtures and tobacco sources, is considered a significant risk factor for the development of heart disease in humans. The goal of this study was to determine the influence of PAHs present at a Superfund site on human coronary artery endothelial cell (HCAEC) phospholipase A(2) (PLA(2)) activity and apoptosis. Extremely high levels of 12 out of 15 EPA high-priority PAHs were present in both the streambed and floodplain sediments at a site where an urban creek and its adjacent floodplain were extensively contaminated by PAHs and other coal tar compounds. Nine of the 12 compounds and a coal tar mixture (SRM 1597A) activated group IVC PLA(2) in HCAECs, and activation of this enzyme was associated with histone fragmentation and poly (ADP) ribose polymerase (PARP) cleavage. Genetic silencing of group IVC PLA(2) inhibited both (3)H-fatty acid release and histone fragmentation by PAHs and SRM 1597A, indicating that individual PAHs and a coal tar mixture induce apoptosis of HCAECs via a mechanism that involves group IVC PLA(2). Western blot analysis of aortas isolated from feral mice (Peromyscus leucopus) inhabiting the Superfund site showed increased PARP and caspase-3 cleavage when compared to reference mice. These data suggest that PAHs induce apoptosis of HCAECs via activation of group IVC PLA(2). PMID:21132278

  16. Design, synthesis, and biological activities of aromatic gossypol Schiff base derivatives.

    PubMed

    Li, Ling; Li, Zheng; Wang, Kailiang; Zhao, Sheng; Feng, Jiming; Li, Jiarui; Yang, Peiwen; Liu, Yuxiu; Wang, Lizhong; Li, Yongqiang; Shang, Hui; Wang, Qingmin

    2014-11-19

    A series of aromatic gossypol Schiff bases have been successfully synthesized via a feasible chemical modification. The antiviral activity against tobacco mosaic virus (TMV) of these gossypol Schiff bases has been tested for the first time. The bioassay studies indicated most of these derivatives exhibited excellent anti-TMV activity, in which o-trifluoromethylaniline Schiff base (19) displayed the best antiviral activities. Furthermore, compound 19 exhibited an eminent anti-TMV effect in the field and low toxicity to mice. These results suggest it is a promising candidate for the inhibitor of plant virus.

  17. Heterogeneous three-site lattice model for adsorption of aromatics in ZSM-5 zeolites: Temperature dependence of adsorption isotherms

    SciTech Connect

    Narkiewicz-Michalek, J.; Szabelski, P.; Rudzinski, W.; Chiang, A.S.T.

    1999-08-31

    The three-site lattice model of collective localized adsorption of aromatics in ZSM-5 zeolites, presented in previous publications, is extended by taking into account the effects of energetic heterogeneity of the sites of the same type. The appropriate theoretical equations are derived and used for simultaneous description of the experimental adsorption isotherms and heats of adsorption of benzene and p-xylene in silicalite at 303 K. It is shown that taking into account this additional level of heterogeneity leads to a much better description of both the adsorption isotherms and the related heats of adsorption in these systems. The extended model also allows one to predict correctly the adsorption isotherms of benzene and p-xylene in silicalite at different temperatures using the parameters found at one temperature.

  18. Effect of Polarity of Activated Carbon Surface, Solvent and Adsorbate on Adsorption of Aromatic Compounds from Liquid Phase.

    PubMed

    Goto, Tatsuru; Amano, Yoshimasa; Machida, Motoi; Imazeki, Fumio

    2015-01-01

    In this study, introduction of acidic functional groups onto a carbon surface and their removal were carried out through two oxidation methods and outgassing to investigate the adsorption mechanism of aromatic compounds which have different polarity (benzene and nitrobenzene). Adsorption experiments for these aromatics in aqueous solution and n-hexane solution were conducted in order to obtain the adsorption isotherms for commercial activated carbon (BAC) as a starting material, its two types of oxidized BAC samples (OXs), and their outgassed samples at 900 °C (OGs). Adsorption and desorption kinetics of nitrobenzene for the BAC, OXs and OGs in aqueous solution were also examined. The results showed that the adsorption of benzene molecules was significantly hindered by abundant acidic functional groups in aqueous solution, whereas the adsorbed amount of nitrobenzene on OXs gradually increased as the solution concentration increased, indicating that nitrobenzene can adsorb favourably on a hydrophilic surface due to its high dipole moment, in contrast to benzene. In n-hexane solution, it was difficult for benzene to adsorb on any sample owing to the high affinity between benzene and n-hexane solvent. On the other hand, adsorbed amounts of nitrobenzene on OXs were larger than those of OGs in n-hexane solution, implying that nitrobenzene can adsorb two adsorption sites, graphene layers and surface acidic functional groups. The observed adsorption and desorption rate constants of nitrobenzene on the OXs were lower than those on the BAC due to disturbance of diffusion by the acidic functional groups.

  19. Radiation inactivation study of aminopeptidase: probing the active site

    NASA Astrophysics Data System (ADS)

    Jamadar, V. K.; Jamdar, S. N.; Mohan, Hari; Dandekar, S. P.; Harikumar, P.

    2004-04-01

    Ionizing radiation inactivated purified chicken intestinal aminopeptidase in media saturated with gases in the order N 2O>N 2>air. The D 37 values in the above conditions were 281, 210 and 198 Gy, respectively. OH radical scavengers such as t-butanol and isopropanol effectively nullified the radiation-induced damage in N 2O. The radicals (SCN) 2•-, Br 2•- and I 2•- inactivated the enzyme, pointing to the involvement of aromatic amino acids and cysteine in its catalytic activity. The enzyme exhibited fluorescence emission at 340 nm which is characteristic of tryptophan. The radiation-induced loss of activity was accompanied by a decrease in the fluorescence of the enzyme suggesting a predominant influence on tryptophan residues. The enzyme inhibition was associated with a marked increase in the Km and a decrease in the Vmax and kcat values, suggesting an irreversible alteration in the catalytic site. The above observations were confirmed by pulse radiolysis studies.

  20. Contrasts between subsurface microbial communities and their metabolic adaptation to polycyclic aromatic hydrocarbons at a forested and an urban coal-tar disposal site.

    PubMed

    Madsen, E L; Winding, A; Malachowsky, K; Thomas, C T; Ghiorse, W C

    1992-09-01

    The abundance and distribution of microorganisms and their potential for mineralizing polycyclic aromatic hydrocarbons (PAHs) were measured in subsurface sediment samples at two geographically separate buried coal-tar sites. At a relatively undisturbed forested site in the northeastern United States, metabolic adaptation to the PAHs was evident: Radiolabeled naphthalene and phenanthrene were converted to (14)CO2 in core material from inside but not outside a plume of groundwater contamination. However, at the urban site in the midwestern United States these PAHs were mineralized in sediments from both contaminated and uncontaminated boreholes. Thus, clear qualitative evidence showing an adaptational response by the subsurface microbial community was not obtained at the urban site. Instead, subtler clues suggesting metabolic adaptation by subsurface microorganisms from the urban site were discerned by comparing lag periods and extents of (14)CO2 production from radiolabeled PAHs added to samples from contaminated and uncontaminated boreholes. Despite slightly higher PAH mineralization activity in contaminated borehole samples, p-hydroxybenzoate was mineralized equally in all samples from the urban site regardless of location. No striking trends in the abundances of actinomycetes, fungi, and either viable or total bacteria were encountered. However, colonies of the soil bacterium, Bacillus mycoides, were detected on enumeration plates of several samples from unsaturated and saturated zones in both urban boreholes. Furthermore, other common soil bacteria, Myxococcus xanthus and Chromobacterium violaceum, were identified in samples from the uncontaminated urban borehole. The occurrence of bacteria usually restricted to surface soil, combined with the observation of fragments of building materials in many of the core samples, suggested that past excavation and backfilling operations may have caused mixing of surface soil with subsurface materials at the urban site. We

  1. Polycyclic aromatic hydrocarbons in sediments, mussels and crustacea around a former gasworks site in Shoreham-by-Sea, UK.

    PubMed

    Law, R J; Kelly, C A; Baker, K L; Langford, K H; Bartlett, T

    2002-09-01

    Concentrations of polycyclic aromatic hydrocarbons have been determined in sediments, mussels and crustacea in the vicinity of a former gasworks site by Shoreham Harbour, UK. Very high concentrations of PAH were found in the substrate, an ash-like material deposited on the former gasworks site, which exhibited a profile consistent with the major source of contamination being coal or coke tar produced during the period of gas production at the site. Elevated PAH concentrations were also found in mussels both from the beach below the former gasworks site, and from sites further to the east in Portslade and Hove. The significance of these concentrations were assessed using an approach which involved the calculation of benzo[a]pyrene equivalent conoentrations (BaPEs), summing concentrations of individual PAH on the basis of their comparative potency as carcinogens. BaPE ranged from values of, or close to, zero for crustacea, to 336 microg kg(-1) wet weight in mussels from Southwick Beach. The contaminated mussels are not exploited commercially but may be taken by casual gatherers, and notices have been posted to warn potential consumers. PMID:12405215

  2. Polycyclic aromatic hydrocarbons in sediments, mussels and crustacea around a former gasworks site in Shoreham-by-Sea, UK.

    PubMed

    Law, R J; Kelly, C A; Baker, K L; Langford, K H; Bartlett, T

    2002-09-01

    Concentrations of polycyclic aromatic hydrocarbons have been determined in sediments, mussels and crustacea in the vicinity of a former gasworks site by Shoreham Harbour, UK. Very high concentrations of PAH were found in the substrate, an ash-like material deposited on the former gasworks site, which exhibited a profile consistent with the major source of contamination being coal or coke tar produced during the period of gas production at the site. Elevated PAH concentrations were also found in mussels both from the beach below the former gasworks site, and from sites further to the east in Portslade and Hove. The significance of these concentrations were assessed using an approach which involved the calculation of benzo[a]pyrene equivalent conoentrations (BaPEs), summing concentrations of individual PAH on the basis of their comparative potency as carcinogens. BaPE ranged from values of, or close to, zero for crustacea, to 336 microg kg(-1) wet weight in mussels from Southwick Beach. The contaminated mussels are not exploited commercially but may be taken by casual gatherers, and notices have been posted to warn potential consumers.

  3. New lipophilic piceatannol derivatives exhibiting antioxidant activity prepared by aromatic hydroxylation with 2-iodoxybenzoic acid (IBX).

    PubMed

    Bernini, Roberta; Barontini, Maurizio; Spatafora, Carmela

    2009-01-01

    Piceatannol (E-3,5,3',4'-tetrahydroxystilbene) is a phytoalexin synthesized in grapes in response to stress conditions. It exhibits strong antioxidant and antileukaemic activities due to the presence of the catechol moiety. To modify some physical properties like solubility, and miscibility in non-aqueous media some new previously unreported piceatannol derivatives having lipophilic chains on the A-ring were prepared in good yields by a simple and efficient procedure. The key step was a chemo- and regioselective aromatic hydroxylation with 2-iodoxybenzoic acid (IBX). The new compounds showed antioxidant activity and seemed promising for possible applications as multifunctional emulsifiers in food, cosmetic and pharmaceutical fields.

  4. Active Site and Laminarin Binding in Glycoside Hydrolase Family 55*

    PubMed Central

    Bianchetti, Christopher M.; Takasuka, Taichi E.; Deutsch, Sam; Udell, Hannah S.; Yik, Eric J.; Bergeman, Lai F.; Fox, Brian G.

    2015-01-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100–10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  5. The biochemical mechanisms of the plant activation of promutagenic aromatic amines

    SciTech Connect

    Wagner, E.D.; Verdier, M.M.; Plewa, M.J. )

    1990-01-01

    Using specific monooxygenase and oxidase inhibitors in a plant cell/microbe coincubation assay, the biochemical mechanisms of the plant activation of two aromatic amines were compared. The biological endpoints included mutation induction, inhibition of mutagenicity, viability of the plant cells (activating system), and viability of the microbial cells. The activation of m-phenylenediamine by TX1 cells was mediated by enzyme systems that were inhibited by diethyldithiocarbamate, potassium cyanide, methimazole, (+)-catechin or acetaminophen. The inhibition by metyrapone was attended by toxicity in the plant cells. These data implicate a TX1 cell peroxidase and a FAD-dependent monoxygenase in the plant activation of m-phenylenediamine. The TX1 cell activation of 2-aminofluorene was inhibited by diethyldithiocarbamate, 7,8-benzoflavone, acetaminophen or (+)-catechin.

  6. Antimicrobial activity of essential oils from Mediterranean aromatic plants against several foodborne and spoilage bacteria.

    PubMed

    Silva, Nuno; Alves, Sofia; Gonçalves, Alexandre; Amaral, Joana S; Poeta, Patrícia

    2013-12-01

    The antimicrobial activity of essential oils extracted from a variety of aromatic plants, often used in the Portuguese gastronomy was studied in vitro by the agar diffusion method. The essential oils of thyme, oregano, rosemary, verbena, basil, peppermint, pennyroyal and mint were tested against Gram-positive (Listeria monocytogenes, Clostridium perfringens, Bacillus cereus, Staphylococcus aureus, Enterococcus faecium, Enterococcus faecalis, and Staphylococcus epidermidis) and Gram-negative strains (Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa). For most essential oils examined, S. aureus, was the most susceptible bacteria, while P. aeruginosa showed, in general, least susceptibility. Among the eight essential oils evaluated, thyme, oregano and pennyroyal oils showed the greatest antimicrobial activity, followed by rosemary, peppermint and verbena, while basil and mint showed the weakest antimicrobial activity. Most of the essential oils considered in this study exhibited a significant inhibitory effect. Thyme oil showed a promising inhibitory activity even at low concentration, thus revealing its potential as a natural preservative in food products against several causal agents of foodborne diseases and food spoilage. In general, the results demonstrate that, besides flavoring the food, the use of aromatic herbs in gastronomy can also contribute to a bacteriostatic effect against pathogens.

  7. Antimicrobial activity of essential oils from Mediterranean aromatic plants against several foodborne and spoilage bacteria.

    PubMed

    Silva, Nuno; Alves, Sofia; Gonçalves, Alexandre; Amaral, Joana S; Poeta, Patrícia

    2013-12-01

    The antimicrobial activity of essential oils extracted from a variety of aromatic plants, often used in the Portuguese gastronomy was studied in vitro by the agar diffusion method. The essential oils of thyme, oregano, rosemary, verbena, basil, peppermint, pennyroyal and mint were tested against Gram-positive (Listeria monocytogenes, Clostridium perfringens, Bacillus cereus, Staphylococcus aureus, Enterococcus faecium, Enterococcus faecalis, and Staphylococcus epidermidis) and Gram-negative strains (Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa). For most essential oils examined, S. aureus, was the most susceptible bacteria, while P. aeruginosa showed, in general, least susceptibility. Among the eight essential oils evaluated, thyme, oregano and pennyroyal oils showed the greatest antimicrobial activity, followed by rosemary, peppermint and verbena, while basil and mint showed the weakest antimicrobial activity. Most of the essential oils considered in this study exhibited a significant inhibitory effect. Thyme oil showed a promising inhibitory activity even at low concentration, thus revealing its potential as a natural preservative in food products against several causal agents of foodborne diseases and food spoilage. In general, the results demonstrate that, besides flavoring the food, the use of aromatic herbs in gastronomy can also contribute to a bacteriostatic effect against pathogens. PMID:23444311

  8. Antitumor and antiparasitic activity of novel ruthenium compounds with polycyclic aromatic ligands.

    PubMed

    Miserachs, Helena Guiset; Cipriani, Micaella; Grau, Jordi; Vilaseca, Marta; Lorenzo, Julia; Medeiros, Andrea; Comini, Marcelo A; Gambino, Dinorah; Otero, Lucía; Moreno, Virtudes

    2015-09-01

    Five novel ruthenium(II)-arene complexes with polycyclic aromatic ligands were synthesized, comprising three compounds of the formula [RuCl(η(6)-p-cym)(L)][PF6], where p-cym = 1-isopropyl-4-methylbenzene and L are the bidentate aromatic ligands 1,10-phenanthroline-5,6-dione, 1, 5-amine-1,10-phenanthroline, 4, or 5,6-epoxy-5,6-dihydro-phenanthroline, 5. In the other two complexes [RuCl2(η(6)-p-cym)(L')], the metal is coordinated to a monodentate ligand L', where L' is phenanthridine, 2, or 9-carbonylanthracene, 3. All compounds were fully characterized by mass spectrometry and elemental analysis, as well as NMR and IR spectroscopic techniques. Obtained ruthenium compounds as well as their respective ligands were tested for their antiparasitic and antitumoral activities. Even though all compounds showed lower Trypanosoma brucei activity than the free ligands, they also resulted less toxic on mammalian cells. Cytotoxicity assays on HL60 cells showed a moderate antitumoral activity for all ruthenium compounds. Compound 1 was the most potent antitumoral (IC50 = 1.26±0.78 μM) and antiparasitic (IC50 = 0.19 ± 0.05 μM) agent, showing high selectivity towards the parasites (selectivity index >100). As complex 1 was the most promising antitumoral compound, its interaction with ubiquitin as potential target was also studied. In addition, obtained ruthenium compounds were found to bind DNA, and they are thought to interact with this macromolecule mainly through intercalation of the aromatic ligand.

  9. Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library*

    PubMed Central

    Kiefer, Jonathan D.; Srinivas, Raja R.; Lobner, Elisabeth; Tisdale, Alison W.; Mehta, Naveen K.; Yang, Nicole J.; Tidor, Bruce; Wittrup, K. Dane

    2016-01-01

    The Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus is an attractive binding scaffold because of its small size (7 kDa), high thermal stability (Tm of 98 °C), and absence of cysteines and glycosylation sites. However, as a DNA-binding protein, Sso7d is highly positively charged, introducing a strong specificity constraint for binding epitopes and leading to nonspecific interaction with mammalian cell membranes. In the present study, we report charge-neutralized variants of Sso7d that maintain high thermal stability. Yeast-displayed libraries that were based on this reduced charge Sso7d (rcSso7d) scaffold yielded binders with low nanomolar affinities against mouse serum albumin and several epitopes on human epidermal growth factor receptor. Importantly, starting from a charge-neutralized scaffold facilitated evolutionary adaptation of binders to differentially charged epitopes on mouse serum albumin and human epidermal growth factor receptor, respectively. Interestingly, the distribution of amino acids in the small and rigid binding surface of enriched rcSso7d-based binders is very different from that generally found in more flexible antibody complementarity-determining region loops but resembles the composition of antibody-binding energetic hot spots. Particularly striking was a strong enrichment of the aromatic residues Trp, Tyr, and Phe in rcSso7d-based binders. This suggests that the rigidity and small size of this scaffold determines the unusual amino acid composition of its binding sites, mimicking the energetic core of antibody paratopes. Despite the high frequency of aromatic residues, these rcSso7d-based binders are highly expressed, thermostable, and monomeric, suggesting that the hyperstability of the starting scaffold and the rigidness of the binding surface confer a high tolerance to mutation. PMID:27582495

  10. Polycylic aromatic hydrocarbons in rape seeds with relation to their growing site and thermal treatment.

    PubMed

    Bojanowska, M; Czerwiński, J

    2010-01-01

    A significant source of polycyclic aromatic hydrocarbons (PAH) in human diet is vegetable oils, especially those produced from plants grown in regions where the soil and the atmosphere are contaminated with these chemicals. Contamination with PAH of vegetable oils may also occur in the process of plant material drying with smoke or exhaust fumes, or in the course of extraction of that material with solvents containing trace amounts of PAH. The objective of this study was to determine the relationship between the levels of PAH present in rape seeds and the occurrence of these compounds in cultivation region and the relationship of the levels of PAH in rape seeds to thermal treatment after harvest. Rape seeds and pods from experimental fields and rape seeds subjected to thermal treatment in dryers obtained from suppliers of the raw material were examined and compared. Cleanup of extracts was performed with high-resolution size exclusion chromatography (SEC) and final determinations were by Trace Ultra/PolarisQ gas chromatography-mass spectroscopy (GC-MS). The results obtained indicated that during thermal treatment of rape seeds the concentration of PAH increased, but the levels of benzo[a]pyrene did not exceed threshold permissible levels. Data demonstrate that rapeseed cultivation in the presence of PAH results in higher levels of contaminants; however, the PAH levels still did not exceed the maximal allowable levels in Poland.

  11. Polycylic aromatic hydrocarbons in rape seeds with relation to their growing site and thermal treatment.

    PubMed

    Bojanowska, M; Czerwiński, J

    2010-01-01

    A significant source of polycyclic aromatic hydrocarbons (PAH) in human diet is vegetable oils, especially those produced from plants grown in regions where the soil and the atmosphere are contaminated with these chemicals. Contamination with PAH of vegetable oils may also occur in the process of plant material drying with smoke or exhaust fumes, or in the course of extraction of that material with solvents containing trace amounts of PAH. The objective of this study was to determine the relationship between the levels of PAH present in rape seeds and the occurrence of these compounds in cultivation region and the relationship of the levels of PAH in rape seeds to thermal treatment after harvest. Rape seeds and pods from experimental fields and rape seeds subjected to thermal treatment in dryers obtained from suppliers of the raw material were examined and compared. Cleanup of extracts was performed with high-resolution size exclusion chromatography (SEC) and final determinations were by Trace Ultra/PolarisQ gas chromatography-mass spectroscopy (GC-MS). The results obtained indicated that during thermal treatment of rape seeds the concentration of PAH increased, but the levels of benzo[a]pyrene did not exceed threshold permissible levels. Data demonstrate that rapeseed cultivation in the presence of PAH results in higher levels of contaminants; however, the PAH levels still did not exceed the maximal allowable levels in Poland. PMID:20706951

  12. Adsorption of aromatic compounds from the biodegradation of azo dyes on activated carbon

    NASA Astrophysics Data System (ADS)

    Faria, P. C. C.; Órfão, J. J. M.; Figueiredo, J. L.; Pereira, M. F. R.

    2008-03-01

    The adsorption of three selected aromatic compounds (aniline, sulfanilic acid and benzenesulfonic acid) on activated carbons with different surface chemical properties was investigated at different solution pH. A fairly basic commercial activated carbon was modified by means of chemical treatment with HNO 3, yielding an acid activated carbon. The textural properties of this sample were not significantly changed after the oxidation treatment. Equilibrium isotherms of the selected compounds on the mentioned samples were obtained and the results were discussed in relation to their surface chemistry. The influence of electrostatic and dispersive interactions involved in the uptake of the compounds studied was evaluated. The Freundlich model was used to fit the experimental data. Higher uptakes are attained when the compounds are present in their molecular form. In general, adsorption was disfavoured by the introduction of oxygen-containing groups on the surface of the activated carbon.

  13. Improvement of aromatic thiol release through the selection of yeasts with increased β-lyase activity.

    PubMed

    Belda, Ignacio; Ruiz, Javier; Navascués, Eva; Marquina, Domingo; Santos, Antonio

    2016-05-16

    The development of a selective medium for the rapid differentiation of yeast species with increased aromatic thiol release activity has been achieved. The selective medium was based on the addition of S-methyl-l-cysteine (SMC) as β-lyase substrate. In this study, a panel of 245 strains of Saccharomyces cerevisiae strains was tested for their ability to grow on YCB-SMC medium. Yeast strains with an increased β-lyase activity grew rapidly because of their ability to release ammonium from SMC in comparison to others, and allowed for the easy isolation and differentiation of yeasts with promising properties in oenology, or another field, for aromatic thiol release. The selective medium was also helpful for the discrimination between those S. cerevisiae strains, which present a common 38-bp deletion in the IRC7 sequence (present in around 88% of the wild strains tested and are likely to be less functional for 4-mercapto-4-methylpentan-2-one (4MMP) production), and those S. cerevisiae strains homozygous for the full-length IRC7 allele. The medium was also helpful for the selection of non-Saccharomyces yeasts with increased β-lyase activity. Based on the same medium, a highly sensitive, reproducible and non-expensive GC-MS method for the evaluation of the potential volatile thiol release by different yeast isolates was developed. PMID:26971012

  14. Improvement of aromatic thiol release through the selection of yeasts with increased β-lyase activity.

    PubMed

    Belda, Ignacio; Ruiz, Javier; Navascués, Eva; Marquina, Domingo; Santos, Antonio

    2016-05-16

    The development of a selective medium for the rapid differentiation of yeast species with increased aromatic thiol release activity has been achieved. The selective medium was based on the addition of S-methyl-l-cysteine (SMC) as β-lyase substrate. In this study, a panel of 245 strains of Saccharomyces cerevisiae strains was tested for their ability to grow on YCB-SMC medium. Yeast strains with an increased β-lyase activity grew rapidly because of their ability to release ammonium from SMC in comparison to others, and allowed for the easy isolation and differentiation of yeasts with promising properties in oenology, or another field, for aromatic thiol release. The selective medium was also helpful for the discrimination between those S. cerevisiae strains, which present a common 38-bp deletion in the IRC7 sequence (present in around 88% of the wild strains tested and are likely to be less functional for 4-mercapto-4-methylpentan-2-one (4MMP) production), and those S. cerevisiae strains homozygous for the full-length IRC7 allele. The medium was also helpful for the selection of non-Saccharomyces yeasts with increased β-lyase activity. Based on the same medium, a highly sensitive, reproducible and non-expensive GC-MS method for the evaluation of the potential volatile thiol release by different yeast isolates was developed.

  15. Tumour-promoting activity of polycyclic aromatic hydrocarbons and their oxygenated or nitrated derivatives.

    PubMed

    Misaki, Kentaro; Takamura-Enya, Takeji; Ogawa, Hideoki; Takamori, Kenji; Yanagida, Mitsuaki

    2016-03-01

    Various types of polycyclic aromatic compounds (PACs) in diesel exhaust particles are thought to contribute to carcinogenesis in mammals. Although the carcinogenicity, mutagenicity and tumour-initiating activity of these compounds have been evaluated, their tumour-promoting activity is unclear. In the present study, to determine the tumour-inducing activity of PACs, including previously known mutagenic compounds in atmospheric environments, a transformation assay for promoting activity mediated by the release of contact inhibition was conducted for six polycyclic aromatic hydrocarbons (PAHs), seven oxygenated PAHs (oxy-PAHs) and seven nitrated PAHs (nitro-PAHs) using mouse embryonic fibroblast cells transfected with the v-Ha-ras gene (Bhas 42 cells). Of these, two PAHs [benzo[k]fluoranthene (B[k]FA) and benzo[b]fluoranthene (B[b]FA)], one oxy-PAH [6H-benzo[cd]pyren-6-one (BPO)] and two nitro-PAHs (3-nitro-7H-benz[de]anthracen-7-one and 6-nitrochrysene) were found to exhibit particularly powerful tumour-promoting activity (≥10 foci following exposure to <100nM). In addition, clear mRNA expression of CYP1A1, which is associated with aryl hydrocarbon receptor (AhR)-mediated activation, was observed following the exposure of cells to two PAHs (B[k]FA and B[b]FA) and three oxy-PAHs (1,2-naphthoquinone, 11H-benzo[b]fluoren-11-one and BPO). Further, an HO-1 antioxidant response activation was observed following exposure to B[k]FA, B[b]FA and BPO, suggesting that the induction of tumour-promoting activity in these compounds is correlated with the dysfunction of signal transduction via AhR-mediated responses and/or oxidative stress responses.

  16. The mechanism of action of dipeptidyl aminopeptidase. Inhibition by amino acid derivatives and amines; activation by aromatic compounds.

    PubMed

    Metrione, R M; MacGeorge, N L

    1975-12-01

    A variety of amino acid and peptide amides have been shown to be inhibitors of dipeptidyl aminopeptidase. Among these compounds derivatives of strongly hydrophobic amino acids are the strongest inhibitors (Phe-NH2, Ki = 1.0 +/- 0.2 mM), while amides of basic amino acids were somewhat less effective (Lys-NH2, Ki = 36 +/- 3 mM). Short chain amino acid amides are notably weaker inhibitors (Gly-NH2, Ki = 293 +/- 50 mM). The interaction of the side chains of compounds with the enzyme appears to be at a site other than that at which the side chain of the amino-penultimate residue of the substrate interacts since the specificity of binding is different. Primary amines have been shown to inhibit, e.g., butylamine, Ki = 340 +/- 40 mM, and aromatic compounds have been shown to stimulate activity toward Gly-Gly-NH2 and Gly-Gly-OEt (phenol, 35% stimulation of activity at a 1:1 molar ratio with the substrate). The data suggest that inhibition involves binding at the site occupied by the free alpha-amino group and the N-terminal amino acid.

  17. Use of bioassays and sediment polycyclic aromatic hydrocarbon concentrations to assess toxicity at coastal sites impacted by Hurricane Katrina.

    PubMed

    Weston, James; Warren, Crystal; Chaudhary, Amit; Emerson, Beth; Argote, Kate; Khan, Shabana; Willett, Kristine L

    2010-07-01

    The goal of the present study was twofold: to rapidly assess the potential environmental toxicological response following the storm surge and flooding caused by Hurricane Katrina along the Gulf Coast of Mississippi, USA, in August 2005, and to establish post-Katrina baseline toxicological profiles for three environmental matrices (water, suspended sediments, and sediments) within the intertidal zone. Sediment and water samples were collected monthly from September 2005 to 2006 from 10 sites along the Gulf Coast from Gulfport, Mississippi, to Mobile Bay, Alabama. Water samples and suspended sediment matrices were extracted, assayed, and toxic equivalent values calculated for compounds with estrogenic potential, using the yeast estrogen screen, and CYP1A induction potential, using the H4IIE rat hepatoma ethoxyresorufin-O-deethylase assay. Polycyclic aromatic hydrocarbons (PAHs) were measured in surface sediments. It was hypothesized that the more heavily storm impacted sites, those closest to Katrina's path and time of landfall (e.g., Gulfport, September-October 2005), would elicit higher bioassay responses and PAH concentrations compared to those further east or approximately a year post-Katrina (e.g., Mobile Bay, August- September 2006). Benzo[a]pyrene equivalents decreased along spatial and temporal storm intensity gradients, but estrogenic compounds and sediment PAHs did not. Estrogen equivalents (approximately 1 ng/L) from water and suspended sediment samples occurred primarily in samples collected within a few months post-Katrina. Site-averaged surface sediment total PAHs varied significantly between sites and were higher than the U.S. National Oceanic and Atmospheric Administration's probable effects level at the Gulfport Marina and Back Biloxi Bay, Mississippi, sites. Results from the present study suggest that CYP1A inducing compounds elicited a short-term bioassay response in the water matrix shortly (within weeks) after Katrina's passing but were quickly

  18. The kinetics and QSAR of abiotic reduction of mononitro aromatic compounds catalyzed by activated carbon.

    PubMed

    Gong, Wenwen; Liu, Xinhui; Gao, Ding; Yu, Yanjun; Fu, Wenjun; Cheng, Dengmiao; Cui, Baoshan; Bai, Junhong

    2015-01-01

    The kinetics of abiotic reduction of mono-nitro aromatic compounds (mono-NACs) catalyzed by activated carbon (AC) in an anaerobic system were examined. There were 6 types of substituent groups on nitrobenzene, including methyl, chlorine, amino, carboxyl, hydroxyl and cyanogen groups, at the ortho, meta or para positions. Our results showed that reduction followed pseudo-first order reaction kinetics, and that the rate constant (logkSA) varied widely, ranging between -4.77 and -2.82, depending upon the type and position of the substituent. A quantitative structure-activity relationship (QSAR) model using 15 theoretical molecular descriptors and partial-least-squares (PLS) regression was developed for the reduction rates of mono-NACs catalyzed by AC. The cross-validated regression coefficient (Qcum(2), 0.861) and correlation coefficient (R(2), 0.898) indicated significantly high robustness of the model. The VIP (variable importance in the projection) values of energy of the lowest unoccupied molecular orbital (ELUMO) and the maximum net atomic charge on the aromatic carbon bound to the nitro group (QC(-)) were 1.15 and 1.01, respectively. These values indicated that the molecular orbital energies and the atomic net charges might play important roles in the reduction of mono-NACs catalyzed by AC in anaerobic systems.

  19. Aromatic Cyanoalkylation through Double C-H Activation Mediated by Ni(III).

    PubMed

    Zhou, Wen; Zheng, Shuai; Schultz, Jason W; Rath, Nigam P; Mirica, Liviu M

    2016-05-11

    Herein we report an atom- and step-economic aromatic cyanoalkylation reaction that employs nitriles as building blocks and proceeds through Csp(2)-H and Csp(3)-H bond activation steps mediated by Ni(III). In addition to cyanomethylation with MeCN, regioselective α-cyanoalkylation was observed with various nitrile substrates to generate secondary and tertiary nitriles. Importantly, to the best of our knowledge these are the first examples of C-H bond activation reactions occurring at a Ni(III) center, which may exhibit different reactivity and selectivity profiles than those corresponding to analogous Ni(II) centers. These studies provide guiding principles to design catalytic C-H activation and functionalization reactions involving high-valent Ni species. PMID:27120207

  20. Catalysis: Elusive active site in focus

    NASA Astrophysics Data System (ADS)

    Labinger, Jay A.

    2016-08-01

    The identification of the active site of an iron-containing catalyst raises hopes of designing practically useful catalysts for the room-temperature conversion of methane to methanol, a potential fuel for vehicles. See Letter p.317

  1. Identification and quantification of biomarkers and polycyclic aromatic hydrocarbons (PAHs) in an aged mixed contaminated site: from source to soil.

    PubMed

    Kao, Nien-Hsin; Su, Ming-Chien; Fan, Jheng-Rong; Chung, Ying-Yung

    2015-05-01

    The sources of the spill and the contaminated soils of an aged oil spill contaminated site with unknown mixed pollutants were investigated by using a set of developed forensic chemical procedures which include analysis of oil products, site investigation, gas chromatography/mass spectrometry (GC/MS) screening, biomarker identification, and finally, the confirmation of pollutants. Adamantanes (17 compounds), 10 bicyclic sesquiterpanes, 6 newly detected compounds, 16 polycyclic aromatic hydrocarbons, and 10 alkylated naphthalenes compounds in several gasoline, diesel oil samples, and contaminated soil samples were examined and quantified. GC/MS method, retention indices, relative response factors, and diagnostic ratio were used to identify and quantify pollutant compounds. The study revealed the key factors for distinguishing among gasoline and diesel oil products in the market, created a new set of retention indices for 10 bicyclic sesquiterpane compounds, and discovered 6 quantifiable compounds in analysis of fresh oil products. The suggested diagnostic ratios for BSs and the new compounds in the analysis of the biomarker show the differences among diesel products, link between the source of pollutants with contaminated soil, and the recognition of the signs of an aged spill, and the indications of weathering effects. PMID:25712884

  2. Role of weathered coal tar pitch in the partitioning of polycyclic aromatic hydrocarbons in manufactured gas plant site sediments

    SciTech Connect

    Muhammad F. Khalil; Upal Ghosh; Joseph P. Kreitinger

    2006-09-15

    Polycyclic aromatic hydrocarbons (PAHs) in manufactured gas plant (MGP) site sediments are often associated with carbonaceous particles that reduce contaminant bioavailability. Although black carbon inclusive partitioning models have been proposed to describe elevated PAH partitioning behavior, questions remain on the true loading and association of PAHs in different particle types in industrially impacted sediments. In the studied MGP sediments, the light density organic particles (coal, coke, wood, and coal tar pitch) comprised 10-20% of the total mass and 70-95% of the PAHs. The remainder of the PAHs in sediment was associated with the heavy density particles (i.e., sand, silt, and clays). Among the different particle types, coal tar pitch (quantified by a quinoline extraction method) contributed the most to the bulk sediment PAH concentration. Aqueous partition coefficients for PAHs measured using a weathered pitch sample from the field were generally an order of magnitude higher than reported for natural organic matter partitioning, and match well with theoretical predictions based on a coal tar-water partitioning model. A pitch-partitioning inclusive model is proposed that gives better estimates of the measured site-specific PAH aqueous equilibrium values than standard estimation based on natural organic matter partitioning only. Thus, for MGP impacted sediments containing weathered pitch particles, the partitioning behavior may be dominated by the sorption characteristics of pitch and not by natural organic matter or black carbon. 25 refs., 5 figs., 1 tab.

  3. Assessment of polycyclic aromatic hydrocarbons (PAHs) contamination in surface soil of coal stockpile sites in South Kalimantan, Indonesia.

    PubMed

    Mizwar, Andy; Priatmadi, Bambang Joko; Abdi, Chairul; Trihadiningrum, Yulinah

    2016-03-01

    Concentrations, spatial distribution, and sources of 16 polycyclic aromatic hydrocarbons (PAHs), listed as priority pollutants by the United States Environmental Protection Agency (USEPA), were investigated in surface soils of three different coal stockpile, agricultural, and residential sites in South Kalimantan Province, Indonesia. Total PAHs concentration ranged from 4.69 to 22.67 mg kg(-1)-dw. PAHs concentrations in soil of coal stockpile sites were higher than those in agricultural and residential soil. A complex of petrogenic origin and pyrolytic sources was found within the study area, as suggested by the isomeric ratios of PAHs. The results of principal component analysis and multiple linear regressions (PCA/MLR) showed that three sources contributed to the PAHs in the study area, including biomass and coal combustion (48.46%), raw coal (35.49%), and vehicular emission (16.05%). The high value of total benzo[a]pyrene equivalent concentration (B[a]Peq) suggests that local residents are exposed to a high carcinogenic potential.

  4. Virucidal activity of essential oils from aromatic plants of San Luis, Argentina.

    PubMed

    García, C C; Talarico, L; Almeida, N; Colombres, S; Duschatzky, C; Damonte, E B

    2003-11-01

    Essential oils obtained from eight aromatic plants of San Luis Province, Argentina, were screened for virucidal activity against herpes simplex virus type 1 (HSV-1), Junin virus (JUNV) and dengue virus type 2 (DEN-2). The most potent inhibition was observed with the essential oil of Lippia junelliana and Lippia turbinata against JUNV with virucidal concentration 50% (VC(50)) values in the range 14-20 ppm, whereas Aloysia gratissima, Heterotheca latifolia and Tessaria absinthioides inhibited JUNV in the range 52-90 ppm. The virucidal activity was time- and temperature-dependent. The essential oils of A. gratissima, Artemisia douglasiana, Eupatorium patens and T. absinthioides inactivated HSV-1 at 65-125 ppm. However, only A. douglasiana and E. patens had any discernible effect on DEN-2 infectivity with VC(50) values of 60 and 150 ppm, respectively. PMID:14595590

  5. Double group transfer reactions: role of activation strain and aromaticity in reaction barriers.

    PubMed

    Fernández, Israel; Bickelhaupt, F Matthias; Cossío, Fernando P

    2009-12-01

    Double group transfer (DGT) reactions, such as the bimolecular automerization of ethane plus ethene, are known to have high reaction barriers despite the fact that their cyclic transition states have a pronounced in-plane aromatic character, as indicated by NMR spectroscopic parameters. To arrive at a way of understanding this somewhat paradoxical and incompletely understood phenomenon of high-energy aromatic transition states, we have explored six archetypal DGT reactions using density functional theory (DFT) at the OLYP/TZ2P level. The main trends in reactivity are rationalized using the activation strain model of chemical reactivity. In this model, the shape of the reaction profile DeltaE(zeta) and the height of the overall reaction barrier DeltaE( not equal)=DeltaE(zeta=zeta(TS)) is interpreted in terms of the strain energy DeltaE(strain)(zeta) associated with deforming the reactants along the reaction coordinate zeta plus the interaction energy DeltaE(int)(zeta) between these deformed reactants: DeltaE(zeta)=DeltaE(strain)(zeta)+DeltaE(int)(zeta). We also use an alternative fragmentation and a valence bond model for analyzing the character of the transition states. PMID:19852009

  6. Effect of different solvent on the photocatalytic activity of ZnIn2S4 for selective oxidation of aromatic alcohols to aromatic aldehydes under visible light irradiation

    NASA Astrophysics Data System (ADS)

    Su, Li; Ye, Xiangju; Meng, Sugang; Fu, Xianliang; Chen, Shifu

    2016-10-01

    A series of ternary chalcogenides, zinc indium sulphide (ZnIn2S4), were synthesized by a simple solvothermal method with different solvents. The structure, textural, and optical properties of the resulting materials were thoroughly characterized by several techniques. The as-prepared ZnIn2S4 samples could all be employed as excellent photocatalysts to activate O2 for selective oxidation of aromatic alcohols to aromatic aldehydes under visible light illumination. The results showed that ZnIn2S4 prepared in ethanol solvent (ZIS-EtOH) exhibited the highest photocatalytic activity among the screened samples. The differences of photocatalytic performance for ZnIn2S4 samples prepared in different media were mainly attributed to the different levels of exposed {0001} special facets caused by the exposure extent of the basic crystal plane. In addition, rad O2- and positive holes were proved to be the main active species during the photocatalytic process. Combined with the previous reports, a possible photocatalytic mechanism for the selective oxidation of benzyl alcohol to benzaldehyde over ZnIn2S4 sample was proposed.

  7. Gas chromatography-mass spectrometric determination of polycyclic aromatic hydrocarbons in five species of fish from three sites in the Arabian Gulf.

    PubMed

    Al-Saleh, Iman; Al-Doush, Inaam

    2002-06-01

    A gas chromatography-mass spectrmetroic (GC-MS) method was developed to measure six polycyclic aromatic hydrocarbons (PAHs) in 54 fish samples. Five fish species highly consumed by the local population (shrimps, Emperors, Rabbitfish, Doublebar Bream and Greasy Grouper) were selected from three different sites on the Gulf coast of Saudi Arabia where agricultural, municipal and petroleum industry activities take place. Variations in PAH levels among the three sites were not significant. Total concentrations of PAHs benzo(a)anthracene, chrysene, and benzo(b)fluoranthene ranged from non-detectable to 44.9 microg kg(-1). In this study, concentrations of benzo(a)anthracene, chrysene, benzo(b)fluoranthene and total PAHs greater than the acceptable tolerance limit (1 microg kg(-1)) were found in 68.5, 40.7, 51.9 and 83.3% of the fish samples, respectively. PAH contents in fish vary considerably with species; Doublebar bream contain the highest while shrimps contain the lowest. This pilot study clearly shows that the consumption of fish could be a source of exposure of the local population to PAHs. Since there is a consensus on the substantial contribution of PAHs to cancer in humans, it would be interesting to conduct further research in order to determine the magnitude of the problem along other coastal regions of Saudi Arabia.

  8. Urinary 1-hydroxypyrene as a biomarker of polycyclic aromatic hydrocarbons exposure of workers on a contaminated site: influence of exposure conditions.

    PubMed

    Dor, F; Haguenoer, J M; Zmirou, D; Empereur-Bissonnet, P; Jongeneelen, F J; Nedellec, V; Person, A; Ferguson, C C; Dab, W

    2000-04-01

    The aim of the study was to determine the exposure levels of workers to polycyclic aromatic hydrocarbons on gasworks sites by the measurement of urinary 1-hydroxypyrene. Start-shift and end-shift urine samples were taken every day during an entire week (Monday to Friday), once in November and a second time in June. Four groups of workers were selected according to their activity. Increased exposure was only found among volunteers involved in the remediation of a site, 0.16 to 2.31 mumol/mol creatinine in non-smokers. The median of the non-smoker referent group was 0.02 mumol/mol creatinine (95% confidence interval, 0.01 to 0.04). Smokers had greater exposure levels than non-smokers in every group. Within and between variability was around 200%. Assessment of the exposure of persons on contaminated soil is possible, with the condition that the exposed subjects come in direct contact with the soil. PMID:10774508

  9. Comparison of mussels and semi-permeable membrane devices as intertidal monitors of polycyclic aromatic hydrocarbons at oil spill sites.

    PubMed

    Boehm, Paul D; Page, David S; Brown, John S; Neff, Jerry M; Edward Bence, A

    2005-07-01

    Side-by-side comparisons of polycyclic aromatic hydrocarbon (PAH) concentrations in resident blue mussels (Mytilus trossulus) and in semi-permeable membrane devices (SPMDs) were made at four sites in Prince William Sound, Alaska. SPMDs were deployed for approximately 30 days on the surface of the beach sediment at three tidal elevations on each shore and in 0.5 m deep open pits in the middle intertidal zone. Total PAH (TPAH) concentrations in mussels and in SPMDs were correlated, but the PAH compositions were different. The lower molecular weight PAH were relatively more abundant in the SPMDs than in the mussels at oiled and HA sites. TPAH concentrations in SPMDs deployed in pits and mussels collected adjacent to those pits at oiled sites were higher than in SPMDs and mussels from non-pitted SPMD locations approximately 3-15 m from the pits. Pitting released buried oil making its PAH bioavailable. SPMDs deployed in the supratidal zone (+4.0 m tidal elevation) were exposed to atmospheric contaminants for a large fraction of the deployment time and accumulated primarily pyrogenic (combustion-sourced) PAH from the atmosphere. The SPMD strips supplied by the manufacturer contained significant amounts (approximately 125 ng/strip) of primarily alkylated 2-3 ring PAH. These blank levels make SPMDs unsuitable for shoreline assessments when environmental PAH concentrations are low. Consequently, where available, mussels are recommended for use in assessments of the bioavailability of buried oil residues sequestered in intertidal sediments following an oil spill. Mussels are the preferred monitoring tool when the assessments involve food-chain effects. At locations where the absence of mussels necessitates the use of SPMDs or other passive sampling devices, their limitations need to be carefully considered in the interpretation of results.

  10. Concentrations of polycyclic aromatic hydrocarbons: Their potential health risks and sources at three non-urban sites in Japan.

    PubMed

    Jadoon, Waqar A; Sakugawa, Hiroshi

    2016-09-18

    This investigation was undertaken to monitor particulate polycyclic aromatic hydrocarbons (PAHs) concentrations in order to determine their emission sources and potential human health risks in remote and rural areas of Japan. Seventeen PAHs in aerosol samples collected in remote (Kamihaya), coastal (Hiki) and inland (Higashi-Hiroshima) areas of Japan during 2013-2014 were analyzed using gas chromatography/mass spectrometry. Total PAH (Σ17PAH) concentrations in aerosol samples were in the range of 0.08-6.51 ng m(-3), 0.09-4.74 ng m(-3), and 0.21-6.53 ng m(-3) at Kamihaya, Hiki, and Higashi-Hiroshima sites, with mean concentrations of 1.63, 1.18, and 2.43 ng m(-3), respectively. Significant seasonal variation in concentrations occurred at Hiki and Higashi-Hiroshima, while no significant variation occurred at Kamihaya. Ambient air temperature greatly affected PAH concentrations in Higashi-Hiroshima, but had only moderate effects in Kamihaya and Hiki. Wind direction also influenced the concentrations of PAHs. Vehicle exhaust, industrial emissions, biomass combustion, and domestic heating and cooking were identified as the main PAH emission sources using principal component analysis. Backward trajectory calculations showed that domestically generated PAHs were significant in Kamihaya and Hiki, while in Higashi-Hiroshima concentrations were mainly influenced by long-range transport. The incremental lifetime lung cancer risk had values of 3.38 × 10(-5) and 1.84 × 10(-5) at Higashi-Hiroshima and Hiki, which are greater than the US EPA acceptable level (10(-6)). Typically, 5-6-ring PAHs contributed 95% to this overall health risk, of which benzo(a)pyrene was the largest contributor, followed by dibenz(a,h)anthracene at both residential sites. Clearly, stricter guidelines for PAHs need to be implemented at these sites to protect the population.

  11. Concentrations of polycyclic aromatic hydrocarbons: Their potential health risks and sources at three non-urban sites in Japan.

    PubMed

    Jadoon, Waqar A; Sakugawa, Hiroshi

    2016-09-18

    This investigation was undertaken to monitor particulate polycyclic aromatic hydrocarbons (PAHs) concentrations in order to determine their emission sources and potential human health risks in remote and rural areas of Japan. Seventeen PAHs in aerosol samples collected in remote (Kamihaya), coastal (Hiki) and inland (Higashi-Hiroshima) areas of Japan during 2013-2014 were analyzed using gas chromatography/mass spectrometry. Total PAH (Σ17PAH) concentrations in aerosol samples were in the range of 0.08-6.51 ng m(-3), 0.09-4.74 ng m(-3), and 0.21-6.53 ng m(-3) at Kamihaya, Hiki, and Higashi-Hiroshima sites, with mean concentrations of 1.63, 1.18, and 2.43 ng m(-3), respectively. Significant seasonal variation in concentrations occurred at Hiki and Higashi-Hiroshima, while no significant variation occurred at Kamihaya. Ambient air temperature greatly affected PAH concentrations in Higashi-Hiroshima, but had only moderate effects in Kamihaya and Hiki. Wind direction also influenced the concentrations of PAHs. Vehicle exhaust, industrial emissions, biomass combustion, and domestic heating and cooking were identified as the main PAH emission sources using principal component analysis. Backward trajectory calculations showed that domestically generated PAHs were significant in Kamihaya and Hiki, while in Higashi-Hiroshima concentrations were mainly influenced by long-range transport. The incremental lifetime lung cancer risk had values of 3.38 × 10(-5) and 1.84 × 10(-5) at Higashi-Hiroshima and Hiki, which are greater than the US EPA acceptable level (10(-6)). Typically, 5-6-ring PAHs contributed 95% to this overall health risk, of which benzo(a)pyrene was the largest contributor, followed by dibenz(a,h)anthracene at both residential sites. Clearly, stricter guidelines for PAHs need to be implemented at these sites to protect the population. PMID:27314274

  12. Aromatic plants play an important role in promoting soil biological activity related to nitrogen cycling in an orchard ecosystem.

    PubMed

    Chen, Xinxin; Song, Beizhou; Yao, Yuncong; Wu, Hongying; Hu, Jinghui; Zhao, Lingling

    2014-02-15

    Aromatic plants can substantially improve the diversity and structure of arthropod communities, as well as reduce the number of herbivore pests and regulate the abundance of predators and parasitoids. However, it is not clear whether aromatic plants are also effective in improving soil quality by enhancing nutrient cycling. Here, field experiments are described involving intercropping with aromatic plants to investigate their effect on soil nitrogen (N) cycling in an orchard ecosystem. The results indicate that the soil organic nitrogen and available nitrogen contents increased significantly in soils intercropped with aromatic plants. Similarly, the activities of soil protease and urease increased, together with total microbial biomass involved in N cycling, including nitrifying bacteria, denitrifying bacteria and azotobacters, as well as the total numbers of bacteria and fungi. This suggests that aromatic plants improve soil N cycling and nutrient levels by enriching the soil in organic matter through the regulation of both the abundance and community structure of microorganisms, together with associated soil enzyme activity, in orchard ecosystems. PMID:24342101

  13. Aromatic plants play an important role in promoting soil biological activity related to nitrogen cycling in an orchard ecosystem.

    PubMed

    Chen, Xinxin; Song, Beizhou; Yao, Yuncong; Wu, Hongying; Hu, Jinghui; Zhao, Lingling

    2014-02-15

    Aromatic plants can substantially improve the diversity and structure of arthropod communities, as well as reduce the number of herbivore pests and regulate the abundance of predators and parasitoids. However, it is not clear whether aromatic plants are also effective in improving soil quality by enhancing nutrient cycling. Here, field experiments are described involving intercropping with aromatic plants to investigate their effect on soil nitrogen (N) cycling in an orchard ecosystem. The results indicate that the soil organic nitrogen and available nitrogen contents increased significantly in soils intercropped with aromatic plants. Similarly, the activities of soil protease and urease increased, together with total microbial biomass involved in N cycling, including nitrifying bacteria, denitrifying bacteria and azotobacters, as well as the total numbers of bacteria and fungi. This suggests that aromatic plants improve soil N cycling and nutrient levels by enriching the soil in organic matter through the regulation of both the abundance and community structure of microorganisms, together with associated soil enzyme activity, in orchard ecosystems.

  14. Low dielectric response in enzyme active site

    PubMed Central

    Mertz, Edward L.; Krishtalik, Lev I.

    2000-01-01

    The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

  15. Depth heterogeneity of fully aromatic polyamide active layers in reverse osmosis and nanofiltration membranes.

    PubMed

    Coronell, Orlando; Mariñas, Benito J; Cahill, David G

    2011-05-15

    We studied the depth heterogeneity of fully aromatic polyamide (PA) active layers in commercial reverse osmosis (RO) and nanofiltration (NF) membranes by quantifying near-surface (i.e., top 6 nm) and volume-averaged properties of the active layers using X-ray photoelectron spectrometry (XPS) and Rutherford backscattering spectrometry (RBS), respectively. Some membranes (e.g., ESPA3 RO) had active layers that were depth homogeneous with respect to the concentration and pK(a) distribution of carboxylic groups, degree of polymer cross-linking, concentration of barium ion probe that associated with ionized carboxylic groups, and steric effects experienced by barium ion. Other membranes (e.g., NF90 NF) had active layers that were depth heterogeneous with respect to the same properties. Our results therefore support the existence of both depth-homogeneous and depth-heterogeneous active layers. It remains to be assessed whether the depth heterogeneity consists of gradually changing properties throughout the active layer depth or of distinct sublayers with different properties.

  16. New Quantitative Structure-Activity Relationship Models Improve Predictability of Ames Mutagenicity for Aromatic Azo Compounds.

    PubMed

    Manganelli, Serena; Benfenati, Emilio; Manganaro, Alberto; Kulkarni, Sunil; Barton-Maclaren, Tara S; Honma, Masamitsu

    2016-10-01

    Existing Quantitative Structure-Activity Relationship (QSAR) models have limited predictive capabilities for aromatic azo compounds. In this study, 2 new models were built to predict Ames mutagenicity of this class of compounds. The first one made use of descriptors based on simplified molecular input-line entry system (SMILES), calculated with the CORAL software. The second model was based on the k-nearest neighbors algorithm. The statistical quality of the predictions from single models was satisfactory. The performance further improved when the predictions from these models were combined. The prediction results from other QSAR models for mutagenicity were also evaluated. Most of the existing models were found to be good at finding toxic compounds but resulted in many false positive predictions. The 2 new models specific for this class of compounds avoid this problem thanks to a larger set of related compounds as training set and improved algorithms.

  17. [Assessment of exposure to cancerogenic aromatic hydrocarbon during controlled-access highways management activities].

    PubMed

    Martinotti, I; Cirla, A M; Cottica, D; Cirla, P E

    2011-01-01

    The purpose of this study was an integrated assessment of exposure to benzene and Polycyclic Aromatic Hydrocarbons (PAH) in 29 workers employed to manage a controlled-access highways. A campaign was performed in summertime by environmental monitoring (active and passive airborne personal sampler), as well as by biological monitoring (urine samples of the beginning and of the end of daily shift, baseline after two days of vacation). The measured environmental levels did not differ from background environmental concentrations found in a metropolitan area (i.e. benzo[a]pyrene < 1 ng/m3; benzene < 5 mcg/m3), and the results of biological monitoring were in agreement and were compatible with extra-professional habits of the investigated subjects (1-hydroxipyrene 50-990 ng/g creatinine; unmetabolized benzene 15-2010 ng/I; t-t muconic acid < 4-222 mcg/g creatinine).

  18. [Distribution, formation, carcinogenic and mutagenic activities of nitro derivatives of polycyclic aromatic hydrocarbons].

    PubMed

    Khesina, A Ia; Makhover, M S; Khitrovo, I A

    1989-01-01

    Nitro-PAHs (nitro-substituted derivatives of polycyclic aromatic hydrocarbons) are a class of chemical compounds with high biologic activity. They have been detected in samples of air pollutants, diesel and gasoline engine exhausts, in airplane exhaust emissions, cigarette smoke condensate, emissions of coke ovens, wood-burning fireplaces, coal-fired plants, in food and tea. Concentrations of nitro-PAHs have been compared with those of PAHs present in air pollutant samples and emissions from different sources. Information on the environmental occurrence, formation, and decomposition of nitro-PAHs in the atmosphere is given. Biologic effects (carcinogenic and mutagenic) of pure nitro-PAHs and nitro-PAHs-containing complex mixtures are discussed.

  19. New Quantitative Structure-Activity Relationship Models Improve Predictability of Ames Mutagenicity for Aromatic Azo Compounds.

    PubMed

    Manganelli, Serena; Benfenati, Emilio; Manganaro, Alberto; Kulkarni, Sunil; Barton-Maclaren, Tara S; Honma, Masamitsu

    2016-10-01

    Existing Quantitative Structure-Activity Relationship (QSAR) models have limited predictive capabilities for aromatic azo compounds. In this study, 2 new models were built to predict Ames mutagenicity of this class of compounds. The first one made use of descriptors based on simplified molecular input-line entry system (SMILES), calculated with the CORAL software. The second model was based on the k-nearest neighbors algorithm. The statistical quality of the predictions from single models was satisfactory. The performance further improved when the predictions from these models were combined. The prediction results from other QSAR models for mutagenicity were also evaluated. Most of the existing models were found to be good at finding toxic compounds but resulted in many false positive predictions. The 2 new models specific for this class of compounds avoid this problem thanks to a larger set of related compounds as training set and improved algorithms. PMID:27413112

  20. Photoactivated polycyclic aromatic hydrocarbon toxicity in medaka (Oryzias latipes) embryos: relevance to environmental risk in contaminated sites.

    PubMed

    Diamond, Stephen A; Mount, David R; Mattson, Vincent R; Heinis, Larry J; Highland, Terry L; Adams, Andy D; Simcik, Matthew F

    2006-11-01

    The hazard for photoactivated toxicity of polycyclic aromatic hydrocarbons (PAHs) has been clearly demonstrated; however, to our knowledge, the risk in contaminated systems has not been characterized. To address this question, a median lethal dose (LD50) for fluoranthene photoactivated toxicity in medaka (Orvzias latipes) embryos was determined experimentally and then compared with ultraviolet-A (UV-A; 320-400 nm) radiation exposures in a PAH-contaminated field site. The dose metric, J/cm2/ microg fluoranthene/g egg wet weight, provided the means to estimate risk as the depth where the LD50 level would be exceeded at realistic field PAH concentrations, based on estimates of UV-A exposure. The estimates were made using 30 years of solar radiation data for Duluth (MN, USA) and measurements of water-column UV-A transmittance in a PAH-contaminated field site. Medaka embryo failure was strongly related to tissue PAH concentration and UV-A exposure. The LD50 was estimated to be 12.64 J/cm2/ microg fluoranthene/g egg wet weight; the 95% confidence interval was 8.46 to 19.7 J/cm2/microg fluoranthene/g egg wet weight. Embryo failures were characterized by undifferentiated cell proliferation that occurred very early in development. No partial effects or embryo/larval malformations were observed. Estimates of the depth at which the LD50 would be exceeded in the contaminated field site ranged from 10.7 cm (clear-sky conditions and lowest attenuation) to 0.0 cm (cloudy conditions and highest attenuation). Similar calculations were done using water-column attenuation estimates from 12 sites across the Great Lakes (USA). For these, the depths at which the LD50 would be exceeded ranged from 0.00 to 271.6 cm under the conditions described above. These results suggest that PAH phototoxicity may be a risk factor in specific contaminated sites, and they provide a framework for assessing that risk. PMID:17089726

  1. Antibacterial activities of essential oils from eight Greek aromatic plants against clinical isolates of Staphylococcus aureus.

    PubMed

    Alexopoulos, A; Kimbaris, A C; Plessas, S; Mantzourani, I; Theodoridou, I; Stavropoulou, E; Polissiou, M G; Bezirtzoglou, E

    2011-12-01

    Aromatic plants have been used widely to extend the shelf life of foods but at the same time research is undergoes for their properties as antibacterial agents in clinical use. Although there are promising results for the antimicrobial properties of various essential oils against environmental or food-isolated strains of Staphylococcus aureus, limited work has been done concerning these properties against clinical isolates of this pathogen. S. aureus is responsible for an increase number of nosocomial infections and at the same time exhibits increased resistance to synthetic agents. In this study, essential oils from eight aromatic plants common in Greece were isolated by hydrodistillation, analyzed by gas chromatography (GC) and GC/mass spectrometry (GC/MS) for their chemical components and tested for their antimicrobial activities against 24 clinical isolates of S. aureus. The methods used were disk diffusion and broth dilution in order to determine the Minimum Inhibitory Concentration (MIC). Our results showed that essential oils from Origanum vulgare and Origanum dictamnus were active against S. aureus when tested by disk diffusion, but exhibited increased MIC values (>256 mg/L) with the dilution method. In contrast, the reference strain NCTC 6571 showed to be extremely sensitive in most of the oils tested (MICs 0.25-32.0 mg/L) and resistant only to the essential oil from Ocimum basilicum. Therefore, there is no evidence of a potential clinical use for those essential oils and further research is needed in order to determine if they could substitute efficiently synthetic antibiotics or, perhaps be used in combination. PMID:21521657

  2. Chemical composition and antimicrobial activity of the essential oil from the edible aromatic plant Aristolochia delavayi.

    PubMed

    Li, Zhi-Jian; Njateng, Guy S S; He, Wen-Jia; Zhang, Hong-Xia; Gu, Jian-Long; Chen, Shan-Na; Du, Zhi-Zhi

    2013-11-01

    The essential oil obtained by hydrodistillation from the aerial parts of Aristolochia delavayi Franch. (Aristolochiaceae), a unique edible aromatic plant consumed by the Nakhi (Naxi) people in Yunnan, China, was investigated using GC/MS analysis. In total, 95 components, representing more than 95% of the oil composition, were identified, and the main constituents found were (E)-dec-2-enal (52.0%), (E)-dodec-2-enal (6.8%), dodecanal (3.35%), heptanal (2.88%), and decanal (2.63%). The essential oil showed strong inhibitory activity (96% reduction) of the production of bacterial volatile sulfide compounds (VSC) by Klebsiella pneumoniae, an effect that was comparable with that of the reference compound citral (91% reduction). Moreover, the antimicrobial activity of the essential oil and the isolated major compound against eight bacterial and six fungal strains were evaluated. The essential oil showed significant antibacterial activity against Providencia stuartii and Escherichia coli, with minimal inhibitory concentrations (MIC) ranging from 3.9 to 62.5 μg/ml. The oil also showed strong inhibitory activity against the fungal strains Trichophyton ajelloi, Trichophyton terrestre, Candida glabrata, Candida guilliermondii, and Cryptococcus neoformans, with MIC values ranging from 3.9 to 31.25 μg/ml, while (E)-dec-2-enal presented a lower antifungal activity than the essential oil. PMID:24243612

  3. Accumulation and bioconcentration of polycyclic aromatic hydrocarbons in a nearshore estuarine environment near a Pensacola (Florida) creosote contamination site

    USGS Publications Warehouse

    Elder, J.F.; Dresler, P.V.

    1988-01-01

    Long-term accumulation of creosote wastes at a wood-preserving facility near Pensacola, Florida, has produced high levels of organic contamination of groundwaters near Pensacola Bay. Impacts of this contamination on the nearshore environment of the bay were examined by analysis of water, sediment and tissues of two mollusc species. One of the species (Thais haemastoma) was native to the study area. Individuals of the other test species (Crassostrea virginica) were placed in cages at the test sites for a 6-week period. Contamination at the nearshore estuarine sites was assessed by comparison to a control site in an uncontaminated area of the bay, as well as a small stream which forms a direct surface-water link between the creosote storage ponds and the bay. The study focused on polycyclic aromatic hydrocarbons (PAH), the primary components of creosote. Very little PAH in water or in the surface layer of estuarine sediments was detected, despite heavy pollution of the stream sediments. This is attributed to various degradation processes which attack the PAH compounds once they discharge into the estuary, and to the likelihood of intermittent and localised release of contaminants to the estuary. Examination of sediment cores and mollusc tissues, which provide a record integrated over time and space, revealed some accumulation of a few PAH, notably fluoranthene, pyrene, benzo(a)anthracene, chrysene and phenanthrene. In the sediments, the highest concentrations of these compounds appeared below the surface, within a depth range of 8-13 cm. Bioaccumulation of fluoranthene, pyrene and phenanthrene in both mollusc species was up to ten times greater at test sites than at the control site. This contrasts with naphthalene, the bioaccumulation of which was no greater at test sites than at the control site. These differences in bioaccumulation factors relate to structural chemistry of the compounds which control their solubility, bioavailability, susceptibility to degradation

  4. Cytosolic activation of aromatic and heterocyclic amines. Inhibition by dicoumarol and enhancement in viral hepatitis B.

    PubMed Central

    De Flora, S; Bennicelli, C; D'Agostini, F; Izzotti, A; Camoirano, A

    1994-01-01

    The aromatic amines 2-aminofluorene (2AF), 2-acetylaminofluorene, and 2-aminoanthracene, and the heterocyclic amines 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), 2-amino-3,4-dimethylimidazo[4,5-f]quinoline, and 3-amino-1-methyl-SH-pyrido[4,3-b]indole (Trp-P-2) were activated by rat liver cytosolic fractions to form mutagenic metabolites in Salmonella typhimurium strains TA98, TA98NR, and TA98/1,8-DNP6. In the case of the Trp-P-2, the cytosolic activation was even more potent than the microsomal activation, which is classically ascribed to N-hydroxylation and subsequent esterification. The cytosolic activation was a) NADPH-dependent, b) induced by pretreatment of rats with 3-methylcholanthrene and especially Aroclor 1254 but not by phenobarbital, and c) inhibited by dicoumarol. The hypothesis is that, following a preliminary oxidative step in the cytosol (pure cytosolic activation) or in microsomes via prostaglandin H synthase (mixed microsomal-cytosolic activation), an oxidized intermediate of amino compounds may serve as substrate for DT diaphorase activity and bielectronically reduced to the corresponding N-hydroxyamino derivative. Purified DT diaphorase, in the presence of either NADPH or NADH as electron donor, produced mutagenic derivatives from IQ and Trp-P-2. An NADPH-dependent activation of Trp-P-2 also occurred in the liver cytosol of woodchucks (Marmota monax), but was not inhibited by dicoumarol. As previously demonstrated with liver S-12 fractions in both humans and woodchucks, the cytosolic activation of Trp-P-2 was enhanced in animals affected by hepatitis B virus infection. This enhanced metabolism, which persisted even after appearance of primary hepatocellular carcinoma in virus carriers, is likely to be ascribed to mechanisms other than DT diaphorase induction, such as glutathione depletion. PMID:7534225

  5. Induction of mixed-function oxidase activity in mouse lymphoid tissues by polycyclic aromatic hydrocarbons

    SciTech Connect

    Griffin, G.D.; Egan, B.Z.; Lee, N.E.; Burtis, C.A.

    1986-01-01

    Polycyclic aromatic hydrocarbon (PAH) exposure can cause mixed-function oxidase (MFO) enzyme induction in certain tissues of various organisms. Measurements of such induction might serve as a useful bioindicator of human exposure to PAHs, provided readily obtainable human tissues can be utilized for such measurements. The authors have investigated the MFO activity in various lymphoid tissues of the C3H mouse as a model system and have studied the effect of systemic PAH treatment on such enzyme activity. An MFO enzyme assay was used to measure the activity of 7-ethoxyresorufin deethylase, an enzyme activity that may be specific for the cytochrome P-448 subset of MFO enzymes (those enzymes that are induced in cells or tissues following PAH administration). Intraperitoneal injection of mice with 180 mg/kg (4.6 mg) benzo(a)pyrene (BaP) or 160 mg/kg (4.0 mg) 3-methylcholanthrene (MC) produced a significant induction in MFO activity in mouse spleen S9 fractions 48 h after the injection. Induction ratios (induced activity/control activity) between 4 and 5 were seen with BaP; MC produced induction ratios of 2.5-3.0. Enzyme activity was not induced in the spleen within 16 h following BaP or MC administration. Other experiments indicated that MFO activity could be induced in thymus cells 48 h after either BaP or MC treatment. Treatment with BaP or MC did produce significant enzyme induction in the liver and lung tissues from the animals both 16 and 48 h after chemical treatment.

  6. Pilot study of aromatic hydrocarbon adsorption characteristics of disposable filtering facepiece respirators that contain activated carbon.

    PubMed

    Rozzi, Tony; Snyder, Jay; Novak, Debra

    2012-01-01

    Disposable filtering facepiece respirators (FFRs) used by health care workers are not designed to reduce the inhalation of volatile organic compounds (VOCs). Smoke-generating surgical procedures release VOCs and have been associated with the following complaints: foul smell, headaches, nausea, irritated throat and lungs, and asthma. Organic vapor FFRs that contain activated carbon are used by industrial workers to provide odor relief. These respirators remove irritating odors but are not marketed as respirators that provide respiratory protection against a gas or vapor. This study investigated the aromatic hydrocarbon adsorption capabilities of nuisance organic vapor (OV) FFRs. Three OV FFR models were tested to determine the 10% breakthrough time of three aromatic hydrocarbons at ambient room temperature and relative humidity. All respirator models were exposed to each vapor separately in three duplicate tests (n = 27). The respirator was sealed with silicone to an AVON-ISI headform that was placed in a chamber and exposed to VOC-laden air (20 ppm, 37 L/min). Periodically, gas samples were directed to an SRI gas chromatograph (Model 8610C) for analysis. All respirators performed similarly. The average 10% breakthrough values for all tests were at least 64 min, 96 min, and 110 min for benzene, toluene, and xylene, respectively. Respirators were tested with challenge concentrations at nuisance levels (20 ppm) and did not exceed 10% breakthrough values for at least 61 min. While the results of this pilot study hold promise, there is a need for further investigation and validation to determine the effectiveness of nuisance FFRs in mitigating organic vapors such as benzene, toluene, and xylene. PMID:22978813

  7. PHOTOACTIVATED POLYCYCLIC AROMATIC HYDROCARBON TOXICITY IN MEDAKA (ORYZIAS LATIPES) EMBRYOS: RELEVANCE TO ENVIRONMENTAL RISK IN CONTAMINATED SITES

    EPA Science Inventory

    The hazard for photoactivated toxicity of polycyclic aromatic hydrocarbons (PAHs) has been clearly demonstrated; however, to our knowledge, the risk in contaminated systems has not been characterized. To address this question, a median lethal dose (LD50) for fluoranthene photoa...

  8. Aromatic L-amino acids activate the calcium-sensing receptor.

    PubMed

    Conigrave, Arthur D; Mun, Hee-Chang; Lok, Hiu-Chuen

    2007-06-01

    The calcium-sensing receptor (CaR) is recognized as a member of class 3 of the G-protein coupled receptor superfamily. Members of this subgroup, which have large N-terminal extracellular domains, include receptors that respond specifically to the amino acid glutamate; receptors that respond to the glutamate analogue, gamma-amino butyric acid; and several receptors that act as broad-spectrum amino acid sensors. The CaR is one of these broad-spectrum amino acid sensors that, along with several other members of the subgroup, also responds to extracellular Ca2+. In this mini-review, we consider evidence that the CaR is a sensor of aromatic amino acids, that it has broad-spectrum amino acid sensing properties, that it provides an amino acid binding site in its extracellular N-terminal Venus Fly Trap domain, and that amino acids have a physiological impact on systems in which the CaR is expressed.

  9. Antimicrobial Activity of Seven Essential Oils From Iranian Aromatic Plants Against Common Causes of Oral Infections

    PubMed Central

    Zomorodian, Kamiar; Ghadiri, Pooria; Saharkhiz, Mohammad Jamal; Moein, Mohammad Reza; Mehriar, Peiman; Bahrani, Farideh; Golzar, Tahereh; Pakshir, Keyvan; Fani, Mohammad Mehdi

    2015-01-01

    Background: Over the past two decades, there has been a growing trend in using oral hygienic products originating from natural resources such as essential oils (EOs) and plant extracts. Seven aromatic plants used in this study are among popular traditional Iranian medicinal plants with potential application in modern medicine as anti-oral infectious diseases. Objectives: This study was conducted to determine the chemical composition and antimicrobial activities of essential oils from seven medicinal plants against pathogens causing oral infections. Materials and Methods: The chemical compositions of EOs distilled from seven plants were analyzed by gas chromatography/mass spectrometry (GC/MS). These plants included Satureja khuzestanica, S. bachtiarica, Ocimum sanctum, Artemisia sieberi, Zataria multiflora, Carum copticum and Oliveria decumbens. The antimicrobial activity of the essential oils was evaluated by broth micro-dilution in 96 well plates as recommended by the Clinical and Laboratory Standards Institute (CLSI) methods. Results: The tested EOs inhibited the growth of examined oral pathogens at concentrations of 0.015-16 µL/mL. Among the examined oral pathogens, Enterococcus faecalis had the highest Minimum Inhibitory Concentrations (MICs) and Minimum Microbicidal Concentrations (MMCs). Of the examined EOs, S. khuzestanica, Z. multiflora and S. bachtiarica, showed the highest antimicrobial activities, respectively, while Artemisia sieberi exhibited the lowest antimicrobial activity. Conclusions: The excellent antimicrobial activities of the tested EOs might be due to their major phenolic or alcoholic monoterpenes with known antimicrobial activities. Hence, these EOs can be possibly used as an antimicrobial agent in treatment and control of oral pathogens. PMID:25793100

  10. Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity

    DOE PAGES

    Johnson, Christopher W.; Salvachua, Davinia; Khanna, Payal; Smith, Holly; Peterson, Darren J.; Beckham, Gregg T.

    2016-04-22

    The conversion of biomass-derived sugars and aromatic molecules to cis,cis-muconic acid (referred to hereafter as muconic acid or muconate) has been of recent interest owing to its facile conversion to adipic acid, an important commodity chemical. Metabolic routes to produce muconate from both sugars and many lignin-derived aromatic compounds require the use of a decarboxylase to convert protocatechuate (PCA, 3,4-dihydroxybenzoate) to catechol (1,2-dihydroxybenzene), two central aromatic intermediates in this pathway. Several studies have identified the PCA decarboxylase as a metabolic bottleneck, causing an accumulation of PCA that subsequently reduces muconate production. A recent study showed that activity of the PCAmore » decarboxylase is enhanced by co-expression of two genetically associated proteins, one of which likely produces a flavin-derived cofactor utilized by the decarboxylase. Using entirely genome-integrated gene expression, we have engineered Pseudomonas putida KT2440-derived strains to produce muconate from either aromatic molecules or sugars and demonstrate in both cases that co-expression of these decarboxylase associated proteins reduces PCA accumulation and enhances muconate production relative to strains expressing the PCA decarboxylase alone. In bioreactor experiments, co-expression increased the specific productivity (mg/g cells/h) of muconate from the aromatic lignin monomer p-coumarate by 50% and resulted in a titer of >15 g/L. In strains engineered to produce muconate from glucose, co-expression more than tripled the titer, yield, productivity, and specific productivity, with the best strain producing 4.92+/-0.48 g/L muconate. Furthermore, this study demonstrates that overcoming the PCA decarboxylase bottleneck can increase muconate yields from biomass-derived sugars and aromatic molecules in industrially relevant strains and cultivation conditions.« less

  11. Aromaticity and Antiaromaticity in Transition-Metal Systems

    SciTech Connect

    Zubarev, Dmitry Y.; Averkiev, Boris B.; Zhai, Hua Jin; Wang, Lai S.; Boldyrev, Alexander I.

    2007-11-05

    Aromaticity is an important concept in chemistry primarily for hydrocarbon compounds, but it has been extended to compounds containing transition-metal atoms. Recent findings of aromaticity and antiaromaticy in all-metal clusters have stimulated further researches in describing the chemical bonding, structures, and stability in transition-metal clusters and compounds on the basis of aromaticity and antiaromaticity, which are reviewed here. The presence of d-orbitals endows much more diverse chemistry, structure, and chemical bonding to transition-metal clusters and compounds. One interesting feature is the existence of a new type of δ-aromaticity, in addition to σ- and π-aromaticity that are only possible for main group compounds. Another striking characteristic in the chemical bonding of transition-metal systems is the multi-fold nature of aromaticity, antiaromaticity, or even conflicting aromaticity. Separate sets of counting rules have been proposed for cyclic transition-metal systems to account for the three types of σ-, π-, and δ-aromaticity/antiaromaticity. The diverse transition-metal clusters and compounds reviewed here indicate that multiple aromaticity and antiaromaticity may be much more common in chemistry than one would anticipate. It is hoped that the current review will stimulate interest in further understanding the structure and bonding, on the basis of aromaticity and antiaromaticity, of other known or unknown transition-metal systems, such as the active sites of enzymes or other biomolecules, which contain transition-metal atoms and clusters.

  12. Mycelia promote active transport and spatial dispersion of polycyclic aromatic hydrocarbons.

    PubMed

    Furuno, Shoko; Foss, Susan; Wild, Ed; Jones, Kevin C; Semple, Kirk T; Harms, Hauke; Wick, Lukas Y

    2012-05-15

    To cope with heterogeneous subsurface environments mycelial microorganisms have developed a unique ramified growth form. By extending hyphae, they can obtain nutrients from remote places and transport them even through air gaps and in small pore spaces, repectively. To date, studies have been focusing on the role that networks play in the distribution of nutrients. Here, we investigated the role of mycelia for the translocation of nonessential substances, using polycyclic aromatic hydrocarbons (PAHs) as model compounds. We show that the hyphae of the mycelial soil oomycete Pythium ultimum function as active translocation vectors for a wide range of PAHs. Visualization by two-photon excitation microscopy (TPEM) demonstrated the uptake and accumulation of phenanthrene (PHE) in lipid vesicles and its active transport by cytoplasmic streaming of the hyphae ('hyphal pipelines'). In mycelial networks, contaminants were translocated over larger distances than by diffusion. Given their transport capacity and ubiquity, hyphae may substantially distribute remote hydrophobic contaminants in soil, thereby improving their bioavailability to bacterial degradation. Hyphal contaminant dispersal may provide an untapped potential for future bioremediation approaches. PMID:22559873

  13. Autonomic nervous function and localization of cerebral activity during lavender aromatic immersion.

    PubMed

    Duan, Xudong; Tashiro, Manabu; Wu, Di; Yambe, Tomoyuki; Wang, Qingtian; Sasaki, Takehisa; Kumagai, Kazuaki; Luo, Yun; Nitta, Shin-ichi; Itoh, Masatoshi

    2007-01-01

    Changes in the autonomic nervous activity can be induced by various sensory and emotional stimuli. The authors examined whether the power spectral analysis of heart rate variability (HRV) could detect changes in autonomic tone following a lavender aroma treatment or not. Healthy young women (n=10, 23+/-3 years old) underwent continuous electrocardiographic (ECG) monitoring before and after (10, 20, 30 minutes) the lavender fragrance stimuli. HRV was expressed by three indices: low (0.04-0.15 Hz) and high (0.15-0.40 Hz) frequency components (nLF and nHF, respectively) as well as LF/HF ratio. Increases in the parasympathetic tone were observed after the lavender fragrance stimulus as seen as increases in the HF component and decreases in the LF/HF. Additional measurement with positron emission tomography (PET) demonstrated the regional metabolic activation in the orbitofrontal, posterior cingulate gyrus, brainstem, thalamus and cerebellum, as well as the reductions in the pre/post-central gyrus and frontal eye field. These results suggested that lavender aromatic treatment induced not only relaxation but also increased arousal level in these subjects. PMID:17361051

  14. Mosquito larvicidal activity of aromatic medicinal plant oils against Aedes aegypti and Culex pipiens pallens.

    PubMed

    Lee, Hoi-Seon

    2006-06-01

    Larvicidal activity of essential oils derived from 11 aromatic medicinal plants against early 4th-stage larvae of Aedes aegypti and Culex pipiens pallens was tested in the laboratory. At 100 ppm, the essential oils of all plants caused 100% mortality against Ae. aegypti and Cx. pipiens pallens. At 25 ppm, the essential oils of Citrus bergamia, Cuminum myrrha, and Pimenta racemosa caused 100% mortality against larvae of Ae. aegypti and Cx. pipiens pallens. The oil of C. begamia caused 32.5% and 24.5% mortality against Ae. aegypti and Cx. pipiens pallens at 12.5 ppm, but 24.2% and 0% mortality against Ae. aegypti and Cx. pipiens pallens at 6.25 ppm, respectively. The oil of P. racemosa caused 52.3% and 38.5% mortality against Ae. aegypti and Cx. pipiens pallens at 12.5 ppm, but 32.2% and 0% mortality against Ae. aegypti and Cx. pipiens pallens at 6.25 ppm, respectively. The larvicidal activity of oils of C. bergamia, C. myrrha, and P. racemosa was significantly reduced when used at 6.25 ppm. These plants warrant further studies as possible agents for mosquito control.

  15. Autonomic nervous function and localization of cerebral activity during lavender aromatic immersion.

    PubMed

    Duan, Xudong; Tashiro, Manabu; Wu, Di; Yambe, Tomoyuki; Wang, Qingtian; Sasaki, Takehisa; Kumagai, Kazuaki; Luo, Yun; Nitta, Shin-ichi; Itoh, Masatoshi

    2007-01-01

    Changes in the autonomic nervous activity can be induced by various sensory and emotional stimuli. The authors examined whether the power spectral analysis of heart rate variability (HRV) could detect changes in autonomic tone following a lavender aroma treatment or not. Healthy young women (n=10, 23+/-3 years old) underwent continuous electrocardiographic (ECG) monitoring before and after (10, 20, 30 minutes) the lavender fragrance stimuli. HRV was expressed by three indices: low (0.04-0.15 Hz) and high (0.15-0.40 Hz) frequency components (nLF and nHF, respectively) as well as LF/HF ratio. Increases in the parasympathetic tone were observed after the lavender fragrance stimulus as seen as increases in the HF component and decreases in the LF/HF. Additional measurement with positron emission tomography (PET) demonstrated the regional metabolic activation in the orbitofrontal, posterior cingulate gyrus, brainstem, thalamus and cerebellum, as well as the reductions in the pre/post-central gyrus and frontal eye field. These results suggested that lavender aromatic treatment induced not only relaxation but also increased arousal level in these subjects.

  16. Human aldo-keto reductases and the metabolic activation of polycyclic aromatic hydrocarbons.

    PubMed

    Penning, Trevor M

    2014-11-17

    Aldo-keto reductases (AKRs) are promiscuous NAD(P)(H) dependent oxidoreductases implicated in the metabolic activation of polycyclic aromatic hydrocarbons (PAH). These enzymes catalyze the oxidation of non-K-region trans-dihydrodiols to the corresponding o-quinones with the concomitant production of reactive oxygen species (ROS). The PAH o-quinones are Michael acceptors and can form adducts but are also redox-active and enter into futile redox cycles to amplify ROS formation. Evidence exists to support this metabolic pathway in humans. The human recombinant AKR1A1 and AKR1C1-AKR1C4 enzymes all catalyze the oxidation of PAH trans-dihydrodiols to PAH o-quinones. Many human AKRs also catalyze the NADPH-dependent reduction of the o-quinone products to air-sensitive catechols, exacerbating ROS formation. Moreover, this pathway of PAH activation occurs in a panel of human lung cell lines, resulting in the production of ROS and oxidative DNA damage in the form of 8-oxo-2'-deoxyguanosine. Using stable-isotope dilution liquid chromatography tandem mass spectrometry, this pathway of benzo[a]pyrene (B[a]P) metabolism was found to contribute equally with the diol-epoxide pathway to the activation of this human carcinogen in human lung cells. Evaluation of the mutagenicity of anti-B[a]P-diol epoxide with B[a]P-7,8-dione on p53 showed that the o-quinone produced by AKRs was the more potent mutagen, provided that it was permitted to redox cycle, and that the mutations observed were G to T transversions, reminiscent of those observed in human lung cancer. It is concluded that there is sufficient evidence to support the role of human AKRs in the metabolic activation of PAH in human lung cell lines and that they may contribute to the causation of human lung cancer.

  17. Human Aldo-Keto Reductases and the Metabolic Activation of Polycyclic Aromatic Hydrocarbons

    PubMed Central

    2015-01-01

    Aldo-keto reductases (AKRs) are promiscuous NAD(P)(H) dependent oxidoreductases implicated in the metabolic activation of polycyclic aromatic hydrocarbons (PAH). These enzymes catalyze the oxidation of non-K-region trans-dihydrodiols to the corresponding o-quinones with the concomitant production of reactive oxygen species (ROS). The PAH o-quinones are Michael acceptors and can form adducts but are also redox-active and enter into futile redox cycles to amplify ROS formation. Evidence exists to support this metabolic pathway in humans. The human recombinant AKR1A1 and AKR1C1–AKR1C4 enzymes all catalyze the oxidation of PAH trans-dihydrodiols to PAH o-quinones. Many human AKRs also catalyze the NADPH-dependent reduction of the o-quinone products to air-sensitive catechols, exacerbating ROS formation. Moreover, this pathway of PAH activation occurs in a panel of human lung cell lines, resulting in the production of ROS and oxidative DNA damage in the form of 8-oxo-2′-deoxyguanosine. Using stable-isotope dilution liquid chromatography tandem mass spectrometry, this pathway of benzo[a]pyrene (B[a]P) metabolism was found to contribute equally with the diol-epoxide pathway to the activation of this human carcinogen in human lung cells. Evaluation of the mutagenicity of anti-B[a]P-diol epoxide with B[a]P-7,8-dione on p53 showed that the o-quinone produced by AKRs was the more potent mutagen, provided that it was permitted to redox cycle, and that the mutations observed were G to T transversions, reminiscent of those observed in human lung cancer. It is concluded that there is sufficient evidence to support the role of human AKRs in the metabolic activation of PAH in human lung cell lines and that they may contribute to the causation of human lung cancer. PMID:25279998

  18. C-O cleavage of aromatic oxygenates over ruthenium catalysts. A computational study of reactions at step sites.

    PubMed

    Chiu, Cheng-chau; Genest, Alexander; Borgna, Armando; Rösch, Notker

    2015-06-21

    We studied the C-O cleavage of phenolate and catecholate at step sites of a Ru catalyst using periodic DFT methods at the GGA level. Both C-O scission steps are associated with activation barriers of about 75 kJ mol(-1), hence are significantly more facile than the analogous reactions on Ru terraces. With these computational results, we offer an interpretation of recent experiments on the hydrodeoxygenation of guaiacol (2-methoxyphenol) over Ru/C. We hypothesize that the experimentally observed dependency of the product selectivity on the H2 pressure is related to the availability of step sites on a Ru catalyst.

  19. Active Sites Environmental Monitoring Program: Action levels

    SciTech Connect

    Ashwood, J.S.; Ashwood, T.L.

    1991-10-01

    The Active Sites Environmental Monitoring Program (ASEMP) was established at Oak Ridge National Laboratory to provide for early leak detection and to monitor performance of the active low-level waste disposal facilities in Solid Waste Storage Area (SWSA) 6 and the transuranic waste storage areas in SWSA 5 North. Early leak detection is accomplished by sampling runoff, groundwater, and perched water in burial trenches. Sample results are compared to action levels that represent background contamination by naturally occurring and fallout-derived radionuclides. 15 refs., 3 figs., 12 tabs.

  20. Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations.

    PubMed

    Rahimi, Mehran; van der Meer, Jan-Ytzen; Geertsema, Edzard M; Poddar, Harshwardhan; Baas, Bert-Jan; Poelarends, Gerrit J

    2016-07-01

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which catalyzes enol-keto tautomerization as part of a degradative pathway for aromatic hydrocarbons, promiscuously catalyzes various carbon-carbon bond-forming reactions. These include the aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde. Here, we demonstrate that 4-OT can be engineered into a more efficient aldolase for this condensation reaction, with a >5000-fold improvement in catalytic efficiency (kcat /Km ) and a >10(7) -fold change in reaction specificity, by exploring small libraries in which only "hotspots" are varied. The hotspots were identified by systematic mutagenesis (covering each residue), followed by a screen for single mutations that give a strong improvement in the desired aldolase activity. All beneficial mutations were near the active site of 4-OT, thus underpinning the notion that new catalytic activities of a promiscuous enzyme are more effectively enhanced by mutations close to the active site. PMID:27238293

  1. Warm dust and aromatic bands as quantitative probes of star-formation activity

    NASA Astrophysics Data System (ADS)

    Förster Schreiber, N. M.; Roussel, H.; Sauvage, M.; Charmandaris, V.

    2004-05-01

    We combine samples of spiral galaxies and starburst systems observed with ISOCAM on board ISO to investigate the reliability of mid-infrared dust emission as a quantitative tracer of star formation activity. The total sample covers very diverse galactic environments and probes a much wider dynamic range in star formation rate density than previous similar studies. We find that both the monochromatic 15 μm continuum and the 5-8.5 μm emission constitute excellent indicators of the star formation rate as quantified by the Lyman continuum luminosity LLyc, within specified validity limits which are different for the two tracers. Normalized to projected surface area, the 15 μm continuum luminosity Σ15 μm,ct is directly proportional to ΣLyc over several orders of magnitude. Two regimes are distinguished from the relative offsets in the observed relationship: the proportionality factor increases by a factor of ≈5 between quiescent disks in spiral galaxies, and moderate to extreme star-forming environments in circumnuclear regions of spirals and in starburst systems. The transition occurs near ΣLyc ˜ 102 L⊙ pc-2 and is interpreted as due to very small dust grains starting to dominate the emission at 15 μm over aromatic species above this threshold. The 5-8.5 μm luminosity per unit projected area is also directly proportional to the Lyman continuum luminosity, with a single conversion factor from the most quiescent objects included in the sample up to ΣLyc ˜ 104 L⊙ pc-2, where the relationship then flattens. The turnover is attributed to depletion of aromatic band carriers in the harsher conditions prevailing in extreme starburst environments. The observed relationships provide empirical calibrations useful for estimating star formation rates from mid-infrared observations, much less affected by extinction than optical and near-infrared tracers in deeply embedded H II regions and obscured starbursts, as well as for theoretical predictions from evolutionary

  2. Genetic engineering activates biosynthesis of aromatic fumaric acid amides in the human pathogen Aspergillus fumigatus.

    PubMed

    Kalb, Daniel; Heinekamp, Thorsten; Lackner, Gerald; Scharf, Daniel H; Dahse, Hans-Martin; Brakhage, Axel A; Hoffmeister, Dirk

    2015-03-01

    The Aspergillus fumigatus nonribosomal peptide synthetase FtpA is among the few of this species whose natural product has remained unknown. Both FtpA adenylation domains were characterized in vitro. Fumaric acid was identified as preferred substrate of the first and both l-tyrosine and l-phenylalanine as preferred substrates of the second adenylation domain. Genetically engineered A. fumigatus strains expressed either ftpA or the regulator gene ftpR, encoded in the same cluster of genes, under the control of the doxycycline-inducible tetracycline-induced transcriptional activation (tet-on) cassette. These strains produced fumaryl-l-tyrosine and fumaryl-l-phenylalanine which were identified by liquid chromatography and high-resolution mass spectrometry. Modeling of the first adenylation domain in silico provided insight into the structural requirements to bind fumaric acid as peptide synthetase substrate. This work adds aromatic fumaric acid amides to the secondary metabolome of the important human pathogen A. fumigatus which was previously not known as a producer of these compounds.

  3. Mineralisation and primary biodegradation of aromatic organophosphorus flame retardants in activated sludge.

    PubMed

    Jurgens, Sharona S; Helmus, Rick; Waaijers, Susanne L; Uittenbogaard, Dirk; Dunnebier, Dorien; Vleugel, Melissa; Kraak, Michiel H S; de Voogt, Pim; Parsons, John R

    2014-09-01

    Halogen-free flame retardants (HFFRs), such as the aromatic organophosphorus flame retardants (OPFRs) triphenyl phosphate (TPHP), resorcinol bis(diphenylphosphate) (PBDPP) and bisphenol A bis(diphenylphosphate) (BPA-BDPP) have been proposed as potential replacements for brominated flame retardants in polymers and textiles. Although these OPFRs are already marketed, their environmental fate and effects are poorly characterised. The aim of this study was therefore to determine the mineralisation and primary biodegradation of these OPFRs by activated sludge. Mineralisation was monitored by measuring CO2 production by means of GC analysis, whereas primary biodegradation was monitored by LC-MS/MS analysis of the OPFRs and their potential metabolites. TPHP was biodegraded and mineralised most rapidly and achieved the requirement for ready biodegradability (60% of theoretical maximum mineralisation). Primary biodegradation was also rapid for PBDPP, but 60% mineralisation was not achieved within the time of the test, suggesting that transformation products of PBDPP may accumulate. Primary degradation of BPA-BDPP was very slow and very low CO2 production was also observed. Based on these results, TPHP and to a lesser extent PBDPP appear to be suitable replacements for the more environmentally persistent brominated flame retardants. PMID:24997924

  4. Genetic Engineering Activates Biosynthesis of Aromatic Fumaric Acid Amides in the Human Pathogen Aspergillus fumigatus

    PubMed Central

    Kalb, Daniel; Heinekamp, Thorsten; Lackner, Gerald; Scharf, Daniel H.; Dahse, Hans-Martin; Brakhage, Axel A.

    2014-01-01

    The Aspergillus fumigatus nonribosomal peptide synthetase FtpA is among the few of this species whose natural product has remained unknown. Both FtpA adenylation domains were characterized in vitro. Fumaric acid was identified as preferred substrate of the first and both l-tyrosine and l-phenylalanine as preferred substrates of the second adenylation domain. Genetically engineered A. fumigatus strains expressed either ftpA or the regulator gene ftpR, encoded in the same cluster of genes, under the control of the doxycycline-inducible tetracycline-induced transcriptional activation (tet-on) cassette. These strains produced fumaryl-l-tyrosine and fumaryl-l-phenylalanine which were identified by liquid chromatography and high-resolution mass spectrometry. Modeling of the first adenylation domain in silico provided insight into the structural requirements to bind fumaric acid as peptide synthetase substrate. This work adds aromatic fumaric acid amides to the secondary metabolome of the important human pathogen A. fumigatus which was previously not known as a producer of these compounds. PMID:25527545

  5. Aerobic metabolism and cardiac activity in the descendants of zebrafish exposed to pyrolytic polycyclic aromatic hydrocarbons.

    PubMed

    Lucas, Julie; Perrichon, Prescilla; Nouhaud, Marine; Audras, Alexandre; Leguen, Isabelle; Lefrancois, Christel

    2014-12-01

    The increase of anthropogenic activities on coastal areas induces discharges of polycyclic aromatic hydrocarbons (PAHs) in aquatic ecosystem. PAH effects depend not only on their concentration and the way of contamination but also on the different developmental stages of the organism. Zebrafish were exposed to relevant concentration of pyrolytic PAHs from the first meal (i.e., 5-day post fertilization, dpf) to mature adults. Parental effect of this type of exposure was evaluated through the assessment of aerobic metabolic scope, cardiac frequency, and cardiac mRNA expression on larval and/or embryo progeny of contaminated fish. Our results suggest that cardiac frequency increased in larval descendants of fish exposed to the environmental concentration of pyrolytic PAHs (i.e., 5 ng.g(-1) of food), while a lack of effect on aerobic metabolism in 5 dpf larvae was highlighted. A surexpression of mRNA related to the cardiac calcium transporting ATPase atp2a2a, a protein essential for contraction, is in accordance with this increasing cardiac frequency. Even if cardiac development genes cmlc1 and tnnt2a were not affected at early life stages tested, complementary work on cardiac structure could be interesting to better understand PAHs action.

  6. Targeting of Arenavirus RNA Synthesis by a Carboxamide-Derivatized Aromatic Disulfide with Virucidal Activity

    PubMed Central

    Sepúlveda, Claudia S.; García, Cybele C.; Levingston Macleod, Jesica M.

    2013-01-01

    Several arenaviruses can cause severe hemorrhagic fever (HF) in humans, representing a public health threat in endemic areas of Africa and South America. The present study characterizes the potent virucidal activity of the carboxamide-derivatized aromatic disulfide NSC4492, an antiretroviral zinc finger-reactive compound, against Junín virus (JUNV), the causative agent of Argentine HF. The compound was able to inactivate JUNV in a time and temperature-dependent manner, producing more than 99 % reduction in virus titer upon incubation with virions at 37°C for 90 min. The ability of NSC4492-treated JUNV to go through different steps of the multiplication cycle was then evaluated. Inactivated virions were able to bind and enter into the host cell with similar efficiency as control infectious particles. In contrast, treatment with NSC4492 impaired the capacity of JUNV to drive viral RNA synthesis, as measured by quantitative RT-PCR, and blocked viral protein expression, as determined by indirect immunofluorescence. These results suggest that the disulfide NSC4492 targets on the arenavirus replication complex leading to impairment in viral RNA synthesis. Additionally, analysis of VLP produced in NSC4492-treated cells expressing JUNV matrix Z protein revealed that the compound may interact with Z resulting in an altered aggregation behavior of this protein, but without affecting its intrinsic self-budding properties. The potential perspectives of NSC4492 as an inactivating vaccinal compound for pathogenic arenaviruses are discussed. PMID:24278404

  7. Polybenzimidazole via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G. (Inventor)

    1994-01-01

    Di(hydroxyphenyl)benzimidazole monomers were prepared from phenyl-4-hydroxybenzoate and aromatic bis(o-diamine)s. These monomers were used in the synthesis of soluble polybenzimidazoles. The reaction involved the aromatic nucleophilic displacement of various di(hydroxyphenyl)benzimidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds in the presence of an alkali metal base. These polymers exhibited lower glass transition temperatures, improved solubility, and better compression moldability over their commercial counterparts.

  8. Characterization of active sites in zeolite catalysts

    SciTech Connect

    Eckert, J.; Bug, A.; Nicol, J.M.

    1997-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Atomic-level details of the interaction of adsorbed molecules with active sites in catalysts are urgently needed to facilitate development of more effective and/or environmentally benign catalysts. To this end the authors have carried out neutron scattering studies combined with theoretical calculations of the dynamics of small molecules inside the cavities of zeolite catalysts. The authors have developed the use of H{sub 2} as a probe of adsorption sites by observing the hindered rotations of the adsorbed H{sub 2} molecule, and they were able to show that an area near the four-rings is the most likely adsorption site for H{sub 2} in zeolite A while adsorption of H{sub 2} near cations located on six-ring sites decreases in strength as Ni {approximately} Co > Ca > Zn {approximately} Na. Vibrational and rotational motions of ethylene and cyclopropane adsorption complexes were used as a measure for zeolite-adsorbate interactions. Preliminary studies of the binding of water, ammonia, and methylamines were carried out in a number of related guest-host materials.

  9. Identification of acidic and aromatic residues in the Zta activation domain essential for Epstein-Barr virus reactivation.

    PubMed

    Deng, Z; Chen, C J; Zerby, D; Delecluse, H J; Lieberman, P M

    2001-11-01

    Epstein-Barr virus (EBV) lytic cycle transcription and DNA replication require the transcriptional activation function of the viral immediate-early protein Zta. We describe a series of alanine substitution mutations in the Zta activation domain that reveal two functional motifs based on amino acid composition. Alanine substitution of single or paired hydrophobic aromatic amino acid residues resulted in modest transcription activation defects, while combining four substitutions of aromatic residues (F22/F26/W74/F75) led to more severe transcription defects. Substitution of acidic amino acid residue E27, D35, or E54 caused severe transcription defects on most viral promoters. Promoter- and cell-specific defects were observed for some substitution mutants. Aromatic residues were required for Zta interaction with TFIIA-TFIID and the CREB-binding protein (CBP) and for stimulation of CBP histone acetyltransferase activity in vitro. In contrast, acidic amino acid substitution mutants interacted with TFIIA-TFIID and CBP indistinguishably from the wild type. The nuclear domain 10 (ND10) protein SP100 was dispersed by most Zta mutants, but acidic residue mutations led to reduced, while aromatic substitution mutants led to increased SP100 nuclear staining. Acidic residue substitution mutants had more pronounced defects in transcription activation of endogenous viral genes in latently infected cells and for viral replication, as measured by the production of infectious virus. One mutant, K12/F13, was incapable of stimulating EBV lytic replication but had only modest transcription defects. These results indicate that Zta stimulates viral reactivation through two nonredundant structural motifs, one of which interacts with general transcription factors and coactivators, and the other has an essential but as yet not understood function in lytic transcription.

  10. Iridium-catalyzed intermolecular dehydrogenative silylation of polycyclic aromatic compounds without directing groups.

    PubMed

    Murai, Masahito; Takami, Keishi; Takai, Kazuhiko

    2015-03-16

    This study describes the iridium-catalyzed intermolecular dehydrogenative silylation of C(sp(2))-H bonds of polycyclic aromatic compounds without directing groups. The reaction produced various arylsilanes through both Si-H and C-H bond activation, with hydrogen as the sole byproduct. Reactivity was affected by the electronic nature of the aromatic compounds, and silylation of electron-deficient and polycyclic aromatic compounds proceeded efficiently. Site-selectivity was controlled predominantly by steric factors. Therefore, the current functionalization proceeded with opposite chemo- and site-selectivity compared to that observed for general electrophilic functionalization of aromatic compounds.

  11. Ring flips revisited: (13)C relaxation dispersion measurements of aromatic side chain dynamics and activation barriers in basic pancreatic trypsin inhibitor.

    PubMed

    Weininger, Ulrich; Modig, Kristofer; Akke, Mikael

    2014-07-22

    Intramolecular motions of proteins are critical for biological function. Transient structural fluctuations underlie a wide range of processes, including enzyme catalysis, ligand binding to buried sites, and generic protein motions, such as 180° rotation of aromatic side chains in the protein interior, but remain poorly understood. Understanding the dynamics and molecular nature of concerted motions requires characterization of their rates and energy barriers. Here we use recently developed (13)C transverse relaxation dispersion methods to improve our current understanding of aromatic ring flips in basic pancreatic trypsin inhibitor (BPTI). We validate these methods by benchmarking ring-flip rates against the three previously characterized cases in BPTI, namely, Y23, Y35, and F45. Further, we measure conformational exchange for one additional aromatic ring, F22, which can be interpreted in terms of a flip rate of 666 s(-1) at 5 °C. Upon inclusion of our previously reported result that Y21 also flips slowly [Weininger, U., et al. (2013) J. Phys. Chem. B 117, 9241-9247], the (13)C relaxation dispersion experiments thus reveal relatively slow ring-flip rates for five of eight aromatic residues in BPTI. These results are in contrast with previous reports, which have estimated that all rings, except Y23, Y35, and F45, flip with a high rate at ambient temperature. The (13)C relaxation dispersion data result in an updated rank order of ring-flip rates in BPTI, which agrees considerably better with that estimated from a recent 1 ms molecular dynamics trajectory than do previously published NMR data. However, significant quantitative differences remain between experiment and simulation, in that the latter yields flip rates that are in many cases too fast by 1-2 orders of magnitude. By measuring flip rates across a temperature range of 5-65 °C, we determined the activation barriers of ring flips for Y23, Y35, and F45. Y23 and F45 have identical activation parameters

  12. Activation of the cnidarian oxidative stress response by ultraviolet radiation, polycyclic aromatic hydrocarbons and crude oil

    PubMed Central

    Tarrant, A. M.; Reitzel, A. M.; Kwok, C. K.; Jenny, M. J.

    2014-01-01

    Organisms are continuously exposed to reactive chemicals capable of causing oxidative stress and cellular damage. Antioxidant enzymes, such as superoxide dismutases (SODs) and catalases, are present in both prokaryotes and eukaryotes and provide an important means of neutralizing such oxidants. Studies in cnidarians have previously documented the occurrence of antioxidant enzymes (transcript expression, protein expression and/or enzymatic activity), but most of these studies have not been conducted in species with sequenced genomes or included phylogenetic analyses, making it difficult to compare results across species due to uncertainties in the relationships between genes. Through searches of the genome of the sea anemone Nematostella vectensis Stephenson, one catalase gene and six SOD family members were identified, including three copper/zinc-containing SODs (CuZnSODs), two manganese-containing SODs (MnSODs) and one copper chaperone of SOD (CCS). In 24 h acute toxicity tests, juvenile N. vectensis showed enhanced sensitivity to combinations of ultraviolet radiation (UV) and polycyclic aromatic hydrocarbons (PAHs, specifically pyrene, benzo[a]pyrene and fluoranthene) relative to either stressor alone. Adult N. vectensis exhibited little or no mortality following UV, benzo[a]pyrene or crude oil exposure but exhibited changes in gene expression. Antioxidant enzyme transcripts were both upregulated and downregulated following UV and/or chemical exposure. Expression patterns were most strongly affected by UV exposure but varied between experiments, suggesting that responses vary according to the intensity and duration of exposure. These experiments provide a basis for comparison with other cnidarian taxa and for further studies of the oxidative stress response in N. vectensis. PMID:24436378

  13. Aromatic plants essential oils activity on Fusarium verticillioides Fumonisin B(1) production in corn grain.

    PubMed

    López, A G; Theumer, M G; Zygadlo, J A; Rubinstein, H R

    2004-10-01

    The minimum inhibitory concentration (MIC) of Origanum vulgare, Aloysia triphylla, Aloysia polystachya and Mentha piperita essential oils (EOs) against Fusarium verticillioides M 7075 (F. moniliforme, Sheldon) were assessed, using the semisolid agar antifungal susceptibility (SAAS) technique. O. vulgare, A. triphylla, A. polystachya and M. piperita EOs were evaluated at final concentrations of 10, 20, 40, 50, 100, 200, 250, 500, 1000 and 1500 epsilonl per litre (epsilonl/l) of culture medium. A. triphylla and O. vulgare EOs showed the highest inhibitory effects on F. verticillioides mycelial development. This inhibition was observed at 250 and 500 epsilonl/l for EOs coming from Aloysia triphylla and O. vulgare, respectively. Thus, the effects of EOs on FB(1) production were evaluated using corn grain (Zea mays) as substrate. The EOs were inserted on the 5th, 10th, 15th and 20th day of maize postinoculation with a conidia suspension of F. verticillioides. O. vulgare and A. triphylla were applied to give final concentrations of 30 ppm and 45 ppm, respectively. Different effects were observed in the toxicogenicity at the 20th day treatment. The O. vulgare EO decreased the production level of FB(1) (P < 0.01) while A. triphyla EO increased it (P < 0.001) with respect to those obtained in the inoculated maize, not EOs treated. Results obtained in the present work indicate that fumonisin production could be inhibited or stimulated by some constituents of EOs coming from aromatic plants. Further studies should be performed to identify the components of EOs with modulatory activity on the growth and fumonisins production of Fusarium verticillioides.

  14. Aromatic plants essential oils activity on Fusarium verticillioides Fumonisin B(1) production in corn grain.

    PubMed

    López, A G; Theumer, M G; Zygadlo, J A; Rubinstein, H R

    2004-10-01

    The minimum inhibitory concentration (MIC) of Origanum vulgare, Aloysia triphylla, Aloysia polystachya and Mentha piperita essential oils (EOs) against Fusarium verticillioides M 7075 (F. moniliforme, Sheldon) were assessed, using the semisolid agar antifungal susceptibility (SAAS) technique. O. vulgare, A. triphylla, A. polystachya and M. piperita EOs were evaluated at final concentrations of 10, 20, 40, 50, 100, 200, 250, 500, 1000 and 1500 epsilonl per litre (epsilonl/l) of culture medium. A. triphylla and O. vulgare EOs showed the highest inhibitory effects on F. verticillioides mycelial development. This inhibition was observed at 250 and 500 epsilonl/l for EOs coming from Aloysia triphylla and O. vulgare, respectively. Thus, the effects of EOs on FB(1) production were evaluated using corn grain (Zea mays) as substrate. The EOs were inserted on the 5th, 10th, 15th and 20th day of maize postinoculation with a conidia suspension of F. verticillioides. O. vulgare and A. triphylla were applied to give final concentrations of 30 ppm and 45 ppm, respectively. Different effects were observed in the toxicogenicity at the 20th day treatment. The O. vulgare EO decreased the production level of FB(1) (P < 0.01) while A. triphyla EO increased it (P < 0.001) with respect to those obtained in the inoculated maize, not EOs treated. Results obtained in the present work indicate that fumonisin production could be inhibited or stimulated by some constituents of EOs coming from aromatic plants. Further studies should be performed to identify the components of EOs with modulatory activity on the growth and fumonisins production of Fusarium verticillioides. PMID:15702272

  15. Adsorption of aromatic organic acids onto high area activated carbon cloth in relation to wastewater purification.

    PubMed

    Ayranci, Erol; Duman, Osman

    2006-08-25

    Adsorption of aromatic organic acids: benzoic acid (BA), salicylic acid (SA), p-aminobenzoic acid (pABA) and nicotinic acid (NA), onto high area activated carbon cloth from solutions in 0.4 M H(2)SO(4), in water at natural pH, in 0.1 M NaOH and also from solutions having pH 7.0 were studied by in situ UV-spectroscopic technique. The first-order rate law was found to be applicable for the kinetic data of adsorption. The rates and extents of adsorption of the organic acids were the highest from water or 0.4 M H(2)SO(4) solutions and the lowest from 0.1 M NaOH solution. The order of rates and extents of adsorption of the four organic acids in each of the four solutions (0.4 M H(2)SO(4), water, solution of pH 7.0 and 0.1 M NaOH) was determined as SA>BA>NA approximately pABA. These observed orders were explained in terms of electrostatic, dispersion and hydrogen bonding interactions between the surface and the adsorbate species, taking the charge of the carbon surface and the adsorbate in each solution into account. Adsorption of BA in molecular form or in benzoate form was analyzed by treating the solution as a mixture of two components and applying Lambert-Beer law to two-component system. The adsorption isotherm data of the systems studied were derived at 30 degrees C and fitted to Langmuir and Freundlich equations. PMID:16442224

  16. Crystallographic Analysis of Active Site Contributions to Regiospecificity in the Diiron Enzyme Toluene 4-Monooxygenase

    SciTech Connect

    Bailey, Lucas J.; Acheson, Justin F.; McCoy, Jason G.; Elsen, Nathaniel L.; Phillips, Jr., George N.; Fox, Brian G.

    2014-10-02

    Crystal structures of toluene 4-monooxygenase hydroxylase in complex with reaction products and effector protein reveal active site interactions leading to regiospecificity. Complexes with phenolic products yield an asymmetric {mu}-phenoxo-bridged diiron center and a shift of diiron ligand E231 into a hydrogen bonding position with conserved T201. In contrast, complexes with inhibitors p-NH{sub 2}-benzoate and p-Br-benzoate showed a {mu}-1,1 coordination of carboxylate oxygen between the iron atoms and only a partial shift in the position of E231. Among active site residues, F176 trapped the aromatic ring of products against a surface of the active site cavity formed by G103, E104 and A107, while F196 positioned the aromatic ring against this surface via a {pi}-stacking interaction. The proximity of G103 and F176 to the para substituent of the substrate aromatic ring and the structure of G103L T4moHD suggest how changes in regiospecificity arise from mutations at G103. Although effector protein binding produced significant shifts in the positions of residues along the outer portion of the active site (T201, N202, and Q228) and in some iron ligands (E231 and E197), surprisingly minor shifts (<1 {angstrom}) were produced in F176, F196, and other interior residues of the active site. Likewise, products bound to the diiron center in either the presence or absence of effector protein did not significantly shift the position of the interior residues, suggesting that positioning of the cognate substrates will not be strongly influenced by effector protein binding. Thus, changes in product distributions in the absence of the effector protein are proposed to arise from differences in rates of chemical steps of the reaction relative to motion of substrates within the active site channel of the uncomplexed, less efficient enzyme, while structural changes in diiron ligand geometry associated with cycling between diferrous and diferric states are discussed for their potential

  17. Active site of ribulosebisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.; Stringer, C.D.; Milanez, S.; Lee, E.H.

    1985-01-01

    Previous affinity labeling studies and comparative sequence analyses have identified two different lysines at the active site of ribulosebisphosphate carboxylase/oxygenase and have suggested their essentiality to function. The essential lysines occupy positions 166 and 329 in the Rhodospirillum rubrum enzyme and positions 175 and 334 in the spinach enzyme. Based on the pH-dependencies of inactivations of the two enzymes by trinitrobenzene sulfonate, Lys-166 (R. rubrum enzyme) exhibits a pK/sub a/ of 7.9 and Lys-334 (spinach enzyme) exhibits a pK/sub a/ of 9.0. These low pK/sub a/ values as well as the enhanced nucleophilicities of the lysyl residues argue that both are important to catalysis rather than to substrate binding. Lys-166 may correspond to the essential base that initiates catalysis and that displays a pK/sub a/ of 7.5 in the pH-curve for V/sub max//K/sub m/. Cross-linking experiments with 4,4'-diisothiocyano-2,2'-disulfonate stilbene demonstrate that the two active-site lysines are within 12 A. 50 refs., 7 figs., 1 tab.

  18. GC-MS-olfactometric characterization of the most aroma-active components in a representative aromatic extract from Iranian saffron (Crocus sativus L.).

    PubMed

    Amanpour, Asghar; Sonmezdag, A Salih; Kelebek, Hasim; Selli, Serkan

    2015-09-01

    Aroma and aroma-active compounds of Iranian saffron (Crocus sativus L.) were analyzed by gas chromatography-mass spectrometry-olfactometry. The saffron aromatic extracts were obtained by four different extraction techniques including solvent-assisted flavour evaporation (SAFE), liquid-liquid extraction (LLE), solid phase extraction (SPE), and simultaneous distillation extraction (SDE) and compared to achieve a representative aromatic extract from saffron. According to sensory analysis, the aromatic extract obtained by SAFE was the most representative of saffron odour. A total of 28 aroma compounds were identified in saffron. Ketones were quantitatively the most dominant volatiles in saffron, followed by aldehydes and acids. Aroma extract dilution analysis (AEDA) was used for the determination of aroma-active compounds of saffron. A total of nine aroma-active compounds were detected in the aromatic extract. On the basis of the flavour dilution (FD) factor, the most powerful aroma active compounds were safranal (FD = 512), 4-ketoisophorone (FD = 256) and dihydrooxophorone (FD = 128).

  19. The doping effect of fluorinated aromatic hydrocarbon solvents on the performance of common olefin metathesis catalysts: application in the preparation of biologically active compounds.

    PubMed

    Samojłowicz, Cezary; Bieniek, Michał; Zarecki, Andrzej; Kadyrov, Renat; Grela, Karol

    2008-12-21

    Aromatic fluorinated hydrocarbons, used as solvents for olefin metathesis reactions, catalysed by standard commercially available Ru precatalysts, allow substantially higher yields to be obtained, especially of challenging substrates, including natural and biologically active compounds.

  20. Synthesis of high specific activity (+)- and (-)-6-( sup 18 F)fluoronorepinephrine via the nucleophilic aromatic substitution reaction

    SciTech Connect

    Ding, Y.S.; Fowler, J.S.; Gatley, S.J.; Dewey, S.L.; Wolf, A.P. )

    1991-02-01

    The first example of a no-carrier-added {sup 18}F-labeled catecholamine, 6-({sup 18}F)fluoronorepinephrine (6-({sup 18}F)FNE), has been synthesized via nucleophilic aromatic substitution. The racemic mixture was resolved on a chiral HPLC column to obtain pure samples of (-)-6-({sup 18}F)FNE and (+)6-({sup 18}F)FNE. Radiochemical yields of 20% at the end of bombardment (EOB) for the racemic mixture (synthesis time 93 min), 6% for each enantiomer (synthesis time 128 min) with a specific activity of 2-5 Ci/mumol at EOB were obtained. Chiral HPLC peak assignment for the resolved enantiomers was achieved by using two independent methods: polarimetric determination and reaction with dopamine beta-hydroxylase. Positron emission tomography (PET) studies with racemic 6-({sup 18}F)FNE show high uptake and retention in the baboon heart. This work demonstrates that nucleophilic aromatic substitution by ({sup 18}F)fluoride ion is applicable to systems having electron-rich aromatic rings, leading to high specific activity radiopharmaceuticals. Furthermore, the suitably protected dihydroxynitrobenzaldehyde 1 may serve as a useful synthetic precursor for the radiosynthesis of other complex {sup 18}F-labeled radiotracers.

  1. A quantum chemical study for exploring the inhibitory effect of nitrogen containing species on the adsorption of polynuclear aromatic hydrocarbons over a Bronsted acid site

    NASA Astrophysics Data System (ADS)

    Celis-Cornejo, C. M.; Garnica Mantilla, M. M.; Baldovino-Medrano, V. G.; Ramírez-Caballero, G. E.

    2016-08-01

    The analysis of the inhibitory effect of nitrogenated compounds on the hydroprocessing and hydropurification of oil derived fuels is important to produce cleaner fuels. In this work, density functional theory calculations were performed to investigate the effect of the nitrogen containing molecules on the adsorption of Polynuclear Aromatic Hydrocarbons (PAHs). Mordenite was chosen as a zeolitic structure for simulating a Bronsted acid site. The character of the acid site was confirmed by both a vibrational frequency calculation and a Bader charge analysis. From the adsorption calculations, it was found that the adsorption energy of PAHs increases with the number of aromatic rings in the structure. Also, the nitrogen containing species possibly inhibit more extensively two and three rings PAHs because of their lower adsorption energies. Finally, it was observed that the nitrogen species tend to drag the proton from the mordenite acid site. This explains the inhibitory effect in the adsorption of PAHs and contributes to understanding the dynamics of hydrocarbon hydroprocessing in refineries.

  2. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  3. Haemolytic activity of aromatic heptaenes. A group of polyene macrolide antifungal antibiotics.

    PubMed

    Cybulska, B; Mazerski, J; Borowski, E; Gary-Bobo, C M

    1984-01-01

    The aromatic heptaene vacidin A induces ion selective channels in human red blood cells. The ion flux induced leads to a secondary effect--colloid osmotic haemolysis. Molecular variations at ionizable polar groups of the antibiotic modify the properties of the permeability pathway concerning intercationic selectivity and the symmetry of ion flux. PMID:6704143

  4. Evaluation of heavy metal and polycyclic aromatic hydrocarbons accumulation in plants from typical industrial sites: potential candidate in phytoremediation for co-contamination.

    PubMed

    Sun, Lu; Liao, Xiaoyong; Yan, Xiulan; Zhu, Ganghui; Ma, Dong

    2014-11-01

    The heavy metal and polycyclic aromatic hydrocarbons (PAHs) contents were evaluated in surface soil and plant samples of 18 wild species collected from 3 typical industrial sites in South Central China. The accumulative characteristics of the plant species for both heavy metal and PAHs were discussed. The simultaneous accumulation of heavy metal and PAHs in plant and soil was observed at all the investigated sites, although disparities in spatial distributions among sites occurred. Both plant and soil samples were characterized by high accumulation for heavy metal at smelting site, moderate enrichment at coke power and coal mining sites, whereas high level of PAHs (16 priority pollutants according to US Environmental Protection Agency) at coke power site, followed sequentially by coal mining and smelting sites. Based on the differences of heavy metal and PAH accumulation behaviors of the studied plant species, heavy metal and PAH accumulation strategies were suggested: Pteris vittata L. and Pteris cretica L. for As and PAHs, Boehmeria nivea (L.) Gaud for Pb, As, and PAHs, and Miscanthus floridulu (Labnll.) Warb for Cu and PAHs. These native plant species could be proposed as promising materials for heavy metal and PAHs combined pollution remediation.

  5. Nucleophilic Aromatic Substitution.

    ERIC Educational Resources Information Center

    Avila, Walter B.; And Others

    1990-01-01

    Described is a microscale organic chemistry experiment which demonstrates one feasible route in preparing ortho-substituted benzoic acids and provides an example of nucleophilic aromatic substitution chemistry. Experimental procedures and instructor notes for this activity are provided. (CW)

  6. C2-substituted aromatic cytokinin sugar conjugates delay the onset of senescence by maintaining the activity of the photosynthetic apparatus.

    PubMed

    Vylíčilová, Hana; Husičková, Alexandra; Spíchal, Lukáš; Srovnal, Josef; Doležal, Karel; Plíhal, Ondřej; Plíhalová, Lucie

    2016-02-01

    Cytokinins are plant hormones with biological functions ranging from coordination of plant growth and development to the regulation of senescence. A series of 2-chloro-N(6)-(halogenobenzylamino)purine ribosides was prepared and tested for cytokinin activity in detached wheat leaf senescence, tobacco callus and Amaranthus bioassays. The synthetic compounds showed significant activity, especially in delaying senescence in detached wheat leaves. They were also tested in bacterial receptor bioassays using both monocot and dicot members of the cytokinin receptor family. Most of the derivatives did not trigger cytokinin signaling via the AHK3 and AHK4 receptors from Arabidopsis thaliana in the bacterial assay, but some of them specifically activated the ZmHK1 receptor from Zea mays and were also more active than the aromatic cytokinin BAP in an ARR5::GUS cytokinin bioassay using transgenic Arabidopsis plants. Whole transcript expression analysis was performed using an Arabidopsis model to gather information about the reprogramming of gene transcription when senescent leaves were treated with selected C2-substituted aromatic cytokinin ribosides. Genome-wide expression profiling revealed that the synthetic halogenated derivatives induced the expression of genes related to cytokinin signaling and metabolism. They also prompted both up- and down-regulation of a unique combination of genes coding for components of the photosystem II (PSII) reaction center, light-harvesting complex II (LHCII), and the oxygen-evolving complex, as well as several stress factors responsible for regulating photosynthesis and chlorophyll degradation. Chlorophyll content and fluorescence analyses demonstrated that treatment with the halogenated derivatives increased the efficiency of PSII photochemistry and the abundance of LHCII relative to DMSO- and BAP-treated controls. These findings demonstrate that it is possible to manipulate and fine-tune leaf longevity using synthetic aromatic cytokinin

  7. Synthesis and antifungal activity of C-21 steroids with an aromatic D ring.

    PubMed

    Sonego, Juan M; Cirigliano, Adriana M; Cabrera, Gabriela M; Burton, Gerardo; Veleiro, Adriana S

    2013-07-01

    Six analogues of salpichrolides with a simplified side chain (6-11) were synthesized using a new methodology to obtain steroids with an aromatic D-ring. The key step was the elimination of HBr in a vicinal dibromo D-homosteroid by treatment with 1,4-diazabicyclo[2.2.2]octane (DABCO). All new compounds were completely characterized by 2D NMR techniques and tested on two fungal pathogenic species, Fusarium virguliforme and Fusarium solani.

  8. Quantitative structure-activity relationship modeling of polycyclic aromatic hydrocarbon mutagenicity by classification methods based on holistic theoretical molecular descriptors.

    PubMed

    Gramatica, Paola; Papa, Ester; Marrocchi, Assunta; Minuti, Lucio; Taticchi, Aldo

    2007-03-01

    Various polycyclic aromatic hydrocarbons (PAHs), ubiquitous environmental pollutants, are recognized mutagens and carcinogens. A homogeneous set of mutagenicity data (TA98 and TA100,+S9) for 32 benzocyclopentaphenanthrenes/chrysenes was modeled by the quantitative structure-activity relationship classification methods k-nearest neighbor and classification and regression tree, using theoretical holistic molecular descriptors. Genetic algorithm provided the selection of the best subset of variables for modeling mutagenicity. The models were validated by leave-one-out and leave-50%-out approaches and have good performance, with sensitivity and specificity ranges of 90-100%. Mutagenicity assessment for these PAHs requires only a few theoretical descriptors of their molecular structure.

  9. Synthesis of Aromatic Retinoids and Curcuminoids and Evaluation of their Antiproliferative, Antiradical, and Anti‐inflammatory Activities

    PubMed Central

    Morzycki, Jacek W.; Rárová, Lucie; Grúz, Jiři; Sawczuk, Tomasz; Kiełczewska, Urszula; Siergiejczyk, Leszek

    2016-01-01

    Abstract Natural retinoids and curcuminoids are known for their broad spectrum of biological properties, such as antioxidant, anti‐inflammatory, antitumor, and so forth. In this work, a convenient synthesis of aromatic retinoids and curcuminoids from vinyl or allyl ketones, and the corresponding alcohols, using olefin metathesis as a key reaction, was elaborated. The best yields and diastereoselectivities were obtained from allylic or homoallylic alcohols by employing the two‐step cross‐metathesis/oxidation procedure. The synthesized analogues were tested for their antiproliferative activity on human cancer cell lines of various origin (leukemia CEM, adenocarcinoma MCF7, cervical carcinoma HeLa) as well as for their antioxidant and anti‐inflammatory activity in vitro. All examined derivatives exhibited strong anti‐inflammatory activity in vitro without affecting cell viability. They also showed strong cytotoxicity against leukemia cell line CEM, except for 18 and 35. The antioxidant activity of the tested compounds was rather weak. PMID:27547644

  10. Synthesis of Aromatic Retinoids and Curcuminoids and Evaluation of their Antiproliferative, Antiradical, and Anti-inflammatory Activities.

    PubMed

    Morzycki, Jacek W; Rárová, Lucie; Grúz, Jiři; Sawczuk, Tomasz; Kiełczewska, Urszula; Siergiejczyk, Leszek; Wojtkielewicz, Agnieszka

    2016-08-01

    Natural retinoids and curcuminoids are known for their broad spectrum of biological properties, such as antioxidant, anti-inflammatory, antitumor, and so forth. In this work, a convenient synthesis of aromatic retinoids and curcuminoids from vinyl or allyl ketones, and the corresponding alcohols, using olefin metathesis as a key reaction, was elaborated. The best yields and diastereoselectivities were obtained from allylic or homoallylic alcohols by employing the two-step cross-metathesis/oxidation procedure. The synthesized analogues were tested for their antiproliferative activity on human cancer cell lines of various origin (leukemia CEM, adenocarcinoma MCF7, cervical carcinoma HeLa) as well as for their antioxidant and anti-inflammatory activity in vitro. All examined derivatives exhibited strong anti-inflammatory activity in vitro without affecting cell viability. They also showed strong cytotoxicity against leukemia cell line CEM, except for 18 and 35. The antioxidant activity of the tested compounds was rather weak. PMID:27547644

  11. Control of active sites in flocculation: Concept of equivalent active sites''

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Flocculation and dispersion of solids are strong functions of the amount and conformation of the adsorbed polymer. Regions of dispersion and flocculation of solids with particular polymer molecules may be deduced from saturation adsorption data. The concept of equivalent active sites'' is proposed to explain flocculation and dispersion behavior irrespective of the amount or conformation of the adsorbed polymer. The concept has been further extended to study the selective flocculation process.

  12. Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase

    PubMed Central

    Piontek, Klaus; Strittmatter, Eric; Ullrich, René; Gröbe, Glenn; Pecyna, Marek J.; Kluge, Martin; Scheibner, Katrin; Hofrichter, Martin; Plattner, Dietmar A.

    2013-01-01

    Aromatic peroxygenases (APOs) represent a unique oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity and were thus recently assigned a distinct EC classification (EC 1.11.2.1). They catalyze, inter alia, oxyfunctionalization reactions of aromatic and aliphatic hydrocarbons with remarkable regio- and stereoselectivities. When compared with cytochrome P450, APOs appear to be the choice enzymes for oxyfunctionalizations in organic synthesis due to their independence from a cellular environment and their greater chemical versatility. Here, the first two crystal structures of a heavily glycosylated fungal aromatic peroxygenase (AaeAPO) are described. They reveal different pH-dependent ligand binding modes. We model the fitting of various substrates in AaeAPO, illustrating the way the enzyme oxygenates polycyclic aromatic hydrocarbons. Spatial restrictions by a phenylalanine pentad in the active-site environment govern substrate specificity in AaeAPO. PMID:24126915

  13. The effect of wind direction on the observed size distribution of particle adsorbed polycyclic aromatic hydrocarbons on an inner city sampling site.

    PubMed

    Schnelle-Kreis, J; Jänsch, T; Wolf, K; Gebefügi, I; Kettrup, A

    1999-08-01

    An investigation of the variability in the size distribution of particle adsorbed polycyclic aromatic hydrocarbons (PAHs) on an inner city sampling site showed differences depending on the wind direction. Particle size distributions of PAHs from outdoor air sampling were measured in Munich from 1994 to 1997. The sampling site is located northeast of a crossing with heavy traffic and southwest of a large inner city park. Depending on the wind direction, three different size distributions of particle adsorbed PAHs were observed. The maximum PAH concentration on very small particles (geometric mean diameter 75 nm) was observed with wind from west to southwest coming directly from the crossing area or the roads with heavy traffic. The maximum PAH concentration on particles with geometric mean diameter of 260 nm was found on days with wind from the built-up area north of the sampling site. On particles with geometric mean diameter of 920 nm the maximum PAH concentration was found on days with main wind directions from northeast to east. On these days the wind is blowing from the direction of the city park nearby. The distribution of particle adsorbed PAHs within different particle size classes is substantially influenced by the distance of the sampling site from strong sources of PAH loaded particulate matter. PMID:11529136

  14. Aromatic residues in the catalytic center of chitinase A from Serratia marcescens affect processivity, enzyme activity, and biomass converting efficiency.

    PubMed

    Zakariassen, Henrik; Aam, Berit Bjugan; Horn, Svein J; Vårum, Kjell M; Sørlie, Morten; Eijsink, Vincent G H

    2009-04-17

    The processive Serratia marcescens chitinases A (ChiA) and B (ChiB) are thought to degrade chitin in the opposite directions. A recent study of ChiB suggested that processivity is governed by aromatic residues in the +1 and +2 (aglycon) subsites close to the catalytic center. To further investigate the roles of aromatic residues in processivity and to gain insight into the structural basis of directionality, we have mutated Trp(167), Trp(275), and Phe(396) in the -3, +1, and +2 subsites of ChiA, respectively, and characterized the hydrolytic activities of the mutants toward beta-chitin and the soluble chitin-derivative chitosan. Although the W275A and F396A mutants showed only modest reductions in processivity, it was almost abolished by the W167A mutation. Thus, although aglycon subsites seem to steer processivity in ChiB, a glycon (-3) subsite seems to be adapted to do so in ChiA, in line with the notion that the two enzymes have different directionalities. Remarkably, whereas all three single mutants and the W167A/W275A double mutant showed reduced efficiency toward chitin, they showed up to 20-fold higher activities toward chitosan. These results show that the processive mechanism is essential for an efficient conversion of crystalline substrates but comes at a large cost in terms of intrinsic enzyme speed. This needs to be taken into account when devising enzymatic strategies for biomass turnover.

  15. Structure-Activity study of retinoid agonists bearing substituted dicarba-closo-dodecaborane. Relation between retinoidal activity and conformation of two aromatic nuclei.

    PubMed

    Endo, Y; Iijima, T; Yaguchi, K; Kawachi, E; Inoue, N; Kagechika, H; Kubo, A; Itai, A

    2001-05-21

    We have investigated the structure activity relationships of the potent retinoid agonist, 4-[4-(2-propyl-1,2-dicarba-closo-dodecaboran-l-yl)phenylamino]benzoic acid (BR403), which we have previously reported. Substitution of a methyl group on the aromatic nucleus or a methyl group on the nitrogen atom, or replacement of the amino group with ether, methylene, carboxyl or 1,1-ethylene greatly decreased the activity. The relatively planar conformation at the phenyl-N-phenyl moiety seems to play a critical role in the appearance of the biological activity.

  16. Polyimidazoles via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor)

    1991-01-01

    Polyimidazoles (Pl) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl)imidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The reactions are carried out in polar aprotic solvents such as N,N-dimethylacetamide, sulfolane, N-methylpyrroldinone, dimethylsulfoxide, or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperature under nitrogen. The di(hydroxyphenyl)imidazole monomers are prepared by reacting an aromatic aldehyde with a dimethoxybenzil or by reacting an aromatic dialdehyde with a methoxybenzil in the presence of ammonium acetate. The di(methoxyphenyl)imidazole is subsequently treated with aqueous hydrobromic acid to give the di(hydroxyphenyl)imidazole monomer. This synthetic route has provided high molecular weight Pl of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the availability of a large variety of activated aromatic dihalides and dinitro compounds.

  17. Polyimidazoles via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor)

    1992-01-01

    Polyimidazoles (PI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl) imidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The reactions are carried out in polar aprotic solvents such as N,N-dimethyl acetamide, sulfolane, N-methylpyrrolidinone, dimethylsulfoxide, or diphenylsulfone using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. The di(hydroxyphenyl) imidazole monomers are prepared by reacting an aromatic aldehyde with a dimethoxybenzil or by reacting an aromatic dialdehyde with a methoxybenzil in the presence of ammonium acetate. The di(methoxyphenyl) imidazole is subsequently treated with aqueous hydrobromic acid to give the di(hydroxphenyl) imidazole monomer. This synthetic route has provided high molecular weight PI of new chemical structure, is economically and synthetically more favorable than other routes, and allows for facile chemical structure variation due to the availability of a large variety of activated aromatic dihalides and dinitro compounds.

  18. Dissecting the active site of a photoreceptor protein

    NASA Astrophysics Data System (ADS)

    Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

    While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

  19. Understanding the fate of polycyclic aromatic hydrocarbons at a forest fire site using a conceptual model based on field monitoring.

    PubMed

    Simon, Erwan; Choi, Sung-Deuk; Park, Min-Kyu

    2016-11-01

    Forest fires are a well-known source of polycyclic aromatic hydrocarbons (PAHs). After forest fires, residual ash above a soil layer can be highly contaminated with PAHs. However, little is known about the fate of these contaminants, particularly about their susceptibility to be transferred deeper into underlying soil or downstream during rainfall events. In this study, meteorological conditions, organic carbon (OC) content, and the 16 US-EPA priority PAHs in unburnt control soil, burnt soil, and ash were monitored for 16 months after a forest fire. Whereas the ash was significantly contaminated with PAHs, the levels of PAHs in the underlying burnt soil were similar to those of the control soil. In the ash bed, the levels of PAHs normalized by OC also decreased. Neither PAHs nor OC lost from the ash bed was substantially transferred to the underlying soil. Instead, significant amounts of PAHs in the ash bed were likely removed by surface runoff. Light PAHs were dominantly emitted from the forest fire, but they showed higher decreasing rates with total precipitation. These findings were explained by a conceptual model for the fate of PAHs, involving four distinct processes related to precipitation and two states of the ash bed.

  20. Understanding the fate of polycyclic aromatic hydrocarbons at a forest fire site using a conceptual model based on field monitoring.

    PubMed

    Simon, Erwan; Choi, Sung-Deuk; Park, Min-Kyu

    2016-11-01

    Forest fires are a well-known source of polycyclic aromatic hydrocarbons (PAHs). After forest fires, residual ash above a soil layer can be highly contaminated with PAHs. However, little is known about the fate of these contaminants, particularly about their susceptibility to be transferred deeper into underlying soil or downstream during rainfall events. In this study, meteorological conditions, organic carbon (OC) content, and the 16 US-EPA priority PAHs in unburnt control soil, burnt soil, and ash were monitored for 16 months after a forest fire. Whereas the ash was significantly contaminated with PAHs, the levels of PAHs in the underlying burnt soil were similar to those of the control soil. In the ash bed, the levels of PAHs normalized by OC also decreased. Neither PAHs nor OC lost from the ash bed was substantially transferred to the underlying soil. Instead, significant amounts of PAHs in the ash bed were likely removed by surface runoff. Light PAHs were dominantly emitted from the forest fire, but they showed higher decreasing rates with total precipitation. These findings were explained by a conceptual model for the fate of PAHs, involving four distinct processes related to precipitation and two states of the ash bed. PMID:27368087

  1. Increased concentrations of polycyclic aromatic hydrocarbons in Alpine streams during annual snowmelt: investigating effects of sampling method, site characteristics, and meteorology.

    PubMed

    Shahpoury, Pourya; Hageman, Kimberly J; Matthaei, Christoph D; Alumbaugh, Robert E; Cook, Michelle E

    2014-10-01

    Silicone passive samplers and macroinvertebrates were used to measure time-integrated concentrations of polycyclic aromatic hydrocarbons (PAHs) in alpine streams during annual snowmelt. The three sampling sites were located near a main highway in Arthur's Pass National Park in the Southern Alps of New Zealand. A similar set of PAH congeners, composed of 2-4 rings, were found in silicone passive samplers and macroinvertebrates. The background PAH concentrations were similar at all sites, implying that proximity to the highway did not affect concentrations. In passive samplers, an increase of PAH concentrations by up to seven times was observed during snowmelt. In macroinvertebrates, the concentration changes were moderate; however, macroinvertebrate sampling did not occur during the main pulse observed in the passive samplers. The extent of vegetation in the catchment appeared to affect the concentration patterns seen at the different stream sites. A strong correlation was found between PAH concentrations in passive samplers and the amount of rainfall in the study area, indicating that the washout of contaminants from snowpack by rainfall was an important process.

  2. Mosquito repellent activity of essential oils of aromatic plants growing in Argentina.

    PubMed

    Gillij, Y G; Gleiser, R M; Zygadlo, J A

    2008-05-01

    Mosquitoes are important vectors of diseases and nuisance pests. Repellents minimize contact with mosquitoes. Repellents based on essential oils (EO) are being developed as an alternative to DEET (N,N-diethyl-m-methylbenzamide), an effective compound that has disadvantages including toxic reactions, and damage to plastic and synthetic fabric. This work evaluated the repellency against Aedes aegypti of EO from aromatic plants that grow in Argentina: Acantholippia seriphioides, Achyrocline satureioides, Aloysia citriodora, Anemia tomentosa, Baccharis spartioides, Chenopodium ambrosioides, Eucalyptus saligna, Hyptis mutabilis, Minthostachys mollis, Rosmarinus officinalis, Tagetes minuta and Tagetes pusilla. Most EO were effective. Variations depending on geographic origin of the plant were detected. At a 90% EO concentration, A. satureoides and T. pusilla were the least repellent. At concentrations of 12.5% B. spartioides, R. officinalis and A. citriodora showed the longest repellency times. Comparisons of the principal components of each EO suggest that limonene and camphor were the main components responsible for the repellent effects.

  3. Mosquito repellent activity of essential oils of aromatic plants growing in Argentina.

    PubMed

    Gillij, Y G; Gleiser, R M; Zygadlo, J A

    2008-05-01

    Mosquitoes are important vectors of diseases and nuisance pests. Repellents minimize contact with mosquitoes. Repellents based on essential oils (EO) are being developed as an alternative to DEET (N,N-diethyl-m-methylbenzamide), an effective compound that has disadvantages including toxic reactions, and damage to plastic and synthetic fabric. This work evaluated the repellency against Aedes aegypti of EO from aromatic plants that grow in Argentina: Acantholippia seriphioides, Achyrocline satureioides, Aloysia citriodora, Anemia tomentosa, Baccharis spartioides, Chenopodium ambrosioides, Eucalyptus saligna, Hyptis mutabilis, Minthostachys mollis, Rosmarinus officinalis, Tagetes minuta and Tagetes pusilla. Most EO were effective. Variations depending on geographic origin of the plant were detected. At a 90% EO concentration, A. satureoides and T. pusilla were the least repellent. At concentrations of 12.5% B. spartioides, R. officinalis and A. citriodora showed the longest repellency times. Comparisons of the principal components of each EO suggest that limonene and camphor were the main components responsible for the repellent effects. PMID:17583499

  4. The Toluene o-Xylene Monooxygenase Enzymatic Activity for the Biosynthesis of Aromatic Antioxidants

    PubMed Central

    Pizzo, Elio; Notomista, Eugenio; Pezzella, Alessandro; Di Cristo, Carlo; De Lise, Federica; Di Donato, Alberto; Izzo, Viviana

    2015-01-01

    Monocyclic phenols and catechols are important antioxidant compounds for the food and pharmaceutic industries; their production through biotransformation of low-added value starting compounds is of major biotechnological interest. The toluene o-xylene monooxygenase (ToMO) from Pseudomonas sp. OX1 is a bacterial multicomponent monooxygenase (BMM) that is able to hydroxylate a wide array of aromatic compounds and has already proven to be a versatile biochemical tool to produce mono- and dihydroxylated derivatives of aromatic compounds. The molecular determinants of its regioselectivity and substrate specificity have been thoroughly investigated, and a computational strategy has been developed which allows designing mutants able to hydroxylate non-natural substrates of this enzyme to obtain high-added value compounds of commercial interest. In this work, we have investigated the use of recombinant ToMO, expressed in cells of Escherichia coli strain JM109, for the biotransformation of non-natural substrates of this enzyme such as 2-phenoxyethanol, phthalan and 2-indanol to produce six hydroxylated derivatives. The hydroxylated products obtained were identified, isolated and their antioxidant potential was assessed both in vitro, using the DPPH assay, and on the rat cardiomyoblast cell line H9c2. Incubation of H9c2 cells with the hydroxylated compounds obtained from ToMO-catalyzed biotransformation induced a differential protective effect towards a mild oxidative stress induced by the presence of sodium arsenite. The results obtained confirm once again the versatility of the ToMO system for oxyfunctionalization reactions of biotechnological importance. Moreover, the hydroxylated derivatives obtained possess an interesting antioxidant potential that encourages the use of the enzyme for further functionalization reactions and their possible use as scaffolds to design novel bioactive molecules. PMID:25915063

  5. The Toluene o-Xylene Monooxygenase Enzymatic Activity for the Biosynthesis of Aromatic Antioxidants.

    PubMed

    Donadio, Giuliana; Sarcinelli, Carmen; Pizzo, Elio; Notomista, Eugenio; Pezzella, Alessandro; Di Cristo, Carlo; De Lise, Federica; Di Donato, Alberto; Izzo, Viviana

    2015-01-01

    Monocyclic phenols and catechols are important antioxidant compounds for the food and pharmaceutic industries; their production through biotransformation of low-added value starting compounds is of major biotechnological interest. The toluene o-xylene monooxygenase (ToMO) from Pseudomonas sp. OX1 is a bacterial multicomponent monooxygenase (BMM) that is able to hydroxylate a wide array of aromatic compounds and has already proven to be a versatile biochemical tool to produce mono- and dihydroxylated derivatives of aromatic compounds. The molecular determinants of its regioselectivity and substrate specificity have been thoroughly investigated, and a computational strategy has been developed which allows designing mutants able to hydroxylate non-natural substrates of this enzyme to obtain high-added value compounds of commercial interest. In this work, we have investigated the use of recombinant ToMO, expressed in cells of Escherichia coli strain JM109, for the biotransformation of non-natural substrates of this enzyme such as 2-phenoxyethanol, phthalan and 2-indanol to produce six hydroxylated derivatives. The hydroxylated products obtained were identified, isolated and their antioxidant potential was assessed both in vitro, using the DPPH assay, and on the rat cardiomyoblast cell line H9c2. Incubation of H9c2 cells with the hydroxylated compounds obtained from ToMO-catalyzed biotransformation induced a differential protective effect towards a mild oxidative stress induced by the presence of sodium arsenite. The results obtained confirm once again the versatility of the ToMO system for oxyfunctionalization reactions of biotechnological importance. Moreover, the hydroxylated derivatives obtained possess an interesting antioxidant potential that encourages the use of the enzyme for further functionalization reactions and their possible use as scaffolds to design novel bioactive molecules.

  6. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, Virginia C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program --now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history The missions will develop technology and acquire data necessary for eventual human Exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines be opportunities for the Mars community to provide input into the landing site selection process.

  7. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, V. C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program -- now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history. The missions will develop technology and acquire data necessary for eventual human exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines the opportunities for the Mars community to provide input into the landing site selection process.

  8. The luminous polycyclic aromatic hydrocarbon emission features: Applications to high redshift galaxies and active galactic nuclei

    NASA Astrophysics Data System (ADS)

    Shipley, Heath Vernon

    The co-evolution of star-formation and supermassive black hole (SMBH) accretion in galaxies is one of the key problems in galaxy formation theory. Understanding the formation of galaxies, and their subsequent evolution, will be coupled to intensive study of the evolution of SMBHs. This thesis focuses on studying diagnostics of star-formation and SMBH accretion to develop tools to study this co-evolution. Chapter 2 consists of using mid-infrared (mid-IR) spectroscopy from the Spitzer Infrared Spectrograph (IRS) to study the nature of star-formation and SMBH accretion. The mid-IR spectra cover wavelengths 5-38mum, spanning the polycyclic aromatic hydrocarbon (PAH) features and important atomic diagnostic lines. We divide our sample into a subsample of galaxies with Spitzer IRAC colors indicative of warm dust heated by an AGN (IRAGN) and those galaxies whose colors indicate star-formation processes (non-IRAGN). In both the IRAGN and star-forming samples, the luminosity in the PAH features correlates strongly with [Ne II]lambda12.8&mum emission line, from which we conclude that the PAH luminosity directly traces the instantaneous star-formation rate (SFR) in both the IRAGN and star-forming galaxies. There is no measurable difference between the PAH luminosity ratios of L11:3/L7:7 and L6:2/L7:7 for the IRAGN and non-IRAGN, suggesting that AGN do not significantly excite or destroy PAH molecules on galaxy-wide scales. In chapter 3, I calibrate the PAH luminosity as a SFR indicator. We provide a new robust SFR calibration using the luminosity emitted from PAH molecules at 6.2mum, 7.7mum and 11.3mum. The PAH features emit strongly in the mid-IR mitigating dust extinction, containing on average 5--10% of the total IR luminosity in galaxies. We use mid-IR spectroscopy from the Spitzer/IRS, and data covering other SFR indicators (Halpha emission and rest-frame 24mum continuum emission). The PAH luminosity correlates linearly with the SFR as measured by the Halpha luminosity

  9. Activation of Inhibitors by Sortase Triggers Irreversible Modification of the Active Site*S

    PubMed Central

    Maresso, Anthony W.; Wu, Ruiying; Kern, Justin W.; Zhang, Rongguang; Janik, Dorota; Missiakas, Dominique M.; Duban, Mark-Eugene; Joachimiak, Andrzej; Schneewind, Olaf

    2011-01-01

    Sortases anchor surface proteins to the cell wall of Gram-positive pathogens through recognition of specific motif sequences. Loss of sortase leads to large reductions in virulence, which identifies sortase as a target for the development of antibacterials. By screening 135,625 small molecules for inhibition, we report here that aryl (β-amino)ethyl ketones inhibit sortase enzymes from staphylococci and bacilli. Inhibition of sortases occurs through an irreversible, covalent modification of their active site cysteine. Sortases specifically activate this class of molecules via β-elimination, generating a reactive olefin intermediate that covalently modifies the cysteine thiol. Analysis of the three-dimensional structure of Bacillus anthracis sortase B with and without inhibitor provides insights into the mechanism of inhibition and reveals binding pockets that can be exploited for drug discovery. PMID:17545669

  10. The bifunctional active site of s-adenosylmethionine synthetase. Roles of the active site aspartates.

    PubMed

    Taylor, J C; Markham, G D

    1999-11-12

    S-Adenosylmethionine (AdoMet) synthetase catalyzes the biosynthesis of AdoMet in a unique enzymatic reaction. Initially the sulfur of methionine displaces the intact tripolyphosphate chain (PPP(i)) from ATP, and subsequently PPP(i) is hydrolyzed to PP(i) and P(i) before product release. The crystal structure of Escherichia coli AdoMet synthetase shows that the active site contains four aspartate residues. Aspartate residues Asp-16* and Asp-271 individually provide the sole protein ligand to one of the two required Mg(2+) ions (* denotes a residue from a second subunit); aspartates Asp-118 and Asp-238* are proposed to interact with methionine. Each aspartate has been changed to an uncharged asparagine, and the metal binding residues were also changed to alanine, to assess the roles of charge and ligation ability on catalytic efficiency. The resultant enzyme variants all structurally resemble the wild type enzyme as indicated by circular dichroism spectra and are tetramers. However, all have k(cat) reductions of approximately 10(3)-fold in AdoMet synthesis, whereas the MgATP and methionine K(m) values change by less than 3- and 8-fold, respectively. In the partial reaction of PPP(i) hydrolysis, mutants of the Mg(2+) binding residues have >700-fold reduced catalytic efficiency (k(cat)/K(m)), whereas the D118N and D238*N mutants are impaired less than 35-fold. The catalytic efficiency for PPP(i) hydrolysis by Mg(2+) site mutants is improved by AdoMet, like the wild type enzyme. In contrast AdoMet reduces the catalytic efficiency for PPP(i) hydrolysis by the D118N and D238*N mutants, indicating that the events involved in AdoMet activation are hindered in these methionyl binding site mutants. Ca(2+) uniquely activates the D271A mutant enzyme to 15% of the level of Mg(2+), in contrast to the approximately 1% Ca(2+) activation of the wild type enzyme. This indicates that the Asp-271 side chain size is a discriminator between the activating ability of Ca(2+) and the

  11. Aromatics saturation over hydrotreating catalysts: Reactivity and susceptibility to poisons

    SciTech Connect

    Kokayeff, P.

    1994-12-31

    Aromatics saturation over hydrotreating catalysts has been investigated by processing a synthetic feedstock to which naphthalene, biphenyl, tetralin, and cyclohexylbenzene have been added as model aromatic compounds. The saturation reactions were successfully correlated with a kinetic model of consecutive first order reactions. The rates of saturation of the di-aromatics, naphthalene and biphenyl, were approximately 5--40 times faster than the rate of saturation of the mono-aromatics, tetralin and cyclohexylbenzene. The nature of the di-aromatic is a significant determinant of its reactivity for saturation. The rate of saturation of naphthalene is 10--20 times faster than the rate of saturation of biphenyl. The two mono-aromatics, tetralin and cyclohexylbenzene, exhibited nearly identical reactivities for saturation. An investigation of the effect of organo-nitrogen compounds on saturation activity revealed a very severe poisoning and attenuation of saturation activity. Since activity was recoverable upon the removal of the poisoning agent the chemical effect was conjectured to be due to adsorption of the poison on the active sites of the catalyst. The adsorption constants were determined for three model nitrogen compounds--quinoline, indole, and tert-butylamine. The poisoning action of an organo-nitrogen compound was found to be dependent on both basicity and chemical structure.

  12. Pattern of aromatic and hydrophobic amino acids critical for one of two subdomains of the VP16 transcriptional activator.

    PubMed Central

    Regier, J L; Shen, F; Triezenberg, S J

    1993-01-01

    Structural features of the transcriptional activation domain of the herpes simplex virion protein VP16 were examined by oligonucleotide-directed mutagenesis. Extensive mutagenesis at position 442 of the truncated VP16 activation domain (delta 456), normally occupied by a phenylalanine residue, demonstrated the importance of an aromatic amino acid at that position. On the basis of an alignment of the VP16 sequence surrounding Phe-442 and the sequences of other transcriptional activation domains, we subjected leucine residues at positions 439 and 444 of VP16 to mutagenesis. Results from these experiments suggest that bulky hydrophobic residues flanking Phe-442 also contribute significantly to the function of the truncated VP16 activation domain. Restoration of amino acids 457-490 to various Phe-442 mutants partially restored activity. Although the pattern of amino acids surrounding Phe-473 resembles that surrounding Phe-442, mutations of Phe-473 did not dramatically affect activity; in fact, Phe-475 appears more sensitive to mutations than does Phe-473. We infer that the two regions of VP16 (amino acids 413-456 and 457-490) possess unique structural features, although neither is likely to be an amphipathic alpha-helix or an "acidic blob." These results, considered with previous in vitro activation and inhibition studies, suggest that the two subdomains of VP16 affect transcription by different mechanisms. Images PMID:8381535

  13. Effects of heterocyclic aromatic substituents on binding affinities at two distinct sites of somatostatin receptors. Correlation with the electrostatic potential of the substituents.

    PubMed

    Prasad, Vidya; Birzin, Elizabeth T; McVaugh, Cheryl T; Van Rijn, Rachel D; Rohrer, Susan P; Chicchi, Gary; Underwood, Dennis J; Thornton, Edward R; Smith, Amos B; Hirschmann, Ralph

    2003-05-01

    In our continuing program exploring glucose-based peptidomimetics of somatostatin (SRIF-14), we sought to improve the water solubility of our glycosides. This led to insights into the nature of the ligand binding sites at the SRIF receptor. Replacement of the C4 benzyl substituent in glucoside (+)-2 with pyridinylmethyl or pyrazin-2-ylmethyl congeners increased water solubility and enhanced affinity for the human SRIF subtype receptor 4 (sst4). We attribute this effect to hydrogen bond formation. The pyridin-3-ylmethyl substituent at C4, when combined with the imidazol-4-ylmethyl group at C2, generated (-)-19, which has the highest affinity of a glucose-based peptidomimetic at a human SRIF receptor to date (K(i) 53 +/- 23 nM, n = 6 at sst4). The C4 heterocyclic congeners of glucosides bearing a 1-methoxy substituent rather than an indole side chain at the anomeric carbon, such as (+)-16, also provided information about the Trp(8) binding pocket. We correlated the SARs at both the C4 and the Trp(8) binding pockets with calculations of the electrostatic potentials of the diverse C4 aromatic substituents using Spartan 3-21G(*) MO analysis. These calculations provide an approximate analysis of a molecule's ability to interact within a receptor binding site. Our binding studies show that benzene and indole rings, but not pyridinylmethyl nor pyrazin-2-ylmethyl rings, can bind the hydrophobic Trp(8) binding pocket of sst4. The Spartan 3-21G(*) MO analysis reveals significant negative electrostatic potential in the region of the pi-clouds for the benzene and indole rings but not for the pyridinylmethyl or pyrazin-2-ylmethyl congeners. Our data further demonstrate that the replacement of benzene or indole side chains by heterocyclic aromatic rings typified by pyridine and pyrazine not only enhances water solubility and hydrogen bonding capacity as expected, but can also profoundly diminish the ability of the pi-cloud of the aromatic substituent to interact with side chains

  14. POLYCYCLIC AROMATIC HYDROCARBONS IN GALAXIES AT z approx 0.1: THE EFFECT OF STAR FORMATION AND ACTIVE GALACTIC NUCLEI

    SciTech Connect

    O'Dowd, Matthew J.; Schiminovich, David; Johnson, Benjamin D.; Treyer, Marie A.; Martin, Christopher D.; Wyder, Ted K.; Charlot, S.; Heckman, Timothy M.; Martins, Lucimara P.; Seibert, Mark; Van der Hulst, J. M.

    2009-11-01

    We present the analysis of the polycyclic aromatic hydrocarbon (PAH) spectra of a sample of 92 typical star-forming galaxies at 0.03 < z < 0.2 observed with the Spitzer intensified Reticon spectrograph (IRS). We compare the relative strengths of PAH emission features with Sloan Digital Sky Survey optical diagnostics to probe the relationship between PAH grain properties and star formation and active galactic nuclei (AGNs) activity. Short-to-long wavelength PAH ratios, and in particular the 7.7 mum-to-11.3 mum feature ratio, are strongly correlated with the star formation diagnostics D{sub n} (4000) and Halpha equivalent width, increasing with younger stellar populations. This ratio also shows a significant difference between active and non-active galaxies, with the active galaxies exhibiting weaker 7.7 mum emission. A hard radiation field as measured by [O{sub III}]/Hbeta and [Ne{sub III}]{sub 15.6m}u{sub m}/[Ne{sub II}]{sub 12.8m}u{sub m} effects PAH ratios differently depending on whether this field results from starburst activity or an AGN. Our results are consistent with a picture in which larger PAH molecules grow more efficiently in richer media and in which smaller PAH molecules are preferentially destroyed by the AGN.

  15. The active site of ribulose-bisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.

    1991-01-01

    The active site of ribulose-bisphosphate carboxylase/oxygenase requires interacting domains of adjacent, identical subunits. Most active-site residues are located within the loop regions of an eight-stranded {beta}/{alpha}-barrel which constitutes the larger C-terminal domain; additional key residues are located within a segment of the smaller N-terminal domain which partially covers the mouth of the barrel. Site-directed mutagenesis of the gene encoding the enzyme from Rhodospirillum rubrum has been used to delineate functions of active-site residues. 6 refs., 2 figs.

  16. Influence of urban activities on polycyclic aromatic hydrocarbons in precipitation: distribution, sources and depositional flux in a developing metropolis, Fortaleza, Brazil.

    PubMed

    Cavalcante, Rivelino M; Sousa, Francisco W; Nascimento, Ronaldo F; Silveira, Edilberto R; Viana, Rommel B

    2012-01-01

    We measured polycyclic aromatic hydrocarbons (PAHs) in bulk precipitation in the Fortaleza metropolitan area, Ceará, Brazil, for the first time. Because little information is available concerning PAHs in tropical climatic regions, we assessed their spatial distribution and possible sources and the influence of urban activities on the depositional fluxes of PAHs in bulk precipitation. The concentrations of individual and total PAHs (Σ(PAHs)) in bulk precipitation ranged from undetectable to 133.9 ng.L(-1) and from 202.6 to 674.8 ng.L(-1), respectively. The plume of highest concentrations was most intense in a zone with heavy automobile traffic and favorable topography for the concentration of emitted pollutants. The depositional fluxes of PAHs in bulk precipitation calculated in this study (undetectable to 0.87 μg.m(-2).month(-1)) are 4 to 27 times smaller than those reported from tourist sites and industrial and urban areas in the Northern Hemisphere. Diagnostic ratio analyses of PAH samples showed that the major source of emissions is gasoline exhaust, with a small percentage originating from diesel fuel. Contributions from coal and wood combustion were also found. Major economic activities appear to contribute to pollutant emissions.

  17. Indole-3-acetic acid biosynthetic pathway and aromatic amino acid aminotransferase activities in Pantoea dispersa strain GPK.

    PubMed

    Kulkarni, G B; Nayak, A S; Sajjan, S S; Oblesha, A; Karegoudar, T B

    2013-05-01

    This investigation deals with the production of IAA by a bacterial isolate Pantoea dispersa strain GPK (PDG) identified by 16S rRNA gene sequence analysis. HPLC and Mass spectral analysis of metabolites from bacterial spent medium revealed that, IAA production by PDG is Trp-dependent and follows indole-3-pyruvic acid (IPyA) pathway. Substrate specificity study of aromatic amino acid aminotransferase (AAT) showed high activities, only when tryptophan (Trp) and α-ketoglutarate (α-kg) were used as substrates. AAT is highly specific for Trp and α-kg as amino group donor and acceptor, respectively. The effect of exogenous IAA on bacterial growth was established. Low concentration of exogenous IAA induced the growth, whereas high concentration decreased the growth of bacterium. PDG treatment significantly increased the root length, shoot length and dry mass of the chickpea and pigeon pea plants. PMID:23448265

  18. Savannah River Site prioritization of transition activities

    SciTech Connect

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D&D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities.

  19. DOE site performance assessment activities. Radioactive Waste Technical Support Program

    SciTech Connect

    Not Available

    1990-07-01

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions.

  20. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    SciTech Connect

    Zull, Lawrence M.; Yeniscavich, William

    2008-01-15

    The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive material contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.

  1. DELTA-13C VALUES OF POLYCYCLIC AROMATIC HYDROCARBONS (PAHS) COLLECTED FROM TWO CREOSOTE-CONTAMINATED WASTE SITES

    EPA Science Inventory

    Groundwater samples were collected from the American Creosote Works (ACW) Superfund site in Pensacola, Florida in June and September 1994. Sampling wells were located along a transect leading away from the most contaminated area. PAHs were extracted from the groundwater samples w...

  2. Temporal variability of Polycyclic Aromatic Hydrocarbons (PAHs) in a receptor site of the Puebla-Tlaxcala Valley

    NASA Astrophysics Data System (ADS)

    Padilla, Z. V.; Torres, R.; Ruiz Suarez, L.; Molina, L. T.

    2013-05-01

    This contribution documents the presence and possible origin of PAHs, their temporal concentration patterns and correlations with other air pollutants in the so-called Puebla-Tlaxcala valley. This valley is located to the east of the Mexico City Metropolitan Area and is a very populated region which suffers of air pollution problems. Emission sources of PAHs include open burning, industrial boilers, automobiles and trucks, but vehicle emissions vary significantly depending on the use of: fuel, engine type and catalytic converter. An important emission source in the Puebla-Tlaxcala region is wood burning for cooking. Therefore, it is expected to have contributions of PAHS from this type of sources. PAHs measurements were performed in an air pollution semi-rural receptor site (Chipilo) southwest the City of Puebla, using an aerosol photoelectric sensor (PAS 2000 CE) to measure the concentration of PAHs and a diffuser charger (DC 2000 CE) to evaluate the active surface (DC) of the particles. The measuring period included March and April of 2012 during the ozne season in central Mexico. The use of these two sensors in parallel has been identified as a fingerprint technique to identify different types of particles from several combustion processes and is a useful tool to identify quantitatively the major source of emissions, as well as to describe thephysical and chemical characteristics of the particles. Correlations between PAHs and DC, with NOx and CO, together with an analysis of atmospheric transport may approximate the possible origin of these particles. The coefficient PAHs / DC associated with backward trajectory analysis represents a tool to identify potential areas of emission. The correlation between PAHs and NOx emissions reflects association with diesel combustion, while the correlation between PAHs and CO, the combustion of gasoline. The results show that vehicle emissions are the major source of PAHs with an associated increase in the concentration of

  3. Non-ovarian aromatization is required to activate female sexual motivation in testosterone-treated ovariectomized quail.

    PubMed

    de Bournonville, Catherine; Balthazart, Jacques; Ball, Gregory F; Cornil, Charlotte A

    2016-07-01

    Although aromatase is expressed in both male and female brains, its functional significance in females remains poorly understood. In female quail, sexual receptivity is activated by estrogens. However it is not known whether sexual motivation is similarly estrogen-dependent and whether estrogens locally produced in the brain contribute to these behavioral responses. Four main experiments were designed to address these questions. In Experiment 1 chronic treatment of females with the anti-estrogen tamoxifen decreased their receptivity, confirming that this response is under the control of estrogens. In Experiment 2 chronic treatment with tamoxifen significantly decreased sexual motivation as treated females no longer approached a sexual partner. In Experiment 3 (a) ovariectomy (OVX) induced a significant decrease of time spent near the male and a significantly decreased receptivity compared to gonadally intact females, (b) treatment with testosterone (OVX+T) partially restored these responses and (c) this effect of T was prevented when estradiol synthesis was inhibited by the potent aromatase inhibitor Vorozole (OVX+T+VOR). Serum estradiol concentration was significantly higher in OVX+T than in OVX or OVX+T+VOR females. Together these data demonstrate that treatment of OVX females with T increases sexual motivation and that these effects are mediated at least in part by non-gonadal aromatization of the androgen. Finally, assays of aromatase activity on brain and peripheral tissues (Experiment 4) strongly suggest that brain aromatization contributes to behavioral effects observed here following T treatment but alternative sources of estrogens (e.g. liver) should also be considered. PMID:27189762

  4. Non-ovarian aromatization is required to activate female sexual motivation in testosterone-treated ovariectomized quail.

    PubMed

    de Bournonville, Catherine; Balthazart, Jacques; Ball, Gregory F; Cornil, Charlotte A

    2016-07-01

    Although aromatase is expressed in both male and female brains, its functional significance in females remains poorly understood. In female quail, sexual receptivity is activated by estrogens. However it is not known whether sexual motivation is similarly estrogen-dependent and whether estrogens locally produced in the brain contribute to these behavioral responses. Four main experiments were designed to address these questions. In Experiment 1 chronic treatment of females with the anti-estrogen tamoxifen decreased their receptivity, confirming that this response is under the control of estrogens. In Experiment 2 chronic treatment with tamoxifen significantly decreased sexual motivation as treated females no longer approached a sexual partner. In Experiment 3 (a) ovariectomy (OVX) induced a significant decrease of time spent near the male and a significantly decreased receptivity compared to gonadally intact females, (b) treatment with testosterone (OVX+T) partially restored these responses and (c) this effect of T was prevented when estradiol synthesis was inhibited by the potent aromatase inhibitor Vorozole (OVX+T+VOR). Serum estradiol concentration was significantly higher in OVX+T than in OVX or OVX+T+VOR females. Together these data demonstrate that treatment of OVX females with T increases sexual motivation and that these effects are mediated at least in part by non-gonadal aromatization of the androgen. Finally, assays of aromatase activity on brain and peripheral tissues (Experiment 4) strongly suggest that brain aromatization contributes to behavioral effects observed here following T treatment but alternative sources of estrogens (e.g. liver) should also be considered.

  5. Simultaneous removal of sulfur dioxide and polycyclic aromatic hydrocarbons from incineration flue gas using activated carbon fibers.

    PubMed

    Liu, Zhen-Shu; Li, Wen-Kai; Hung, Ming-Jui

    2014-09-01

    Incineration flue gas contains polycyclic aromatic hydrocarbons (PAHs) and sulfur dioxide (SO2). The effects of SO2 concentration (0, 350, 750, and 1000 ppm), reaction temperature (160, 200, and 280 degrees C), and the type of activated carbon fibers (ACFs) on the removal of SO2 and PAHs by ACFs were examined in this study. A fluidized bed incinerator was used to simulate practical incineration flue gas. It was found that the presence of SO2 in the incineration flue gas could drastically decrease removal of PAHs because of competitive adsorption. The effect of rise in the reaction temperature from 160 to 280 degrees C on removal of PAHs was greater than that on SO2 removal at an SO2 concentration of 750 ppm. Among the three ACFs studied, ACF-B, with the highest microporous volume, highest O content, and the tightest structure, was the best adsorbent for removing SO2 and PAHs when these gases coexisted in the incineration flue gas. Implications: Simultaneous adsorption of sulfur dioxide (SO2) and polycyclic aromatic hydrocarbons (PAHs) emitted from incineration flue gas onto activated carbon fibers (ACFs) meant to devise a new technique showed that the presence of SO2 in the incineration flue gas leads to a drastic decrease in removal of PAHs because of competitive adsorption. Reaction temperature had a greater influence on PAHs removal than on SO2 removal. ACF-B, with the highest microporous volume, highest O content, and tightest structure among the three studied ACFs, was found to be the best adsorbent for removing SO2 and PAHs.

  6. Downward fluxes of elemental carbon, metals and polycyclic aromatic hydrocarbons in settling particles from the deep Ionian Sea (NESTOR site), Eastern Mediterranean

    NASA Astrophysics Data System (ADS)

    Theodosi, C.; Parinos, C.; Gogou, A.; Kokotos, A.; Stavrakakis, S.; Lykousis, V.; Hatzianestis, J.; Mihalopoulos, N.

    2013-07-01

    To assess sources and major processes controlling the vertical transport of both anthropogenic and natural chemical species in a deep basin of the Eastern Mediterranean Sea (SE Ionian Sea, Nestor site), we performed chemical characterization (elemental carbon, major and trace metals and polycyclic aromatic hydrocarbons) of marine sinking particles. Sediment traps were deployed at five successive depths, 700, 1200, 2000, 3200 and 4300 m from the sea surface from May 2007 to October 2008. Fluxes of all measured chemical species, attributed to both natural and anthropogenic sources, exhibited minimum values from January to March 2008 and maximum from April to September 2008. Crustal matter flux from atmospheric inputs - either "freshly" deposited or stored in the surface layers - plays an important role in the temporal variability of particulate marine matter fluxes along with particulate organic carbon export, imposing ballast effects. Tracers (elemental carbon, retene) of the devastating forest fires that occurred in August 2007 in southern Greece were detected in sediment trap material from all depths with a delay of 15 days at 4300 m, indicating a rapid and well-coupled transport of sinking particulate material between the sea-surface and deep layers of the Eastern Mediterranean Sea. This is in accordance with an evident covariance between certain compounds, suggesting common sources and/or transport mechanisms to depth. Lateral inputs of pollutants at the deepest trap (4300 m) are probably of importance, related to the periodic influence of deep Adriatic water at the study site.

  7. Measurement of total polycyclic aromatic hydrocarbon concentrations in sediments and toxic units used for estimating risk to benthic invertebrates at manufactured gas plant sites.

    PubMed

    Hawthorne, Steven B; Miller, David J; Kreitinger, Joseph P

    2006-01-01

    The U.S. Environmental Protection Agency's (U.S. EPA) narcosis model requires the measurement of 18 parent and 16 groups of alkyl polycyclic aromatic hydrocarbons (PAHs) (so-called 34 PAHs) in sediments to calculate the number of PAH toxic units (TU) available to benthic organisms. If data for the 34 PAHs are not available, the U.S. EPA proposes estimating the risk by multiplying the TU for 13 parent PAHs by 11.5 (95% confidence interval) based on data from 488 sediments. This estimate is overly conservative for PAHs from pyrogenic manufactured gas plant (MGP) processes based on the analysis of 45 sediments from six sites. Parent PAHs contributed approximately 40% of the total concentrations and TU for MGP sediments. In contrast, parent PAHs from diesel fuel and petroleum crude oil contributed only 2 and 1%, respectively, of the PAH concentrations and TU, compared to approximately 98 to 99% contributed by the alkyl PAHs. Statistical comparison of the TU based on the measured 34 alkyl and parent PAHs and those based on only 13 parent PAHs demonstrated that a factor of 4.2 (rather than 11.5) is sufficient to estimate total TU within a 95% confidence level for MGP sites. Similarly, measurement of parent PAHs is sufficient to accurately estimate the total 34 alkyl and parent PAH concentrations for MGP-impacted sediments. PMID:16494254

  8. Downward fluxes of elemental carbon, metals and polycyclic aromatic hydrocarbons in settling particles from the deep Ionian Sea (NESTOR site), Eastern Mediterranean

    NASA Astrophysics Data System (ADS)

    Theodosi, C.; Parinos, C.; Gogou, A.; Kokotos, A.; Stavrakakis, S.; Lykousis, V.; Hatzianestis, J.; Mihalopoulos, N.

    2012-12-01

    To assess sources and major processes controlling vertical transport of both anthropogenic and natural chemical species in deep basins of the Eastern Mediterranean Sea (SE Ionian Sea, Nestor site), we performed chemical characterization (elemental carbon, major and trace metals and polycyclic aromatic hydrocarbons) of marine sinking particles. Sediment traps were deployed at five successive depths, 700 m, 1200 m, 2000 m, 3200 m and 4300 m from the sea surface, during the period of May 2007 to October 2008. Fluxes of all measured species exhibited minimum values from January to March 2008 and maximum from April to September 2008, with an evident covariance revealing a common and rapid vertical transport mechanism from 700 m down to 4300 m depth. Crustal matter flux from atmospheric deposition plays an important role in the temporal variability of particulate matter with significant contribution from biogenic constituents namely the seasonal succession in the export of planktonic biomass, expressed by particulate organic carbon (POC), carbonates and biogenic Si fluxes (Stavrakakis et al., 2012). Tracers (elemental carbon, retene) of the devastating forest fires occurred in August 2007 in southern Greece, were detected at sediment trap material in all depths with a delay of 15 days at 4300 m, indicating a rapid and well-coupled transport of sinking particulate material between the sea-surface and deep layers of the Eastern Mediterranean Sea. Lateral inputs of pollutants at the deepest trap (4300 m) are probably of importance, due to the influence of deep Adriatic water at the study site.

  9. Health risks of polycyclic aromatic hydrocarbons via fish consumption in Haimen bay (China), downstream of an e-waste recycling site (Guiyu).

    PubMed

    Shi, Jingchun; Zheng, Gene Jin-Shu; Wong, Ming-Hung; Liang, Hong; Li, Yuelin; Wu, Yinglin; Li, Ping; Liu, Wenhua

    2016-05-01

    Guiyu, China has been one of the largest e-waste recycling sites of the world for more than 20 years. Abundant data show that local dwellers there suffered from severe health risks from e-waste contaminants. In this study, polycyclic aromatic hydrocarbons (PAHs) were used as candidates to test the contamination levels and their possible adverse effects on residents in Haimen Bay, the estuary of Lian River (less than 30km from Guiyu), which has been totally neglected. The concentrations of 16PAHs were determined in collected marine fish with a median ΣPAH concentration of 1478ng/g (wet weight), and the contamination may be mainly influenced by Lian River runoff, specifically from Guiyu. The lifetime excess cancer risk for local dwellers was much higher than the serious risk level (10(-4)). More seriously, outflows of PAHs from the e-waste recycling site (Guiyu) seemed to exert health risks of a much larger scale of population downstream.

  10. Distribution and sources of polycyclic aromatic hydrocarbons in sediments of the Mai Po Inner Deep Bay Ramsar Site in Hong Kong.

    PubMed

    Zhao, Zhen-Ye; Chu, Yan-ling; Gu, Ji-Dong

    2012-08-01

    The concentration of total polycyclic aromatic hydrocarbons (∑PAHs) and the 16 US EPA priority individual PAH compounds were analyzed in surface sediments from the Mai Po Inner Deep Bay, Ramsar Site of Hong Kong from December 2001 to Jun 2005, to investigate the spatial variability of anthropogenic pollutants. ∑PAHs concentrations ranged from 36.5 to 256.3 ng g(-1) dry weight with an average of 148.9 ng g(-1), comparable to other urbanized areas of the world, and there was little difference among different sampling times from December 2001 to June 2005. Based on comparison to the results from earlier study, it appears that a decrease of total PAHs concentration has occurred since 1992. Meanwhile, the concentrations of ∑PAHs were positive correlated with total organic carbon contents except sites F and G, suggesting the characteristics of the sediment influences the distribution and concentration of PAHs. There was relatively a good relationship among the individual PAHs and the compounds of fluorene, phenanthrene, anthracene, fluoranthene, pyrene, benzo[a]pyrene and indeno[cd]pyrene yielded a good correlation (r(2) > 0.5) with total PAHs. Principal component analysis and specific PAHs compound ratios (Phe/Ant vs. Flt/Pyr) indicate the pyrogenic origins, especially traffic exhausts, are the dominant sources of PAHs in the Mai Po Inner Deep Bay Nature Reserve. PMID:22695981

  11. Health risks of polycyclic aromatic hydrocarbons via fish consumption in Haimen bay (China), downstream of an e-waste recycling site (Guiyu).

    PubMed

    Shi, Jingchun; Zheng, Gene Jin-Shu; Wong, Ming-Hung; Liang, Hong; Li, Yuelin; Wu, Yinglin; Li, Ping; Liu, Wenhua

    2016-05-01

    Guiyu, China has been one of the largest e-waste recycling sites of the world for more than 20 years. Abundant data show that local dwellers there suffered from severe health risks from e-waste contaminants. In this study, polycyclic aromatic hydrocarbons (PAHs) were used as candidates to test the contamination levels and their possible adverse effects on residents in Haimen Bay, the estuary of Lian River (less than 30km from Guiyu), which has been totally neglected. The concentrations of 16PAHs were determined in collected marine fish with a median ΣPAH concentration of 1478ng/g (wet weight), and the contamination may be mainly influenced by Lian River runoff, specifically from Guiyu. The lifetime excess cancer risk for local dwellers was much higher than the serious risk level (10(-4)). More seriously, outflows of PAHs from the e-waste recycling site (Guiyu) seemed to exert health risks of a much larger scale of population downstream. PMID:26897061

  12. Size-dependent distribution and inhalation cancer risk of particle-bound polycyclic aromatic hydrocarbons at a typical e-waste recycling and an urban site.

    PubMed

    Luo, Pei; Bao, Lian-Jun; Li, Shao-Meng; Zeng, Eddy Y

    2015-05-01

    Atmospheric particle size distribution of polycyclic aromatic hydrocarbons (PAHs) in a typical e-waste recycling zone and an urban site (Guangzhou) in southern China featured a unimodal peak in 0.56-1.8 μm for 4-6 ring PAHs but no obvious peak for 2-3 ring PAHs at both sites. The atmospheric deposition fluxes of PAHs were estimated at 5.4 ± 2.3 μg m(-2) d(-1) in the e-waste recycling zone and 3.1 ± 0.6 μg m(-2) d(-1) in Guangzhou. In addition, dry and wet deposition fluxes of PAHs were dominated by coarse (Dp > 1.8 μm) and fine particles (Dp < 1.8 μm), respectively. Fine particles predominated the deposition of PAHs in the lung. The results estimated by incremental inhalation cancer risk suggested that particle-bound PAHs posed serious threat to human health within the e-waste recycling zone and Guangzhou.

  13. Metabolic Activation of Polycyclic Aromatic Hydrocarbons and Aryl and Heterocyclic Amines by Human Cytochromes P450 2A13 and 2A6

    PubMed Central

    Shimada, Tsutomu; Murayama, Norie; Yamazaki, Hiroshi; Tanaka, Katsuhiro; Takenaka, Shigeo; Komori, Masayuki; Kim, Donghak; Guengerich, F. Peter

    2013-01-01

    Human cytochrome P450 (P450) 2A13 was found to interact with several polycyclic aromatic hydrocarbons (PAHs) to produce Type I binding spectra, including acenaphthene, acenaphthylene, benzo[c]phenanthrene, fluoranthene, fluoranthene-2,3-diol, and 1-nitropyrene. P450 2A6 also interacted with acenaphthene and acenaphthylene, but not with fluoranthene, fluoranthene-2,3-diol, or 1-nitropyrene. P450 1B1 is well known to oxidize many carcinogenic PAHs, and we found that several PAHs (i.e., 7,12-dimethylbenz[a]anthracene, 7,12-dimethylbenz[a]anthracene-5,6-diol, benzo[c]phenanthrene, fluoranthene, fluoranthene-2,3-diol, 5-methylchrysene, benz[a]pyrene-4,5-diol, benzo[a]pyrene-7,8-diol, 1-nitropyrene, 2-aminoanthracene, 2-aminofluorene, and 2-acetylaminofluorene) interacted with P450 1B1, producing Reverse Type I binding spectra. Metabolic activation of PAHs and aryl- and heterocyclic amines to genotoxic products was examined in Salmonella typhimurium NM2009, and we found that P450 2A13 and 2A6 (as well as P450 1B1) were able to activate several of these procarcinogens. The former two enzymes were particularly active in catalyzing 2-aminofluorene and 2-aminoanthracene activation, and molecular docking simulations supported the results with these procarcinogens, in terms of binding in the active sites of P450 2A13 and 2A6. These results suggest that P450 2A enzymes, as well as P450 Family 1 enzymes including P450 1B1, are major enzymes involved in activating PAHs and aryl- and heterocyclic amines, as well as tobacco-related nitrosamines. PMID:23432465

  14. Aromatic Interactions in Organocatalyst Design: Augmenting Selectivity Reversal in Iminium Ion Activation.

    PubMed

    Holland, Mareike C; Metternich, Jan Benedikt; Daniliuc, Constantin; Schweizer, W Bernd; Gilmour, Ryan

    2015-07-01

    Substituting N-methylpyrrole for N-methyindole in secondary-amine-catalysed Friedel-Crafts reactions leads to a curious erosion of enantioselectivity. In extreme cases, this substrate dependence can lead to an inversion in the sense of enantioinduction. Indeed, these closely similar transformations require two structurally distinct catalysts to obtain comparable selectivities. Herein a focussed molecular editing study is disclosed to illuminate the structural features responsible for this disparity, and thus identify lead catalyst structures to further exploit this selectivity reversal. Key to effective catalyst re-engineering was delineating the non-covalent interactions that manifest themselves in conformation. Herein we disclose preliminary validation that intermolecular aromatic (CH-π and cation-π) interactions between the incipient iminium cation and the indole ring system is key to rationalising selectivity reversal. This is absent in the N-methylpyrrole alkylation, thus forming the basis of two competing enantio-induction pathways. A simple L-valine catalyst has been developed that significantly augments this interaction. PMID:25982418

  15. Isolation and identification of aromatic compounds in Lion's Mane Mushroom and their anticancer activities.

    PubMed

    Li, Wei; Zhou, Wei; Kim, Eun-Ji; Shim, Sang Hee; Kang, Hee Kyoung; Kim, Young Ho

    2015-03-01

    Lion's Mane Mushroom (Hericium erinaceum) is a traditional edible mushroom widely used in culinary applications and as an herbal medicine in East Asian countries. In the present study, two new aromatic compounds, hericerin A (1) and isohericenone J (5), along with five known compounds, isoericerin (2), hericerin (3), N-De phenylethyl isohericerin (4), hericenone J (6), and 4-[3',7'-dimethyl-2',6'-octadienyl]-2-formyl-3-hydroxy-5-methyoxybenzylalcohol (7), were isolated from a methanol extract of the fruiting bodies of H. erinaceum. The chemical structures of the compounds were determined from mass spectra and 1D- and 2D NMR spectroscopy. The anticancer effects of the isolated compounds were examined in HL-60 human acute promyelocytic leukaemia cells. Hericerin A (1) and hericerin (3) significantly reduced cell proliferation with IC50 values of 3.06 and 5.47 μM, respectively. These same compounds also induced apoptosis of HL-60 cells, accompanied by time-dependent down-regulation of p-AKT and c-myc levels. These data suggest that compounds 1 and 3 from H. erinaceum are suitable for use in potential cancer treatments.

  16. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.

    PubMed Central

    Weaver, T.; Lees, M.; Banaszak, L.

    1997-01-01

    Two mutant forms of fumarase C from E. coli have been made using PCR and recombinant DNA. The recombinant form of the protein included a histidine arm on the C-terminal facilitating purification. Based on earlier studies, two different carboxylic acid binding sites, labeled A- and B-, were observed in crystal structures of the wild type and inhibited forms of the enzyme. A histidine at each of the sites was mutated to an asparagine. H188N at the A-site resulted in a large decrease in specific activity, while the H129N mutation at the B-site had essentially no effect. From the results, we conclude that the A-site is indeed the active site, and a dual role for H188 as a potential catalytic base is proposed. Crystal structures of the two mutant proteins produced some unexpected results. Both mutations reduced the affinity for the carboxylic acids at their respective sites. The H129N mutant should be particularly useful in future kinetic studies because it sterically blocks the B-site with the carboxyamide of asparagine assuming the position of the ligand's carboxylate. In the H188N mutation at the active site, the new asparagine side chain still interacts with an active site water that appears to have moved slightly as a result of the mutation. PMID:9098893

  17. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

    Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

  18. Structure-plant phytotoxic activity relationship of 7,7'-epoxylignanes, (+)- and (-)-verrucosin: simplification on the aromatic ring substituents.

    PubMed

    Yamauchi, Satoshi; Nakayama, Kumiko; Nishiwaki, Hisashi; Shuto, Yoshihiro

    2014-10-15

    The synthesized 7-aryl derivatives of (7R,7'S,8S,8'S)-(+)-verrucosin were applied to growth inhibitory activity test against ryegrass at 1mM. 7-(3-Ethoxy-4-hydroxyphenyl) derivative 12 and 7-(2-hydroxyphenyl) derivative 4 showed comparable activity to those of (+)-verrucosin against the root (-95%) and the shoot (-60%), respectively. The growth inhibitory activity test against lettuce using synthesized 7-aryl derivatives of (7S,7'R,8R,8'R)-(-)-verrucosin at 1mM showed that the activities of 7-(3-hydroxyphenyl) derivative 20 and 7-(3-ethoxy-4-hydroxyphenyl) derivative 28 are similar to that of (-)-verrucosin against the root (-95%). Against the shoot, 7-(3-hydroxyphenyl) derivative 20 showed higher activity (-80%) than that of (-)-verrucosin (-60%). As the next step, (7S,7'R,8R,8'R)-7-(3-hydroxyphenyl)-7'-aryl-(-)-verrucosin derivatives, in which the most effective 3-hydroxyphenyl group is employed as 7-aromatic ring, were synthesized for the assay against lettuce. In this experiment, 7'-(2-hydroxyphenyl) derivative 37 and 7'-(3-hydroxyphenyl) derivative 38 showed similar activity to that of derivative 20. The effect of 7- and 7'-aryl structures of 7,7'-epoxylignanes on the plant growth inhibitory activity was clarified. The 7- and 7'-aryl structures were simplified to show comparable activity to or higher activity than that of (-)-verrucosin. The plant growth inhibitory activity of a nutmeg component, (+)-fragransin C3b, was estimated as -80% inhibition at 1mM against ryegrass roots. PMID:25248684

  19. Metal-ligand cooperation by aromatization-dearomatization: a new paradigm in bond activation and "green" catalysis.

    PubMed

    Gunanathan, Chidambaram; Milstein, David

    2011-08-16

    In view of global concerns regarding the environment and sustainable energy resources, there is a strong need for the discovery of new, green catalytic reactions. For this purpose, fresh approaches to catalytic design are desirable. In recent years, complexes based on "cooperating" ligands have exhibited remarkable catalytic activity. These ligands cooperate with the metal center by undergoing reversible structural changes in the processes of substrate activation and product formation. We have discovered a new mode of metal-ligand cooperation, involving aromatization-dearomatization of ligands. Pincer-type ligands based on pyridine or acridine exhibit such cooperation, leading to unusual bond activation processes and to novel, environmentally benign catalysis. Bond activation takes place with no formal change in the metal oxidation state, and so far the activation of H-H, C-H (sp(2) and sp(3)), O-H, and N-H bonds has been demonstrated. Using this approach, we have demonstrated a unique water splitting process, which involves consecutive thermal liberation of H(2) and light-induced liberation of O(2), using no sacrificial reagents, promoted by a pyridine-based pincer ruthenium complex. An acridine pincer complex displays unique "long-range" metal-ligand cooperation in the activation of H(2) and in reaction with ammonia. In this Account, we begin by providing an overview of the metal-ligand cooperation based on aromatization-dearomatization processes. We then describe a range of novel catalytic reactions that we developed guided by these new modes of metal-ligand cooperation. These reactions include the following: (1) acceptorless dehydrogenation of secondary alcohols to ketones, (2) acceptorless dehydrogenative coupling of alcohols to esters, (3) acylation of secondary alcohols by esters with dihydrogen liberation, (4) direct coupling of alcohols and amines to form amides and polyamides with liberation of dihydrogen, (5) coupling of esters and amines to form amides

  20. Aromatic-turmerone attenuates invasion and expression of MMP-9 and COX-2 through inhibition of NF-κB activation in TPA-induced breast cancer cells.

    PubMed

    Park, Sun Young; Kim, Young Hun; Kim, YoungHee; Lee, Sang-Joon

    2012-12-01

    Recent evidence suggests that breast cancer is one of the most common forms of malignancy in females, and metastasis from the primary cancer site is the main cause of death. Aromatic (ar)-turmerone is present in Curcuma longa and is a common remedy and food. In the present study, we investigated the inhibitory effects of ar-turmerone on expression and enzymatic activity levels of 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced matrix metalloproteinase (MMP)-9 and cyclooxygenaase-2 (COX-2) in breast cancer cells. Our data indicated that ar-turmerone treatment significantly inhibited enzymatic activity and expression of MMP-9 and COX-2 at non-cytotoxic concentrations. However, the expression of tissue inhibitor of metalloproteinase (TIMP)-1, TIMP-2, MMP-2, and COX-1 did not change upon ar-turmerone treatment. We found that ar-turmerone inhibited the activation of NF-κB, whereas it did not affect AP-1 activation. Moreover, The ChIP assay revealed that in vivo binding activities of NF-κB to the MMP-9 and COX-2 promoter were significantly inhibited by ar-turmerone. Our data showed that ar-turmerone reduced the phosphorylation of PI3K/Akt and ERK1/2 signaling, whereas it did not affect phosphorylation of JNK or p38 MAPK. Thus, transfection of breast cancer cells with PI3K/Akt and ERK1/2 siRNAs significantly decreased TPA-induced MMP-9 and COX-2 expression. These results suggest that ar-turmerone suppressed the TPA-induced up-regulation of MMP-9 and COX-2 expression by blocking NF-κB, PI3K/Akt, and ERK1/2 signaling in human breast cancer cells. Furthermore, ar-turmerone significantly inhibited TPA-induced invasion, migration, and colony formation in human breast cancer cells.

  1. The Luminous Polycyclic Aromatic Hydrocarbon Emission Features: Applications to High Redshift Galaxies and Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Shipley, Heath; Papovich, Casey

    2015-08-01

    We provide a new robust star-formation rate (SFR) calibration using the luminosity from polycyclic aromatic hydrogen (PAH) molecules. The PAH features emit strongly in the mid-infrared (mid-IR; 3-19μm), mitigating dust extinction, and they are very luminous, containing 5-10% of the total IR luminosity in galaxies. We derive the calibration of the PAH luminosity as a SFR indicator using a sample of 105 star-forming galaxies covering a range of total IR luminosity, LIR = L(8-1000μm) = 109 - 1012 L⊙ and redshift 0 < z < 0.6. The PAH luminosity correlates linearly with the SFR as measured by the dust-corrected Hα luminosity (using the sum of the Hα and rest-frame 24μm luminosity from Kennicutt et al. 2009), with tight scatter of ~0.15 dex, comparable to the scatter in the dust-corrected Hα SFRs and Paα SFRs. We show this relation is sensitive to galaxy metallicity, where the PAH luminosity of galaxies with Z < 0.7 Z⊙ departs from the linear SFR relationship but in a behaved manor. We derive for this a correction to galaxies below solar metallicity. As a case study for observations with JWST, we apply the PAH SFR calibration to a sample of lensed galaxies at 1 < z < 3 with Spitzer Infrared Spectrograph (IRS) data, and we demonstrate the utility of PAHs to derive SFRs as accurate as those available from any other indicator. This new SFR indicator will be useful for probing the peak of the SFR density of the universe (1 < z < 3) and for studying the coevolution of star-formation and supermassive blackhole accretion contemporaneously in a galaxy.

  2. Uptake and toxicity of polycyclic aromatic hydrocarbons in terrestrial springtails--studying bioconcentration kinetics and linking toxicity to chemical activity.

    PubMed

    Schmidt, Stine Nørgaard; Smith, Kilian Eric Christopher; Holmstrup, Martin; Mayer, Philipp

    2013-02-01

    Passive dosing applies a polymer loaded with test compound(s) to establish and maintain constant exposure in laboratory experiments. Passive dosing with the silicone poly(dimethylsiloxane) was used to control exposure of the terrestrial springtail Folsomia candida to six polycyclic aromatic hydrocarbons (PAHs) in bioconcentration and toxicity experiments. Folsomia candida could move freely on the PAH-loaded silicone, resulting in exposure via air and direct contact. The bioconcentration kinetics indicated efficient uptake of naphthalene, anthracene, and pyrene through air and (near) equilibrium partitioning of these PAHs to lipids and possibly the waxy layer of the springtail cuticle. Toxicities of naphthalene, phenanthrene, and pyrene were related to chemical activity, which quantifies the energetic level and drives spontaneous processes including diffusive biouptake. Chemical activity-response relationships yielded effective lethal chemical activities (La50s) well within the expected range for baseline toxicity (0.01-0.1). Effective lethal body burdens for naphthalene and pyrene exceeded the expected range of 2 to 8 mmol kg(-1) fresh weight, which again indicated the waxy layer to be a sorbing phase. Finally, chemical activities were converted into equilibrium partitioning concentrations in lipids yielding effective lethal concentrations for naphthalene and phenanthrene in good correspondence with the lethal membrane burden for baseline toxicity (40-160 mmol kg(-1) lipid). Passive dosing was a practical approach for tightly controlling PAH exposure, which in turn provided new experimental possibilities and findings. PMID:23147567

  3. Characterization of EPA's 16 priority pollutant polycyclic aromatic hydrocarbons (PAHs) in tank bottom solids and associated contaminated soils at oil exploration and production sites in Texas.

    PubMed

    Bojes, Heidi K; Pope, Peter G

    2007-04-01

    The purpose of this study was to determine the concentration and types of polycyclic aromatic hydrocarbons (PAHs), a group of environmentally toxic and persistent chemicals, at contaminated oil exploration and production (E&P) sites located in environmentally sensitive and geographically distinct areas throughout Texas. Samples of tank bottom solids, the oily sediment that collects at the bottom of the tanks, were collected from inactive crude oil storage tanks at E&P sites and hydrocarbon contaminated soil samples were collected from the area surrounding each tank that was sampled. All samples were analyzed for the 16 PAH priority pollutant listed by US EPA and for total petroleum hydrocarbons (TPH). The results demonstrate that overall average PAH concentrations were significantly higher in tank bottom solids than in contaminated soils. Total PAH concentrations decreased predictably with diminishing hydrocarbon concentrations; but the percent fraction of carcinogenic PAHs per total measured PAH content increased from approximately 12% in tank bottom solids to about 46% in the contaminated soils. These results suggest that the PAH content found in tank bottom solids cannot reliably be used to predict the PAH content in associated contaminated soil. Comparison of PAHs to conservative risk-based screening levels for direct exposure to soil and leaching from soil to groundwater indicate that PAHs are not likely to exceed default risk-based thresholds in soils containing TPH of 1% (10,000mg/kg) or less. These results show that the magnitude of TPH concentration may be a useful indicator of potential risk from PAHs in crude oil-contaminated soils. The results also provide credibility to the 1% (10,000mg/kg) TPH cleanup level, used in Texas as a default management level at E&P sites located in non-sensitive areas, with respect to PAH toxicity.

  4. Concentration profiles, source apportionment and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in dumpsite soils from Agbogbloshie e-waste dismantling site, Accra, Ghana.

    PubMed

    Daso, Adegbenro P; Akortia, Eric; Okonkwo, Jonathan O

    2016-06-01

    The concentrations of eighteen (18) polycyclic aromatic hydrocarbons (PAHs), including the 16 USEPA's priority PAHs as well as two alkyl-substituted naphthalenes were determined in dumpsite soils collected from different sampling sites within the Agbogbloshie e-waste dismantling site in Accra, Ghana. Following their isolation with ultrasonic-assisted extraction technique, the concentrations of the PAHs were determined by gas chromatography mass spectrometry (GC-MS). Loss-on-ignition (LOI) method was employed for the determination of total organic carbon (TOC) of the soil samples. The mean Σ18PAHs obtained were 3006, 5627, 3046, 5555, and 7199 ng g(-1) dry weight (dw) for sampling sites A (mosque), B (dismantling site), C (residential house/police station), D (personal computer repairers' shop) and E (e-waste open burning area), respectively. In all cases, the prevalence of phenanthrene, fluoranthene and pyrene was generally observed across the sampling sites. In this study, PAHs with two to three rings and four to six rings exhibited strong positive correlations, whereas BbF and BkF showed weak positive and negative correlations with other PAHs investigated. With the exception of BbF and BkF, all the PAHs had moderate to strong positive correlations with the TOC. Benzo[a]pyrene equivalent (BaPeq) concentration is a useful indicator of the carcinogenic potency of environmental matrices and these ranged between 111 and 454 ng g(-1), which are generally below the 'safe' level of 600 ng g(-1) established for the protection of the environment and human health. Interestingly, the seven carcinogenic PAHs were the major contributors to the BaPeq concentrations accounting between 97.7 and 98.3 %. Despite the minimal risk to cancer via exposure to the investigated dumpsite soil as indicated in the present study, the prolonged exposure to these pollutants via various exposure pathways may result in increased risk to cancer over time. The application of several

  5. Concentration profiles, source apportionment and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in dumpsite soils from Agbogbloshie e-waste dismantling site, Accra, Ghana.

    PubMed

    Daso, Adegbenro P; Akortia, Eric; Okonkwo, Jonathan O

    2016-06-01

    The concentrations of eighteen (18) polycyclic aromatic hydrocarbons (PAHs), including the 16 USEPA's priority PAHs as well as two alkyl-substituted naphthalenes were determined in dumpsite soils collected from different sampling sites within the Agbogbloshie e-waste dismantling site in Accra, Ghana. Following their isolation with ultrasonic-assisted extraction technique, the concentrations of the PAHs were determined by gas chromatography mass spectrometry (GC-MS). Loss-on-ignition (LOI) method was employed for the determination of total organic carbon (TOC) of the soil samples. The mean Σ18PAHs obtained were 3006, 5627, 3046, 5555, and 7199 ng g(-1) dry weight (dw) for sampling sites A (mosque), B (dismantling site), C (residential house/police station), D (personal computer repairers' shop) and E (e-waste open burning area), respectively. In all cases, the prevalence of phenanthrene, fluoranthene and pyrene was generally observed across the sampling sites. In this study, PAHs with two to three rings and four to six rings exhibited strong positive correlations, whereas BbF and BkF showed weak positive and negative correlations with other PAHs investigated. With the exception of BbF and BkF, all the PAHs had moderate to strong positive correlations with the TOC. Benzo[a]pyrene equivalent (BaPeq) concentration is a useful indicator of the carcinogenic potency of environmental matrices and these ranged between 111 and 454 ng g(-1), which are generally below the 'safe' level of 600 ng g(-1) established for the protection of the environment and human health. Interestingly, the seven carcinogenic PAHs were the major contributors to the BaPeq concentrations accounting between 97.7 and 98.3 %. Despite the minimal risk to cancer via exposure to the investigated dumpsite soil as indicated in the present study, the prolonged exposure to these pollutants via various exposure pathways may result in increased risk to cancer over time. The application of several

  6. Conserved tyrosine 182 residue in hyperthermophilic esterase EstE1 plays a critical role in stabilizing the active site.

    PubMed

    Truongvan, Ngoc; Chung, Hye-Shin; Jang, Sei-Heon; Lee, ChangWoo

    2016-03-01

    An aromatic amino acid, Tyr or Trp, located in the esterase active site wall, is highly conserved, with hyperthermophilic esterases showing preference for Tyr and lower temperature esterases showing preference for Trp. In this study, we investigated the role of Tyr(182) in the active site wall of hyperthermophilic esterase EstE1. Mutation of Tyr to Phe or Ala had a moderate effect on EstE1 thermal stability. However, a small-to-large mutation such as Tyr to His or Trp had a devastating effect on thermal stability. All mutant EstE1 enzymes showed reduced catalytic rates and enhanced substrate affinities as compared with wild-type EstE1. Hydrogen bond formation involving Tyr(182) was unimportant for maintaining EstE1 thermal stability, as the EstE1 structure is already adapted to high temperatures via increased intramolecular interactions. However, removal of hydrogen bond from Tyr(182) significantly decreased EstE1 catalytic activity, suggesting its role in stabilization of the active site. These results suggest that Tyr is preferred over a similarly sized Phe residue or bulky His or Trp residue in the active site walls of hyperthermophilic esterases for stabilizing the active site and regulating catalytic activity at high temperatures. PMID:26838013

  7. Probing the active site tryptophan of Staphylococcus aureus thioredoxin with an analog

    PubMed Central

    Englert, Markus; Nakamura, Akiyoshi; Wang, Yane-Shih; Eiler, Daniel; Söll, Dieter; Guo, Li-Tao

    2015-01-01

    Genetically encoded non-canonical amino acids are powerful tools of protein research and engineering; in particular they allow substitution of individual chemical groups or atoms in a protein of interest. One such amino acid is the tryptophan (Trp) analog 3-benzothienyl-l-alanine (Bta) with an imino-to-sulfur substitution in the five-membered ring. Unlike Trp, Bta is not capable of forming a hydrogen bond, but preserves other properties of a Trp residue. Here we present a pyrrolysyl-tRNA synthetase-derived, engineered enzyme BtaRS that enables efficient and site-specific Bta incorporation into proteins of interest in vivo. Furthermore, we report a 2.1 Å-resolution crystal structure of a BtaRS•Bta complex to show how BtaRS discriminates Bta from canonical amino acids, including Trp. To show utility in protein mutagenesis, we used BtaRS to introduce Bta to replace the Trp28 residue in the active site of Staphylococcus aureus thioredoxin. This experiment showed that not the hydrogen bond between residues Trp28 and Asp58, but the bulky aromatic side chain of Trp28 is important for active site maintenance. Collectively, our study provides a new and robust tool for checking the function of Trp in proteins. PMID:26582921

  8. The Luminous Polycyclic Aromatic Hydrocarbon Emission Features: Applications to High Redshift Galaxies and Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Shipley, Heath V.

    2016-01-01

    For decades, significant work has been applied to calibrating emission from the ultra-violet, nebular emission lines, far-infrared, X-ray and radio as tracers of the star-formation rate (SFR) in distant galaxies. Understanding the exact rate of star-formation and how it evolves with time and galaxy mass has deep implications for how galaxies form. The co-evolution of star-formation and supermassive black hole (SMBH) accretion is one of the key problems in galaxy formation theory. But, many of these SFR indicators are influenced by SMBH accretion in galaxies and result in unreliable SFRs. Utilizing the luminous polycyclic aromatic hydrocarbon (PAH) emission features, I provide a new robust SFR calibration using the luminosity emitted from the PAHs at 6.2μm, 7.7μm and 11.3μm to solve this. The PAH features emit strongly in the mid-infrared (mid-IR; 5-25μm) mitigating dust extinction, containing on average 5-10% of the total IR luminosity in galaxies. I use a sample of 105 star-forming galaxies covering a range of total IR luminosity, LIR = L(8-1000μm) = 109 - 1012 L⊙ and redshift 0 < z < 0.4, with mid-IR spectroscopy from the Spitzer Infrared Spectrograph (IRS), and data covering other SFR indicators (Hα emission and rest-frame 24μm continuum emission). The PAH luminosity correlates linearly with the SFR as measured by the Hα luminosity (corrected for attenuation using the mono-chromatic rest-frame 24μm emission), with a tight scatter of <0.15 dex. The scatter is comparable to that between SFRs derived from the Paα and dust-corrected Hα emission lines. We present a case study in advance of JWST, which will be capable of measuring SFRs (from 8μm rest-frame photometry, i.e. PAHs) in distant galaxies (z ≤ 2) with JWST/MIRI to SFRs as low as ~10 M⊙yr-1, because the PAH features are so bright. We use Spitzer/IRS observations of PAH features in lensed star-forming galaxies at 1 < z < 3 to demonstrate the utility of the PAHs to derive SFRs that agree with

  9. {Polycyclic aromatic hydrocarbons (PAHs) and aliphatic hydrocarbons in gas and particle phases in two sites of Mexico: MILAGRO project}

    NASA Astrophysics Data System (ADS)

    Amador-Muñoz, O.; Villalobos-Pietrini, R.; Castro, T.; Gaspariano-Larino, R.

    2009-04-01

    Aliphatic hydrocarbons are markers of anthropogenic and biogenic emission sources1; meanwhile PAHs are generated by incomplete combustion sources2. The last ones are important compounds due to their carcinogenic and mutagenic properties3,4. The aim of this study was to identify and quantify aliphatic hydrocarbons and PAHs in gas and particles phases of the atmospheric aerosol and to determine the day and night time behavior during the MILAGRO (Megacity Initiative: Local Global and Research Observations) campaign. The gas phase was collected on polyurethane foam, while particles less than 2.5 m (PM2.5) were collected on glass fiber filters covered with Teflon (TIGF, pallflex) of 8x10 in. Samplings were carried out with a high volume sampler (Tisch) with a flow of 1.13 m3 min-1 at two sites: Instituto Mexicano del Petróleo (T0) and Tecamac (T1) located at North and Northeast of Mexico City, respectively during day (7:00 am-7:00 pm) and night time (7:00 pm-7:00 am) from 1 to 29 of March, 2006. Ninteen PAHs and 23 aliphatic hydrocarbons from n-C13H28 to n-C35H72 were analyzed by gas chromatography coupled to mass spectrometry in impact mode. The samples were spiked with deuterads PAHs and aliphatics hydrocarbons before ultrasound extraction. Medians comparisons were made with Mann-Whitney U test. PAHs with molecular weight (MW) less than 228 g mol-1 were distributed in the gas phase, in both sites. Higher concentrations of PAHs ≥ 228 g mol-1 in PM2.5, were observed during night period (p

  10. Supercritical carbon dioxide extraction as a predictor of polycyclic aromatic hydrocarbon bioaccumulation and toxicity by earthworms in manufactured-gas plant site soils.

    PubMed

    Kreitinger, Joseph P; Quiñones-Rivera, Antonio; Neuhauser, Edward F; Alexander, Martin; Hawthorne, Steven B

    2007-09-01

    The toxicity and uptake of polycyclic aromatic hydrocarbons (PAHs) by earthworms were measured in soil samples collected from manufactured-gas plant sites having a wide range in PAH concentrations (170-42,000 mg/kg) and soil characteristics. Samples varied from vegetated soils to pure lampblack soot and had total organic carbon contents ranging from 3 to 87%. The biota-soil accumulation factors (BSAFs) observed for individual PAHs in field-collected earthworms (Aporrectodea caliginosa) were up to 50-fold lower than the BSAFs predicted using equilibrium-partitioning theory. Acute toxicity to the earthworm Eisenia fetida was unrelated to total PAH concentration: Mortality was not observed in some soils having high concentrations of total PAHs (>42,000 mg/kg), whereas 100% mortality was observed in other soils having much lower concentrations of total PAHs (1,520 mg/kg). Instead, toxicity appeared to be related to the rapidly released fraction of PAHs determined by mild supercritical CO2 extraction (SFE). The results demonstrate that soils having approximately 16,000 mg rapidly released total PAH/kg organic carbon can be acutely toxic to earthworms and that the concentration of PAHs in soil that is rapidly released by SFE can estimate toxicity to soil invertebrates.

  11. Supercritical carbon dioxide extraction as a predictor of polycyclic aromatic hydrocarbon bioaccumulation and toxicity by earthworms in manufactured-gas plant site soils.

    PubMed

    Kreitinger, Joseph P; Quiñones-Rivera, Antonio; Neuhauser, Edward F; Alexander, Martin; Hawthorne, Steven B

    2007-09-01

    The toxicity and uptake of polycyclic aromatic hydrocarbons (PAHs) by earthworms were measured in soil samples collected from manufactured-gas plant sites having a wide range in PAH concentrations (170-42,000 mg/kg) and soil characteristics. Samples varied from vegetated soils to pure lampblack soot and had total organic carbon contents ranging from 3 to 87%. The biota-soil accumulation factors (BSAFs) observed for individual PAHs in field-collected earthworms (Aporrectodea caliginosa) were up to 50-fold lower than the BSAFs predicted using equilibrium-partitioning theory. Acute toxicity to the earthworm Eisenia fetida was unrelated to total PAH concentration: Mortality was not observed in some soils having high concentrations of total PAHs (>42,000 mg/kg), whereas 100% mortality was observed in other soils having much lower concentrations of total PAHs (1,520 mg/kg). Instead, toxicity appeared to be related to the rapidly released fraction of PAHs determined by mild supercritical CO2 extraction (SFE). The results demonstrate that soils having approximately 16,000 mg rapidly released total PAH/kg organic carbon can be acutely toxic to earthworms and that the concentration of PAHs in soil that is rapidly released by SFE can estimate toxicity to soil invertebrates. PMID:17705650

  12. Active site - a site of binding of affinity inhibitors in baker's yeast inorganic pyrophosphatase

    SciTech Connect

    Svyato, I.E.; Sklyankina, V.A.; Avaeva, S.M.

    1986-03-20

    The interaction of the enzyme-substrate complex with methyl phosphate, O-phosphoethanolamine, O-phosphopropanolamine, N-acetylphosphoserine, and phosphoglyolic acid, as well as pyrophosphatase, modified by monoesters of phosphoric acid, with pyrophosphate and tripolyphosphate, was investigated. It was shown that the enzyme containing the substrate in the active site does not react with monophosphates, but modified pyrophosphatase entirely retains the ability to bind polyanions to the regulatory site. It is concluded that the inactivation of baker's yeast inorganic pyrophosphatase by monoesters of phosphoric acid, which are affinity inhibitors of it, is the result of modification of the active site of the enzyme.

  13. A critical evaluation of magnetic activated carbon's potential for the remediation of sediment impacted by polycyclic aromatic hydrocarbons.

    PubMed

    Han, Zhantao; Sani, Badruddeen; Akkanen, Jarkko; Abel, Sebastian; Nybom, Inna; Karapanagioti, Hrissi K; Werner, David

    2015-04-01

    Addition of activated carbon (AC) or biochar (BC) to sediment to reduce the chemical and biological availability of organic contaminants is a promising in-situ remediation technology. But concerns about leaving the adsorbed pollutants in place motivate research into sorbent recovery methods. This study explores the use of magnetic sorbents. A coal-based magnetic activated carbon (MAC) was identified as the strongest of four AC and BC derived magnetic sorbents for polycyclic aromatic hydrocarbons (PAHs) remediation. An 8.1% MAC amendment (w/w, equal to 5% AC content) was found to be as effective as 5% (w/w) pristine AC in reducing aqueous PAHs within three months by 98%. MAC recovery from sediment after three months was 77%, and incomplete MAC recovery had both, positive and negative effects. A slight rebound of aqueous PAH concentrations was observed following the MAC recovery, but aqueous PAH concentrations then dropped again after six months, likely due to the presence of the 23% unrecovered MAC. On the other hand, the 77% recovery of the 8.1% MAC dose was insufficient to reduce ecotoxic effects of fine grained AC or MAC amendment on the egestion rate, growth and reproduction of the AC sensitive species Lumbriculus variegatus.

  14. Polycyclic aromatic hydrocarbon-induced CYP1B1 activity is suppressed by perillyl alcohol in MCF-7 cells

    SciTech Connect

    Chan, Nelson L.S.; Wang Huan; Wang Yun; Leung, H.Y.; Leung, Lai K. . E-mail: laikleung@yahoo.com

    2006-06-01

    Perillyl alcohol (POH) is a dietary monoterpene with potential applications in chemoprevention and chemotherapy. Although clinical trials are under way, POH's physiological and pharmacological properties are still unclear. In the present study, the effect of POH on polycyclic aromatic hydrocarbon (PAH)-induced genotoxicity, and the related expression were examined in MCF-7 cells. Exposure to environmental toxicant increases the risk of cancer. Many of these compounds are pro-carcinogens and are biotransformed into their ultimate genotoxic structures by xenobiotic metabolizing enzymes. CYP1A1 and 1B1 are enzymes that catalyze the biotransformation of dimethylbenz[a]anthracene (DMBA). Our data revealed that 0.5 {mu}M of POH was effective in blocking DMBA-DNA binding. Ethoxyresorufin-O-deethylase (EROD) assay indicated that the administration of POH inhibited the DMBA-induced enzyme activity in MCF-7 cells. Enzyme kinetic analysis revealed that POH inhibited CYP1B1 but not CYP1A1 activity. Quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) assay also demonstrated that the monoterpene reduced CYP1B1 mRNA abundance induced by DMBA. The present study illustrated that POH might inhibit and downregulate CYP1B1, which could protect against PAH-induced carcinogenesis.

  15. Gas-particle partitioning of polycyclic aromatic hydrocarbons (PAHs) in an urban traffic site in Eskisehir, Turkey

    NASA Astrophysics Data System (ADS)

    Gaga, Eftade O.; Ari, Akif

    2011-02-01

    Gas and particle-phase ambient air samples were collected at a traffic site in Eskisehir over a six-month period between January and October 2006. Gas/particle concentrations of 15 PAHs were determined by analyzing integrated glass fiber and polyurethane foam samples. On average, 66% of the total concentrations of PAHs were found in the gas-phase in heating and 69% in the non-heating period samples. Heating period PAH concentrations were found to be 7 to 8 times greater than concentrations in non-heating period samples. Multiple linear regression analysis was carried out to determine the effect of meteorological parameters on measured individual PAH concentrations. Temperature, wind speed and wind direction explained 43% (dibenzo[ a,h]anthracene and benzo[ a]pyrene) to 78% (phenanthrene) of the variability in atmospheric PAH concentrations. Results of the multiple linear regression analysis indicated that temperature and wind speed were statistically significant factors for the measured concentrations of PAHs. Gas-particle partitioning coefficients, (K p) and particle-phase fractions (Φ) of PAHs, were correlated with supercooled vapor pressures ( PLo). Application of non-linear fitting for Φ versus log PLo plots was found to be more robust than linear logarithmic regressions of log K p versus log PLo plots. Particle-phase fractions (Φ) for each PAH were also calculated using octanol-air and soot-air partitioning models. Soot model resulted better predictions of Φ for fluorene, phenanthrene, anthracene, fluoranthene and pyrene. Both two models yielded very similar particle-phase fractions having very close results to experimentally obtained Φ values for the rest of PAHs measured.

  16. Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation*

    PubMed Central

    Payne, Christina M.; Bomble, Yannick J.; Taylor, Courtney B.; McCabe, Clare; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.

    2011-01-01

    Proteins employ aromatic residues for carbohydrate binding in a wide range of biological functions. Glycoside hydrolases, which are ubiquitous in nature, typically exhibit tunnels, clefts, or pockets lined with aromatic residues for processing carbohydrates. Mutation of these aromatic residues often results in significant activity differences on insoluble and soluble substrates. However, the thermodynamic basis and molecular level role of these aromatic residues remain unknown. Here, we calculate the relative ligand binding free energy by mutating tryptophans in the Trichoderma reesei family 6 cellulase (Cel6A) to alanine. Removal of aromatic residues near the catalytic site has little impact on the ligand binding free energy, suggesting that aromatic residues immediately upstream of the active site are not directly involved in binding, but play a role in the glucopyranose ring distortion necessary for catalysis. Removal of aromatic residues at the entrance and exit of the Cel6A tunnel, however, dramatically impacts the binding affinity, suggesting that these residues play a role in chain acquisition and product stabilization, respectively. The roles suggested from differences in binding affinity are confirmed by molecular dynamics and normal mode analysis. Surprisingly, our results illustrate that aromatic-carbohydrate interactions vary dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, these results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for biomass utilization. Generally, these results suggest that nature employs aromatic-carbohydrate interactions with a wide range of binding affinities for diverse functions. PMID:21965672

  17. Bioaccumulation of native polycyclic aromatic hydrocarbons from sediment by a polychaete and a gastropod: freely dissolved concentrations and activated carbon amendment.

    PubMed

    Cornelissen, Gerard; Breedveld, Gijs D; Naes, Kristoffer; Oen, Amy M P; Ruus, Anders

    2006-09-01

    The present paper describes a study on the bioaccumulation of native polycyclic aromatic hydrocarbons (PAHs) from three harbors in Norway using the polychaete Nereis diversicolor and the gastropod Hinia reticulata. First, biota-sediment accumulation factors (BSAFs) were measured in laboratory bioassays using the original sediments. Median BSAFs were 0.004 to 0.01 kg organic carbon/kg lipid (10 PAHs and 6 organism-sediment combinations), which was a factor of 89 to 240 below the theoretical BSAF based on total sediment contents (which is approximately one). However, if BSAFs were calculated on the basis of measured freely dissolved PAH concentrations in the pore water (measured with polyoxymethylene passive samplers), it appeared that these BSAFfree values agreed well with the measured BSAFs, within a factor of 1.7 to 4.3 (median values for 10 PAHs and six organism-sediment combinations). This means that for bioaccumulation, freely dissolved pore-water concentrations appear to be a much better measure than total sediment contents. Second, we tested the effect of 2% (of sediment dry wt) activated carbon (AC) amendments on BSAE The BSAFs were significantly reduced by a factor of six to seven for N. diversicolor in two sediments (i.e., two of six organism-sediment combinations), whereas no significant reduction was observed for H. reticulata. This implies that either site-specific evaluations of AC amendment are necessary, using several site-relevant benthic organisms, or that the physiology of H. reticulata caused artifactually high BSAF values in the presence of AC.

  18. A novel approach to predict active sites of enzyme molecules.

    PubMed

    Chou, Kuo-Chen; Cai, Yu-dong

    2004-04-01

    Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. PMID:14997541

  19. Growth exponents in surface models with non-active sites

    NASA Astrophysics Data System (ADS)

    Santos, M.; Figueiredo, W.; Aarão Reis, F. D. A.

    2006-11-01

    In this work, we studied the role played by the inactive sites present on the substrate of a growing surface. In our model, one particle sticks at the surface if the site where it falls is an active site. However, we allow the deposited particle to diffuse along the surface in accordance with some mechanism previously defined. Using Monte Carlo simulations, and some analytical results, we have investigated the model in (1+1) and (2+1) dimensions considering different relaxation mechanisms. We show that the consideration of non-active sites is a crucial point in the model. In fact, we have seen that the saturation regime is not observed for any value of the density of inactive sites. Besides, the growth exponent β turns to be one, at long times, whatever the mechanism of diffusion we consider in one and two dimensions.

  20. Spectral Response and Diagnostics of Biological Activity of Hydroxyl-Containing Aromatic Compounds

    NASA Astrophysics Data System (ADS)

    Tolstorozhev, G. B.; Mayer, G. V.; Bel'kov, M. V.; Shadyro, O. I.

    2016-08-01

    Using IR Fourier spectra and employing quantum-chemical calculations of electronic structure, spectra, and proton-acceptor properties, synthetic derivatives of aminophenol exhibiting biological activity in the suppression of herpes, influenza, and HIV viruses have been investigated from a new perspective, with the aim of establishing the spectral response of biological activity of the molecules. It has been experimentally established that the participation of the aminophenol hydroxyl group in intramolecular hydrogen bonds is characteristic of structures with antiviral properties. A quantum-chemical calculation of the proton-acceptor ability of the investigated aminophenol derivatives has shown that biologically active structures are characterized by a high proton-acceptor ability of oxygen of the hydroxyl group. A correlation that has been obtained among the formation of an intramolecular hydrogen bond, high proton-acceptor ability, and antiviral activity of substituted aminophenols enables us to predict the pharmacological properties of new medical preparations of the given class of compounds.

  1. A small ribozyme with dual-site kinase activity

    PubMed Central

    Biondi, Elisa; Maxwell, Adam W.R.; Burke, Donald H.

    2012-01-01

    Phosphoryl transfer onto backbone hydroxyls is a recognized catalytic activity of nucleic acids. We find that kinase ribozyme K28 possesses an unusually complex active site that promotes (thio)phosphorylation of two residues widely separated in primary sequence. After allowing the ribozyme to radiolabel itself by phosphoryl transfer from [γ-32P]GTP, DNAzyme-mediated cleavage yielded two radiolabeled cleavage fragments, indicating phosphorylation sites within each of the two cleavage fragments. These sites were mapped by alkaline digestion and primer extension pausing. Enzymatic digestion and mutational analysis identified nucleotides important for activity and established the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose the two reactive sites. Nuclease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPγS, indicating donor-induced folding. The 5′ target site was more strongly favored in full-length ribozyme K28 (128 nt) than in truncated RNAs (58 nt). Electrophoretic mobilities of self-thiophosphorylated products on organomercurial gels are distinct from the 5′ mono-thiophosphorylated product produced by reaction with polynucleotide kinase, potentially indicating simultaneous labeling of both sites within individual RNA strands. Our evidence supports a single, compact structure with local dynamics, rather than global rearrangement, as being responsible for dual-site phosphorylation. PMID:22618879

  2. Aromatic graphene

    NASA Astrophysics Data System (ADS)

    Das, D. K.; Sahoo, S.

    2016-04-01

    In recent years graphene attracts the scientific and engineering communities due to its outstanding electronic, thermal, mechanical and optical properties and many potential applications. Recently, Popov et al. [1] have studied the properties of graphene and proved that it is aromatic but without fragrance. In this paper, we present a theory to prepare graphene with fragrance. This can be used as scented pencils, perfumes, room and car fresheners, cosmetics and many other useful household substances.

  3. Dehalogenation of aromatics by nucleophilic aromatic substitution.

    PubMed

    Sadowsky, Daniel; McNeill, Kristopher; Cramer, Christopher J

    2014-09-16

    Nucleophilic aromatic substitution has been implicated as a mechanism for both the biotic and abiotic hydrodehalogenation of aromatics. Two mechanisms for the aqueous dehalogenation of aromatics involving nucleophilic aromatic substitution with hydride as a nucleophile are investigated using a validated density functional and continuum solvation protocol. For chlorinated and brominated aromatics, nucleophilic addition ortho to carbon-halogen bonds via an anionic intermediate is predicted to be the preferred mechanism in the majority of cases, while concerted substitution is predicted to be preferred for most fluorinated aromatics. Nucleophilic aromatic substitution reactions with the hydroxide and hydrosulfide anions as nucleophiles are also investigated and compared.

  4. Multiple, Ligand-Dependent Routes from the Active Site of Cytochrome P450 2C9

    SciTech Connect

    Cojocaru, Vlad; Winn, Peter J.; Wade, Rebecca C.

    2012-02-13

    The active site of liver-specific, drug-metabolizing cytochrome P450 (CYP) monooxygenases is deeply buried in the protein and is connected to the protein surface through multiple tunnels, many of which were found open in different CYP crystal structures. It has been shown that different tunnels could serve as ligand passage routes in different CYPs. However, it is not understood whether one CYP uses multiple routes for substrate access and product release and whether these routes depend on ligand properties. From 300 ns of molecular dynamics simulations of CYP2C9, the second most abundant CYP in the human liver we found four main ligand exit routes, the occurrence of each depending on the ligand type and the conformation of the F-G loop, which is likely to be affected by the CYP-membrane interaction. A non-helical F-G loop favored exit towards the putative membrane-embedded region. Important protein features that direct ligand exit include aromatic residues that divide the active site and whose motions control access to two pathways. The ligands interacted with positively charged residues on the protein surface through hydrogen bonds that appear to select for acidic substrates. The observation of multiple, ligand-dependent routes in a CYP aids understanding of how CYP mutations affect drug metabolism and provides new possibilities for CYP inhibition.

  5. New aromatic activated dihalides and bisphenol monomers for the preparation of novel poly(arylene ethers)

    NASA Technical Reports Server (NTRS)

    Wolfe, James F.

    1993-01-01

    The goal of this research program was to synthesize a series of unique monomers of type I to be utilized at NASA-Langley in the preparation of new poly(arylene ether ketones), poly(arylene ether ketosulfones), and poly(arylene ether ketophosphine oxides). These A-A and A-B monomer systems, which possess activated aryl halide and/or phenolic end groups, are accessible via condensation reactions of appropriately substituted aryl acetonitrile carbanions with activated aryl dihalides followed by oxidative decyanation.

  6. Polyimidazoles Via Aromatic Nucleophilic Displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W.; Hergenrother, Paul M.

    1990-01-01

    Experiments show variety of polyimidazoles prepared by aromatic nucleophilic displacement, from reactions of bisphenol imidazoles with activated difluoro compounds. Polyimidazoles have good mechanical properties making them suitable for use as films, moldings, and adhesives.

  7. Prenatal Polycyclic Aromatic Hydrocarbon, Adiposity, Peroxisome Proliferator-Activated Receptor (PPAR) γ Methylation in Offspring, Grand-Offspring Mice

    PubMed Central

    Yan, Zhonghai; Zhang, Hanjie; Maher, Christina; Arteaga-Solis, Emilio; Champagne, Frances A.; Wu, Licheng; McDonald, Jacob D.; Yan, Beizhan; Schwartz, Gary J.; Miller, Rachel L.

    2014-01-01

    Rationale Greater levels of prenatal exposure to polycyclic aromatic hydrocarbon (PAH) have been associated with childhood obesity in epidemiological studies. However, the underlying mechanisms are unclear. Objectives We hypothesized that prenatal PAH over-exposure during gestation would lead to weight gain and increased fat mass in offspring and grand-offspring mice. Further, we hypothesized that altered adipose gene expression and DNA methylation in genes important to adipocyte differentiation would be affected. Materials and Methods Pregnant dams were exposed to a nebulized PAH mixture versus negative control aerosol 5 days a week, for 3 weeks. Body weight was recorded from postnatal day (PND) 21 through PND60. Body composition, adipose cell size, gene expression of peroxisome proliferator-activated receptor (PPAR) γ, CCAAT/enhancer-binding proteins (C/EBP) α, cyclooxygenase (Cox)-2, fatty acid synthase (FAS) and adiponectin, and DNA methylation of PPAR γ, were assayed in both the offspring and grand-offspring adipose tissue. Findings Offspring of dams exposed to greater PAH during gestation had increased weight, fat mass, as well as higher gene expression of PPAR γ, C/EBP α, Cox2, FAS and adiponectin and lower DNA methylation of PPAR γ. Similar differences in phenotype and DNA methylation extended through the grand-offspring mice. Conclusions Greater prenatal PAH exposure was associated with increased weight, fat mass, adipose gene expression and epigenetic changes in progeny. PMID:25347678

  8. Purification of Pseudomonas putida acyl coenzyme A ligase active with a range of aliphatic and aromatic substrates.

    PubMed Central

    Fernández-Valverde, M; Reglero, A; Martinez-Blanco, H; Luengo, J M

    1993-01-01

    Acyl coenzyme A (acyl-CoA) ligase (acyl-CoA synthetase [ACoAS]) from Pseudomonas putida U was purified to homogeneity (252-fold) after this bacterium was grown in a chemically defined medium containing octanoic acid as the sole carbon source. The enzyme, which has a mass of 67 kDa, showed maximal activity at 40 degrees C in 10 mM K2PO4H-NaPO4H2 buffer (pH 7.0) containing 20% (wt/vol) glycerol. Under these conditions, ACoAS showed hyperbolic behavior against acetate, CoA, and ATP; the Kms calculated for these substrates were 4.0, 0.7, and 5.2 mM, respectively. Acyl-CoA ligase recognizes several aliphatic molecules (acetic, propionic, butyric, valeric, hexanoic, heptanoic, and octanoic acids) as substrates, as well as some aromatic compounds (phenylacetic and phenoxyacetic acids). The broad substrate specificity of ACoAS from P. putida was confirmed by coupling it with acyl-CoA:6-aminopenicillanic acid acyltransferase from Penicillium chrysogenum to study the formation of several penicillins. Images PMID:8476289

  9. Electrochemically enhanced removal of polycyclic aromatic basic dyes from dilute aqueous solutions by activated carbon cloth electrodes.

    PubMed

    Bayram, Edip; Ayranci, Erol

    2010-08-15

    Open-circuit (OC) adsorption and electrosorption behaviors of three polycyclic aromatic dyes from dilute aqueous solutions onto activated carbon cloth (ACC) were investigated. The selected dyes were crystal violet (BB-3), basic blue7 (BB-7), and basic blue11 (BB-11). OC adsorption and electrosorption processes were monitored by in situ UV-visible spectrophotometry. Electrosorption was carried out by polarization of an ACC electrode, galvanostatically. Considerable enhancements in removal capacity and duration of the dyes were achieved upon polarization of ACC. Kinetic data for OC adsorption and electrosorption were successfully treated according to pseudo-first-order law, and rate constants were determined. Adsorption isotherms were derived, and the data were treated according to Langmuir and Freundlich equations. Both the rate and extent of adsorption and electrosorption of dyes were found to increase in the order of BB-7 < BB-11 < BB-3. This order was discussed in terms of correlation between sizes of dye species and of ACC pores. Electrodesorption experiments were carried out to explore possibilities of regeneration of ACC. PMID:20704233

  10. Architecture and active site of particulate methane monooxygenase

    PubMed Central

    Culpepper, Megen A.; Rosenzweig, Amy C.

    2012-01-01

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O2 binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies. PMID:22725967

  11. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site.

    PubMed

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  12. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

    PubMed Central

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-01-01

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  13. Sulfated Low Molecular Weight Lignins, Allosteric Inhibitors of Coagulation Proteinases via the Heparin Binding Site, Significantly Alter the Active Site of Thrombin and Factor Xa Compared to Heparin

    PubMed Central

    Henry, Brian L.; Desai, Umesh R.

    2014-01-01

    Sulfated low molecular weight lignins (LMWLs) have been found to bind in the heparin binding sites of coagulation proteinases. LMWLs represent a library of diverse non-carbohydrate, aromatic molecules which are structures different from heparin, but still potently inhibit thrombin and factor Xa. To better understand their mechanism of action, we studied the effects of three sulfated LMWLs (CDSO3, FDSO3, and SDSO3) on the active sites of thrombin and factor Xa. LMWLs were found to uniformly inhibit the catalytic activity of thrombin and factor Xa, regardless of the substrate used. Michaelis-Menten kinetic studies indicate that maximal velocity of hydrolysis of each chromogenic substrate decreases significantly in the presence of sulfated LMWLs, while the effect on Michaelis constant is dependent on the nature of the substrate. These studies indicate that LMWLs inhibit thrombin and factor Xa through allosteric disruption of the catalytic apparatus, specifically through the catalytic step. As opposed to heparin, LMWLs significantly alter the binding of the active site fluorescent ligand p-aminobenzamidine. LMWLs also had a greater effect on the molecular orientation of fluorescein-labeled His 57 than heparin. The molecular geometry surrounding the most important catalytic amino acid, Ser 195, was significantly altered by the binding of LMWLs while heparin had no measurable effect on Ser 195. These results further advance the concept of sulfated LMWLs as heparin mimics and will aid the design of anticoagulants based on their novel scaffold. PMID:25242245

  14. Sulfated low molecular weight lignins, allosteric inhibitors of coagulation proteinases via the heparin binding site, significantly alter the active site of thrombin and factor xa compared to heparin.

    PubMed

    Henry, Brian L; Desai, Umesh R

    2014-11-01

    Sulfated low molecular weight lignins (LMWLs) have been found to bind in the heparin binding sites of coagulation proteinases. LMWLs represent a library of diverse non-carbohydrate, aromatic molecules which are structures different from heparin, but still potently inhibit thrombin and factor Xa. To better understand their mechanism of action, we studied the effects of three sulfated LMWLs (CDSO3, FDSO3, and SDSO3) on the active sites of thrombin and factor Xa. LMWLs were found to uniformly inhibit the catalytic activity of thrombin and factor Xa, regardless of the substrate used. Michaelis-Menten kinetic studies indicate that maximal velocity of hydrolysis of each chromogenic substrate decreases significantly in the presence of sulfated LMWLs, while the effect on Michaelis constant is dependent on the nature of the substrate. These studies indicate that LMWLs inhibit thrombin and factor Xa through allosteric disruption of the catalytic apparatus, specifically through the catalytic step. As opposed to heparin, LMWLs significantly alter the binding of the active site fluorescent ligand p-aminobenzamidine. LMWLs also had a greater effect on the molecular orientation of fluorescein-labeled His 57 than heparin. The molecular geometry surrounding the most important catalytic amino acid, Ser 195, was significantly altered by the binding of LMWLs while heparin had no measurable effect on Ser 195. These results further advance the concept of sulfated LMWLs as heparin mimics and will aid the design of anticoagulants based on their novel scaffold. PMID:25242245

  15. Bioassay of polycyclic aromatic hydrocarbons

    SciTech Connect

    Van Kirk, E.A.

    1980-08-01

    A positive relationship was found between the photodynamic activity of 24 polycyclic aromatic hydrocarbons versus published results on the mutagenicity, carcinogenicity, and initiation of unscheduled DNA synthesis. Metabolic activation of benzo(a)pyrene resulted in detection of increased mutagenesis in Paramecium tetraurelia as found also in the Ames Salmonella assay. The utility of P. tetraurelia as a biological detector of hazardous polycyclic aromatic hydrocarbons is discussed.

  16. Anti-plasmodial and insecticidal activities of the essential oils of aromatic plants growing in the Mediterranean area

    PubMed Central

    2012-01-01

    Background Sardinia is a Mediterranean area endemic for malaria up to the last century. During a screening study to evaluate the anti-plasmodial activity of some aromatic plants traditionally used in Sardinia, Myrtus communis (myrtle, Myrtaceae), Satureja thymbra (savory, Lamiaceae), and Thymus herba-barona (caraway thyme, Lamiaceae) were collected in three vegetative periods: before, during and after flowering. Methods The essential oils were obtained by steam distillation, fractionated by silica gel column chromatography and analysed by GC-FID-MS. Total oil and three main fractions were tested on D10 and W2 strains of Plasmodium falciparum in vitro. Larvicidal and adulticidal activities were tested on Anopheles gambiae susceptible strains. Results The essential oil of savory, rich in thymol, was the most effective against P. falciparum with an inhibitory activity independent from the time of collection (IC50 17–26 μg/ml on D10 and 9–11 μg/ml on W2). Upon fractionation, fraction 1 was enriched in mono-sesquiterpenoid hydrocarbons; fraction 2 in thymol (73-83%); and fraction 3 contained thymol, carvacrol and terpinen-4-ol, with a different composition depending on the time of collection. Thymol-enriched fractions were the most active on both strains (IC50 20–22 μg/ml on D10 and 8–10 μg/ml on W2) and thymol was confirmed as mainly responsible for this activity (IC50 19.7± 3.0 and 10.6 ± 2.0 μg/ml on D10 and W2, respectively). The essential oil of S. thymbra L. showed also larvicidal and adulticidal activities. The larvicidal activity, expressed as LC50, was 0.15 ± 0.002; 0.21 ± 0.13; and 0.15 ± 0.09 μg/ml (mean ± sd) depending on the time of collection: before, during and after flowering, respectively. Conclusions This study provides evidence for the use of essential oils for treating malaria and fighting the vector at both the larval and adult stages. These findings open the possibility for further investigation aimed at

  17. Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis.

    PubMed

    Neshat, Armin; Mentz, Almut; Rückert, Christian; Kalinowski, Jörn

    2014-11-20

    The Gram-positive bacterium Corynebacterium glutamicum belongs to the order Corynebacteriales and is used as a producer of amino acids at industrial scales. Due to its economic importance, gene expression and particularly the regulation of amino acid biosynthesis has been investigated extensively. Applying the high-resolution technique of transcriptome sequencing (RNA-seq), recently a vast amount of data has been generated that was used to comprehensively analyze the C. glutamicum transcriptome. By analyzing RNA-seq data from a small RNA cDNA library of C. glutamicum, short transcripts in the known transcriptional attenuators sites of the trp operon, the ilvBNC operon and the leuA gene were verified. Furthermore, whole transcriptome RNA-seq data were used to elucidate the transcriptional organization of these three amino acid biosynthesis operons. In addition, we discovered and analyzed the novel attenuator aroR, located upstream of the aroF gene (cg1129). The DAHP synthase encoded by aroF catalyzes the first step in aromatic amino acid synthesis. The AroR leader peptide contains the amino acid sequence motif F-Y-F, indicating a regulatory effect by phenylalanine and tyrosine. Analysis by real-time RT-PCR suggests that the attenuator regulates the transcription of aroF in dependence of the cellular amount of tRNA loaded with phenylalanine when comparing a phenylalanine-auxotrophic C. glutamicum mutant fed with limiting and excess amounts of a phenylalanine-containing dipeptide. Additionally, the very interesting finding was made that all analyzed attenuators are leaderless transcripts. PMID:24910972

  18. Metabolism and Biomarkers of Heterocyclic Aromatic Amines in Molecular Epidemiology Studies: Lessons Learned from Aromatic Amines

    PubMed Central

    2011-01-01

    Aromatic amines and heterocyclic aromatic amines (HAAs) are structurally related classes of carcinogens that are formed during the combustion of tobacco or during the high-temperature cooking of meats. Both classes of procarcinogens undergo metabolic activation by N-hydroxylation of the exocyclic amine group, to produce a common proposed intermediate, the arylnitrenium ion, which is the critical metabolite implicated in toxicity and DNA damage. However, the biochemistry and chemical properties of these compounds are distinct and different biomarkers of aromatic amines and HAAs have been developed for human biomonitoring studies. Hemoglobin adducts have been extensively used as biomarkers to monitor occupational and environmental exposures to a number of aromatic amines; however, HAAs do not form hemoglobin adducts at appreciable levels and other biomarkers have been sought. A number of epidemiologic studies that have investigated dietary consumption of well-done meat in relation to various tumor sites reported a positive association between cancer risk and well-done meat consumption, although some studies have shown no associations between well-done meat and cancer risk. A major limiting factor in most epidemiological studies is the uncertainty in quantitative estimates of chronic exposure to HAAs and, thus, the association of HAAs formed in cooked meat and cancer risk has been difficult to establish. There is a critical need to establish long-term biomarkers of HAAs that can be implemented in molecular epidemioIogy studies. In this review article, we highlight and contrast the biochemistry of several prototypical carcinogenic aromatic amines and HAAs to which humans are chronically exposed. The biochemical properties and the impact of polymorphisms of the major xenobiotic-metabolizing enzymes on the biological effects of these chemicals are examined. Lastly, the analytical approaches that have been successfully employed to biomonitor aromatic amines and HAAs, and

  19. Computer Simulations Reveal Multiple Functions for Aromatic Residues in Cellulase Enzymes (Fact Sheet)

    SciTech Connect

    Not Available

    2012-07-01

    NREL researchers use high-performance computing to demonstrate fundamental roles of aromatic residues in cellulase enzyme tunnels. National Renewable Energy Laboratory (NREL) computer simulations of a key industrial enzyme, the Trichoderma reesei Family 6 cellulase (Cel6A), predict that aromatic residues near the enzyme's active site and at the entrance and exit tunnel perform different functions in substrate binding and catalysis, depending on their location in the enzyme. These results suggest that nature employs aromatic-carbohydrate interactions with a wide variety of binding affinities for diverse functions. Outcomes also suggest that protein engineering strategies in which mutations are made around the binding sites may require tailoring specific to the enzyme family. Cellulase enzymes ubiquitously exhibit tunnels or clefts lined with aromatic residues for processing carbohydrate polymers to monomers, but the molecular-level role of these aromatic residues remains unknown. In silico mutation of the aromatic residues near the catalytic site of Cel6A has little impact on the binding affinity, but simulation suggests that these residues play a major role in the glucopyranose ring distortion necessary for cleaving glycosidic bonds to produce fermentable sugars. Removal of aromatic residues at the entrance and exit of the cellulase tunnel, however, dramatically impacts the binding affinity. This suggests that these residues play a role in acquiring cellulose chains from the cellulose crystal and stabilizing the reaction product, respectively. These results illustrate that the role of aromatic-carbohydrate interactions varies dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, the results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for

  20. Effect of cyclic aromatics on sodium active transport in frog skin

    SciTech Connect

    Blankemeyer, J.T.; Bowerman, M.C. )

    1993-01-01

    A modified glass Ussing-chamber was used to mount the skin. The electrical potential difference (PD) was measured by two 3% agar-frog Ringer's bridges. Current (i.e. short-circuit current, or ISC) was passed by Ag-AgCl electrodes placed so that current density was uniform across the skin. Ringer's solution, bathing each side of the frog skin, was stirred and aerated by gas-lift pumps. The effect of toxicants on the ISC was determined by using the 15 min prior to toxicant administration as a control period, then calculating the change in ISC during the toxicant period as a percent of the control ISC. Phenol and benzene are components of crude oil and crude oil waste. These hydrocarbons and phenanthrene were tested for their effect on frog skin. The results show that the effect of organics on sodium active transport of an epithelium is to alter the active transport of sodium ions. 5 refs., 3 figs., 1 tab.

  1. Oxidation of polycyclic aromatic hydrocarbons using Bacillus subtilis CotA with high laccase activity and copper independence.

    PubMed

    Zeng, Jun; Zhu, Qinghe; Wu, Yucheng; Lin, Xiangui

    2016-04-01

    Bacterial laccase CueO from Escherichia coli can oxidize polycyclic aromatic hydrocarbons (PAHs); however, its application in the remediation of PAH-contaminated soil mainly suffers from a low oxidation rate and copper dependence. It was reported that a laccase with a higher redox potential tended to have a higher oxidation rate; thus, the present study investigated the oxidation of PAHs using another bacterial laccase CotA from Bacillus subtilis with a higher redox potential (525 mV) than CueO (440 mV). Recombinant CotA was overexpressed in E. coli and partially purified, exhibiting a higher laccase-specific activity than CueO over a broad pH and temperature range. CotA exhibited moderate thermostability at high temperatures. CotA oxidized PAHs in the absence of exogenous copper. Thereby, secondary heavy metal pollution can be avoided, another advantage of CotA over CueO. Moreover, this study also evaluated some unexplained phenomena in our previous study. It was observed that the oxidation of PAHs with bacterial laccases can be promoted by copper. The partially purified bacterial laccase oxidized only two of the 15 tested PAHs, i.e., anthracene and benzo[a]pyrene, indicating the presence of natural redox mediators in crude cell extracts. Overall, the recombinant CotA oxidizes PAHs with high laccase activity and copper independence, indicating that CotA is a better candidate for the remediation of PAHs than CueO. Besides, the findings here provide a better understanding of the oxidation of PAHs using bacterial laccases.

  2. Phytochemical profiles and antimicrobial activity of aromatic Malaysian herb extracts against food-borne pathogenic and food spoilage microorganisms.

    PubMed

    Aziman, Nurain; Abdullah, Noriham; Noor, Zainon Mohd; Kamarudin, Wan Saidatul Syida Wan; Zulkifli, Khairusy Syakirah

    2014-04-01

    Preliminary phytochemical and flavonoid compounds of aqueous and ethanolic extracts of 6 aromatic Malaysian herbs were screened and quantified using Reverse-Phase High Performance Liquid Chromatography (RP-HPLC). The herbal extracts were tested for their antimicrobial activity against 10 food-borne pathogenic and food spoilage microorganisms using disk diffusion assay. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC)/minimum fungicidal concentration (MFC) of herbal extracts were determined. In the phytochemical screening process, both aqueous and ethanolic extracts of P. hydropiper exhibited presence of all 7 tested phytochemical compounds. Among all herbal extracts, the aqueous P. hydropiper and E. elatior extracts demonstrated the highest antibacterial activity against 7 tested Gram-positive and Gram-negative bacteria with diameter ranging from 7.0 to 18.5 mm and 6.5 to 19 mm, respectively. The MIC values for aqueous and ethanolic extracts ranged from 18.75 to 175 mg/mL and 0.391 to 200 mg/mL, respectively while the MBC/MFC values for aqueous and ethanolic extracts ranged from 25 to 200 mg/mL and 3.125 to 50 mg/mL, respectively. Major types of bioactive compounds in aqueous P. hydropiper and E. elatior extracts were identified using RP-HPLC instrument. Flavonoids found in these plants were epi-catechin, quercetin, and kaempferol. The ability of aqueous Persicaria hydropiper (L.) H. Gross and Etlingera elatior (Jack) R.M. Sm. extracts to inhibit the growth of bacteria is an indication of its broad spectrum antimicrobial potential. Hence these herbal extracts may be used as natural preservative to improve the safety and shelf-life of food and pharmaceutical products.

  3. Evaluation of the mutagenic activity of chrysin, a flavonoid inhibitor of the aromatization process.

    PubMed

    Oliveira, G A R; Ferraz, E R A; Souza, A O; Lourenço, R A; Oliveira, D P; Dorta, D J

    2012-01-01

    Chrysin is one of the natural flavonoids present in plants, and large amounts are present in honey and propolis. In addition to anticancer, antioxidation, and anti-inflammatory activities, chrysin has also been reported to be an inhibitor of aromatase, an enzyme converting testosterone into estrogen. The present study evaluated the mutagenicity of this flavonoid using micronucleus (MN) with HepG2 cells and Salmonella. Cell survival after exposure to different concentrations of chrysin was also determined using sulforhodamine B (SRB) colorimetric assay in HepG2 cells and the influence of this flavonoid on growth of cells in relation to the cell cycle and apoptosis. The MN test showed that from 1 to 15 μM of this flavonoid mutagenic activity was noted in HepG2 cells. The Salmonella assay demonstrated a positive response to the TA100 Salmonella strain in the presence or absence of S9, suggesting that this compound acted on DNA, inducing base pair substitution before or after metabolism via cytochrome P-450. The SRB assay illustrated that chrysin promoted growth inhibition of HepG2 cells in both periods studied (24 and 48 h). After 24 h of exposure it was noted that the most significant results were obtained with a concentration of 50 μM, resulting in 83% inhibition and SubG0 percentage of 12%. After 48 h of incubation cell proliferation inhibition rates (97% at 50 μM) were significantly higher. Our results showed that chrysin is a mutagenic and cytotoxic compound in cultured human HepG2 cells and Salmonella typhimurium. Although it is widely accepted that flavonoids are substances beneficial to health, one must evaluate the risk versus benefit relationship and concentrations of these substances to which an individual may be exposed.

  4. Active Sites Environmental Monitoring Program: Mid-FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1991-10-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.

  5. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined.

  6. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined. PMID:27243042

  7. Studies on the active site of pig plasma amine oxidase.

    PubMed Central

    Collison, D; Knowles, P F; Mabbs, F E; Rius, F X; Singh, I; Dooley, D M; Cote, C E; McGuirl, M

    1989-01-01

    Amine oxidase from pig plasma (PPAO) has two bound Cu2+ ions and at least one pyrroloquinoline quinone (PQQ) moiety as cofactors. It is shown that recovery of activity by copper-depleted PPAO is linear with respect to added Cu2+ ions. Recovery of e.s.r. and optical spectral characteristics of active-site copper parallel the recovery of catalytic activity. These results are consistent with both Cu2+ ions contributing to catalysis. Further e.s.r. studies indicate that the two copper sites in PPAO, unlike those in amine oxidases from other sources, are chemically distinct. These comparative studies establish that non-identity of the Cu2+ ions in PPAO is not a requirement for amine oxidase activity. It is shown through the use of a new assay procedure that there are two molecules of PQQ bound per molecule of protein in PPAO; only the more reactive of these PQQ moieties is required for activity. PMID:2559715

  8. Treatment of soil eluate containing nitro aromatic compounds by adsorption on activated coke (AC).

    PubMed

    Zhang, Yiping; Jiang, Zhenming; Zhao, Quanlin; Zhang, Zhenzhong; Su, Hongping; Gao, Xuewen; Ye, Zhengfang

    2016-01-01

    Soil washing is a kind of physical method to remove organic matters from contaminated soil. However, its eluate after washing may result in secondary pollution to the environment. In this study, activated coke (AC) was used to remove organic pollutants from contaminated soil eluate. The effect of temperature, initial chemical oxygen demand (COD) and AC dosage on COD removal efficiency was investigated. The results showed that the organic matter can be removed in the eluate because the COD dropped a lot. When the AC dosage was 20 g·L(-1), 88.92% of COD decreased after 480 min of adsorption at 50 °C. The process of adsorption can be described by the Redlich-Peterson isotherm. The adsorption was spontaneous and endothermic. The pseudo-second-order model can be used to describe the adsorption process. After adsorption, the acute toxicity of the eluate was reduced by 76%, and the water qualities were in agreement with Chinese discharge standard GB 14470.1-2002, which means the eluate could be discharged to the environment. PMID:27003071

  9. Treatment of soil eluate containing nitro aromatic compounds by adsorption on activated coke (AC).

    PubMed

    Zhang, Yiping; Jiang, Zhenming; Zhao, Quanlin; Zhang, Zhenzhong; Su, Hongping; Gao, Xuewen; Ye, Zhengfang

    2016-01-01

    Soil washing is a kind of physical method to remove organic matters from contaminated soil. However, its eluate after washing may result in secondary pollution to the environment. In this study, activated coke (AC) was used to remove organic pollutants from contaminated soil eluate. The effect of temperature, initial chemical oxygen demand (COD) and AC dosage on COD removal efficiency was investigated. The results showed that the organic matter can be removed in the eluate because the COD dropped a lot. When the AC dosage was 20 g·L(-1), 88.92% of COD decreased after 480 min of adsorption at 50 °C. The process of adsorption can be described by the Redlich-Peterson isotherm. The adsorption was spontaneous and endothermic. The pseudo-second-order model can be used to describe the adsorption process. After adsorption, the acute toxicity of the eluate was reduced by 76%, and the water qualities were in agreement with Chinese discharge standard GB 14470.1-2002, which means the eluate could be discharged to the environment.

  10. Visible-Light-Induced Olefin Activation Using 3D Aromatic Boron-Rich Cluster Photooxidants.

    PubMed

    Messina, Marco S; Axtell, Jonathan C; Wang, Yiqun; Chong, Paul; Wixtrom, Alex I; Kirlikovali, Kent O; Upton, Brianna M; Hunter, Bryan M; Shafaat, Oliver S; Khan, Saeed I; Winkler, Jay R; Gray, Harry B; Alexandrova, Anastassia N; Maynard, Heather D; Spokoyny, Alexander M

    2016-06-01

    We report a discovery that perfunctionalized icosahedral dodecaborate clusters of the type B12(OCH2Ar)12 (Ar = Ph or C6F5) can undergo photo-excitation with visible light, leading to a new class of metal-free photooxidants. Excitation in these species occurs as a result of the charge transfer between low-lying orbitals located on the benzyl substituents and an unoccupied orbital delocalized throughout the boron cluster core. Here we show how these species, photo-excited with a benchtop blue LED source, can exhibit excited-state reduction potentials as high as 3 V and can participate in electron-transfer processes with a broad range of styrene monomers, initiating their polymerization. Initiation is observed in cases of both electron-rich and electron-deficient styrene monomers at cluster loadings as low as 0.005 mol%. Furthermore, photo-excitation of B12(OCH2C6F5)12 in the presence of a less activated olefin such as isobutylene results in the production of highly branched poly(isobutylene). This work introduces a new class of air-stable, metal-free photo-redox reagents capable of mediating chemical transformations. PMID:27186856

  11. Conversed mutagenesis of an inactive peptide to ASIC3 inhibitor for active sites determination.

    PubMed

    Osmakov, Dmitry I; Koshelev, Sergey G; Andreev, Yaroslav A; Dyachenko, Igor A; Bondarenko, Dmitry A; Murashev, Arkadii N; Grishin, Eugene V; Kozlov, Sergey A

    2016-06-15

    Peptide Ugr9-1 from the venom of sea anemone Urticina grebelnyi selectively inhibits the ASIC3 channel and significantly reverses inflammatory and acid-induced pain in vivo. A close homolog peptide Ugr 9-2 does not have these features. To find the pharmacophore residues and explore structure-activity relationships of Ugr 9-1, we performed site-directed mutagenesis of Ugr 9-2 and replaced several positions by the corresponding residues from Ugr 9-1. Mutant peptides Ugr 9-2 T9F and Ugr 9-2 Y12H were able to inhibit currents of the ASIC3 channels 2.2 times and 1.3 times weaker than Ugr 9-1, respectively. Detailed analysis of the spatial models of Ugr 9-1, Ugr 9-2 and both mutant peptides revealed the presence of the basic-aromatic clusters on opposite sides of the molecule, each of which is responsible for the activity. Additionally, Ugr9-1 mutant with truncated N- and C-termini retained similar with the Ugr9-1 action in vitro and was equally potent in vivo model of thermal hypersensitivity. All together, these results are important for studying the structure-activity relationships of ligand-receptor interaction and for the future development of peptide drugs from animal toxins. PMID:26686983

  12. Interaction of W-Substituted Analogs of Cyclo-RRRWFW with Bacterial Lipopolysaccharides: the Role of the Aromatic Cluster in Antimicrobial Activity ▿ †

    PubMed Central

    Bagheri, Mojtaba; Keller, Sandro; Dathe, Margitta

    2011-01-01

    The activity of cyclo-RRRWFW (c-WFW) against Escherichia coli has been shown to be modulated by the aromatic motif and the lipopolysaccharides (LPS) in the bacterial outer membrane. To identify interaction sites and to elucidate the mode of c-WFW action, peptides were synthesized by the replacement of tryptophan (W) with analogs having altered hydrophobicity, dipole and quadrupole moments, hydrogen-bonding ability, amphipathicity, and ring size. The peptide activity against Bacillus subtilis and erythrocytes increased with increasing hydrophobicity, whereas the effect on E. coli revealed a more complex pattern. Although they had no effect on the E. coli inner membrane even at concentrations higher than the MIC, peptides permeabilized the outer membrane according to their antimicrobial activity pattern, suggesting a major role of LPS in peptide transport across the wall. For isothermal titration calorimetry (ITC) studies of peptide-lipid bilayer interaction, we used POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline), either alone or in mixtures with 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (POPG), to mimic the charge properties of eukaryotic and bacterial membranes, respectively, as well as in mixtures with lipid A, rough LPS, and smooth LPS as models of the outer membrane of E. coli. Peptide accumulation was determined by both electrostatic and hydrophobic interactions. The susceptibility of the lipid systems followed the order of POPC-smooth LPS >> POPC-rough LPS > POPC-lipid A = POPC-POPG > POPC. Low peptide hydrophobicity and enhanced flexibility reduced binding. The influence of the other properties on the free energy of partitioning was low, but an enhanced hydrogen-bonding ability and dipole moment resulted in remarkable variations in the contribution of enthalpy and entropy. In the presence of rough and smooth LPS, the binding-modulating role of these parameters decreased. The highly differentiated activity pattern against E. coli

  13. 1H NMR analysis of complexation of hydrotropic agents nicotinamide and caffeine with aromatic biologically active molecules in aqueous solution

    NASA Astrophysics Data System (ADS)

    Lantushenko, Anastasia O.; Mukhina, Yulia V.; Veselkov, Kyrill A.; Davies, David B.; Veselkov, Alexei N.

    2004-07-01

    NMR spectroscopy has been used to elucidate the molecular mechanism of solubilization action of hydrotropic agents nicotinamide (NA) and caffeine (CAF). Hetero-association of NA with riboflavine-mononucleotide (FMN) and CAF with low soluble in aqueous solution synthetic analogue of antibiotic actinomycin D, actinocyl-bis-(3-dimethylaminopropyl) amine (Actill), has been investigated by 500 MHz 1H NMR spectroscopy. Concentration and temperature dependences of proton chemical shifts have been analysed in terms of a statistical-thermodynamic model of indefinite self- and heteroassociation of aromatic molecules. The obtained results enable to conclude that NA-FMN and CAF-Actill intermolecular complexes are mainly stabilized by the stacking interactions of the aromatic chromophores. Hetero-association of the investigated molecules plays an important role in solubilization of aromatic drugs by hydrotropic agents nicotinamide and caffeine.

  14. Computer simulation of the active site of human serum cholinesterase

    SciTech Connect

    Kefang Jiao; Song Li; Zhengzheng Lu

    1996-12-31

    The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positive electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.

  15. Polybenzimidazoles via aromatic nucleophilic displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

    1995-01-01

    Novel molecular weight controlled and endcapped polybenzimidazoles (PBI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenyl benzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The PBI are endcapped with mono(hydroxyphenyl) benzimidazoles. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. Mono(hydroxyphenyl) benzimidazoles are synthesizedby reacting phenyl-4-hydroxybenzoate with aromatic (o-diamine)s in diphenylsulfone. Molecular weight controlled and endcapped PBI of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

  16. Polybenzimidazoles Via Aromatic Nucleophilic Displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Hergerrother, Paul M. (Inventor); Smith, Joseph G., Jr. (Inventor)

    1997-01-01

    Novel molecular weight controlled and endcapped polybenzimidazoles (PBI) are prepared by the aromatic nucleophilic displacement reaction of di(hydroxyphenylbenzimidazole) monomers with activated aromatic dihalides or activated aromatic dinitro compounds. The PBI are endcapped with mono(hydroxyphenyl)benzimidazoles. The polymerizations are carried out in polar aprotic solvents such as N-methyl-2-pyrrolidinone or N,N-dimethylacetamide using alkali metal bases such as potassium carbonate at elevated temperatures under nitrogen. Mono(hydroxyphenyl)benzimidazoles are synthesized by reacting phenyl-4-hydroxybenzoate with aromatic (o-diamine)s in diphenylsulfone. Molecular weight controlled and endcapped PBI of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

  17. Resonant active sites in catalytic ammonia synthesis: A structural model

    NASA Astrophysics Data System (ADS)

    Cholach, Alexander R.; Bryliakova, Anna A.; Matveev, Andrey V.; Bulgakov, Nikolai N.

    2016-03-01

    Adsorption sites Mn consisted of n adjacent atoms M, each bound to the adsorbed species, are considered within a realistic model. The sum of bonds Σ lost by atoms in a site in comparison with the bulk atoms was used for evaluation of the local surface imperfection, while the reaction enthalpy at that site was used as a measure of activity. The comparative study of Mn sites (n = 1-5) at basal planes of Pt, Rh, Ir, Fe, Re and Ru with respect to heat of N2 dissociative adsorption QN and heat of Nad + Had → NHad reaction QNH was performed using semi-empirical calculations. Linear QN(Σ) increase and QNH(Σ) decrease allowed to specify the resonant Σ for each surface in catalytic ammonia synthesis at equilibrium Nad coverage. Optimal Σ are realizable for Ru2, Re2 and Ir4 only, whereas other centers meet steric inhibition or unreal crystal structure. Relative activity of the most active sites in proportion 5.0 × 10- 5: 4.5 × 10- 3: 1: 2.5: 3.0: 1080: 2270 for a sequence of Pt4, Rh4, Fe4(fcc), Ir4, Fe2-5(bcc), Ru2, Re2, respectively, is in agreement with relevant experimental data. Similar approach can be applied to other adsorption or catalytic processes exhibiting structure sensitivity.

  18. Multi-site Phosphorylation Regulates Bim Stability and Apoptotic Activity

    PubMed Central

    Hübner, Anette; Barrett, Tamera; Flavell, Richard A.; Davis, Roger J.

    2008-01-01

    The pro-apoptotic BH3-only protein Bim is established to be an important mediator of signaling pathways that induce cell death. Multi-site phosphorylation of Bim by several members of the MAP kinase group is implicated as a regulatory mechanism that controls the apoptotic activity of Bim. To test the role of Bim phosphorylation in vivo, we constructed mice with a series of mutant alleles that express phosphorylation-defective Bim proteins. We show that mutation of the phosphorylation site Thr-112 causes decreased binding of Bim to the anti-apoptotic protein Bcl2 and can increase cell survival. In contrast, mutation of the phosphorylation sites Ser-55, Ser-65, and Ser-73 can cause increased apoptosis because of reduced proteasomal degradation of Bim. Together, these data indicate that phosphorylation can regulate Bim by multiple mechanisms and that the phosphorylation of Bim on different sites can contribute to the sensitivity of cellular apoptotic responses. PMID:18498746

  19. Manganese peroxidase mRNA and enzyme activity levels during bioremediation of polycyclic aromatic hydrocarbon-contaminated soil with Phanerochaete chrysosporium

    SciTech Connect

    Bogan, B.W.; Schoenike, B.; Lamar, R.T.; Cullen, D.

    1996-07-01

    mRNA extraction from soil and quantitation by competitive reverse transcription-PCR were combined to study the expression of three manganese peroxidase (MnP) genes during removal of polycyclic aromatic hydrocarbons from cultures of Phanerochaete chrysosporium grown in presterilized soil. Periods of high mnp transcript levels and extractable MnP enzyme activity were temporally correlated, although separated by a short (1- to 2-day) lag period. This time frame also coincided with maximal rates of fluorene oxidation and chrysene disappearance in soil cultures, supporting the hypothesis that high ionization potential polycyclic aromatic hydrocarbons are oxidized in soil via MnP-dependent mechanisms. The patterns of transcript abundance over time in soil-grown P. chrysosporium were similar for all three of the mnp mRNAs studied, indicating that transcription of this gene family may be coordinately regulated under these growth conditions. 47 refs., 6 figs., 1 tab.

  20. Water in the Active Site of Ketosteroid Isomerase

    PubMed Central

    Hanoian, Philip; Hammes-Schiffer, Sharon

    2011-01-01

    Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

  1. Rapid microwave hydrothermal synthesis of ZnGa{sub 2}O{sub 4} with high photocatalytic activity toward aromatic compounds in air and dyes in liquid water

    SciTech Connect

    Sun Meng; Li Danzhen; Zhang Wenjuan; Chen Zhixin; Huang Hanjie; Li Wenjuan; He Yunhui; Fu Xianzhi

    2012-06-15

    ZnGa{sub 2}O{sub 4} was synthesized from Ga(NO{sub 3}){sub 3} and ZnCl{sub 2} via a rapid and facile microwave-assisted hydrothermal method. The photocatalytic properties of the as-prepared ZnGa{sub 2}O{sub 4} were evaluated by the degradation of pollutants in air and aqueous solution under ultraviolet (UV) light illumination. The results demonstrated that ZnGa{sub 2}O{sub 4} had exhibited efficient photocatalytic activities higher than that of commercial P25 (Degussa Co.) in the degradation of benzene, toluene, and ethylbenzene, respectively. In the liquid phase degradation of dyes (methyl orange, Rhodamine B, and methylene blue), ZnGa{sub 2}O{sub 4} has also exhibited remarkable activities higher than that of P25. After 32 min of UV light irradiation, the decomposition ratio of methyl orange (10 ppm, 150 mL) over ZnGa{sub 2}O{sub 4} (0.06 g) was up to 99%. The TOC tests revealed that the mineralization ratio of MO (10 ppm, 150 mL) was 88.1% after 90 min of reaction. A possible mechanism of the photocatalysis over ZnGa{sub 2}O{sub 4} was also proposed. - Graphical abstract: In the degradation of RhB under UV light irradiation, ZnGa{sub 2}O{sub 4} had exhibited efficient photo-activity, and after only 24 min of irradiation the decomposition ratio was up to 99.8%. Highlights: Black-Right-Pointing-Pointer A rapid and facile M-H method to synthesize ZnGa{sub 2}O{sub 4} photocatalyst. Black-Right-Pointing-Pointer The photocatalyst exhibits high activity toward benzene and dyes. Black-Right-Pointing-Pointer The catalyst possesses more surface hydroxyl sites than TiO{sub 2} (P25). Black-Right-Pointing-Pointer Deep oxidation of different aromatic compounds and dyes over catalyst.

  2. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

    PubMed

    Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

    2014-12-16

    Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

  3. Chemical Modification of Papain and Subtilisin: An Active Site Comparison

    ERIC Educational Resources Information Center

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

    An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

  4. Energy transfer at the active sites of heme proteins

    SciTech Connect

    Dlott, D.D.; Hill, J.R.

    1995-12-31

    Experiments using a picosecond pump-probe apparatus at the Picosecond Free-electron Laser Center at Stanford University, were performed to investigate the relaxation of carbon monoxide bound to the active sites of heme proteins. The significance of these experiments is two-fold: (1) they provide detailed information about molecular dynamics occurring at the active sites of proteins; and (2) they provide insight into the nature of vibrational relaxation processes in condensed matter. Molecular engineering is used to construct various molecular systems which are studied with the FEL. We have studied native proteins, mainly myoglobin obtained from different species, mutant proteins produced by genetic engineering using recombinant DNA techniques, and a variety of model systems which mimic the structures of the active sites of native proteins, which are produced using molecular synthesis. Use of these different systems permits us to investigate how specific molecular structural changes affect dynamical processes occurring at the active sites. This research provides insight into the problems of how different species needs are fulfilled by heme proteins which have greatly different functionality, which is induced by rather small structural changes.

  5. Fate of aromatic hydrocarbons in Italian municipal wastewater systems: an overview of wastewater treatment using conventional activated-sludge processes (CASP) and membrane bioreactors (MBRs).

    PubMed

    Fatone, Francesco; Di Fabio, Silvia; Bolzonella, David; Cecchi, Franco

    2011-01-01

    We studied the occurrence, removal, and fate of 16 polycyclic aromatic hydrocarbons (PAHs) and 23 volatile organic compounds (VOCs) in Italian municipal wastewater treatment systems in terms of their common contents and forms, and their apparent and actual removal in both conventional activated-sludge processes (CASP) and membrane bioreactors (MBRs). We studied five representative full-scale CASP treatment plants (design capacities of 12,000 to 700,000 population-equivalent), three of which included MBR systems (one full-scale and two pilot-scale) operating in parallel with the conventional systems. We studied the solid-liquid partitioning and fates of these substances using both conventional samples and a novel membrane-equipped automatic sampler. Among the VOCs, toluene, ethylbenzene, xylenes, styrene, 1,2,4-trimethylbenzene, and 4-chlorotoluene were ubiquitous, whereas naphthalene, acenaphthene, fluorene, and phenanthrene were the most common PAHs. Both PAHs and aromatic VOCs had removal efficiencies of 40-60% in the headworks, even in plants without primary sedimentation. Mainly due to volatilization, aromatic VOCs had comparable removal efficiencies in CASP and MBRs, even for different sludge ages. MBRs did not enhance the retention of PAHs sorbed to suspended particulates compared with CASPs. On the other hand, the specific daily accumulation of PAHs in the MBR's activated sludge decreased logarithmically with increasing sludge age, indicating enhanced biodegradation of PAHs. The PAH and aromatic VOC contents in the final effluent are not a major driver for widespread municipal adoption of MBRs, but MBRs may enhance the biodegradation of PAHs and their removal from the environment.

  6. Changes in active site histidine hydrogen bonding trigger cryptochrome activation.

    PubMed

    Ganguly, Abir; Manahan, Craig C; Top, Deniz; Yee, Estella F; Lin, Changfan; Young, Michael W; Thiel, Walter; Crane, Brian R

    2016-09-01

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions. PMID:27551082

  7. Conformational Transitions in Human AP Endonuclease 1 and Its Active Site Mutant during Abasic Site Repair†

    PubMed Central

    Kanazhevskaya, Lyubov Yu.; Koval, Vladimir V.; Zharkov, Dmitry O.; Strauss, Phyllis R.; Fedorova, Olga S.

    2010-01-01

    AP endonuclease 1 (APE 1) is a crucial enzyme of the base excision repair pathway (BER) in human cells. APE1 recognizes apurinic/apyrimidinic (AP) sites and makes a nick in the phosphodiester backbone 5′ to them. The conformational dynamics and presteady-state kinetics of wild-type APE1 and its active site mutant, Y171F-P173L-N174K, have been studied. To observe conformational transitions occurring in the APE1 molecule during the catalytic cycle, we detected intrinsic tryptophan fluorescence of the enzyme under single turnover conditions. DNA duplexes containing a natural AP site, its tetrahydrofuran analogue, or a 2′-deoxyguanosine residue in the same position were used as specific substrates or ligands. The stopped-flow experiments have revealed high flexibility of the APE1 molecule and the complexity of the catalytic process. The fluorescent traces indicate that wild-type APE1 undergoes at least four conformational transitions during the processing of abasic sites in DNA. In contrast, nonspecific interactions of APE1 with undamaged DNA can be described by a two-step kinetic scheme. Rate and equilibrium constants were extracted from the stopped-flow and fluorescence titration data for all substrates, ligands, and products. A replacement of three residues at the enzymatic active site including the replacement of tyrosine 171 with phenylalanine in the enzyme active site resulted in a 2 × 104-fold decrease in the reaction rate and reduced binding affinity. Our data indicate the important role of conformational changes in APE1 for substrate recognition and catalysis. PMID:20575528

  8. N-methyl-D-aspartate recognition site ligands modulate activity at the coupled glycine recognition site.

    PubMed

    Hood, W F; Compton, R P; Monahan, J B

    1990-03-01

    In synaptic plasma membranes from rat forebrain, the potencies of glycine recognition site agonists and antagonists for modulating [3H]1-[1-(2-thienyl)cyclohexyl]piperidine ([3H]TCP) binding and for displacing strychnine-insensitive [3H]glycine binding are altered in the presence of N-methyl-D-aspartate (NMDA) recognition site ligands. The NMDA competitive antagonist, cis-4-phosphonomethyl-2-piperidine carboxylate (CGS 19755), reduces [3H]glycine binding, and the reduction can be fully reversed by the NMDA recognition site agonist, L-glutamate. Scatchard analysis of [3H]glycine binding shows that in the presence of CGS 19755 there is no change in Bmax (8.81 vs. 8.79 pmol/mg of protein), but rather a decrease in the affinity of glycine (KD of 0.202 microM vs. 0.129 microM). Similar decreases in affinity are observed for the glycine site agonists, D-serine and 1-aminocyclopropane-1-carboxylate, in the presence of CGS 19755. In contrast, the affinity of glycine antagonists, 1-hydroxy-3-amino-2-pyrrolidone and 1-aminocyclobutane-1-carboxylate, at this [3H]glycine recognition site increases in the presence of CGS 19755. The functional consequence of this change in affinity was addressed using the modulation of [3H]TCP binding. In the presence of L-glutamate, the potency of glycine agonists for the stimulation of [3H]TCP binding increases, whereas the potency of glycine antagonists decreases. These data are consistent with NMDA recognition site ligands, through their interactions at the NMDA recognition site, modulating activity at the associated glycine recognition site.

  9. Interaction of smoking, uptake of polycyclic aromatic hydrocarbons, and cytochrome P450IA2 activity among foundry workers.

    PubMed Central

    Sherson, D; Sigsgaard, T; Overgaard, E; Loft, S; Poulsen, H E; Jongeneelen, F J

    1992-01-01

    An increased lung cancer risk has been described among foundry workers. Polycyclic aromatic hydrocarbons (PAHs) and silica are possible aetiological factors. This study describes a urinary PAH metabolite, 1-hydroxypyrene (hpU), as well as the degree of cytochrome P450IA2 activity/induction as reflected by the urinary caffeine ratio (IA2) in 45 foundry workers and 52 controls; IA2 was defined as the ratio of paraxanthine 7-demethylation products to a paraxanthine 8-hydroxylation product (1,7-dimethyluric acid). Mean exposure concentrations for foundry workers were defined by breathing zone hygienic samples (respirable dust 1.2 to 3.52 mg/m3 (93 samples)) and as total PAH (0.46 micrograms/m3) and pyrene concentrations (0.28 micrograms/m3) (six samples). Non-smoking controls and foundry workers had similar IA2 ratios (5.63, 95% confidence interval (95% CI) 4.56-6.70 and 4.40, 95% CI 3.56-5.24). The same was true for smoking controls and foundry workers (9.10, 95% CI 8.00-10.20 and 8.69, 95% CI 7.37-10.01). Both smoking groups had raised IA2 ratios compared with non-smokers (p less than 0.01). Non-smoking controls and foundry workers had similar hpU concentrations (0.16, 95% CI 0.10-0.22 and 0.11, 95% CI 0.09-0.13 mumol/mol creatinine). Smoking foundry workers had raised hpU concentrations (0.42, 95% CI 0.25-0.59) compared with smoking controls (0.26, 95% CI 0.18-0.34) (p less than 0.01). A small subgroup of smoking foundry workers with the highest exposures to both silica and PAH also had the highest hpU concentrations (0.70, 95% CI - 0.07-1.47 mumol/mol creatinine) (p less than 0.04). Increased hpU concentrations in smoking foundry workers suggest a more than additive effect from smoking and foundry exposures resulting in increased PAH uptake. Increased P450IA2 enzyme activity was only found in smokers and no additional effect of foundry exposures was seen. These data suggest that smoking as well as work related PAH exposure may be casually related to increased risk

  10. Anti-Prion Activity of a Panel of Aromatic Chemical Compounds: In Vitro and In Silico Approaches

    PubMed Central

    Ferreira, Natalia C.; Marques, Icaro A.; Conceição, Wesley A.; Macedo, Bruno; Machado, Clarice S.; Mascarello, Alessandra; Chiaradia-Delatorre, Louise Domeneghini; Yunes, Rosendo Augusto; Nunes, Ricardo José; Hughson, Andrew G.; Raymond, Lynne D.; Pascutti, Pedro G.; Caughey, Byron; Cordeiro, Yraima

    2014-01-01

    The prion protein (PrP) is implicated in the Transmissible Spongiform Encephalopathies (TSEs), which comprise a group of fatal neurodegenerative diseases affecting humans and other mammals. Conversion of cellular PrP (PrPC) into the scrapie form (PrPSc) is the hallmark of TSEs. Once formed, PrPSc aggregates and catalyzes PrPC misfolding into new PrPSc molecules. Although many compounds have been shown to inhibit the conversion process, so far there is no effective therapy for TSEs. Besides, most of the previously evaluated compounds failed in vivo due to poor pharmacokinetic profiles. In this work we propose a combined in vitro/in silico approach to screen for active anti-prion compounds presenting acceptable drugability and pharmacokinetic parameters. A diverse panel of aromatic compounds was screened in neuroblastoma cells persistently infected with PrPSc (ScN2a) for their ability to inhibit PK-resistant PrP (PrPRes) accumulation. From ∼200 compounds, 47 were effective in decreasing the accumulation of PrPRes in ScN2a cells. Pharmacokinetic and physicochemical properties were predicted in silico, allowing us to obtain estimates of relative blood brain barrier permeation and mutagenicity. MTT reduction assays showed that most of the active compounds were non cytotoxic. Compounds that cleared PrPRes from ScN2a cells, were non-toxic in the MTT assay, and presented a good pharmacokinetic profile were investigated for their ability to inhibit aggregation of an amyloidogenic PrP peptide fragment (PrP109–149). Molecular docking results provided structural models and binding affinities for the interaction between PrP and the most promising compounds. In summary, using this combined in vitro/in silico approach we have identified new small organic anti-scrapie compounds that decrease the accumulation of PrPRes in ScN2a cells, inhibit the aggregation of a PrP peptide, and possess pharmacokinetic characteristics that support their drugability. These compounds are

  11. Noncomparative scaling of aromaticity through electron itinerancy

    SciTech Connect

    Paul, Satadal; Goswami, Tamal; Misra, Anirban

    2015-10-15

    Aromaticity is a multidimensional concept and not a directly observable. These facts have always stood in the way of developing an appropriate theoretical framework for scaling of aromaticity. In the present work, a quantitative account of aromaticity is developed on the basis of cyclic delocalization of π-electrons, which is the phenomenon leading to unique features of aromatic molecules. The stabilization in molecular energy, caused by delocalization of π-electrons is obtained as a second order perturbation energy for archetypal aromatic systems. The final expression parameterizes the aromatic stabilization energy in terms of atom to atom charge transfer integral, onsite repulsion energy and the population of spin orbitals at each site in the delocalized π-electrons. An appropriate computational platform is framed to compute each and individual parameter in the derived equation. The numerical values of aromatic stabilization energies obtained for various aromatic molecules are found to be in close agreement with available theoretical and experimental reports. Thus the reliable estimate of aromaticity through the proposed formalism renders it as a useful tool for the direct assessment of aromaticity, which has been a long standing problem in chemistry.

  12. Noncomparative scaling of aromaticity through electron itinerancy

    NASA Astrophysics Data System (ADS)

    Paul, Satadal; Goswami, Tamal; Misra, Anirban

    2015-10-01

    Aromaticity is a multidimensional concept and not a directly observable. These facts have always stood in the way of developing an appropriate theoretical framework for scaling of aromaticity. In the present work, a quantitative account of aromaticity is developed on the basis of cyclic delocalization of π-electrons, which is the phenomenon leading to unique features of aromatic molecules. The stabilization in molecular energy, caused by delocalization of π-electrons is obtained as a second order perturbation energy for archetypal aromatic systems. The final expression parameterizes the aromatic stabilization energy in terms of atom to atom charge transfer integral, onsite repulsion energy and the population of spin orbitals at each site in the delocalized π-electrons. An appropriate computational platform is framed to compute each and individual parameter in the derived equation. The numerical values of aromatic stabilization energies obtained for various aromatic molecules are found to be in close agreement with available theoretical and experimental reports. Thus the reliable estimate of aromaticity through the proposed formalism renders it as a useful tool for the direct assessment of aromaticity, which has been a long standing problem in chemistry.

  13. Control of active sites in selective flocculation: I -- Mathematical model

    SciTech Connect

    Behl, S.; Moudgil, B.M.; Prakash, T.S. . Dept. of Materials Science and Engineering)

    1993-12-01

    Heteroflocculation has been determined to be another major reason for loss in selectivity for flocculation process. In a mathematical model developed earlier, conditions for controlling heteroflocculation were discussed. Blocking active sites to control selective adsorption of a flocculant oil a desirable solid surface is discussed. It has been demonstrated that the lower molecular weight fraction of a flocculant which is incapable of flocculating the particles is an efficient site blocking agent. The major application of selective flocculation has been in mineral processing but many potential uses exist in biological and other colloidal systems. These include purification of ceramic powders, separating hazardous solids from chemical waste, and removal of deleterious components from paper pulp.

  14. The site of activation of factor X by cancer procoagulant.

    PubMed

    Gordon, S G; Mourad, A M

    1991-12-01

    Cancer procoagulant (CP) is a cysteine proteinase found in a variety of malignant cells and tissues and in human amnion-chorion tissue. It initiates coagulation by activating factor X. However, the amino acid sequence of the substrate protein that determines the cleavage site of cysteine proteinases is different from that of the serine proteinases that normally activate factor X, such as factor IXa, VIIa and Russell's Viper Venom (RVV). Therefore, it was of interest to determine the site of cleavage of human factor X by CP. Purified CP was incubated with purified factor X and the reaction mixture was electrophoresed on a 10% Tris-tricine SDS-PAGE gel. The proteins were electroeluted on to a polyvinylidene difluoride (PVDF) membrane, and stained with Coomassie blue. The heavy chain of activated factor X was cut out of the PVDF membrane and sequenced with an Applied Biosystems 477A with on-line HPLC. The primary cleavage sequence was Asp-Ala-Ala-Asp-Leu-Asp-Pro-; two other secondary sequences Ser-Ile-Thr-Trp-Lys-Pro- and Glu-Asn-Pro-Phe-Asp-Leu were found. The penultimate amino acid on the carbonyl side of the hydrolysed amide bond plays a critical role for the recognition of the cleavage site of cysteine proteinases. These data indicate that the penultimate amino acid for the primary cleavage site of factor X by CP is proline-20 and for the secondary sites, proline-13 and proline-28. This is in contrast to arginine-52 that determines the specificity of the cleavage by normal serine proteinase activation.(ABSTRACT TRUNCATED AT 250 WORDS)

  15. Polycyclic Aromatic Hydrocarbon Affects Acetic Acid Production during Anaerobic Fermentation of Waste Activated Sludge by Altering Activity and Viability of Acetogen.

    PubMed

    Luo, Jingyang; Chen, Yinguang; Feng, Leiyu

    2016-07-01

    Till now, almost all the studies on anaerobic fermentation of waste activated sludge (WAS) for bioproducts generation focused on the influences of operating conditions, pretreatment methods and sludge characteristics, and few considered those of widespread persistent organic pollutants (POPs) in sludge, for example, polycyclic aromatic hydrocarbons (PAHs). Herein, phenanthrene, which was a typical PAH and widespread in WAS, was selected as a model compound to investigate its effect on WAS anaerobic fermentation for short-chain fatty acids (SCFAs) accumulation. Experimental results showed that the concentration of SCFAs derived from WAS was increased in the presence of phenanthrene during anaerobic fermentation. The yield of acetic acid which was the predominant SCFA in the fermentation reactor with the concentration of 100 mg/kg dry sludge was 1.8 fold of that in the control. Mechanism exploration revealed that the present phenanthrene mainly affected the acidification process of anaerobic fermentation and caused the shift of the microbial community to benefit the accumulation of acetic acid. Further investigation showed that both the activities of key enzymes (phosphotransacetylase and acetate kinase) involved in acetic acid production and the quantities of their corresponding encoding genes were enhanced in the presence of phenanthrene. Viability tests by determining the adenosine 5'-triphosphate content and membrane potential confirmed that the acetogens were more viable in anaerobic fermentation systems with phenanthrene, which resulted in the increased production of acetic acid. PMID:27267805

  16. Comparison of carbon-sulfur and carbon-amine bond in therapeutic drug: 4β-S-aromatic heterocyclic podophyllum derivatives display antitumor activity

    PubMed Central

    Li, Jian-Long; Zhao, Wei; Zhou, Chen; Zhang, Ya-Xuan; Li, Hong-Mei; Tang, Ya-Ling; Liang, Xin-Hua; Chen, Tao; Tang, Ya-Jie

    2015-01-01

    Herein is a first effort to systematically study the significance of carbon-sulfur (C-S) and carbon-amine (C-NH) bonds on the antitumor proliferation activity of podophyllum derivatives and their precise mechanism of apoptosis. Compared with the derivative modified by a C-NH bond, the derivative modified by a C-S bond exhibited superior antitumor activity, the inhibition activity of target proteins tubulin or Topo II, cell cycle arrest, and apoptosis induction. Antitumor mechanistic studies showed that the death receptor and the mitochondrial apoptotic pathways were simultaneously activated by the C-S bond modified aromatic heterocyclic podophyllum derivatives with a higher cellular uptake percentage of 60–90% and induction of a higher level of reactive oxygen species (ROS). Only the mitochondrial apoptotic pathway was activated by the C-NH bond modified aromatic heterocyclic podophyllum derivatives, with a lower cellular uptake percentage of 40–50%. This study provided insight into effects of the C-S and C-NH bond modification on the improvement of the antitumor activity of Podophyllum derivatives. PMID:26443888

  17. Comparison of carbon-sulfur and carbon-amine bond in therapeutic drug: 4β-S-aromatic heterocyclic podophyllum derivatives display antitumor activity.

    PubMed

    Li, Jian-Long; Zhao, Wei; Zhou, Chen; Zhang, Ya-Xuan; Li, Hong-Mei; Tang, Ya-Ling; Liang, Xin-Hua; Chen, Tao; Tang, Ya-Jie

    2015-10-07

    Herein is a first effort to systematically study the significance of carbon-sulfur (C-S) and carbon-amine (C-NH) bonds on the antitumor proliferation activity of podophyllum derivatives and their precise mechanism of apoptosis. Compared with the derivative modified by a C-NH bond, the derivative modified by a C-S bond exhibited superior antitumor activity, the inhibition activity of target proteins tubulin or Topo II, cell cycle arrest, and apoptosis induction. Antitumor mechanistic studies showed that the death receptor and the mitochondrial apoptotic pathways were simultaneously activated by the C-S bond modified aromatic heterocyclic podophyllum derivatives with a higher cellular uptake percentage of 60-90% and induction of a higher level of reactive oxygen species (ROS). Only the mitochondrial apoptotic pathway was activated by the C-NH bond modified aromatic heterocyclic podophyllum derivatives, with a lower cellular uptake percentage of 40-50%. This study provided insight into effects of the C-S and C-NH bond modification on the improvement of the antitumor activity of Podophyllum derivatives.

  18. Retinobenzoic acids. 4. Conformation of aromatic amides with retinoidal activity. Importance of trans-amide structure for the activity.

    PubMed

    Kagechika, H; Himi, T; Kawachi, E; Shudo, K

    1989-10-01

    N-Methylation of two retinoidal amide compounds, 4-[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)carbamoyl]benz oic acid (3, Am80) and 4-[[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2- naphthalenyl)carbonyl]amino]benzoic acid (5, Am580), resulted in the disappearance of their potent differentiation-inducing activity on human promyelocytic leukemia cell line HL-60. Studies with 1H NMR and UV spectroscopy indicated that large conformational differences exist between the active secondary amides and the inactive N-methyl amides. From a comparison of the spectroscopic results of these amides with those of stilbene derivatives, the conformations of the active amides are expected to resemble that of (E)-stilbene, whereas the inactive amides resemble the Z isomer: 3 (Am80) and 5 (Am580) have a trans-amide bond and their whole structures are elongated, while the N-methylated compounds [4 (Am90) and 6 (Am590)] have a cis-amide bond, resulting in the folding of the two benzene rings. These structures in the crystals were related to those in solution by 13C NMR spectroscopic comparison between the two phases (solid and solution).

  19. Production of alkyl-aromatics from light oxygenates over zeolite catalysts for bio-oil refining

    NASA Astrophysics Data System (ADS)

    Hoang, Trung Q.

    Upgrading of light oxygenates derived from biomass conversion, such as propanal and glycerol, to more valuable aromatics for biofuels has been demonstrated on zeolite catalysts. Aromatics with a high ratio of C 9/(C8+C7) and little benzene are produced at much higher yield from oxygenates than from olefins at mild conditions over HZSM-5. It is proposed that C9 aromatics are predominantly produced via acid-catalyzed aldol condensation. This reaction pathway is different from the pathway of propylene and other hydrocarbon aromatization that occurs via a hydrocarbon pool at more severe conditions with major aromatic products C6 and C7. In fact, investigation on the effect of crystallite size HZSM-5 has shown a higher ratio of C9/(C8+C 7) aromatics on small crystallite. This is due to faster removal of products from the shorter diffusion path length. As a result, a longer catalyst lifetime, less isomerization, and less cracking were observed on small crystallites. Beside crystallite size, pore geometry of zeolites was also found to significantly affect aromatic production for both conversion of propanal and glycerol. It is shown that the structure of the HZSM-22, with a one-dimensional and narrower channel system, restricts the formation of aromatics. In contrast, a higher yield of aromatic products is observed over HZSM-5 with its three-dimensional channel system. By increasing channel dimension and connectivity of the channels, increasing catalyst activity was also observed due to more accessible acid sites. It was also found that glycerol is highly active for dehydration on zeolites to produce high yields of acrolein (propenal), a high value chemical. To maximize aromatics from glycerol conversion, HZSM-5 and HY were found to be effective. A two-bed reactor of Pd/ZnO and HZSM-5 was used to first deoxygenate/hydrogenate glycerol over Pd/ZnO to intermediate oxygenates that can further aromatize on HZSM-5. The end results are very promising with significant improvement

  20. Structural Dissection of the Active Site of Thermotoga maritima β-Galactosidase Identifies Key Residues for Transglycosylating Activity.

    PubMed

    Talens-Perales, David; Polaina, Julio; Marín-Navarro, Julia

    2016-04-13

    Glycoside hydrolases, specifically β-galactosidases, can be used to synthesize galacto-oligosaccharides (GOS) due to the transglycosylating (secondary) activity of these enzymes. Site-directed mutagenesis of a thermoresistant β-galactosidase from Thermotoga maritima has been carried out to study the structural basis of transgalactosylation and to obtain enzymatic variants with better performance for GOS biosynthesis. Rational design of mutations was based on homologous sequence analysis and structural modeling. Analysis of mutant enzymes indicated that residue W959, or an alternative aromatic residue at this position, is critical for the synthesis of β-3'-galactosyl-lactose, the major GOS obtained with the wild-type enzyme. Mutants W959A and W959C, but not W959F, showed an 80% reduced synthesis of this GOS. Other substitutions, N574S, N574A, and F571L, increased the synthesis of β-3'-galactosyl-lactose about 40%. Double mutants F571L/N574S and F571L/N574A showed an increase of about 2-fold.

  1. Active-Site-Accessible, Porphyrinic Metal;#8722;Organic Framework Materials

    SciTech Connect

    Farha, Omar K.; Shultz, Abraham M.; Sarjeant, Amy A.; Nguyen, SonBinh T.; Hupp, Joseph T.

    2012-02-06

    On account of their structural similarity to cofactors found in many metallo-enzymes, metalloporphyrins are obvious potential building blocks for catalytically active, metal-organic framework (MOF) materials. While numerous porphyrin-based MOFs have already been described, versions featuring highly accessible active sites and permanent microporosity are remarkably scarce. Indeed, of the more than 70 previously reported porphyrinic MOFs, only one has been shown to be both permanently microporous and contain internally accessible active sites for chemical catalysis. Attempts to generalize the design approach used in this single successful case have failed. Reported here, however, is the synthesis of an extended family of MOFs that directly incorporate a variety of metalloporphyrins (specifically Al{sup 3+}, Zn{sup 2+}, Pd{sup 2+}, Mn{sup 3+}, and Fe{sup 3+} complexes). These robust porphyrinic materials (RPMs) feature large channels and readily accessible active sites. As an illustrative example, one of the manganese-containing RPMs is shown to be catalytically competent for the oxidation of alkenes and alkanes.

  2. Gallium Zeolites for Light Paraffin Aromatization

    SciTech Connect

    Price, G.L.; Dooley, K.M.

    1999-02-10

    The primary original goal of this project was to investigate the active state of gallium-containing MFI catalysts for light paraffin aromatization, in particular the state of gallium in the active material. Our original hypothesis was that the most active and selective materials were those which contained gallium zeolitic cations, and that previously reported conditions for the activation of gallium-containing catalysts served to create these active centers. We believed that in high silica materials such as MFI, ion-exchange is most effectively accomplished with metals in their 1+ oxidation state, both because of the sparsity of the anionic ion-exchange sites associated with the zeolite, and because the large hydration shells associated with aqueous 3+ cations hinder transport. Metals such as Ga which commonly exist in higher oxidation states need to be reduced to promote ion-exchange and this is the reason that reduction of gallium-containing catalysts for light paraffin aromatization often yields a dramatic enhancement in catalytic activity. We have effectively combined reduction with ion-exchange and we term this combined process ''reductive solid-state ion-exchange''. Our hypothesis has largely been proven true, and a number of the papers we have published directly address this hypothesis.

  3. Functional constituents of the active site of human neutrophil collagenase.

    PubMed

    Mookhtiar, K A; Wang, F; Van Wart, H E

    1986-05-01

    A series of chemical modification reactions has been carried out to identify functional constituents of the active site of human neutrophil collagenase. The enzyme is reversibly inhibited by the transition metal chelating agent 1,10-phenanthroline, and inhibition is fully reversed by zinc. Removal of weakly bound metal ions by gel filtration inactivates collagenase, and activity is fully restored on immediate readdition of calcium. The enzyme is unaffected by reagents that modify serine, cysteine, and arginine residues. However, reaction with the carboxyl reagents cyclohexylmorpholinocarbodiimide and Woodward's Reagent K lowers the activity of the enzyme substantially. Acetylimidazole inactivates the enzyme, but activity is completely restored on addition of hydroxylamine. The enzyme is also inactivated by tetranitromethane, indicating that it contains an essential tyrosine residue. Acylation of collagenase with diethyl pyrocarbonate, diketene, acetic anhydride, or trinitrobenzenesulfonate inactivates the enzyme, and activity is not restored on addition of hydroxylamine, indicating the presence of an essential lysine residue.

  4. Inhibition of peripheral aromatization in baboons by an enzyme-activated aromatase inhibitor (MDL 18,962)

    SciTech Connect

    Longcope, C.; Femino, A.; Johnston, J.O.

    1988-05-01

    The peripheral aromatization ((rho)BM) of androstenedione (A) and testosterone (T) was measured before and after administration of the aromatase inhibitor 10-(2 propynyl)estr-4-ene-3,17-dione (MDL-18,962) to five mature female baboons, Papio annubis. The measurements were made by infusing (3H)androstenedione/(14C)estrone or (3H)testosterone/(14C)estradiol for 3.5 h and collecting blood samples during the infusions and all urine for 96 h from the start of the infusion. Blood samples were analyzed for radioactivity as infused and product steroids, and the data were used to calculate MCRs. An aliquot of the pooled urine was analyzed for the glucuronides of estrone and estradiol and used to calculate the (rho)BM. MDL-18,962 was administered as a pulse in polyethylene glycol-400 (1-5 ml) either iv or via gastric tube 30 min before administration of the radiolabeled steroids. Control studies were done with and without polyethylene glycol-400 administration. When MDL-18,962 was given iv at 4 mg/kg, the aromatization of A was decreased 91.8 +/- 0.9% from the control value of 1.23 +/- 0.13% to 0.11 +/- 0.01%. At the same dose, aromatization of T was decreased 82.0 +/- 7.1%, from a control value of 0.20 +/- 0.03% to 0.037 +/- 0.018%. When MDL-18,962 was given iv at doses of 0.4, 0.1, 0.04, and 0.01 mg/kg, the values for aromatization of A were 0.16 +/- 0.03%, 0.18 +/- 0.06%, 0.37 +/- 11%, and 0.65 +/- 0.09%, respectively. The administration of MDL-18,962 via gastric tube at 4 mg/kg as a pulse decreased the aromatization of A from 1.35 +/- 0.06% to 0.43 +/- 0.12%, an inhibition of 67.2 +/- 10.7%. When administered via gastric tube daily for 5 days at 4 mg/kg, the aromatization of A fell from 1.35 +/- 0.06% to 0.063 +/- 0.003%, an inhibition of 84.4 +/- 0.5%.

  5. Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis

    PubMed Central

    Tian, Li; Liu, Shijia; Wang, Shuai; Wang, Lushan

    2016-01-01

    Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the −2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the −1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes. PMID:27009476

  6. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  7. Active sites in char gasification: Final technical report

    SciTech Connect

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  8. Brownian aggregation rate of colloid particles with several active sites

    SciTech Connect

    Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V.; Polshchitsin, Alexey A.; Yakovleva, Galina E.; Maltsev, Valeri P.

    2014-08-14

    We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.

  9. Active Sites Environmental Monitoring Program: FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Hicks, D.S.; Morrissey, C.M.

    1992-11-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from April 1991 through September 1991. The ASEMP was established in 1989 by Solid Waste Operations (SWO) and the Environmental Sciences Division, both of Oak Ridge National Laboratory, to provide early detection and performance monitoring at active low-level (radioactive) waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. A new set of action levels was developed on the basis of a statistical analysis of background contamination. These new action levels have been used to evaluate results in this report. Results of ASEMP monitoring continue to demonstrate that no LLW (except [sup 3]H) is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II, which began in early FY 1991, was >90% complete at the end of September 1991. Results of sampling of groundwater and surface waters is presented.

  10. Inhibition and active-site modelling of prolidase.

    PubMed

    King, G F; Crossley, M J; Kuchel, P W

    1989-03-15

    Consideration of the active-site model of prolidase led us to examine azetidine, pyrrolidine and piperidine substrate analogs as potential in vivo inhibitors of the enzyme. One of these, N-benzyloxycarbonyl-L-proline, was shown to be a potent competitive inhibitor of porcine kidney prolidase (Ki = 90 microM); its rapid protein-mediated permeation of human and sheep erythrocytes suggests that it may be effective in vivo. The higher homolog, N-benzyloxycarbonyl-L-pipecolic acid, was also a potent inhibitor of the enzyme while the antihypertensive drugs, captopril and enalaprilat, were shown to have mild and no inhibitory effects, respectively. Analysis of inhibitor action and consideration of X-ray crystallographic data of relevant Mn2+ complexes allowed the active-site model of prolidase to be further refined; a new model is presented in which the substrate acts as a bidentate ligand towards the active-site manganous ion. Various aspects of the new model help to explain why Mn2+ has been 'chosen' by the enzyme in preference to other biologically available metal ions. PMID:2924773

  11. Studies on the Simultaneous Formation of Aroma-Active and Toxicologically Relevant Vinyl Aromatics from Free Phenolic Acids during Wheat Beer Brewing.

    PubMed

    Langos, Daniel; Granvogl, Michael

    2016-03-23

    During the brewing process of wheat beer, the desired aroma-active vinyl aromatics 2-methoxy-4-vinylphenol and 4-vinylphenol as well as the undesired and toxicologically relevant styrene are formed from their respective precursors, free ferulic acid, p-coumaric acid, and cinnamic acid, deriving from the malts. Analysis of eight commercial wheat beers revealed high concentrations of 2-methoxy-4-vinylphenol and 4-vinylphenol always in parallel with high concentrations of styrene or low concentrations of the odorants in parallel with low styrene concentrations, suggesting a similar pathway. To better understand the formation of these vinyl aromatics, each process step of wheat beer brewing and the use of different strains of Saccharomyces cerevisiae were evaluated. During wort boiling, only a moderate decarboxylation of free phenolic acids and formation of desired and undesired vinyl aromatics were monitored due to the thermal treatment. In contrast, this reaction mainly occurred enzymatically catalyzed during fermentation with S. cerevisiae strain W68 with normal Pof(+) activity (phenolic off-flavor) resulting in a wheat beer eliciting the typical aroma requested by consumers due to high concentrations of 2-methoxy-4-vinylphenol (1790 μg/L) and 4-vinylphenol (937 μg/L). Unfortunately, also a high concentration of undesired styrene (28.3 μg/L) was observed. Using a special S. cerevisiae strain without Pof(+) activity resulted in a significant styrene reduction (

  12. Studies on the Simultaneous Formation of Aroma-Active and Toxicologically Relevant Vinyl Aromatics from Free Phenolic Acids during Wheat Beer Brewing.

    PubMed

    Langos, Daniel; Granvogl, Michael

    2016-03-23

    During the brewing process of wheat beer, the desired aroma-active vinyl aromatics 2-methoxy-4-vinylphenol and 4-vinylphenol as well as the undesired and toxicologically relevant styrene are formed from their respective precursors, free ferulic acid, p-coumaric acid, and cinnamic acid, deriving from the malts. Analysis of eight commercial wheat beers revealed high concentrations of 2-methoxy-4-vinylphenol and 4-vinylphenol always in parallel with high concentrations of styrene or low concentrations of the odorants in parallel with low styrene concentrations, suggesting a similar pathway. To better understand the formation of these vinyl aromatics, each process step of wheat beer brewing and the use of different strains of Saccharomyces cerevisiae were evaluated. During wort boiling, only a moderate decarboxylation of free phenolic acids and formation of desired and undesired vinyl aromatics were monitored due to the thermal treatment. In contrast, this reaction mainly occurred enzymatically catalyzed during fermentation with S. cerevisiae strain W68 with normal Pof(+) activity (phenolic off-flavor) resulting in a wheat beer eliciting the typical aroma requested by consumers due to high concentrations of 2-methoxy-4-vinylphenol (1790 μg/L) and 4-vinylphenol (937 μg/L). Unfortunately, also a high concentration of undesired styrene (28.3 μg/L) was observed. Using a special S. cerevisiae strain without Pof(+) activity resulted in a significant styrene reduction (

  13. Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase

    PubMed Central

    2015-01-01

    The class I terpenoid cyclase epi-isozizaene synthase (EIZS) utilizes the universal achiral isoprenoid substrate, farnesyl diphosphate, to generate epi-isozizaene as the predominant sesquiterpene cyclization product and at least five minor sesquiterpene products, making EIZS an ideal platform for the exploration of fidelity and promiscuity in a terpenoid cyclization reaction. The hydrophobic active site contour of EIZS serves as a template that enforces a single substrate conformation, and chaperones subsequently formed carbocation intermediates through a well-defined mechanistic sequence. Here, we have used the crystal structure of EIZS as a guide to systematically remold the hydrophobic active site contour in a library of 26 site-specific mutants. Remolded cyclization templates reprogram the reaction cascade not only by reproportioning products generated by the wild-type enzyme but also by generating completely new products of diverse structure. Specifically, we have tripled the overall number of characterized products generated by EIZS. Moreover, we have converted EIZS into six different sesquiterpene synthases: F96A EIZS is an (E)-β-farnesene synthase, F96W EIZS is a zizaene synthase, F95H EIZS is a β-curcumene synthase, F95M EIZS is a β-acoradiene synthase, F198L EIZS is a β-cedrene synthase, and F96V EIZS and W203F EIZS are (Z)-γ-bisabolene synthases. Active site aromatic residues appear to be hot spots for reprogramming the cyclization cascade by manipulating the stability and conformation of critical carbocation intermediates. A majority of mutant enzymes exhibit only relatively modest 2–100-fold losses of catalytic activity, suggesting that residues responsible for triggering substrate ionization readily tolerate mutations deeper in the active site cavity. PMID:24517311

  14. A Hydrophobic Pocket in the Active Site of Glycolytic Aldolase Mediates Interactions with Wiskott-Aldrich Syndrome Protein

    SciTech Connect

    St-Jean,M.; Izard, T.; Sygusch, J.

    2007-01-01

    Aldolase plays essential catalytic roles in glycolysis and gluconeogenesis. However, aldolase is a highly abundant protein that is remarkably promiscuous in its interactions with other cellular proteins. In particular, aldolase binds to highly acidic amino acid sequences, including the C-terminus of the Wiskott-Aldrich syndrome protein, an actin nucleation promoting factor. Here we report the crystal structure of tetrameric rabbit muscle aldolase in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein. Aldolase recognizes a short, 4-residue DEWD motif (residues 498-501), which adopts a loose hairpin turn that folds about the central aromatic residue, enabling its tryptophan side chain to fit into a hydrophobic pocket in the active site of aldolase. The flanking acidic residues in this binding motif provide further interactions with conserved aldolase active site residues, Arg-42 and Arg-303, aligning their side chains and forming the sides of the hydrophobic pocket. The binding of Wiskott-Aldrich syndrome protein to aldolase precludes intramolecular interactions of its C-terminus with its active site, and is competitive with substrate as well as with binding by actin and cortactin. Finally, based on this structure a novel naphthol phosphate-based inhibitor of aldolase was identified and its structure in complex with aldolase demonstrated mimicry of the Wiskott-Aldrich syndrome protein-aldolase interaction. The data support a model whereby aldolase exists in distinct forms that regulate glycolysis or actin dynamics.

  15. Graphene stabilized ultra-small CuNi nanocomposite with high activity and recyclability toward catalysing the reduction of aromatic nitro-compounds

    NASA Astrophysics Data System (ADS)

    Fang, Hao; Wen, Ming; Chen, Hanxing; Wu, Qingsheng; Li, Weiying

    2015-12-01

    Nowadays, it is of great significance and a challenge to design a noble-metal-free catalyst with high activity and a long lifetime for the reduction of aromatic nitro-compounds. Here, a 2D structured nanocomposite catalyst with graphene supported CuNi alloy nanoparticles (NPs) is prepared, and is promising for meeting the requirements of green chemistry. In this graphene/CuNi nanocomposite, the ultra-small CuNi nanoparticles (~2 nm) are evenly anchored on graphene sheets, which is not only a breakthrough in the structures, but also brings about an outstanding performance in activity and stability. Combined with a precise optimization of the alloy ratios, the reaction rate constant of graphene/Cu61Ni39 reached a high level of 0.13685 s-1, with a desirable selectivity as high as 99% for various aromatic nitro-compounds. What's more, the catalyst exhibited a unprecedented long lifetime because it could be recycled over 25 times without obvious performance decay or even a morphology change. This work showed the promise and great potential of noble-metal-free catalysts in green chemistry.Nowadays, it is of great significance and a challenge to design a noble-metal-free catalyst with high activity and a long lifetime for the reduction of aromatic nitro-compounds. Here, a 2D structured nanocomposite catalyst with graphene supported CuNi alloy nanoparticles (NPs) is prepared, and is promising for meeting the requirements of green chemistry. In this graphene/CuNi nanocomposite, the ultra-small CuNi nanoparticles (~2 nm) are evenly anchored on graphene sheets, which is not only a breakthrough in the structures, but also brings about an outstanding performance in activity and stability. Combined with a precise optimization of the alloy ratios, the reaction rate constant of graphene/Cu61Ni39 reached a high level of 0.13685 s-1, with a desirable selectivity as high as 99% for various aromatic nitro-compounds. What's more, the catalyst exhibited a unprecedented long lifetime

  16. Role of cytochrome p4501 family members in the metabolic activation of polycyclic aromatic hydrocarbons in mouse epidermis.

    PubMed

    Kleiner, Heather E; Vulimiri, Suryanarayana V; Hatten, William B; Reed, Melissa J; Nebert, Daniel W; Jefcoate, Colin R; DiGiovanni, John

    2004-12-01

    Polycyclic aromatic hydrocarbons (PAHs) are known to be activated by the cytochrome P450 (P450) 1 family. However, the precise role of individual P4501 family members in PAH bioactivation remains to be fully elucidated. We therefore investigated the formation of PAH-DNA adducts in the epidermis of Cyp1a2(-/-), Cyp1b1(-/-), and Ahr(-/-) knockout mice. A panel of different PAHs was used, ranging in carcinogenic potency. Mice were treated topically on the dorsal skin with the following tritium-labeled PAHs: dibenzo[a,l]pyre-ne (DB[a,l]P), 7,12-dimethylbenz[a]anthracene (DMBA), benzo[a]pyrene (B[a]P), dibenzo[a,h]anthracene (DB[a,h]A), benzo[g]chrysene (B[g]C), and benzo[c]phenanthrene (B[c]P). At 24 h after treatment, mice (two male and two female mice per group) were sacrificed, and epidermal DNA was isolated and hydrolyzed with DNase I; subsequently, DNA adducts were quantitated by liquid scintillation counting. In the DB[a,l]P-treated mice, levels of DNA adducts were significantly lower in Cyp1a2(-/-) and Cyp1b1(-/-) mice by 57 and 46%, respectively, as compared to wild-type (WT) mice (C57BL/6 background). The levels of DB[a,l]P DNA adducts formed in Ahr(-/-) mice were 26% lower, but this was not statistically significant. The levels of DMBA-DNA adducts in Cyp1a2(-/-) mice were not different than the WT mice but were significantly lower in Cyp1b1(-/-) and Ahr(-/-) mice by 64 and 52%, respectively. DMBA-DNA adduct samples were further analyzed by HPLC following further digestion to deoxyribonucleosides. HPLC analysis of individual DMBA-DNA adducts revealed differences in the ratio of syn-DMBA-diol epoxide- to anti-DMBA-diol epoxide-derived adducts in the Ahr(-/-) and Cyp1b1(-/-) mice. The ratio of syn-/anti-derived adducts in WT mice was 0.49. This ratio was 0.23 in the Cyp1b1(-/-) mice and 0.87 in the Ahr(-/-) mice. In contrast to the results with DB[a,l]P and DMBA, the levels of B[a]P-, DB[a,h]A-, B[g]C-, and B[c]P-DNA adducts were significantly lower in Ahr

  17. Druggability analysis and classification of protein tyrosine phosphatase active sites

    PubMed Central

    Ghattas, Mohammad A; Raslan, Noor; Sadeq, Asil; Al Sorkhy, Mohammad; Atatreh, Noor

    2016-01-01

    Protein tyrosine phosphatases (PTP) play important roles in the pathogenesis of many diseases. The fact that no PTP inhibitors have reached the market so far has raised many questions about their druggability. In this study, the active sites of 17 PTPs were characterized and assessed for its ability to bind drug-like molecules. Consequently, PTPs were classified according to their druggability scores into four main categories. Only four members showed intermediate to very druggable pocket; interestingly, the rest of them exhibited poor druggability. Particularly focusing on PTP1B, we also demonstrated the influence of several factors on the druggability of PTP active site. For instance, the open conformation showed better druggability than the closed conformation, while the tight-bound water molecules appeared to have minimal effect on the PTP1B druggability. Finally, the allosteric site of PTP1B was found to exhibit superior druggability compared to the catalytic pocket. This analysis can prove useful in the discovery of new PTP inhibitors by assisting researchers in predicting hit rates from high throughput or virtual screening and saving unnecessary cost, time, and efforts via prioritizing PTP targets according to their predicted druggability. PMID:27757011

  18. [Inhibitory activity of hydrosols prepared from 18 Japanese herbs of weak aromatic flavor against filamentous formation and growth of Candida albicans].

    PubMed

    Inouye, Shigeharu; Takahashi, Miki; Abe, Shigeru

    2012-01-01

    Leaf hydrosols prepared from 18 weakly aromatic Japanese herbs used traditionally were tested on the filamentation-inhibitory activity of Candida albicans. These hydrosols were divided into two classes, A and B. The inhibitory activity of 13 hydrosols belonging to class A was markedly altered depending on the drying process of the parent herbs. On the other hand, the remaining 5 hydrosols belonging to class B showed no significant change on the composition and inhibitory activity upon drying. The change of the bioactivity was correlated with the change and concentration of the respective major constituents. Especially strong bioactivity shown by hydrosols of dried Houttuynia cordata and fresh Prunus pendula was ascribed to n-capric acid and cyanide, respectively. Eight hydrosols exhibited weak or moderate activity against the growth of C. albicans.

  19. [Inhibitory activity of hydrosols prepared from 18 Japanese herbs of weak aromatic flavor against filamentous formation and growth of Candida albicans].

    PubMed

    Inouye, Shigeharu; Takahashi, Miki; Abe, Shigeru

    2012-01-01

    Leaf hydrosols prepared from 18 weakly aromatic Japanese herbs used traditionally were tested on the filamentation-inhibitory activity of Candida albicans. These hydrosols were divided into two classes, A and B. The inhibitory activity of 13 hydrosols belonging to class A was markedly altered depending on the drying process of the parent herbs. On the other hand, the remaining 5 hydrosols belonging to class B showed no significant change on the composition and inhibitory activity upon drying. The change of the bioactivity was correlated with the change and concentration of the respective major constituents. Especially strong bioactivity shown by hydrosols of dried Houttuynia cordata and fresh Prunus pendula was ascribed to n-capric acid and cyanide, respectively. Eight hydrosols exhibited weak or moderate activity against the growth of C. albicans. PMID:22467129

  20. Current activities handbook: formerly utilized sites remedial action program

    SciTech Connect

    1981-02-27

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified.

  1. SiRNAs conjugated with aromatic compounds induce RISC-mediated antisense strand selection and strong gene-silencing activity

    SciTech Connect

    Kubo, Takanori; Yanagihara, Kazuyoshi; Takei, Yoshifumi; Mihara, Keichiro; Sato, Yuichiro; Seyama, Toshio

    2012-10-05

    Highlights: Black-Right-Pointing-Pointer SiRNAs conjugated with aromatic compounds (Ar-siRNAs) at 5 Prime -sense strand were synthesized. Black-Right-Pointing-Pointer Ar-siRNAs increased resistance against nuclease degradation. Black-Right-Pointing-Pointer Ar-siRNAs were thermodynamically stable compared with the unmodified siRNA. Black-Right-Pointing-Pointer High levels of cellular uptake and cytoplasmic localization were found. Black-Right-Pointing-Pointer Strong gene-silencing efficacy was exhibited in the Ar-siRNAs. -- Abstract: Short interference RNA (siRNA) is a powerful tool for suppressing gene expression in mammalian cells. In this study, we focused on the development of siRNAs conjugated with aromatic compounds in order to improve the potency of RNAi and thus to overcome several problems with siRNAs, such as cellular delivery and nuclease stability. The siRNAs conjugated with phenyl, hydroxyphenyl, naphthyl, and pyrenyl derivatives showed strong resistance to nuclease degradation, and were thermodynamically stable compared with unmodified siRNA. A high level of membrane permeability in HeLa cells was also observed. Moreover, these siRNAs exhibited enhanced RNAi efficacy, which exceeded that of locked nucleic acid (LNA)-modified siRNAs, against exogenous Renilla luciferase in HeLa cells. In particular, abundant cytoplasmic localization and strong gene-silencing efficacy were found in the siRNAs conjugated with phenyl and hydroxyphenyl derivatives. The novel siRNAs conjugated with aromatic compounds are promising candidates for a new generation of modified siRNAs that can solve many of the problems associated with RNAi technology.

  2. Electrostatic fields in the active sites of lysozymes.

    PubMed

    Sun, D P; Liao, D I; Remington, S J

    1989-07-01

    Considerable experimental evidence is in support of several aspects of the mechanism that has been proposed for the catalytic activity of lysozyme. However, the enzymatically catalyzed hydrolysis of polysaccharides proceeds over 5 orders of magnitude faster than that of model compounds that mimic the configuration of the substrate in the active site of the enzyme. Although several possible explanations for this rate enhancement have been discussed elsewhere, a definitive mechanism has not emerged. Here we report striking results obtained by classical electrodynamics, which suggest that bond breakage and the consequent separation of charge in lysozyme is promoted by a large electrostatic field across the active site cleft, produced in part by a very asymmetric distribution of charged residues on the enzyme surface. Lysozymes unrelated in amino acid sequence have similar distributions of charged residues and electric fields. The results reported here suggest that the electrostatic component of the rate enhancement is greater than 9 kcal.mol-1. Thus, electrostatic interactions may play a more important role in the enzymatic mechanism than has generally been appreciated.

  3. Histidine at the active site of Neurospora tyrosinase.

    PubMed

    Pfiffner, E; Lerch, K

    1981-10-13

    The involvement of histidyl residues as potential ligands to the binuclear active-site copper of Neurospora tyrosinase was explored by dye-sensitized photooxidation. The enzymatic activity of the holoenzyme was shown to be unaffected by exposure to light in the presence of methylene blue; however, irradiation of the apoenzyme under the same conditions led to a progressive loss of its ability to be reactivated with Cu2+. This photoinactivation was paralleled by a decrease in the histidine content whereas the number of histidyl residues in the holoenzyme remained constant. Copper measurements of photooxidized, reconstituted apoenzyme demonstrated the loss of binding of one copper atom per mole of enzyme as a consequence of photosensitized oxidation of three out of nine histidine residues. Their sequence positions were determined by a comparison of the relative yields of the histidine containing peptides of photooxidized holo- and apotyrosinases. The data obtained show the preferential modification of histidyl residues 188, 193, and 289 and suggest that they constitute metal ligands to one of the two active-site copper atoms. Substitution of copper by cobalt was found to afford complete protection of the histidyl residues from being modified by dye-sensitized photooxidation. PMID:6458322

  4. Mechanistic quantitative structure-activity relationship model for the photoinduced toxicity of polycyclic aromatic hydrocarbons. 2: An empirical model for the toxicity of 16 polycyclic aromatic hydrocarbons to the duckweed Lemna gibba L. G-3

    SciTech Connect

    Huang, X.D.; Krylov, S.N.; Ren, L.; McConkey, B.J.; Dixon, D.G.; Greenberg, B.M.

    1997-11-01

    Photoinduced toxicity of polycyclic aromatic hydrocarbons (PAHs) occurs via photosensitization reactions (e.g., generation of singlet-state oxygen) and by photomodification (photooxidation and/or photolysis) of the chemicals to more toxic species. The quantitative structure-activity relationship (QSAR) described in the companion paper predicted, in theory, that photosensitization and photomodification additively contribute to toxicity. To substantiate this QSAR modeling exercise it was necessary to show that toxicity can be described by empirically derived parameters. The toxicity of 16 PAHs to the duckweed Lemna gibba was measured as inhibition of leaf production in simulated solar radiation (a light source with a spectrum similar to that of sunlight). A predictive model for toxicity was generated based on the theoretical model developed in the companion paper. The photophysical descriptors required of each PAH for modeling were efficiency of photon absorbance, relative uptake, quantum yield for triplet-state formation, and the rate of photomodification. The photomodification rates of the PAHs showed a moderate correlation to toxicity, whereas a derived photosensitization factor (PSF; based on absorbance, triplet-state quantum yield, and uptake) for each PAH showed only a weak, complex correlation to toxicity. However, summing the rate of photomodification and the PSF resulted in a strong correlation to toxicity that had predictive value. When the PSF and a derived photomodification factor (PMF; based on the photomodification rate and toxicity of the photomodified PAHs) were summed, an excellent explanatory model of toxicity was produced, substantiating the additive contributions of the two factors.

  5. Dithiane Induced Cycloaddition/Aromatization Tactic for the Synthesis of Multisubstituted Furans.

    PubMed

    Lai, Junshan; Liang, Yongping; Liu, Teng; Tang, Shouchu

    2016-05-01

    The development of a new transition-metal-free tactic for convergent, one-pot synthesis of multisubstituted furans by β-chloro-vinyl dithiane cyclization with aldehydes is described. Key to the success was the development of a new vinylidene dithiane site as a donor allene that generates the active dihydrofuran, which undergoes in situ aromatization under mild conditions.

  6. Seminal vesicles and urinary bladder as sites of aromatization of androgens in men, evidenced by a CYP19A1-driven luciferase reporter mouse and human tissue specimens.

    PubMed

    Strauss, Leena; Rantakari, Pia; Sjögren, Klara; Salminen, Anu; Lauren, Eve; Kallio, Jenny; Damdimopoulou, Pauliina; Boström, Minna; Boström, Peter J; Pakarinen, Pirjo; Zhang, FuPing; Kujala, Paula; Ohlsson, Claes; Mäkelä, Sari; Poutanen, Matti

    2013-04-01

    The human CYP19A1 gene is expressed in various tissues by the use of tissue-specific promoters, whereas the rodent cyp19a1 gene is expressed mainly in the gonads and brain. We generated a transgenic mouse model containing a >100-kb 5' region of human CYP19A1 gene connected to a luciferase reporter gene. The luciferase activity in mouse tissues mimicked the CYP19A1 gene expression pattern in humans. Interestingly, the reporter gene activity was 16 and 160 times higher in the urinary bladder and seminal vesicles, respectively, as compared with the activity in the testis. Accordingly, CYP19A1 gene and P450arom protein expression was detected in those human tissues. Moreover, the data revealed that the expression of CYP19A1 gene is driven by promoters PII, I.4, and I.3 in the seminal vesicles, and by promoters PII and I.4 in the urinary bladder. Furthermore, the reporter gene expression in the seminal vesicles was androgen dependent: Castration decreased the expression ∼20 times, and testosterone treatment restored it to the level of an intact mouse. This reporter mouse model facilitates studies of tissue-specific regulation of the human CYP19A1 gene, and our data provide evidence for seminal vesicles as important sites for estrogen production in males.

  7. Oxidant-dependent metabolic activation of polycyclic aromatic hydrocarbons by phorbol ester-stimulated human polymorphonuclear leukocytes: possible link between inflammation and cancer

    SciTech Connect

    Trush, M.A.; Seed, J.L.; Kensler, T.W.

    1985-08-01

    Oxidants, such as those generated by metabolically activated phagocytes in inflammation, have been implicated in the metabolic activation of carcinogens, and in this study the authors demonstrate that the interaction of (+/-)-trans-7,8-dihydroxy-7,8-dihydrobenzo(a)pyrene (BP 7,8-dihydrodiol) with phorbol ester-stimulated polymorphonuclear leukocytes (PMNs) results in the generation of both a chemiluminescent intermediate and one that covalently binds to DNA. Concordant with the formation of a carcinogen-DNA adduct, the admixture of BP 7,8-dihydrodiol and phorbol ester-stimulated PMNs elicited mutagenesis in Salmonella typhimurium strain TA100. These results demonstrate that oxidants generated by metabolically stimulated PMNs can activate penultimate polycyclic aromatic hydrocarbons to a genotoxic metabolite and further defines a role for inflammation in carcinogenesis.

  8. The Role of Human Aldo-Keto Reductases in the Metabolic Activation and Detoxication of Polycyclic Aromatic Hydrocarbons: Interconversion of PAH Catechols and PAH o-Quinones.

    PubMed

    Zhang, Li; Jin, Yi; Huang, Meng; Penning, Trevor M

    2012-01-01

    Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants. They are procarcinogens requiring metabolic activation to elicit their deleterious effects. Aldo-keto reductases (AKR) catalyze the oxidation of proximate carcinogenic PAH trans-dihydrodiols to yield electrophilic and redox-active PAH o-quinones. AKRs are also found to be capable of reducing PAH o-quinones to form PAH catechols. The interconversion of o-quinones and catechols results in the redox-cycling of PAH o-quinones to give rise to the generation of reactive oxygen species and subsequent oxidative DNA damage. On the other hand, PAH catechols can be intercepted through phase II metabolism by which PAH o-quinones could be detoxified and eliminated. The aim of the present review is to summarize the role of human AKRs in the metabolic activation/detoxication of PAH and the relevance of phase II conjugation reactions to human lung carcinogenesis.

  9. Trichodiene synthase. Identification of active site residues by site-directed mutagenesis.

    PubMed

    Cane, D E; Shim, J H; Xue, Q; Fitzsimons, B C; Hohn, T M

    1995-02-28

    Derivatization of 5,5'-dithiobis(2-nitrobenzoic acid)-treated trichodiene synthase with [methyl-14C]methyl methanethiosulfonate and analysis of the derived tryptic peptides suggested the presence of two cysteine residues at the active site. The corresponding C146A and C190A mutants were constructed by site-directed mutagenesis. The C190A mutant displayed partial but significantly reduced activity, with a reduction in kcat/Km of 3000 compared to the wild-type trichodiene synthase, while the C146A mutant was essentially inactive. A hybrid trichodiene synthase, constructed from amino acids 1-309 of the Fusarium sporotrichioides enzyme and amino acids 310-383 of the Gibberella pulicaris cyclase, had steady state kinetic parameters nearly identical to those of the wild-type F. sporotrichioides enzyme. From this parent hybrid, a series of mutants was constructed by site-directed mutagenesis in which the amino acids in the base-rich region, 302-306 (DRRYR), were systematically modified. Three of these mutants were overexpressed and purified to homogeneity. The importance of Arg304 for catalysis was established by the observation that the R304K mutant showed a more than 25-fold increase in Km, as well as a 200-fold reduction in kcat. In addition, analysis of the incubation products of the R304K mutant by gas chromatography-mass spectrometry (GC-MS) indicated that farnesyl diphosphate was converted not only to trichodiene but to at least two additional C15H24 hydrocarbons, mle 204. Replacement of the Tyr305 residue of trichodiene synthase with Phe had little effect on kcat, while increasing the Km by a factor of ca. 7-8.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7873527

  10. The copper active site of CBM33 polysaccharide oxygenases.

    PubMed

    Hemsworth, Glyn R; Taylor, Edward J; Kim, Robbert Q; Gregory, Rebecca C; Lewis, Sally J; Turkenburg, Johan P; Parkin, Alison; Davies, Gideon J; Walton, Paul H

    2013-04-24

    The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme's three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

  11. Activation of muscarinic acetylcholine receptors via their allosteric binding sites.

    PubMed Central

    Jakubík, J; Bacáková, L; Lisá, V; el-Fakahany, E E; Tucek, S

    1996-01-01

    Ligands that bind to the allosteric-binding sites on muscarinic acetylcholine receptors alter the conformation of the classical-binding sites of these receptors and either diminish or increase their affinity for muscarinic agonists and classical antagonists. It is not known whether the resulting conformational change also affects the interaction between the receptors and the G proteins. We have now found that the muscarinic receptor allosteric modulators alcuronium, gallamine, and strychnine (acting in the absence of an agonist) alter the synthesis of cAMP in Chinese hamster ovary (CHO) cells expressing the M2 or the M4 subtype of muscarinic receptors in the same direction as the agonist carbachol. In addition, most of their effects on the production of inositol phosphates in CHO cells expressing the M1 or the M3 muscarinic receptor subtypes are also similar to (although much weaker than) those of carbachol. The agonist-like effects of the allosteric modulators are not observed in CHO cells that have not been transfected with the gene for any of the subtypes of muscarinic receptors. The effects of alcuronium on the formation of cAMP and inositol phosphates are not prevented by the classical muscarinic antagonist quinuclidinyl benzilate. These observations demonstrate for the first time that the G protein-mediated functional responses of muscarinic receptors can be evoked not only from their classical, but also from their allosteric, binding sites. This represents a new mechanism of receptor activation. PMID:8710935

  12. Mimicking enzymatic active sites on surfaces for energy conversion chemistry.

    PubMed

    Gutzler, Rico; Stepanow, Sebastian; Grumelli, Doris; Lingenfelder, Magalí; Kern, Klaus

    2015-07-21

    Metal-organic supramolecular chemistry on surfaces has matured to a point where its underlying growth mechanisms are well understood and structures of defined coordination environments of metal atoms can be synthesized in a controlled and reproducible procedure. With surface-confined molecular self-assembly, scientists have a tool box at hand which can be used to prepare structures with desired properties, as for example a defined oxidation number and spin state of the transition metal atoms within the organic matrix. From a structural point of view, these coordination sites in the supramolecular structure resemble the catalytically active sites of metallo-enzymes, both characterized by metal centers coordinated to organic ligands. Several chemical reactions take place at these embedded metal ions in enzymes and the question arises whether these reactions also take place using metal-organic networks as catalysts. Mimicking the active site of metal atoms and organic ligands of enzymes in artificial systems is the key to understanding the selectivity and efficiency of enzymatic reactions. Their catalytic activity depends on various parameters including the charge and spin configuration in the metal ion, but also on the organic environment, which can stabilize intermediate reaction products, inhibits catalytic deactivation, and serves mostly as a transport channel for the reactants and products and therefore ensures the selectivity of the enzyme. Charge and spin on the transition metal in enzymes depend on the one hand on the specific metal element, and on the other hand on its organic coordination environment. These two parameters can carefully be adjusted in surface confined metal-organic networks, which can be synthesized by virtue of combinatorial mixing of building synthons. Different organic ligands with varying functional groups can be combined with several transition metals and spontaneously assemble into ordered networks. The catalytically active metal

  13. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-06-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.

  14. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    PubMed Central

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-01-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  15. Spectroscopic Definition of the Ferroxidase Site in M Ferritin: Comparison of Binuclear Substrate vs. Cofactor Active Sites

    PubMed Central

    Schwartz, Jennifer K.; Liu, Xiaofeng S.; Tosha, Takehiko; Theil, Elizabeth C.; Solomon, Edward I.

    2008-01-01

    Maxi ferritins, 24 subunit protein nanocages, are essential in humans, plants, bacteria, and other animals for the concentration and storage of iron as hydrated ferric oxide, while minimizing free radical generation or use by pathogens. Formation of the precursors to these ferric oxides is catalyzed at a non-heme biferrous substrate site, which has some parallels with the cofactor sites in other biferrous enzymes. A combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field MCD (VTVH MCD) has been used to probe Fe(II) binding to the substrate active site in frog M ferritin. These data determined that the active site within each subunit consists of two inequivalent five-coordinate (5C) ferrous centers that are weakly anti-ferromagnetically coupled, consistent with a μ-1,3 carboxylate bridge. The active site ligand set is unusual and likely includes a terminal water bound to each Fe(II) center. The Fe(II) ions bind to the active sites in a concerted manner, and cooperativity among the sites in each subunit is observed, potentially providing a mechanism for the control of ferritin iron loading. Differences in geometric and electronic structure – including a weak ligand field, availability of two water ligands at the biferrous substrate site, and the single carboxylate bridge in ferritin – coincide with the divergent reaction pathways observed between this substrate site and the previously studied cofactor active sites. PMID:18576633

  16. An active-site lysine in avian liver phosphoenolpyruvate carboxykinase

    SciTech Connect

    Guidinger, P.F.; Nowak, T. )

    1991-09-10

    The participation of lysine in the catalysis by avian liver phosphoenolpyruvate carboxykinase was studied by chemical modification and by a characterization of the modified enzyme. The rate of inactivation by 2,4-pentanedione is pseudo-first-order and linearly dependent on reagent concentration with a second-order rate constant of 0.36 {plus minus} 0.025 M{sup {minus}1} min{sup {minus}1}. Inactivation by pyridoxal 5{prime}-phosphate of the reversible reaction catalyzed by phosphoenolpyruvate carboxykinase follows bimolecular kinetics with a second-order rate constant of 7,700 {plus minus} 860 m{sup {minus}1} min{sup {minus}1}. Treatment of the enzyme or one lysine residue modified concomitant with 100% loss in activity. A stoichiometry of 1:1 is observed when either the reversible or the irreversible reactions catalyzed by the enzyme are monitored. A study of k{sub obs} vs pH suggests this active-site lysine has a pK{sub a} of 8.1 and a pH-independent rate constant of inactivation of 47,700 m{sup {minus}1} min{sup {minus}1}. Proton relaxation rate measurements suggest that pyridoxal 5{prime}-phosphate modification alters binding of the phosphate-containing substrates. {sup 31}P NMR relaxation rate measurements show altered binding of the substrates in the ternary enzyme {center dot}Mn{sup 2+}{center dot}substrate complex. Circular dichroism studies show little change in secondary structure of pyridoxal 5{prime}-phosphate modified phosphoenolpyruvate carboxykinase. These results indicate that avian liver phosphoenolpyruvate carboxykinase has one reactive lysine at the active site and it is involved in the binding and activation of the phosphate-containing substrates.

  17. Eel calcitonin binding site distribution and antinociceptive activity in rats

    SciTech Connect

    Guidobono, F.; Netti, C.; Sibilia, V.; Villa, I.; Zamboni, A.; Pecile, A.

    1986-03-01

    The distribution of binding site for (/sup 125/I)-eel-calcitonin (ECT) to rat central nervous system, studied by an autoradiographic technique, showed concentrations of binding in the diencephalon, the brain stem and the spinal cord. Large accumulations of grains were seen in the hypothalamus, the amygdala, in the fasciculus medialis prosencephali, in the fasciculus longitudinalis medialis, in the ventrolateral part of the periventricular gray matter, in the lemniscus medialis and in the raphe nuclei. The density of grains in the reticular formation and in the nucleus tractus spinalis nervi trigemini was more moderate. In the spinal cord, grains were scattered throughout the dorsal horns. Binding of the ligand was displaced equally by cold ECT and by salmon CT(sCT), indicating that both peptides bind to the same receptors. Human CT was much weaker than sCT in displacing (/sup 125/I)-ECT binding. The administration of ECT into the brain ventricles of rats dose-dependently induced a significant and long-lasting enhancement of hot-plate latencies comparable with that obtained with sCT. The antinociceptive activity induced by ECT is compatible with the topographical distribution of binding sites for the peptide and is a further indication that fish CTs are active in the mammalian brain.

  18. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  19. Metal active site elasticity linked to activation of homocysteine in methionine synthases

    SciTech Connect

    Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.; Matthews, Rowena G.; Smith, Janet L.; Ludwig, Martha L.

    2008-04-02

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  20. Active Sites Environmental Monitoring Program: Program plan. Revision 1

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  1. Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

    DOE PAGES

    Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.; Nash, Connor; Steirer, K. Xerxes; Clark, Jared; Robichaud, David J.; Ruddy, Daniel A.

    2016-01-21

    Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo2C) for the deoxygenation of acetic acid, anmore » abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

  2. Gas-particle concentrations of atmospheric polycyclic aromatic hydrocarbons at an urban and a residential site in Osaka, Japan: effect of the formation of atmospherically stable layer on their temporal change.

    PubMed

    Kishida, Masao; Nishikawa, Ayako; Fujimori, Keiichi; Shibutani, Yasuhiko

    2011-09-15

    A comparative study on atmospheric polycyclic aromatic hydrocarbons (PAHs) in particulate matter and the gaseous phase was performed at an urban and a residential site in Osaka, Japan, during 2005-2006. PAH concentrations at the urban site were found to be approximately twice higher than those at the residential site. At both sites, particulate PAH concentrations increased mainly in winter while the trends of temporal change in gaseous PAH concentrations were not clearly observed. The main sources of PAHs were estimated to be local traffic, e.g., diesel engines with catalytic converter. PAH concentrations did not significantly negatively correlate with ozone concentrations and meteorological parameters. Gas-particle partitioning coefficients of representative PAHs with low molecular weight (LMW) significantly negatively correlated with ambient temperature, showing that temporal change in the LMW PAH concentrations in PM could be attributable to the shift of their gas-particle distribution caused by the change in ambient temperature. For the first time, we studied the effect of the formation of atmospherically stable layer following an increase in PAH concentrations in Japan. At the urban site, PAHs showed a significant positive correlation with potential temperature gradients, indicating that temporal variability in PAH concentrations would be dominantly controlled by the formation of atmospherically stable layer in Osaka area.

  3. Use of quantitative shape-activity relationships to model the photoinduced toxicity of polycyclic aromatic hydrocarbons: Electron density shape features accurately predict toxicity

    SciTech Connect

    Mezey, P.G.; Zimpel, Z.; Warburton, P.; Walker, P.D.; Irvine, D.G.; Huang, X.D.; Dixon, D.G.; Greenberg, B.M.

    1998-07-01

    The quantitative shape-activity relationship (QShAR) methodology, based on accurate three-dimensional electron densities and detailed shape analysis methods, has been applied to a Lemna gibba photoinduced toxicity data set of 16 polycyclic aromatic hydrocarbon (PAH) molecules. In the first phase of the studies, a shape fragment QShAR database of PAHs was developed. The results provide a very good match to toxicity based on a combination of the local shape features of single rings in comparison to the central ring of anthracene and a more global shape feature involving larger molecular fragments. The local shape feature appears as a descriptor of the susceptibility of PAHs to photomodification and the global shape feature is probably related to photosensitization activity.

  4. Photoinductive activity of humic acid fractions with the presence of Fe(III): the role of aromaticity and oxygen groups involved in fractions.

    PubMed

    Ou, Xiaoxia; Chen, Shuo; Quan, Xie; Zhao, Huimin

    2008-06-01

    Relationship between the photoinductive activity and the properties of humic acids (HA) fractions were investigated with and without Fe(III). Three fractions were separated based on the molecular weight (M(w)) and were obtained following the order of M(w): F(A)>F(B)>F(C). Compared to F(A) and F(B), photodegradation of atrazine under simulated sunlight was much faster in solution containing F(C), whose structure was dominated by greater aromaticity, more oxygen groups and fluorophores. The interaction of HA fractions and Fe(III) was studied using fluorescence spectrometry and F(C) had the largest quenching constant. The capacity of electron transfer, estimated from the amount of photoformed Fe(II), was also highest for F(C). Thus, the Fe(III)-F(C) complex was efficient in phototransformation of atrazine in nearly neutral aqueous solutions. These results suggest that the aromaticity and oxygen groups content of HA exert great influence on the binding ability of metals and on the fate of pollutants in natural waters.

  5. Pathway engineering for production of aromatics in Escherichia coli: Confirmation of stoichiometric analysis by independent modulation of AroG, TktA, and Pps activities

    SciTech Connect

    Patnaik, R.; Spitzer, R.G.; Liao, J.C.

    1995-05-20

    The synthesis of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) is the first commitment of resources toward aromatics production in Escherichia coli. DAHP is produced during the condensation reaction between phosphenolpyruvate (PEP) and erythrose 4-phosphate (E4P) catalyzed by DAHP synthases (coded by aroF, aroG, and aroH). Stoichiometric analysis has shown a severe PEP limitation in the theoretical yield of DAHP production from glucose due to the phosphotransferase system (PTS) for sugar uptake. In the present study the authors confirm the predictions of the stoichiometric analysis by introducing pps, tktA, and aroG into vectors under independently controlled promoters, In glucose medium, although TktA has some positive effect on the final DAHP concentration, it has no effect on the yield (percent conversion). With Pps overexpression, the DAHP concentration produced from glucose is increased almost twofold and the yield is approaching the theoretical maximum, the final DAHP concentration and the yield are completely determined by the AroG activity. TktA and Pps play no or insignificant roles, and the yield can reach the theoretical maximum without overexpression of these two enzymes. The results shown hare are important for both rational design of metabolic pathways and industrial production of aromatics such as tryptophan, phenylalanine, indigo, quinic acid, and catechol.

  6. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426.

    PubMed

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.

  7. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity. PMID:25706379

  8. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. PMID:25902402

  9. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.

  10. General rules for predicting the local aromaticity of carbon polyhedra

    NASA Astrophysics Data System (ADS)

    Abdukadir, Ablimit; Kerim, Ablikim; Tawar, Tursungul

    2016-01-01

    The aromaticity of classical and nonclassical C24 fullerene isomers and their anions were studied using the topological resonance energy (TRE) method. Local aromaticity was studied using the bond resonance energy (BRE) method. On the basis of BRE values, the contributions of different types of chemical bonds to the molecular global aromaticity were analyzed and general rules for predicting the local aromaticity of fullerenes are proposed. It was found that pentagons, heptagons, and squares preferred hexagons as neighbors rather than squares as neighbors. In the hexaanionic state, pentagon pair sites exhibit larger local aromaticity than other places in the same molecule.

  11. Polybenzimidazoles Via Aromatic Nucleophilic Displacement

    NASA Technical Reports Server (NTRS)

    Connell, John W.; Hergenrother, Paul M.; Smith, Joseph G.

    1994-01-01

    Soluble polybenzimidazoles (PBI's) synthesized by nucleophilic displacement reaction of di(hydroxyphenyl)-benzimidazole monomers with activated aromatic difluoride compounds in presence of anhydrous potassium carbonate. These polymers exhibit good thermal, thermo-oxidative, and chemical stability, and high mechanical properties. Using benzimidazole monomers, more economical, and new PBI's processed more easily than commercial PBI, without loss of desirable physical properties.

  12. Biosynthesis of the Aromatic Amino Acids.

    PubMed

    Pittard, James; Yang, Ji

    2008-09-01

    This chapter describes in detail the genes and proteins of Escherichia coli involved in the biosynthesis and transport of the three aromatic amino acids tyrosine, phenylalanine, and tryptophan. It provides a historical perspective on the elaboration of the various reactions of the common pathway converting erythrose-4-phosphate and phosphoenolpyruvate to chorismate and those of the three terminal pathways converting chorismate to phenylalanine, tyrosine, and tryptophan. The regulation of key reactions by feedback inhibition, attenuation, repression, and activation are also discussed. Two regulatory proteins, TrpR (108 amino acids) and TyrR (513 amino acids), play a major role in transcriptional regulation. The TrpR protein functions only as a dimer which, in the presence of tryptophan, represses the expression of trp operon plus four other genes (the TrpR regulon). The TyrR protein, which can function both as a dimer and as a hexamer, regulates the expression of nine genes constituting the TyrR regulon. TyrR can bind each of the three aromatic amino acids and ATP and under their influence can act as a repressor or activator of gene expression. The various domains of this protein involved in binding the aromatic amino acids and ATP, recognizing DNA binding sites, interacting with the alpha subunit of RNA polymerase, and changing from a monomer to a dimer or a hexamer are all described. There is also an analysis of the various strategies which allow TyrR in conjunction with particular amino acids to differentially affect the expression of individual genes of the TyrR regulon. PMID:26443741

  13. Metals in the active site of native protein phosphatase-1.

    PubMed

    Heroes, Ewald; Rip, Jens; Beullens, Monique; Van Meervelt, Luc; De Gendt, Stefan; Bollen, Mathieu

    2015-08-01

    Protein phosphatase-1 (PP1) is a major protein Ser/Thr phosphatase in eukaryotic cells. Its activity depends on two metal ions in the catalytic site, which were identified as manganese in the bacterially expressed phosphatase. However, the identity of the metal ions in native PP1 is unknown. In this study, total reflection X-ray fluorescence (TXRF) was used to detect iron and zinc in PP1 that was purified from rabbit skeletal muscle. Metal exchange experiments confirmed that the distinct substrate specificity of recombinant and native PP1 is determined by the nature of their associated metals. We also found that the iron level associated with native PP1 is decreased by incubation with inhibitor-2, consistent with a function of inhibitor-2 as a PP1 chaperone. PMID:25890482

  14. Experimental and DFT studies on the aggregation behavior of imidazolium-based surface-active ionic liquids with aromatic counterions in aqueous solution.

    PubMed

    Xu, Wenwen; Wang, Tao; Cheng, Ni; Hu, Qiongzheng; Bi, Yanhui; Gong, Yanjun; Yu, Li

    2015-02-01

    Two imidazolium-based surface-active ionic liquids with aromatic counterions, namely, 1-dodecyl-3-methylimidazolium salicylate (C12mimSal) and 1-dodecyl-3-methylimidazolium 3-hydroxy-2-naphthoate (C12mimHNC), were synthesized, and their aggregate behavior in aqueous solutions was systematically explored. Surface tension and conductivity measurements indicate that both C12mimSal and C12mimHNC show superior surface activity compared to the common imidazolium-based SAIL with the same hydrocarbon chain length, 1-dodecyl-3-methylimidazolium bromide (C12mimBr). This result demonstrates that the incorporation of aromatic counterions favors the formation of micelles. C12mimHNC displays a higher surface activity than C12mimSal, resulting from the different hydrophobicities of the counterions. In comparison with C12mimBr, C12mimSal not only can form hexagonal liquid-crystalline phase (H1) in aqueous solution, but also exhibits a broad region of cubic liquid-crystalline phase (V2) at higher concentration. As for the C12mimHNC/H2O system, a lamellar liquid-crystalline (L(α)) phase was observed. These lyotropic liquid crystals (LLCs) were characterized by polarized optical microscopy (POM) and small-angle X-ray scattering (SAXS). Structural parameters calculated from SAXS patterns suggest that a higher concentration of the SAIL leads to a denser arrangement whereas a higher temperature results in the opposite effect. The rheological results manifest that the formed H1 phase in the C12mimSal/H2O system exhibits an impressive viscoelastic behavior, indicated by a modulus (G' and G″) that is 1 order of magnitude higher than that of C12mimBr. Density functional theory (DFT) calculations reveal that C12mimSal has a more negative interaction energy with a water molecule and the Sal(-) counterion presents a stronger electronegativity than the HNC(-) counterion. The specific phase behavior of the C12mimSal/H2O and C12mimHNC/H2O systems can be attributed to the strong synergic

  15. Contorted polycyclic aromatics.

    PubMed

    Ball, Melissa; Zhong, Yu; Wu, Ying; Schenck, Christine; Ng, Fay; Steigerwald, Michael; Xiao, Shengxiong; Nuckolls, Colin

    2015-02-17

    CONSPECTUS: This Account describes a body of research in the design, synthesis, and assembly of molecular materials made from strained polycyclic aromatic molecules. The strain in the molecular subunits severely distorts the aromatic molecules away from planarity. We coined the term "contorted aromatics" to describe this class of molecules. Using these molecules, we demonstrate that the curved pi-surfaces are useful as subunits to make self-assembled electronic materials. We have created and continue to study two broad classes of these "contorted aromatics": discs and ribbons. The figure that accompanies this conspectus displays the three-dimensional surfaces of a selection of these "contorted aromatics". The disc-shaped contorted molecules have well-defined conformations that create concave pi-surfaces. When these disc-shaped molecules are substituted with hydrocarbon side chains, they self-assemble into columnar superstructures. Depending on the hydrocarbon substitution, they form either liquid crystalline films or macroscopic cables. In both cases, the columnar structures are photoconductive and form p-type, hole- transporting materials in field effect transistor devices. This columnar motif is robust, allowing us to form monolayers of these columns attached to the surface of dielectrics such as silicon oxide. We use ultrathin point contacts made from individual single-walled carbon nanotubes that are separated by a few nanometers to probe the electronic properties of short stacks of a few contorted discs. We find that these materials have high mobility and can sense electron-deficient aromatic molecules. The concave surfaces of these disc-shaped contorted molecules form ideal receptors for the molecular recognition and assembly with spherical molecules such as fullerenes. These interfaces resemble ball-and-socket joints, where the fullerene nests itself in the concave surface of the contorted disc. The tightness of the binding between the two partners can be

  16. Contorted polycyclic aromatics.

    PubMed

    Ball, Melissa; Zhong, Yu; Wu, Ying; Schenck, Christine; Ng, Fay; Steigerwald, Michael; Xiao, Shengxiong; Nuckolls, Colin

    2015-02-17

    CONSPECTUS: This Account describes a body of research in the design, synthesis, and assembly of molecular materials made from strained polycyclic aromatic molecules. The strain in the molecular subunits severely distorts the aromatic molecules away from planarity. We coined the term "contorted aromatics" to describe this class of molecules. Using these molecules, we demonstrate that the curved pi-surfaces are useful as subunits to make self-assembled electronic materials. We have created and continue to study two broad classes of these "contorted aromatics": discs and ribbons. The figure that accompanies this conspectus displays the three-dimensional surfaces of a selection of these "contorted aromatics". The disc-shaped contorted molecules have well-defined conformations that create concave pi-surfaces. When these disc-shaped molecules are substituted with hydrocarbon side chains, they self-assemble into columnar superstructures. Depending on the hydrocarbon substitution, they form either liquid crystalline films or macroscopic cables. In both cases, the columnar structures are photoconductive and form p-type, hole- transporting materials in field effect transistor devices. This columnar motif is robust, allowing us to form monolayers of these columns attached to the surface of dielectrics such as silicon oxide. We use ultrathin point contacts made from individual single-walled carbon nanotubes that are separated by a few nanometers to probe the electronic properties of short stacks of a few contorted discs. We find that these materials have high mobility and can sense electron-deficient aromatic molecules. The concave surfaces of these disc-shaped contorted molecules form ideal receptors for the molecular recognition and assembly with spherical molecules such as fullerenes. These interfaces resemble ball-and-socket joints, where the fullerene nests itself in the concave surface of the contorted disc. The tightness of the binding between the two partners can be

  17. Metavanadate at the active site of the phosphatase VHZ.

    PubMed

    Kuznetsov, Vyacheslav I; Alexandrova, Anastassia N; Hengge, Alvan C

    2012-09-01

    Vanadate is a potent modulator of a number of biological processes and has been shown by crystal structures and NMR spectroscopy to interact with numerous enzymes. Although these effects often occur under conditions where oligomeric forms dominate, the crystal structures and NMR data suggest that the inhibitory form is usually monomeric orthovanadate, a particularly good inhibitor of phosphatases because of its ability to form stable trigonal-bipyramidal complexes. We performed a computational analysis of a 1.14 Å structure of the phosphatase VHZ in complex with an unusual metavanadate species and compared it with two classical trigonal-bipyramidal vanadate-phosphatase complexes. The results support extensive delocalized bonding to the apical ligands in the classical structures. In contrast, in the VHZ metavanadate complex, the central, planar VO(3)(-) moiety has only one apical ligand, the nucleophilic Cys95, and a gap in electron density between V and S. A computational analysis showed that the V-S interaction is primarily ionic. A mechanism is proposed to explain the formation of metavanadate in the active site from a dimeric vanadate species that previous crystallographic evidence has shown to be able to bind to the active sites of phosphatases related to VHZ. Together, the results show that the interaction of vanadate with biological systems is not solely reliant upon the prior formation of a particular inhibitory form in solution. The catalytic properties of an enzyme may act upon the oligomeric forms primarily present in solution to generate species such as the metavanadate ion observed in the VHZ structure. PMID:22876963

  18. Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease*

    PubMed Central

    da Palma, Joel Ramos; Burri, Dominique Julien; Oppliger, Joël; Salamina, Marco; Cendron, Laura; de Laureto, Patrizia Polverino; Seidah, Nabil Georges; Kunz, Stefan; Pasquato, Antonella

    2014-01-01

    The proprotein convertase subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P) plays crucial roles in cellular homeostatic functions and is hijacked by pathogenic viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P involves sequential autocatalytic processing of its N-terminal prodomain at sites B′/B followed by the herein newly identified C′/C sites. We found that SKI-1/S1P autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. In contrast to other zymogen proprotein convertases, all incompletely matured intermediates of SKI-1/S1P showed full catalytic activity toward cellular substrates, whereas optimal cleavage of viral glycoproteins depended on B′/B processing. Incompletely matured forms of SKI-1/S1P further process cellular and viral substrates in distinct subcellular compartments. Using a cell-based sensor for SKI-1/S1P activity, we found that 9 amino acid residues at the cleavage site (P1–P8) and P1′ are necessary and sufficient to define the subcellular location of processing and to determine to what extent processing of a substrate depends on SKI-1/S1P maturation. In sum, our study reveals novel and unexpected features of SKI-1/S1P zymogen activation and subcellular specificity of activity toward cellular and pathogen-derived substrates. PMID:25378398

  19. Implications of binding mode and active site flexibility for inhibitor potency against the salicylate synthase from Mycobacterium tuberculosis.

    PubMed

    Chi, Gamma; Manos-Turvey, Alexandra; O'Connor, Patrick D; Johnston, Jodie M; Evans, Genevieve L; Baker, Edward N; Payne, Richard J; Lott, J Shaun; Bulloch, Esther M M

    2012-06-19

    MbtI is the salicylate synthase that catalyzes the first committed step in the synthesis of the iron chelating compound mycobactin in Mycobacterium tuberculosis. We previously developed a series of aromatic inhibitors against MbtI based on the reaction intermediate for this enzyme, isochorismate. The most potent of these inhibitors had hydrophobic substituents, ranging in size from a methyl to a phenyl group, appended to the terminal alkene of the enolpyruvyl group. These compounds exhibited low micromolar inhibition constants against MbtI and were at least an order of magnitude more potent than the parental compound for the series, which carries a native enolpyruvyl group. In this study, we sought to understand how the substituted enolpyruvyl group confers greater potency, by determining cocrystal structures of MbtI with six inhibitors from the series. A switch in binding mode at the MbtI active site is observed for inhibitors carrying a substituted enolpyruvyl group, relative to the parental compound. Computational studies suggest that the change in binding mode, and higher potency, is due to the effect of the substituents on the conformational landscape of the core inhibitor structure. The crystal structures and fluorescence-based thermal shift assays indicate that substituents larger than a methyl group are accommodated in the MbtI active site through significant but localized flexibility in the peptide backbone. These findings have implications for the design of improved inhibitors of MbtI, as well as other chorismate-utilizing enzymes from this family. PMID:22607697

  20. Site-specific PEGylation of lidamycin and its antitumor activity.

    PubMed

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-05-01

    In this study, N-terminal site-specific mono-PEGylation of the recombinant lidamycin apoprotein (rLDP) of lidamycin (LDM) was prepared using a polyethyleneglycol (PEG) derivative (M w 20 kDa) through a reactive terminal aldehyde group under weak acidic conditions (pH 5.5). The biochemical properties of mPEG-rLDP-AE, an enediyne-integrated conjugate, were analyzed by SDS-PAGE, RP-HPLC, SEC-HPLC and MALDI-TOF. Meanwhile, in vitro and in vivo antitumor activity of mPEG-rLDP-AE was evaluated by MTT assays and in xenograft model. The results indicated that mPEG-rLDP-AE showed significant antitumor activity both in vitro and in vivo. After PEGylation, mPEG-rLDP still retained the binding capability to the enediyne AE and presented the physicochemical characteristics similar to that of native LDP. It is of interest that the PEGylation did not diminish the antitumor efficacy of LDM, implying the possibility that this derivative may function as a payload to deliver novel tumor-targeted drugs. PMID:26579455

  1. Differentiation of regioisomeric aromatic ketocarboxylic acids by positive mode atmospheric pressure chemical ionization collision-activated dissociation tandem mass spectrometry in a linear quadrupole ion trap mass spectrometer.

    PubMed

    Amundson, Lucas M; Owen, Benjamin C; Gallardo, Vanessa A; Habicht, Steven C; Fu, Mingkun; Shea, Ryan C; Mossman, Allen B; Kenttämaa, Hilkka I

    2011-04-01

    Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS(n)) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at different collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.

  2. Structure-activity relationship of genotoxic polycyclic aromatic nitro compounds: Further evidence for the importance of hydrophobicity and molecular orbital energies in genetic toxicity

    SciTech Connect

    Debnath, A.K.; Hansch, C. )

    1992-01-01

    A quantitative structure-activity relationship (QSAR) has been formulated for 15 polycyclic aromatic nitro compounds acting on E. coli PQ37. Upon damage of DNA by these substances [beta]-galactosidase is induced and can be easily assayed colorimetrically, hence, this is a short-term test for mutagenicity. The QSAR (log SOSIP = 1.07 log P - 1.57 e[sub LUMO] - 6.41) is strikingly similar to that found earlier with nitroaromatics acting in the Ames test (TA100) and differs significantly for that found using TA98 organisms. The QSAR brings out in a unique manner the underlying similarity in the two test systems. 24 refs., 2 tabs.

  3. Intramolecular CH Activation and Metallacycle Aromaticity in the Photochemistry of [FeFe]-Hydrogenase Model Compounds in Low-Temperature Frozen Matrices.

    PubMed

    Thornley, Wyatt A; Bitterwolf, Thomas E

    2015-12-01

    The [FeFe]-hydrogenase model complexes [(μ-pdt){Fe(CO)3 }2 ], [(μ-edt){Fe(CO)3 }2 ], and [(μ-mdt){Fe(CO)3 }2 ], where pdt=1,3-propanedithiolate, edt=1,2-ethanedithiolate, and mdt=methanedithiolate, undergo wavelength dependent photodecarbonylation in hydrocarbon matrices at 85 K resulting in multiple decarbonylation isomers. As previously reported in time-resolved solution photolysis experiments, the major photoproduct is attributed to a basal carbonyl-loss species. Apical carbonyl-loss isomers are also generated and may undergo secondary photolysis, resulting in β-hydride activation of the alkyldithiolate bridge, as well as formation of bridging carbonyl isomers. For [(μ-bdt){Fe(CO)3 }2 ], (bdt=1,2-benzenedithiolate), apical photodecarbonylation results in generation of a 10 π-electron aromatic FeS2 C6 H4 metallacycle that coordinates the remaining iron through an η(5) mode.

  4. Synthesis of tetra- and octa-aurated heteroaryl complexes towards probing aromatic indoliums

    PubMed Central

    Yuan, Jun; Sun, Tingting; He, Xin; An, Ke; Zhu, Jun; Zhao, Liang

    2016-01-01

    Polymetalated aromatic compounds are particularly challenging synthetic goals because of the limited thermodynamic stability of polyanionic species arising from strong electrostatic repulsion between adjacent carbanionic sites. Here we describe a facile synthesis of two polyaurated complexes including a tetra-aurated indole and an octa-aurated benzodipyrrole. The imido trinuclear gold(I) moiety exhibits nucleophilicity and undergoes an intramolecular attack on a gold(I)-activated ethynyl to generate polyanionic heteroaryl species. Their computed magnetic properties reveal the aromatic character in the five-membered ring. The incorporation of the aurated substituents at the nitrogen atom can convert non-aromaticity in the parent indolium into aromaticity in the aurated one because of hyperconjugation. Thus, the concept of hyperconjugative aromaticity is extended to heterocycles with transition metal substituents. More importantly, further analysis indicates that the aurated substituents can perform better than traditional main-group substituents. This work highlights the difference in aromaticity between polymetalated aryls and their organic prototypes. PMID:27186982

  5. X-ray structure of human aromatase reveals an androgen-specific active site.

    PubMed

    Ghosh, Debashis; Griswold, Jennifer; Erman, Mary; Pangborn, Walter

    2010-02-28

    Aromatase is a unique cytochrome P450 that catalyzes the removal of the 19-methyl group and aromatization of the A-ring of androgens for the synthesis of estrogens. All human estrogens are synthesized via this enzymatic aromatization pathway. Aromatase inhibitors thus constitute a frontline therapy for estrogen-dependent breast cancer. Despite decades of intense investigation, this enzyme of the endoplasmic reticulum membrane has eluded all structure determination efforts. We have determined the crystal structure of the highly active aromatase purified from human placenta, in complex with its natural substrate androstenedione. The structure shows the binding mode of androstenedione in the catalytically active oxidized high-spin ferric state of the enzyme. Hydrogen bond-forming interactions and tight packing hydrophobic side chains that complement the puckering of the steroid backbone provide the molecular basis for the exclusive androgenic specificity of aromatase. Locations of catalytic residues and water molecules shed new light on the mechanism of the aromatization step. The structure also suggests a membrane integration model indicative of the passage of steroids through the lipid bilayer.

  6. Hybrid [FeFe]-hydrogenases with modified active sites show remarkable residual enzymatic activity.

    PubMed

    Siebel, Judith F; Adamska-Venkatesh, Agnieszka; Weber, Katharina; Rumpel, Sigrun; Reijerse, Edward; Lubitz, Wolfgang

    2015-02-24

    [FeFe]-hydrogenases are to date the only enzymes for which it has been demonstrated that the native inorganic binuclear cofactor of the active site Fe2(adt)(CO)3(CN)2 (adt = azadithiolate = [S-CH2-NH-CH2-S](2-)) can be synthesized on the laboratory bench and subsequently inserted into the unmaturated enzyme to yield fully functional holo-enzyme (Berggren, G. et al. (2013) Nature 499, 66-70; Esselborn, J. et al. (2013) Nat. Chem. Biol. 9, 607-610). In the current study, we exploit this procedure to introduce non-native cofactors into the enzyme. Mimics of the binuclear subcluster with a modified bridging dithiolate ligand (thiodithiolate, N-methylazadithiolate, dimethyl-azadithiolate) and three variants containing only one CN(-) ligand were inserted into the active site of the enzyme. We investigated the activity of these variants for hydrogen oxidation as well as proton reduction and their structural accommodation within the active site was analyzed using Fourier transform infrared spectroscopy. Interestingly, the monocyanide variant with the azadithiolate bridge showed ∼50% of the native enzyme activity. This would suggest that the CN(-) ligands are not essential for catalytic activity, but rather serve to anchor the binuclear subsite inside the protein pocket through hydrogen bonding. The inserted artificial cofactors with a propanedithiolate and an N-methylazadithiolate bridge as well as their monocyanide variants also showed residual activity. However, these activities were less than 1% of the native enzyme. Our findings indicate that even small changes in the dithiolate bridge of the binuclear subsite lead to a rather strong decrease of the catalytic activity. We conclude that both the Brønsted base function and the conformational flexibility of the native azadithiolate amine moiety are essential for the high catalytic activity of the native enzyme. PMID:25633077

  7. Heterogeneous photocatalytic reactions of sulfur aromatic compounds.

    PubMed

    Samokhvalov, Alexander

    2011-11-18

    Sulfur aromatic compounds, such as mono-, di-, tri-, and tetraalkyl-substituted thiophene, benzothiophenes, dibenzothiophenes, are the molecular components of many fossils (petroleum, oil shale, tar sands, bitumen). Structural units of natural, cross-linked heteroaromatic polymers present in brown coals, turf, and soil are similar to those of sulfur aromatic compounds. Many sulfur aromatic compounds are found in the streams of petroleum refining and upgrading (naphthas, gas oils) and in the consumer products (gasoline, diesel, jet fuels, heating fuels). Besides fossils, the structural fragments of sulfur aromatic compounds are present in molecules of certain organic semiconductors, pesticides, small molecule drugs, and in certain biomolecules present in human body (pheomelanin pigments). Photocatalysis is the frontier area of physical chemistry that studies chemical reactions initiated by absorption of photons by photocatalysts, that is, upon electronic rather than thermal activation, under "green" ambient conditions. This review provides systematization and critical review of the fundamental chemical and physicochemical information on heterogeneous photocatalysis of sulfur aromatic compounds accumulated in the last 20-30 years. Specifically, the following topics are covered: physicochemical properties of sulfur aromatic compounds, major classes of heterogeneous photocatalysts, mechanisms and reactive intermediates of photocatalytic reactions of sulfur aromatic compounds, and the selectivity of these reactions. Quantum chemical calculations of properties and structures of sulfur aromatic compounds, their reactive intermediates, and the structure of adsorption complexes formed on the surface of the photocatalysts are also discussed.

  8. The presence and distribution of polycyclic aromatic hydrocarbons and inorganic elements in water and lakebed materials and the potential for bioconcentration in biota at established sampling sites on Lake Powell, Utah and Arizona

    USGS Publications Warehouse

    Schonauer, Kurt T.; Hart, Robert J.; Antweiler, Ronald C.

    2014-01-01

    The National Park Service is responsible for monitoring the effects of visitor use on the quality of water, lakebed material (bottom sediments), and biota, in Lake Powell, Utah and Arizona. A sampling program was begun in 2010 to assess the presence, distribution, and concentrations of organic and inorganic compounds in the water column and bottom sediment. In response to an Environmental Impact Statement regarding personal watercraft and as a continuation from previous studies by the U.S. Geological Survey and the National Park Service, Glen Canyon National Recreation Area, water samples were collected and analyzed for polycyclic aromatic hydrocarbons (PAHs) using semipermeable membrane devices and inorganic elements using a fixed-bottle sampler deployed at established monitoring sites during 2010 and 2011. Lakebed material samples were also analyzed for polycyclic aromatic hydrocarbons and inorganic elements, some of which could be harmful to aquatic biota if present at concentrations above established aquatic life criteria. Of the 44 PAH compounds analyzed, 26 individual compounds were detected above the censoring limit in the water column by semipermeable membrane devices. The highest number of compounds detected were at Lone Rock Beach, Wahweap Marina, Rainbow Bridge National Monument, and Antelope Marina which are all located in the southern part of Lake Powell where visitation and boat use is high. Because PAHs can remain near their source, the potential for bioconcentration is highest near these sites. The PAH compound found in the highest concentration was phenol (5,902 nanograms per liter), which is included in the U.S. Environmental Protection Agency’s priority pollutants list. The dissolved inorganic chemistry of water samples measured at the sampling sites in Lake Powell defined three different patterns of elements: (1) concentrations were similar between sites in the upper part of the lake near Farley Canyon downstream to Halls Crossing Marina, a

  9. Extreme Modulation Properties of Aromatic Fluorine

    SciTech Connect

    Burnett, Michael N; Gakh, Andrei A

    2011-01-01

    Thorough examination of the current literature as well as publicly available databases allowed us to qualify aromatic fluorine as a unique modulator of biological properties of organic compounds. In some rare cases, introduction of fluorine increased biological activity 100,000 times and even higher. We have also identified several examples where aromatic fluorine substantially reduced biological activity. Selected individual cases of extreme modulation are presented and discussed in the paper.

  10. A NOVEL METABOLIC ACTIVATION PATHWAY FOR POLYCYCLIC AROMATIC HYDROCARBONS: REACTIVE OXYGEN SPECIES-MEDIATED DNA DAMAGE AND MORPHOLOGICAL CELL TRANSFORMATION IN MOUSE EMBRYO CELLS BY K-REGION DIOL METABOLITES

    EPA Science Inventory

    Benzo[ a ]pyrene (BP) is a well-studied polycyclic aromatic hydrocarbon (P AH) .Many
    mechanisms have been suggested to explain its carcinogenic activity, yet many questions still
    remain. K-region dihydrodiols (diols) ofPAHs are common metabolites and some are genotoxic. W...

  11. Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification

    PubMed Central

    Keating, David H.; Zhang, Yaoping; Ong, Irene M.; McIlwain, Sean; Morales, Eduardo H.; Grass, Jeffrey A.; Tremaine, Mary; Bothfeld, William; Higbee, Alan; Ulbrich, Arne; Balloon, Allison J.; Westphall, Michael S.; Aldrich, Josh; Lipton, Mary S.; Kim, Joonhoon; Moskvin, Oleg V.; Bukhman, Yury V.; Coon, Joshua J.; Kiley, Patricia J.; Bates, Donna M.; Landick, Robert

    2014-01-01

    Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5-hydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts. PMID:25177315

  12. Characterization of the active site of chloroperoxidase using physical techniques

    SciTech Connect

    Hall, K.S.

    1986-01-01

    Chloroperoxidase (CPO) and Cytochrome P-450, two very different hemeproteins, have been shown to have similar active sites by several techniques. Recent work has demonstrated thiolate ligation from a cysteine residue to the iron in P-450. A major portion of this research has been devoted to obtaining direct evidence that CPO also has a thiolate 5th ligand from a cysteine residue. This information will provide the framework for a detailed analysis of the structure-function relationships between peroxidases, catalase and cytochrome P-450 hemeproteins. To determine whether the 5th ligand is a cysteine, methionine or a unique amino acid, specific isotope enrichment experiments were used. Preliminary /sup 1/H-NMR studies show that the carbon monoxide-CPO complex has a peak in the upfield region corresponding to alpha-protons of a thiolate amino acid. C. fumago was grown on 95% D/sub 2/O media with a small amount of /sup 1/H-cysteine added. Under these conditions C. fumago slows down the biosynthesis of cysteine by at least 50% and utilizes the exogenous cysteine in the media. GC-MS was able to show that the methylene protons next to the sulfur atom in cysteine are 80-90% protonated while these positions in methionine are approximately 73% deuterated. Comparison of the /sup 1/H-NMR spectra of CO-CPO and CO-CPO indicate the presence of a cysteine ligand in chloroperoxidase.

  13. N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

    PubMed Central

    Chen, Kai; Deng, Xin; Yu, Miao; Han, Dali; Hao, Ziyang; Liu, Jianzhao; Lu, Xingyu; Dore, Louis C; Weng, Xiaocheng; Ji, Quanjiang; Mets, Laurens; He, Chuan

    2015-01-01

    SUMMARY N6-methyldeoxyadenosine (6mA or m6A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria, and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution, and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms. PMID:25936837

  14. Detection limit for activation measurements in ultralow background sites

    NASA Astrophysics Data System (ADS)

    Trache, Livius; Chesneanu, D.; Margineanu, R.; Pantelica, A.; Ghita, D. G.; Burducea, I.; Straticiuc, M.; Tang, X. D.

    2014-09-01

    We used 12C +13C fusion at the beam energies E = 6, 7 and 8 MeV to determine the sensitivity and the limits of activation method measurements in ultralow background sites. A 13C beam of 0.5 μA from the 3 MV Tandem accelerator of the Horia Hulubei National Institute of Physics and Nuclear Engineering - IFIN HH impinged on thick graphite targets. After about 24 hrs of irradiation targets were measured in two different laboratories: one with a heavy shielded Ge detector in the institute (at the surface) and one located underground in the microBequerel laboratory, in the salt mine of Slanic-Prahova, Romania. The 1369- and 2754 keV peaks from 24Na deactivation were clearly observed in the γ-ray spectra obtained for acquisitions lasting a few hours, or a few days. Determination of the detection limit in evaluating the cross sections for the target irradiated at Ec . m = 3 MeV indicates the fact that it is possible to measure gamma spectrum in underground laboratory down to Ec . m = 2 . 6 MeV. Cleaning the spectra with beta-gamma coincidences and increasing beam intensity 20 times will take as further down. The measurements are motivated by the study of the 12 C +12 C reaction at astrophysical energies.

  15. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    PubMed

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems. PMID:25727891

  16. Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

    PubMed

    Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

    2016-09-01

    A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

  17. A proposed definition of the 'activity' of surface sites on lactose carriers for dry powder inhalation.

    PubMed

    Grasmeijer, Floris; Frijlink, Henderik W; de Boer, Anne H

    2014-06-01

    A new definition of the activity of surface sites on lactose carriers for dry powder inhalation is proposed which relates to drug detachment during dispersion. The new definition is expected to improve the understanding of 'carrier surface site activity', which stimulates the unambiguous communication about this subject and may aid in the rational design and interpretation of future formulation studies. In contrast to the currently prevailing view on carrier surface site activity, it follows from the newly proposed definition that carrier surface site activity depends on more variables than just the physicochemical properties of the carrier surface. Because the term 'active sites' is ambiguous, it is recommended to use the term 'highly active sites' instead to denote carrier surface sites with a relatively high activity. PMID:24613490

  18. Potent Reversible Inhibition of Myeloperoxidase by Aromatic Hydroxamates*

    PubMed Central

    Forbes, Louisa V.; Sjögren, Tove; Auchère, Françoise; Jenkins, David W.; Thong, Bob; Laughton, David; Hemsley, Paul; Pairaudeau, Garry; Turner, Rufus; Eriksson, Håkan; Unitt, John F.; Kettle, Anthony J.

    2013-01-01

    The neutrophil enzyme myeloperoxidase (MPO) promotes oxidative stress in numerous inflammatory pathologies by producing hypohalous acids. Its inadvertent activity is a prime target for pharmacological control. Previously, salicylhydroxamic acid was reported to be a weak reversible inhibitor of MPO. We aimed to identify related hydroxamates that are good inhibitors of the enzyme. We report on three hydroxamates as the first potent reversible inhibitors of MPO. The chlorination activity of purified MPO was inhibited by 50% by a 5 nm concentration of a trifluoromethyl-substituted aromatic hydroxamate, HX1. The hydroxamates were specific for MPO in neutrophils and more potent toward MPO compared with a broad range of redox enzymes and alternative targets. Surface plasmon resonance measurements showed that the strength of binding of hydroxamates to MPO correlated with the degree of enzyme inhibition. The crystal structure of MPO-HX1 revealed that the inhibitor was bound within the active site cavity above the heme and blocked the substrate channel. HX1 was a mixed-type inhibitor of the halogenation activity of MPO with respect to both hydrogen peroxide and halide. Spectral analyses demonstrated that hydroxamates can act variably as substrates for MPO and convert the enzyme to a nitrosyl ferrous intermediate. This property was unrelated to their ability to inhibit MPO. We propose that aromatic hydroxamates bind tightly to the active site of MPO and prevent it from producing hypohalous acids. This mode of reversible inhibition has potential for blocking the activity of MPO and limiting oxidative stress during inflammation. PMID:24194519

  19. One-year study of polycyclic aromatic compounds at an urban site in Grenoble (France): Seasonal variations, gas/particle partitioning and cancer risk estimation.

    PubMed

    Tomaz, Sophie; Shahpoury, Pourya; Jaffrezo, Jean-Luc; Lammel, Gerhard; Perraudin, Emilie; Villenave, Eric; Albinet, Alexandre

    2016-09-15

    21 PAHs, 27 oxy-PAHs and 32 nitro-PAHs were measured every third day over a year in both gaseous (G) and particulate PM10 (P) phases in ambient air of Grenoble (France). Mean total concentrations (G+P) of PAHs and oxy-PAHs were in the same range and about 10ngm(-3). Nitro-PAHs were 50 to 100 times less concentrated averaging 100pgm(-3). Polycyclic aromatic compound (PAC) concentrations were 5 to 7 times higher in "cold" period (October to March) than in "warm" period (April to September). Seasonal variations may be explained by higher primary emissions from residential heating, especially biomass burning in "cold" season. Meteorological conditions and influence of the geomorphology around Grenoble, with the formation of thermal inversion layers leading to the stagnation of pollutants, were additional key parameters. Maximum individual PAC concentrations were observed during two PM10 pollution events in December and February-March. Chemical processes and secondary formation of oxy- and nitro-PAH were probably enhanced by the accumulation of the pollutants during these events. PAC gas/particle partitioning depended on compound molecular weight and vapour pressure. Gas/particle partitioning of oxy- and nitro-PAHs were evaluated using a multi-phase poly-parameter linear free energy relationship model. The PAC cancer risk was assessed using toxic equivalency factors available in the literature (19 PAHs, 10 nitro-PAHs and 1 oxy-PAH). Overall, particle-bound PACs contributed about 76% of the cancer risk. While PAHs accounted for most of the total PAC cancer risk, oxy- and nitro-PAHs could account for up to 24%. The risk quantification across substance classes is limited by toxicological data availability.

  20. One-year study of polycyclic aromatic compounds at an urban site in Grenoble (France): Seasonal variations, gas/particle partitioning and cancer risk estimation.

    PubMed

    Tomaz, Sophie; Shahpoury, Pourya; Jaffrezo, Jean-Luc; Lammel, Gerhard; Perraudin, Emilie; Villenave, Eric; Albinet, Alexandre

    2016-09-15

    21 PAHs, 27 oxy-PAHs and 32 nitro-PAHs were measured every third day over a year in both gaseous (G) and particulate PM10 (P) phases in ambient air of Grenoble (France). Mean total concentrations (G+P) of PAHs and oxy-PAHs were in the same range and about 10ngm(-3). Nitro-PAHs were 50 to 100 times less concentrated averaging 100pgm(-3). Polycyclic aromatic compound (PAC) concentrations were 5 to 7 times higher in "cold" period (October to March) than in "warm" period (April to September). Seasonal variations may be explained by higher primary emissions from residential heating, especially biomass burning in "cold" season. Meteorological conditions and influence of the geomorphology around Grenoble, with the formation of thermal inversion layers leading to the stagnation of pollutants, were additional key parameters. Maximum individual PAC concentrations were observed during two PM10 pollution events in December and February-March. Chemical processes and secondary formation of oxy- and nitro-PAH were probably enhanced by the accumulation of the pollutants during these events. PAC gas/particle partitioning depended on compound molecular weight and vapour pressure. Gas/particle partitioning of oxy- and nitro-PAHs were evaluated using a multi-phase poly-parameter linear free energy relationship model. The PAC cancer risk was assessed using toxic equivalency factors available in the literature (19 PAHs, 10 nitro-PAHs and 1 oxy-PAH). Overall, particle-bound PACs contributed about 76% of the cancer risk. While PAHs accounted for most of the total PAC cancer risk, oxy- and nitro-PAHs could account for up to 24%. The risk quantification across substance classes is limited by toxicological data availability. PMID:27261422

  1. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  2. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  3. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  4. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  5. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  6. Modulation of aromatic amine mutagenicity in Salmonella typhimurium with rat-liver 9000 g supernatant or monolayers of rat hepatocytes as an activation system.

    PubMed

    Holme, J A; Haug, L T; Dybing, E

    1983-04-01

    2-Aminofluorene (AF), 2-acetylaminofluorene (AAF) and N-hydroxy-2-acetylaminofluorene (N-OH-AAF) were studied for mutagenic activity in S. typhimurium and either liver 9000 g supernatant fractions (S9) or monolayer cultures of hepatocytes isolated from Wistar rats were used as an activation system. All 3 compounds were converted into mutagens excreted into the incubation medium by the cell-culture system, with N-OH-AAF greater than AF greater than AAF. Cultures used 24 h after plating were less efficient in promutagen conversion than were cultures used after 2 h. Phenobarbital, but not 3-methylcholanthrene, pretreatment of the rats caused similar effects on AF, AAF and N-OH-AAF mutagenicity with both S9 and hepatocyte cultures. The mutagenicities of AF and AAF were reduced by the cytochrome-P-450 inhibitors metyrapone and alpha-naphthoflavone, whereas the mutagenicity of N-OH-AAF was increased by using both inhibitors. Further, the microsomal deacetylase inhibitor paraoxon caused only a moderate reduction in N-OH-AAF mutagenicity, but a total inhibition of AAF mutagenicity. No significant effect of paraoxon on AF mutagenicity was seen. With the S9 system, no effect of ascorbate on the mutagenicity of AF, AAF or N-OH-AAF was observed. In contrast, the mutagenicity of all 3 compounds was increased by ascorbate when hepatocyte cultures were used as activation system. Incubation of hepatocyte monolayers in a sulfate-free medium did not change the mutagenicity of AF, AAF or N-OH-AAF. Galactosamine, an inhibitor of glucuronidation in cells, increased the mutagenicity of AF, AAF and N-OH-AAF with hepatocyte cultures. The addition of cofactor for glucuronidation in the S9 system, however, had no effect. A reduction in mutagenicity of AF and AAF, but not that of N-OH-AAF, was observed with the addition of glutathione (GSH) in both the S9 and the hepatocyte systems. On the other hand, no effect of cellular GSH depletion was seen on aromatic-amine mutagenicity in the

  7. Quantitative structure-activity relationship investigation of the role of hydrophobicity in regulating mutagenicity in the Ames test: 2. Mutagenicity of aromatic and heteroaromatic nitro compounds in Salmonella typhimurium TA100

    SciTech Connect

    Debnath, A.K.; Hansch, C. ); Shusterman, A.J. ); Lopez de Compadre, R.L. )

    1992-01-01

    A quantitative structure-activity relationship (QSAR) has been derived for the mutagenic activity of 117 aromatic and heteroaromatic nitro compounds acting on Salmonella typhimurium TA100. Relative mutagenic activity is bilinearly dependent on hydrophobicity, with an optimal log P of 5.44, and is linearly dependent on the energy of the lowest unoccupied molecular orbital of the nitro compound. The dependence of mutagenic activity on hydrophobicity and electronic effects is very similar for TA98 and TA100. Mutagenic activity in TA100 does not depend on the size of the aromatic ring system, as it does in TA98. The effect of the choice of assay organism, TA98 versus TA100, on nitroarene QSAR is seen to be similar to the effect previously found for aminoarenes. Lateral verification of QSARs is presented as a tool for establishing the significance of a new QSAR.

  8. Selective Aromatic C–H Hydroxylation Enabled by η6-Coordination to Iridium(III)

    PubMed Central

    D'Amato, Erica M.; Neumann, Constanze N.; Ritter, Tobias

    2016-01-01

    We report an aromatic C–H hydroxylation protocol in which the arene is activated through η6-coordination to an iridium(III) complex. η6-Coordination of the arene increases its electrophilicity and allows for high positional selectivity of hydroxylation at the site of least electron density. Through investigation of intermediate η5-cyclohexadienyl adducts and arene exchange reactions, we evaluate incorporation of arene π-activation into a catalytic cycle for C–H functionalization. PMID:26877574

  9. GAS HYDRATES AT TWO SITES OF AN ACTIVE CONTINENTAL MARGIN.

    USGS Publications Warehouse

    Kvenvolden, K.A.

    1985-01-01

    Sediment containing gas hydrates from two distant Deep Sea Drilling Project sites (565 and 568), located about 670 km apart on the landward flank of the Middle America Trench, was studied to determine the geochemical conditions that characterize the occurrence of gas hydrates. Site 565 was located in the Pacific Ocean offshore the Nicoya Peninsula of Costa Rica in 3,111 m of water. The depth of the hole at this site was 328 m, and gas hydrates were recovered from 285 and 319 m. Site 568 was located about 670 km to the northwest offshore Guatemala in 2,031 m of water. At this site the hole penetrated to 418 m, and gas hydrates were encountered at 404 m.

  10. Control of active sites in selective flocculation: III -- Mechanism of site blocking

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    It has been shown in Parts I and II of this paper that heteroflocculation can be controlled by poisoning the sites for flocculant adsorption using a site blocking agent (SBA). An efficient SBA was determined to be the lower molecular weight fraction of the flocculant. In this paper, the underlying mechanism of SBA action is described. Also, the mathematical model detailed in Part I is used to determine the effect of different SBAs on apatite-dolomite separation efficiency. It has been demonstrated that the depression in flocculation is directly related to the site blocking parameter ([bar [Phi

  11. Dynamically achieved active site precision in enzyme catalysis.

    PubMed

    Klinman, Judith P

    2015-02-17

    CONSPECTUS: The grand challenge in enzymology is to define and understand all of the parameters that contribute to enzymes' enormous rate accelerations. The property of hydrogen tunneling in enzyme reactions has moved the focus of research away from an exclusive focus on transition state stabilization toward the importance of the motions of the heavy atoms of the protein, a role for reduced barrier width in catalysis, and the sampling of a protein conformational landscape to achieve a family of protein substates that optimize enzyme-substrate interactions and beyond. This Account focuses on a thermophilic alcohol dehydrogenase for which the chemical step of hydride transfer is rate determining across a wide range of experimental conditions. The properties of the chemical coordinate have been probed using kinetic isotope effects, indicating a transition in behavior below 30 °C that distinguishes nonoptimal from optimal C-H activation. Further, the introduction of single site mutants has the impact of either enhancing or eliminating the temperature dependent transition in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium exchange and fluorescent lifetimes and Stokes shifts, have also been pursued. These studies allow the correlation of spatially resolved transitions in protein motions with catalysis. It is now possible to define a long-range network of protein motions in ht-ADH that extends from a dimer interface to the substrate binding domain across to the cofactor binding domain, over a distance of ca. 30 Å. The ongoing challenge to obtaining spatial and temporal resolution of catalysis-linked protein motions is discussed.

  12. Lethal Factor Active-Site Mutations Affect Catalytic Activity In Vitro

    PubMed Central

    Hammond, S. E.; Hanna, P. C.

    1998-01-01

    The lethal factor (LF) protein of Bacillus anthracis lethal toxin contains the thermolysin-like active-site and zinc-binding consensus motif HEXXH (K. R. Klimpel, N. Arora, and S. H. Leppla, Mol. Microbiol. 13:1093–1100, 1994). LF is hypothesized to act as a Zn2+ metalloprotease in the cytoplasm of macrophages, but no proteolytic activities have been previously shown on any target substrate. Here, synthetic peptides are hydrolyzed by LF in vitro. Mass spectroscopy and peptide sequencing of isolated cleavage products separated by reverse-phase high-pressure liquid chromatography indicate that LF seems to prefer proline-containing substrates. Substitution mutations within the consensus active-site residues completely abolish all in vitro catalytic functions, as does addition of 1,10-phenanthroline, EDTA, and certain amino acid hydroxamates, including the novel zinc metalloprotease inhibitor ZINCOV. In contrast, the protease inhibitors bestatin and lysine CMK, previously shown to block LF activity on macrophages, did not block LF activity in vitro. These data provide the first direct evidence that LF may act as an endopeptidase. PMID:9573135

  13. Monoclonal antibody against the active site of caeruloplasmin and the ELISA system detecting active caeruloplasmin.

    PubMed

    Hiyamuta, S; Ito, K

    1994-04-01

    Serum caeruloplasmin deficiency is a characteristic biochemical abnormality found in patients with Wilson's disease, but the mechanism of this disease is unknown. Although the phenylenediamine oxidase activity of serum caeruloplasmin is markedly low in patients with Wilson's disease, mRNA of caeruloplasmin exists to some extent. To investigate the deficiency of caeruloplasmin oxidase activity in Wilson's disease, we generated 14 monoclonal antibodies (MAbs) and selected ID1, which had the strongest reactivity, and ID2, which had neutralizing ability. We also established a system to measure active caeruloplasmin specifically using these MAbs. These MAbs and the system will be useful tools in analyzing the active site of caeruloplasmin in patients with Wilson's disease.

  14. Atmospheric Concentrations, Gas/Particle Partitioning And Exposure Risk Of Polycyclic Aromatic Hydrocarbons (PAHs) At Background, Rural Village And Urban Sites In The North China Plain

    NASA Astrophysics Data System (ADS)

    Wang, W.; Simonich, S.; Zhao, J.; Xue, M.; Wang, W.; Tao, S.

    2009-05-01

    Particle- and gas-phase PAHs were measured in air collected from a background site (Xiaolongmen), two rural village sites (Gubeikou and Donghe), and an urban site (Beijing) located in the North China Plain for four seasons from September 2007 to August 2008 in order to evaluate their concentrations, relative abundance, and gas/particle partitioning. Sixteen PAHs, included in the U.S.EPA priority pollutant list, were determined in the particle (PM10) and gas phases. The annual average 15 PAH concentration in Donghe was 730.7±608.0 ng/m3, which was 18.2, 3.0, 1.8 times higher than Xiaolongmen, Gubeikou and Beijing, respectively. A good linear relationship between gas/particle partitioning coefficients, Kp and subcooled liquid vapor pressure, pl was obtained. At the rural and urban sites, the regression slopes were much steeper than -1, indicating that adsorption of PAH to particulate matter dominated over absorption possibly because, at these sites, the freshly emitted particulate matter and PAHs had not yet reached equilibrium. However, gas/particle partitioning of PAHs approached equilibrium at the background site because of long- range transport of PAHs. In addition, the gas/particle partitioning was studied according to three different models: The Junge-Pankow adsorption model, the Koa absorption model, and the dual organic matter absorption model combined with the soot carbon adsorption model. The Junge-Pankow model and Koa model both under-predicted our experimental Kp values. However, the dual model fit our experimental Kp values well suggesting that the main partitioning mechanism was PAH adsorption onto soot carbon in this region of China. The different particulate matter characteristics (including organic matter and elemental carbon fraction and available adsorption sites), temperature variation during sampling, the presence of a non- exchangeable PAH fraction and non-equilibrium were considered possible reasons for why our experimental Kp values deviated

  15. Stochastic fuzzy environmental risk characterization of uncertainty and variability in risk assessments: A case study of polycyclic aromatic hydrocarbons in soil at a petroleum-contaminated site in China.

    PubMed

    Hu, Yan; Wang, Zesen; Wen, Jingya; Li, Yu

    2016-10-01

    Better decisions are made using risk assessment models when uncertainty and variability are explicitly acknowledged. Uncertainty caused by a lack of uniform and scientifically supported environmental quality guidelines and variability in the degree of exposure of environmental systems to contaminants are here incorporated in a stochastic fuzzy environmental risk characterization (SFERC) approach. The approach is based on quotient probability distribution and environmental risk level fuzzy membership function methods. The SFERC framework was used to characterize the environmental risks posed by 16 priority polycyclic aromatic hydrocarbons (PAHs) in soil at a typical petroleum-contaminated site in China. This relied on integrating data from the literature and field and laboratory experiments. The environmental risk levels posed by the PAHs under four risk scenarios were determined using the SFERC approach, using "residential land" and "industrial land" environmental quality guidelines under "loose" and "strict" strictness parameters. The results showed that environmental risks posed by PAHs in soil are primarily caused by oil exploitation, traffic emissions, and coal combustion. The SFERC approach is an effective tool for characterizing uncertainty and variability in environmental risk assessments and for managing contaminated sites.

  16. Stochastic fuzzy environmental risk characterization of uncertainty and variability in risk assessments: A case study of polycyclic aromatic hydrocarbons in soil at a petroleum-contaminated site in China.

    PubMed

    Hu, Yan; Wang, Zesen; Wen, Jingya; Li, Yu

    2016-10-01

    Better decisions are made using risk assessment models when uncertainty and variability are explicitly acknowledged. Uncertainty caused by a lack of uniform and scientifically supported environmental quality guidelines and variability in the degree of exposure of environmental systems to contaminants are here incorporated in a stochastic fuzzy environmental risk characterization (SFERC) approach. The approach is based on quotient probability distribution and environmental risk level fuzzy membership function methods. The SFERC framework was used to characterize the environmental risks posed by 16 priority polycyclic aromatic hydrocarbons (PAHs) in soil at a typical petroleum-contaminated site in China. This relied on integrating data from the literature and field and laboratory experiments. The environmental risk levels posed by the PAHs under four risk scenarios were determined using the SFERC approach, using "residential land" and "industrial land" environmental quality guidelines under "loose" and "strict" strictness parameters. The results showed that environmental risks posed by PAHs in soil are primarily caused by oil exploitation, traffic emissions, and coal combustion. The SFERC approach is an effective tool for characterizing uncertainty and variability in environmental risk assessments and for managing contaminated sites. PMID:27232725

  17. Metabolic activation of N-hydroxy arylamines, N-hydroxy heterocyclic amines and ring-hydroxymethyl polycyclic aromatic hydrocarbons by human sulfotransferases

    SciTech Connect

    Chou, H.C.

    1993-01-01

    Arylamines and polycyclic aromatic hydrocarbons (PAHs) are two major classes of chemical carcinogens. N-Hydroxylation of arylamines is regarded to be a necessary process for their mutagenicity and carcinogenicity, while alkyl-hydroxylation is the major metabolic pathway for alkyl-substituted PAHs. Evidence has been presented that sulfation of several N-hydroxy arylamines and hydroxymethyl PAHs is an important pathway leading to the formation of ultimate carcinogens in experiment animals. Sulfation of these chemicals forms putative sulfuric acid ester intermediates that can rearrange to electrophilic nitrenium or carbenium ions capable of forming covalent adducts with important cellular macromolecules. In order to study the metabolic activation by sulfotransferase(s) in various human tissue preparations an in vitro enzymatic assay was established. A metabolic phenotyping method was also developed for thermostable phenolsulfotransferase (TS-PST) in platelet homogenates (correlated with TS-PST activity in other tissues) based on a simple colorimetric assay using 2-naphthol as substrate. By using a PAPS-regenerating system to supply the activated sulfate and calf thymus DNA to trap the reactive metabolites, we found that N-hydroxy derivatives of the carcinogens, 4-aminobiphenyl (4-ABP), 4,4[prime]-methylene-bis(2-chloroaniline) (MOCA), 2-acetylaminofluorene (2-AAF), 2-aminofluorene (2-AF), 2-amino-1-methyl-6-phenylimidazo [4,5-b]pyridine (PhIP), and 2-amino-6-methyldipyrido [1,2-1:3[prime],2[prime]-d]imidazole (Glu-P-1) were metabolically activated by human TS-PST. On the other hand, three methyl-hydroxylated derivatives (7-OH, 12-OH, and 7,12-diOH) of 7, 12-dimethylbenz[a]anthracene (DMBA) were metabolically activated by human steroid sulfotransferase. Human sulfotransferase(s)-mediated activation of 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) or 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) was not observed.

  18. Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

    SciTech Connect

    Teese, G.D.

    1995-09-28

    The Savannah River Site has successfully used robots, teleoperators, and remote video to reduce exposure to ionizing radiation, improve worker safety, and improve the quality of operations. Previous reports have described the use of mobile teleoperators in coping with a high level liquid waste spill, the removal of highly contaminated equipment, and the inspection of nuclear reactor vessels. This report will cover recent applications at the Savannah River, as well as systems which SRS has delivered to other DOE site customers.

  19. Control of active sites in selective flocculation: II -- Role of site blocking agents

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Control of heteroflocculation using a lower molecular weight fraction of the flocculant as a site blocking agent is demonstrated in the apatite-dolomite-polyethylene oxide system. The most effective SBA (site blocking agent) was determined to be the highest molecular weight fraction of the flocculant itself which was not capable of flocculating any of the components of the mixture. In the presence of the SBA, flocculant adsorption decreased significantly on apatite particles, thereby inhibiting coflocculation.

  20. Passive dosing of polycyclic aromatic hydrocarbon (PAH) mixtures to terrestrial springtails: linking mixture toxicity to chemical activities, equilibrium lipid concentrations, and toxic units.

    PubMed

    Schmidt, Stine N; Holmstrup, Martin; Smith, Kilian E C; Mayer, Philipp

    2013-07-01

    A 7-day mixture toxicity experiment with the terrestrial springtail Folsomia candida was conducted, and the effects were linked to three different mixture exposure parameters. Passive dosing from silicone was applied to tightly control exposure levels and compositions of 12 mixture treatments, containing the polycyclic aromatic hydrocarbons (PAHs) naphthalene, phenanthrene, and pyrene. Springtail lethality was then linked to sum chemical activities (∑a), sum equilibrium lipid concentrations (∑C(lipid eq.)), and sum toxic units (∑TU). In each case, the effects of all 12 mixture treatments could be fitted to one sigmoidal exposure-response relationship. The effective lethal chemical activity (La50) of 0.027 was well within the expected range for baseline toxicity of 0.01-0.1. Linking the effects to the lipid-based exposure parameter yielded an effective lethal concentration (LC(lipid eq 50)) of 133 mmol kg(-1) lipid in good correspondence with the lethal membrane burden for baseline toxicity (40-160 mmol kg(-1) lipid). Finally, the effective lethal toxic unit (LTU50) of 1.20 was rather close to the expected value of 1. Altogether, passive dosing provided tightly controlled mixture exposure in terms of both level and composition, while ∑a, ∑C(lipid eq.), and ∑TU allowed baseline toxicity to be linked to mixture exposure. PMID:23473585

  1. Passive dosing of polycyclic aromatic hydrocarbon (PAH) mixtures to terrestrial springtails: linking mixture toxicity to chemical activities, equilibrium lipid concentrations, and toxic units.

    PubMed

    Schmidt, Stine N; Holmstrup, Martin; Smith, Kilian E C; Mayer, Philipp

    2013-07-01

    A 7-day mixture toxicity experiment with the terrestrial springtail Folsomia candida was conducted, and the effects were linked to three different mixture exposure parameters. Passive dosing from silicone was applied to tightly control exposure levels and compositions of 12 mixture treatments, containing the polycyclic aromatic hydrocarbons (PAHs) naphthalene, phenanthrene, and pyrene. Springtail lethality was then linked to sum chemical activities (∑a), sum equilibrium lipid concentrations (∑C(lipid eq.)), and sum toxic units (∑TU). In each case, the effects of all 12 mixture treatments could be fitted to one sigmoidal exposure-response relationship. The effective lethal chemical activity (La50) of 0.027 was well within the expected range for baseline toxicity of 0.01-0.1. Linking the effects to the lipid-based exposure parameter yielded an effective lethal concentration (LC(lipid eq 50)) of 133 mmol kg(-1) lipid in good correspondence with the lethal membrane burden for baseline toxicity (40-160 mmol kg(-1) lipid). Finally, the effective lethal toxic unit (LTU50) of 1.20 was rather close to the expected value of 1. Altogether, passive dosing provided tightly controlled mixture exposure in terms of both level and composition, while ∑a, ∑C(lipid eq.), and ∑TU allowed baseline toxicity to be linked to mixture exposure.

  2. Activity and viability of polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LB126 in a DC-electrical field typical for electrobioremediation measures.

    PubMed

    Shi, Lei; Müller, Susann; Loffhagen, Norbert; Harms, Hauke; Wick, Lukas Y

    2008-01-01

    There has been growing interest in employing electro-bioremediation, a hybrid technology of bioremediation and electrokinetics for the treatment of contaminated soil. Knowledge however on the effect of weak electrokinetic conditions on the activity and viability of pollutant-degrading microorganisms is scarce. Here we present data about the influence of direct current (DC) on the membrane integrity, adenosine triphosphate (ATP) pools, physico-chemical cell surface properties, degradation kinetics and culturability of fluorene-degrading Sphingomonas sp. LB126. Flow cytometry was applied to quantify the uptake of propidium iodide (PI) and the membrane potential-related fluorescence intensities (MPRFI) of individual cells within a population. Adenosine tri-phosphate contents and fluorene biodegradation rates of bulk cultures were determined and expressed on a per cell basis. The cells' surface hydrophobicity and electric charge were assessed by contact angle and zeta potential measurements respectively. Relative to the control, DC-exposed cells exhibited up to 60% elevated intracellular ATP levels and yet remained unaffected on all other levels of cellular integrity and functionality tested. Our data suggest that direct current (X=1 V cm(-1); J=10.2 mA cm(-2)) as typically used for electrobioremediation measures has no negative effect on the activity of the polycyclic aromatic hydrocarbon (PAH)-degrading soil microorganism, thereby filling a serious gap of the current knowledge of the electrobioremediation methodology. PMID:21261821

  3. A predictive quantitative structure-activity relationship model for the photoinduced toxicity of polycyclic aromatic hydrocarbons to Daphnia magna with the use of factors for photosensitization and photomodification.

    PubMed

    Lampi, Mark A; Gurska, Jolanta; Huang, Xiao-Dong; Dixon, D George; Greenberg, Bruce M

    2007-03-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants that readily absorb environmentally relevant solar ultraviolet radiation. On absorption of a photon, photoinduced toxicity of PAHs is manifested through photosensitization and photomodification. Both of these processes occur under environmentally relevant levels of actinic radiation. An empirical quantitative structure-activity relationship model previously developed was explanatory of photoinduced toxicity of 16 PAHs in Lemna gibba (duckweed). This model was found to be predictive of toxicity to Vibrio fischeri. The L. gibba quantitative structure-activity relationship showed that a photosensitization factor and a photomodification factor could be combined to describe photoinduced toxicity. To further examine this model, we assessed whether it could be applied to Daphnia magna (water flea), a key bioindicator species in aquatic ecosystems. Toxicity was assessed as median effective concentration and median effective time for immobility. As with L. gibba and V. fischeri, neither the photosensitization factor nor the photomodification factor alone correlated to toxicity in D. magna. However, a photosensitization factor modified for D. magna exhibited a correlation to toxicity (r2 = 0.86), which was modestly improved when summed with a modified photomodification factor (r2 = 0.92). The greatest correlation was observed with median effective concentration data. This research provides evidence that models incorporating factors for photosensitization and photomodification have interspecies applicability. PMID:17373503

  4. Mixed ligand complexes of Cu(II)-2-(2-pyridyl)-benzimidazole and aliphatic or aromatic dicarboxylic acids: Synthesis, characterization and biological activity

    NASA Astrophysics Data System (ADS)

    El-Sherif, Ahmed A.; Jeragh, Bakir J. A.

    2007-11-01

    The synthesis and structural characterization of mixed ligand complexes derived from 2-(2-pyridyl)-benzimidazole (PBI) (1ry ligand) and aliphatic or aromatic dicarboxylic acids (2ry ligand) are reported. Cu(II) complexes were characterized on the bases of their elemental analyses, IR, ESR and thermal analyses. The elemental analysis indicated the formation of mixed ligand complexes in a mole ratio 1:1:1 (Cu:L 1:L 2), L 1 = PBI and L 2 = oxalic acid, phthalic acid or malonic acid. IR spectra showed that PBI acts as a neutral bidentate coordinated to the Cu(II) via the pyridyl and imidazolyl nitrogen atoms. The dicarboxylic acids are bidentate with monodentate carboxylate groups. Thermal decomposition study of complexes was monitored by thermogravimetric (TG) and derivative thermogravimetric (DTG) analysis in N 2 atmosphere. The decomposition course and steps were analysed and the activation parameters of the nonisothermal decomposition were calculated from the TG curves and discussed. The isolated metal chelates were screened for their antimicrobial activities and the results are reported, discussed and compared with some known antibiotics.

  5. A predictive quantitative structure-activity relationship model for the photoinduced toxicity of polycyclic aromatic hydrocarbons to Daphnia magna with the use of factors for photosensitization and photomodification.

    PubMed

    Lampi, Mark A; Gurska, Jolanta; Huang, Xiao-Dong; Dixon, D George; Greenberg, Bruce M

    2007-03-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants that readily absorb environmentally relevant solar ultraviolet radiation. On absorption of a photon, photoinduced toxicity of PAHs is manifested through photosensitization and photomodification. Both of these processes occur under environmentally relevant levels of actinic radiation. An empirical quantitative structure-activity relationship model previously developed was explanatory of photoinduced toxicity of 16 PAHs in Lemna gibba (duckweed). This model was found to be predictive of toxicity to Vibrio fischeri. The L. gibba quantitative structure-activity relationship showed that a photosensitization factor and a photomodification factor could be combined to describe photoinduced toxicity. To further examine this model, we assessed whether it could be applied to Daphnia magna (water flea), a key bioindicator species in aquatic ecosystems. Toxicity was assessed as median effective concentration and median effective time for immobility. As with L. gibba and V. fischeri, neither the photosensitization factor nor the photomodification factor alone correlated to toxicity in D. magna. However, a photosensitization factor modified for D. magna exhibited a correlation to toxicity (r2 = 0.86), which was modestly improved when summed with a modified photomodification factor (r2 = 0.92). The greatest correlation was observed with median effective concentration data. This research provides evidence that models incorporating factors for photosensitization and photomodification have interspecies applicability.

  6. Hydroxylation activity of P450 BM-3 mutant F87V towards aromatic compounds and its application to the synthesis of hydroquinone derivatives from phenolic compounds.

    PubMed

    Sulistyaningdyah, Woro Triarsi; Ogawa, Jun; Li, Qing-Shan; Maeda, Chiharu; Yano, Yuki; Schmid, Rolf D; Shimizu, Sakayu

    2005-06-01

    Cytochrome P450 BM-3 from Bacillus megaterium is a fatty acid hydroxylase exhibiting selectivity for long-chain substrates (12-20 carbons). Replacement of Phe87 in P450 BM-3 by Val (F87V) greatly increased its activity towards a variety of aromatic and phenolic compounds. The apparent initial reaction rates of F87V as to benzothiophene, indan, 2,6-dichlorophenol, and 2-(benzyloxy)phenol were 227, 204, 129, and 385 nmol min(-1) nmol(-1) P450, which are 220-, 66-, 99-, and 963-fold those of the wild type, respectively. These results indicate that Phe87 plays a critical role in the control of the substrate specificity of P450 BM-3. Furthermore, F87V catalyzed regioselective hydroxylation at the para position of various phenolic compounds. In particular, F87V showed high activity as to the hydroxylation of 2-(benzyloxy)phenol to 2-(benzyloxy)hydroquinone. With F87V as the catalyst, 0.71 mg ml(-1) 2-(benzyloxy)hydroquinone was produced from 1.0 mg ml(-1) 2-(benzyloxy)phenol in 4 h, with a molar yield of 66%.

  7. Activity and viability of polycyclic aromatic hydrocarbon‐degrading Sphingomonas sp. LB126 in a DC‐electrical field typical for electrobioremediation measures

    PubMed Central

    Shi, Lei; Müller, Susann; Loffhagen, Norbert; Harms, Hauke; Wick, Lukas Y.

    2008-01-01

    Summary There has been growing interest in employing electro‐bioremediation, a hybrid technology of bioremediation and electrokinetics for the treatment of contaminated soil. Knowledge however on the effect of weak electrokinetic conditions on the activity and viability of pollutant‐degrading microorganisms is scarce. Here we present data about the influence of direct current (DC) on the membrane integrity, adenosine triphosphate (ATP) pools, physico‐chemical cell surface properties, degradation kinetics and culturability of fluorene‐degrading Sphingomonas sp. LB126. Flow cytometry was applied to quantify the uptake of propidium iodide (PI) and the membrane potential‐related fluorescence intensities (MPRFI) of individual cells within a population. Adenosine tri‐phosphate contents and fluorene biodegradation rates of bulk cultures were determined and expressed on a per cell basis. The cells' surface hydrophobicity and electric charge were assessed by contact angle and zeta potential measurements respectively. Relative to the control, DC‐exposed cells exhibited up to 60% elevated intracellular ATP levels and yet remained unaffected on all other levels of cellular integrity and functionality tested. Our data suggest that direct current (X = 1 V cm−1; J = 10.2 mA cm−2) as typically used for electrobioremediation measures has no negative effect on the activity of the polycyclic aromatic hydrocarbon (PAH)‐degrading soil microorganism, thereby filling a serious gap of the current knowledge of the electrobioremediation methodology. PMID:21261821

  8. Antioxidant activity, phenolic content, and peroxide value of essential oil and extracts of some medicinal and aromatic plants used as condiments and herbal teas in Turkey.

    PubMed

    Ozcan, Mehmet Musa; Erel, Ozcan; Herken, Emine Etöz

    2009-02-01

    The antioxidant activity, total peroxide values, and total phenol contents of several medicinal and aromatic plant essential oil and extracts from Turkey were examined. Total phenolic contents were determined using a spectrophotometric technique and calculated as gallic acid equivalents. Total antioxidant activity of essential oil and extracts varied from 0.6853 to 1.3113 and 0.3189 to 0.6119 micromol of Trolox equivalents/g, respectively. The total phenolic content of essential oil ranged from 0.0871 to 0.5919 mg of gallic acid/g dry weight. However, the total phenolic contents of extracts were found to be higher compared with those of essential oils. The amount of total peroxide values of oils varied from 7.31 (pickling herb) to 58.23 (bitter fennel flower) mumol of H(2)O(2)/g. As a result, it is shown that medicinal plant derivatives such as extract and essential oils can be useful as a potential source of total phenol, peroxide, and antioxidant capacity for protection of processed foods. PMID:19298216

  9. N-terminal aromatic residues closely impact the cytolytic activity of cupiennin 1a, a major spider venom peptide.

    PubMed

    Kuhn-Nentwig, Lucia; Sheynis, Tania; Kolusheva, Sofiya; Nentwig, Wolfgang; Jelinek, Raz

    2013-12-01

    Cupiennins are small cationic α-helical peptides from the venom of the ctenid spider Cupiennius salei which are characterized by high bactericidal as well as hemolytic activities. To gain insight into the determinants responsible for the broad cytolytic activities, two analogues of cupiennin 1a with different N-terminal hydrophobicities were designed. The insecticidal, bactericidal and hemolytic activities of these analogues were assayed and compared to the native peptide. Specifically, substitution of two N-terminal Phe residues by Ala results in less pronounced insecticidal and cytolytic activity, whereas a substitution by Lys reduces strongly its bactericidal activity and completely diminishes its hemolytic activity up to very high tested concentrations. Biophysical analyses of peptide/bilayer membrane interactions point to distinct interactions of the analogues with lipid bilayers, and dependence upon membrane surface charge. Indeed, we find that lower hemolytic activity was correlated with less surface association of the analogues. In contrast, our data indicate that the reduced bactericidal activity of the two cupiennin 1a analogues likely correspond to greater bilayer-surface localization of the peptides. Overall, ultimate insertion and destruction of the host cell membrane is highly dependent on the presence of Phe-2 and Phe-6 (Cu 1a) or Leu-6 (Cu 2a) in the N-terminal sequences of native cupiennins.

  10. Comparison in the in vitro inhibitory effects of major phytocannabinoids and polycyclic aromatic hydrocarbons contained in marijuana smoke on cytochrome P450 2C9 activity.

    PubMed

    Yamaori, Satoshi; Koeda, Kyoko; Kushihara, Mika; Hada, Yui; Yamamoto, Ikuo; Watanabe, Kazuhito

    2012-01-01

    Inhibitory effects of Δ⁹-tetrahydrocannabinol (Δ⁹-THC), cannabidiol (CBD), and cannabinol (CBN), the three major constituents in marijuana, and polycyclic aromatic hydrocarbons (PAHs) contained in marijuana smoke on catalytic activity of human cytochrome P450 (CYP) 2C9 were investigated. These phytocannabinoids concentration-dependently inhibited S-warfarin 7-hydroxylase and diclofenac 4'-hydroxylase activities of human liver microsomes (HLMs) and recombinant CYP2C9 (rCYP2C9). In contrast, none of the twelve PAHs including benz[a]anthracene and benzo[a]pyrene exerted substantial inhibition (IC₅₀ > 10 µM). The inhibitory potentials of Δ⁹-THC (Ki = 0.937-1.50 µM) and CBN (Ki = 0.882-1.29 µM) were almost equivalent regardless of the enzyme sources used, whereas the inhibitory potency of CBD (Ki > = 0.954-9.88 µM) varied depending on the enzyme sources and substrates used. Δ⁹-THC inhibited both S-warfarin 7-hydroxylase and diclofenac 4'-hydroxylase activities of HLMs and rCYP2C9 in a mixed manner. CBD and CBN competitively inhibited the activities of HLMs and rCYP2C9, with the only notable difference being that CBD and CBN exhibited mixed-type inhibitions against diclofenac 4'-hydroxylation and S-warfarin 7-hydroxylation, respectively, by rCYP2C9. None of Δ⁹-THC, CBD, and CBN exerted metabolism-dependent inhibition. These results indicated that the three major phytocannabinoids but not PAHs contained in marijuana smoke potently inhibited CYP2C9 activity and that these cannabinoids can be characterized as direct inhibitors for CYP2C9.

  11. Effect of steam activated biochar application to industrially contaminated soils on bioavailability of polycyclic aromatic hydrocarbons and ecotoxicity of soils.

    PubMed

    Kołtowski, Michał; Hilber, Isabel; Bucheli, Thomas D; Oleszczuk, Patryk

    2016-10-01

    The aim of this study was to determine the effect of steam activation of biochars on the immobilization of freely dissolved (Cfree) and bioaccessible fraction (Cbioacc) of PAHs in soils. Additionally, the toxicity to various organisms like Vibrio fischeri, Lepidium sativum and Folsomia candida was measured before and after the amendment of biochars to soils. Three biochars produced from willow, coconut and wheat straw were steam activated and added to three different soils with varying content and origin of PAHs (coke vs. bitumen). The soils with the addition of the biochars (activated and non-activated) were incubated for a period of 60days. Steam activation of the biochars resulted in more pronounced reduction of both Cfree and Cbioacc. The range of the increase in effectiveness was from 10 to 84% for Cfree and from 50 to 99% for Cbioacc. In contrast, the effect of activation on the toxicity of the soils studied varied greatly and was specific to a particular test and soil type. Essentially, biochar activation did not result in a change of phytotoxicity, but it increased or decreased (depending on the parameter, type of biochar, contaminant source, and soil and soil type) the toxic effect to F. candida, and decreased the toxicity of leachates to V. fischeri.

  12. Effect of steam activated biochar application to industrially contaminated soils on bioavailability of polycyclic aromatic hydrocarbons and ecotoxicity of soils.

    PubMed

    Kołtowski, Michał; Hilber, Isabel; Bucheli, Thomas D; Oleszczuk, Patryk

    2016-10-01

    The aim of this study was to determine the effect of steam activation of biochars on the immobilization of freely dissolved (Cfree) and bioaccessible fraction (Cbioacc) of PAHs in soils. Additionally, the toxicity to various organisms like Vibrio fischeri, Lepidium sativum and Folsomia candida was measured before and after the amendment of biochars to soils. Three biochars produced from willow, coconut and wheat straw were steam activated and added to three different soils with varying content and origin of PAHs (coke vs. bitumen). The soils with the addition of the biochars (activated and non-activated) were incubated for a period of 60days. Steam activation of the biochars resulted in more pronounced reduction of both Cfree and Cbioacc. The range of the increase in effectiveness was from 10 to 84% for Cfree and from 50 to 99% for Cbioacc. In contrast, the effect of activation on the toxicity of the soils studied varied greatly and was specific to a particular test and soil type. Essentially, biochar activation did not result in a change of phytotoxicity, but it increased or decreased (depending on the parameter, type of biochar, contaminant source, and soil and soil type) the toxic effect to F. candida, and decreased the toxicity of leachates to V. fischeri. PMID:27267727

  13. Carbohydrate–Aromatic Interactions in Proteins

    PubMed Central

    2015-01-01

    Protein–carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C–H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C–H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C–H bonds engage more often in CH−π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate–aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C–H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein–carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein–carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites. PMID:26561965

  14. Docking-based Design of Galantamine Derivatives with Dual-site Binding to Acetylcholinesterase.

    PubMed

    Stavrakov, Georgi; Philipova, Irena; Zheleva, Dimitrina; Atanasova, Mariyana; Konstantinov, Spiro; Doytchinova, Irini

    2016-07-01

    The enzyme acetylcholinesterase is a key target in the treatment of Alzheimer's disease because of its ability to hydrolyze acetylcholine via the catalytic binding site and to accelerate the aggregation of amyloid-β peptide via the peripheral anionic site (PAS). Using docking-based predictions, in the present study we design 20 novel galantamine derivatives with alkylamide spacers of different length ending with aromatic fragments. The galantamine moiety blocks the catalytic site, while the terminal aromatic fragments bind in PAS. The best predicted compounds are synthesized and tested for acetylcholinesterase inhibitory activity. The experimental results confirm the predictions and show that the heptylamide spacer is of optimal length to bridge the galantamine moiety bound in the catalytic site and the aromatic fragments interacting with PAS. Among the tested terminal aromatic fragments, the phenethyl substituent is the most suitable for binding in PAS. PMID:27492242

  15. Mutation at a Strictly Conserved, Active Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity

    SciTech Connect

    Chen, Zhi-wei; Datta, Saumen; DuBois, Jennifer L.; Klinman, Judith P.; Mathews, F. Scott

    2010-09-07

    The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

  16. Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses.

    PubMed

    Eckhard, Ulrich; Huesgen, Pitter F; Schilling, Oliver; Bellac, Caroline L; Butler, Georgina S; Cox, Jennifer H; Dufour, Antoine; Goebeler, Verena; Kappelhoff, Reinhild; Keller, Ulrich Auf dem; Klein, Theo; Lange, Philipp F; Marino, Giada; Morrison, Charlotte J; Prudova, Anna; Rodriguez, David; Starr, Amanda E; Wang, Yili; Overall, Christopher M

    2016-01-01

    Secreted and membrane tethered matrix metalloproteinases (MMPs) are key homeostatic proteases regulating the extracellular signaling and structural matrix environment of cells and tissues. For drug targeting of proteases, selectivity for individual molecules is highly desired and can be met by high yield active site specificity profiling. Using the high throughput Proteomic Identification of protease Cleavage Sites (PICS) method to simultaneously profile both the prime and non-prime sides of the cleavage sites of nine human MMPs, we identified more than 4300 cleavages from P6 to P6' in biologically diverse human peptide libraries. MMP specificity and kinetic efficiency were mainly guided by aliphatic and aromatic residues in P1' (with a ~32-93% preference for leucine depending on the MMP), and basic and small residues in P2' and P3', respectively. A wide differential preference for the hallmark P3 proline was found between MMPs ranging from 15 to 46%, yet when combined in the same peptide with the universally preferred P1' leucine, an unexpected negative cooperativity emerged. This was not observed in previous studies, probably due to the paucity of approaches that profile both the prime and non-prime sides together, and the masking of subsite cooperativity effects by global heat maps and iceLogos. These caveats make it critical to check for these biologically highly important effects by fixing all 20 amino acids one-by-one in the respective subsites and thorough assessing of the inferred specificity logo changes. Indeed an analysis of bona fide MEROPS physiological substrate cleavage data revealed that of the 37 natural substrates with either a P3-Pro or a P1'-Leu only 5 shared both features, confirming the PICS data. Upon probing with several new quenched-fluorescent peptides, rationally designed on our specificity data, the negative cooperativity was explained by reduced non-prime side flexibility constraining accommodation of the rigidifying P3 proline with

  17. Biodegradation of Aromatic Compounds by Escherichia coli

    PubMed Central

    Díaz, Eduardo; Ferrández, Abel; Prieto, María A.; García, José L.

    2001-01-01

    Although Escherichia coli has long been recognized as the best-understood living organism, little was known about its abilities to use aromatic compounds as sole carbon and energy sources. This review gives an extensive overview of the current knowledge of the catabolism of aromatic compounds by E. coli. After giving a general overview of the aromatic compounds that E. coli strains encounter and mineralize in the different habitats that they colonize, we provide an up-to-date status report on the genes and proteins involved in the catabolism of such compounds, namely, several aromatic acids (phenylacetic acid, 3- and 4-hydroxyphenylacetic acid, phenylpropionic acid, 3-hydroxyphenylpropionic acid, and 3-hydroxycinnamic acid) and amines (phenylethylamine, tyramine, and dopamine). Other enzymatic activities acting on aromatic compounds in E. coli are also reviewed and evaluated. The review also reflects the present impact of genomic research and how the analysis of the whole E. coli genome reveals novel aromatic catabolic functions. Moreover, evolutionary considerations derived from sequence comparisons between the aromatic catabolic clusters of E. coli and homologous clusters from an increasing number of bacteria are also discussed. The recent progress in the understanding of the fundamentals that govern the degradation of aromatic compounds in E. coli makes this bacterium a very useful model system to decipher biochemical, genetic, evolutionary, and ecological aspects of the catabolism of such compounds. In the last part of the review, we discuss strategies and concepts to metabolically engineer E. coli to suit specific needs for biodegradation and biotransformation of aromatics and we provide several examples based on selected studies. Finally, conclusions derived from this review may serve as a lead for future research and applications. PMID:11729263

  18. APPLICATION OF TOXICITY-BASED FRACTIONATION TECHNIQUES AND STRUCTURE-ACTIVITY RELATIONSHIP MODELS FOR THE IDENTIFICATION OF PHOTOTOXIC POLYCYCLIC AROMATIC HYDROCARBONS IN SEDIMENT PORE WATER

    EPA Science Inventory

    Studies conducted in our laboratory show that sediments contaminated with complex mixtures of polycyclic aromatic hydrocarbons (PAHs) can exhibit enhanced toxicity (lethality) to a variety of aquatic species when the samples are tested under ultarviolet (UV) light designed to mim...

  19. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations

    PubMed Central

    Steinkellner, Georg; Gruber, Christian C.; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Łyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites (‘catalophores’). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C–C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  20. Nematicidal activity of essential oils and volatiles derived from Portuguese aromatic flora against the pinewood nematode, Bursaphelenchus xylophilus.

    PubMed

    Barbosa, P; Lima, A S; Vieira, P; Dias, L S; Tinoco, M T; Barroso, J G; Pedro, L G; Figueiredo, A C; Mota, M

    2010-03-01

    Twenty seven essential oils, isolated from plants representing 11 families of Portuguese flora, were screened for their nematicidal activity against the pinewood nematode (PWN), Bursaphelenchus xylophilus. The essential oils were isolated by hydrodistillation and the volatiles by distillation-extraction, and both were analysed by GC and GC-MS. High nematicidal activity was achieved with essential oils from Chamaespartium tridentatum, Origanum vulgare, Satureja montana, Thymbra capitata, and Thymus caespititius. All of these essential oils had an estimated minimum inhibitory concentration ranging between 0.097 and 0.374 mg/ml and a lethal concentration necessary to kill 100% of the population (LC(100)) between 0.858 and 1.984 mg/ml. Good nematicidal activity was also obtained with the essential oil from Cymbopogon citratus. The dominant components of the effective oils were 1-octen-3-ol (9%), n-nonanal, and linalool (both 7%) in C. tridentatum, geranial (43%), neral (29%), and β-myrcene (25%) in C. citratus, carvacrol (36% and 39%), γ-terpinene (24% and 40%), and p-cymene (14% and 7%) in O. vulgare and S. montana, respectively, and carvacrol (75% and 65%, respectively) in T. capitata and T. caespititius. The other essential oils obtained from Portuguese flora yielded weak or no activity. Five essential oils with nematicidal activity against PWN are reported for the first time. PMID:22736831

  1. Nematicidal activity of essential oils and volatiles derived from Portuguese aromatic flora against the pinewood nematode, Bursaphelenchus xylophilus

    PubMed Central

    Barbosa, P.; Lima, A. S.; Vieira, P.; Dias, L. S.; Tinoco, M. T.; Barroso, J. G.; Pedro, L. G.; Figueiredo, A. C.

    2010-01-01

    Twenty seven essential oils, isolated from plants representing 11 families of Portuguese flora, were screened for their nematicidal activity against the pinewood nematode (PWN), Bursaphelenchus xylophilus. The essential oils were isolated by hydrodistillation and the volatiles by distillation-extraction, and both were analysed by GC and GC-MS. High nematicidal activity was achieved with essential oils from Chamaespartium tridentatum, Origanum vulgare, Satureja montana, Thymbra capitata, and Thymus caespititius. All of these essential oils had an estimated minimum inhibitory concentration ranging between 0.097 and 0.374 mg/ml and a lethal concentration necessary to kill 100% of the population (LC100) between 0.858 and 1.984 mg/ml. Good nematicidal activity was also obtained with the essential oil from Cymbopogon citratus. The dominant components of the effective oils were 1–octen-3-ol (9%), n–nonanal, and linalool (both 7%) in C. tridentatum, geranial (43%), neral (29%), and β-myrcene (25%) in C. citratus, carvacrol (36% and 39%), γ-terpinene (24% and 40%), and p-cymene (14% and 7%) in O. vulgare and S. montana, respectively, and carvacrol (75% and 65%, respectively) in T. capitata and T. caespititius. The other essential oils obtained from Portuguese flora yielded weak or no activity. Five essential oils with nematicidal activity against PWN are reported for the first time. PMID:22736831

  2. Fruits and vegetables protect against the genotoxicity of heterocyclic aromatic amines activated by human xenobiotic-metabolizing enzymes expressed in immortal mammalian cells.

    PubMed

    Platt, K L; Edenharder, R; Aderhold, S; Muckel, E; Glatt, H

    2010-12-21

    Heterocyclic aromatic amines (HAAs) can be formed during the cooking of meat and fish at elevated temperatures and are associated with an increased risk for cancer. On the other hand, epidemiological findings suggest that foods rich in fruits and vegetables can protect against cancer. In the present study three teas, two wines, and the juices of 15 fruits and 11 vegetables were investigated for their protective effect against the genotoxic effects of 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). To closely mimic the enzymatic activation of these HAAs in humans, genetically engineered V79 Chinese hamster fibroblasts were employed that express human cytochrome P450-dependent monooxygenase (hCYP) 1A2 (responsible for the first step of enzymatic activation) and human N(O)-acetyltransferase (hNAT) 2*4 or human sulfotransferase (hSULT)1A1*1 (responsible for the second step of enzymatic activation): V79-hCYP1A2-hNAT2*4 for IQ activation and V79-hCYP1A2-hSULT1A1*1 for PhIP activation. HAA genotoxicity was determined by use of the comet assay. Black, green and rooibos tea moderately reduced the genotoxicity of IQ (IC(50)=0.8-0.9%), whereas red and white wine were less active. From the fruit juices, sweet cherry juice exhibited the highest inhibitory effect on IQ genotoxicity (IC(50)=0.17%), followed by juices from kiwi fruit, plum and blueberry (IC(50)=0.48-0.71%). The juices from watermelon, blackberry, strawberry, black currant, and Red delicious apple showed moderate suppression, whereas sour cherry, grapefruit, red currant, and pineapple juices were only weakly active. Granny Smith apple juice and orange juice proved inactive. Of the vegetable juices, strong inhibition of IQ genotoxicity was only seen with spinach and onion juices (IC(50)=0.42-0.54%). Broccoli, cauliflower, beetroot, sweet pepper, tomato, chard, and red-cabbage juices suppressed IQ genotoxicity only moderately, whereas cucumber juice was

  3. An ionizable active-site tryptophan imparts catalase activity to a peroxidase core.

    PubMed

    Loewen, Peter C; Carpena, Xavi; Vidossich, Pietro; Fita, Ignacio; Rovira, Carme

    2014-05-21

    Catalase peroxidases (KatG's) are bifunctional heme proteins that can disproportionate hydrogen peroxide (catalatic reaction) despite their structural dissimilarity with monofunctional catalases. Using X-ray crystallography and QM/MM calculations, we demonstrate that the catalatic reaction of KatG's involves deprotonation of the active-site Trp, which plays a role similar to that of the distal His in monofunctional catalases. The interaction of a nearby mobile arginine with the distal Met-Tyr-Trp essential adduct (in/out) acts as an electronic switch, triggering deprotonation of the adduct Trp.

  4. Activation of electrophilicity of stable Y-delocalized carbamate cations in intramolecular aromatic substitution reaction: evidence for formation of diprotonated carbamates leading to generation of isocyanates.

    PubMed

    Kurouchi, Hiroaki; Kawamoto, Kyoko; Sugimoto, Hiromichi; Nakamura, Satoshi; Otani, Yuko; Ohwada, Tomohiko

    2012-10-19

    Although cations with three heteroatoms, such as monoprotonated guanidine and urea, are stabilized by Y-shaped conjugation and such Y-conjugated cations are sufficiently basic to be further protonated (or protosolvated) to dications in strongly acid media, only O-monoprotonated species have been detected in the case of carbamates even in magic acid. We found that the trifluoromethanesulfonic acid-catalyzed cyclization of arylethylcarbamates proceeds to afford dihydroisoquinolones in high yield. In strong acids, methyl carbamates are fully O-monoprotonated, and these monocations do not undergo cyclization even under heating. But, as the acidity of the reaction medium is further increased, the cyclization reaction of methyl phenethylcarbamates starts to proceed as a first-order reaction, with a linear relationship between rate and acidity. The sign and magnitude of the entropy of activation ΔS(‡) were found to be similar to those of other A(Ac)1 reactions. These results strongly support the idea that further protonation of the O-protonated carbamates is involved in the cyclization, but the concentration of the dications is very low and suggests that the rate-determining step is dissociation of methanol from the diprotonated carbamate to generate protonated isocyanate, which reacts with the aromatic ring. Therefore, O-protonated carbamates are weak bases in sharp contrast to other Y-shaped monocations.

  5. Responses of mixtures of polyhalogenated aromatic compounds or single compounds in the CALUX-assay a novel species-specific bioassay for Ah-receptor active compounds

    SciTech Connect

    Murk, A.J.; Aarts, J.M.M.J.G.; Jonas, A.; Brouwer, A.; Denison, M.S.

    1995-12-31

    Polyhalogenated aromatic hydrocarbons (PHAHs) elicit a number of common toxic responses, including reproductive toxicity, teratogenicity, impairment of immune responses, alterations in vitamin A and thyroid hormone metabolism and carcinogenesis. The toxic effects however are highly dependent on the animal species used, The most toxic PHAHs are approximate isostereomeres of 2,3,7,8 tetrachlorinated dibenzo-p-dioxin (TCDD) and share a common mechanism of action mediated by the aryl hydrocarbon receptor (AhR). Based on the common receptor mediated mechanism, the toxic equivalency factor concept was developed, in which the potency of each individual congener is expressed relative to TCDD, thus allowing hazard and risk assessment for mixtures of PHAHs. A number of recombinant cell lines were developed, including hepalclc7 mouse and H4IIE rat hepatoma cell lines, with AhR-mediated firefly (Photinus pyralis) luciferase gene expression. The response in this so-called CALUX (chemical activated luciferase expression) assay is additive for polychlorinated dibenzofurans (PCDFs) and PCDDS, but for polychlorinated biphenyls (PCBs) both synergistic and antagonistic interactions have been demonstrated, which are partially species-dependent. Also some structurally related compounds, like polybrominated diphenyl ether, pentachlorinated phenol, benzo(a)pyrene, pyrene, tetrachlorobenzyltoluene (Ugilec 141) and mixtures of polychlorinated terphenyls have been tested in the CALUX assay. The responses of these compounds were sometimes agonistic, but also antagonistic and synergistic effects on the TCDO response were observed.

  6. Coordinating activation strategy for C(sp(3))-H/C(sp(3))-H cross-coupling to access β-aromatic α-amino acids.

    PubMed

    Li, Kaizhi; Wu, Qian; Lan, Jingbo; You, Jingsong

    2015-01-01

    The past decade has witnessed significant advances in C-H bond functionalizations with the discovery of new mechanisms. Non-precious transition-metal-catalysed radical oxidative coupling for C(sp(3))-H bond transformations is an appealing strategy for C-C bond formations. The radical oxidative C(sp(3))-H/C(sp(3))-H cross-coupling reactions of α-C(sp(3))-H bonds of amines with free radicals represent a conceptual and practical challenge. We herein develop the coordinating activation strategy to illustrate the nickel-catalysed radical oxidative cross-coupling between C(sp(3))-H bonds and (hetero)arylmethyl free radicals. The protocol can tolerate a rich variety of α-amino acids and (hetero)arylmethanes as well as arylmethylenes and arylmethines, affording a large library of α-tertiary and α-quaternary β-aromatic α-amino acids. This process also features low-cost metal catalyst, readily handled and easily removable coordinating group, synthetic simplicity and gram-scale production, which would enable the potential for economical production at commercial scale in the future. PMID:26415985

  7. Removal of Aromatic Pollutant Surrogate from Water by Recyclable Magnetite-Activated Carbon Nanocomposite: An Experiment for General Chemistry

    ERIC Educational Resources Information Center

    Furlan, Ping Y.; Melcer, Michael E.

    2014-01-01

    A general chemistry laboratory experiment using readily available chemicals is described to introduce college students to an exciting class of nanocomposite materials. In a one-step room temperature synthetic process, magnetite nanoparticles are embedded onto activated carbon matrix. The resultant nanocomposite has been shown to combine the…

  8. Nuclear Site Security in the Event of Terrorist Activity

    SciTech Connect

    Thomson, M.L.; Sims, J.

    2008-07-01

    This paper, presented as a poster, identifies why ballistic protection should now be considered at nuclear sites to counter terrorist threats. A proven and flexible form of multi purpose protection is described in detail with identification of trial results that show its suitability for this role. (authors)

  9. Nucleophilic fluorination of aromatic compounds

    DOEpatents

    Satyamurthy, Nagichettiar; Barrio, Jorge R

    2014-03-18

    Iodylbenzene derivatives substituted with electron donating as well as electron withdrawing groups on the aromatic ring are used as precursors in aromatic nucleophilic substitution reactions. The iodyl group (IO.sub.2) is regiospecifically substituted by nucleophilic fluoride to provide the corresponding fluoroaryl derivatives. No-carrier-added [F-18]fluoride ion derived from anhydrous [F-18](F/Kryptofix, [F-18]CsF or a quaternary ammonium fluoride (e.g., Me.sub.4NF, Et.sub.4NF, n-Bu.sub.4NF, (PhCH.sub.2).sub.4NF) exclusively substitutes the iodyl moiety in these derivatives and provides high specific activity F-18 labeled fluoroaryl analogs. Iodyl derivatives of a benzothiazole analog and 6-iodyl-L-dopa derivatives have been synthesized as precursors and have been used in the preparation of no-carrier-added [F-18]fluorobenzothiazole as well as 6-[F-18]fluoro-L-dopa.

  10. Catalytic decomposition of 4-phenoxyphenol to aromatics over Pd/Cs(x)H3.0-x PW12O40/activated carbon aerogel (X = 2.0-3.0).

    PubMed

    Park, Hai Woong; Hong, Ung Gi; Lee, Yoon Jae; Choi, Jung Ho; Song, In Kyu

    2013-12-01

    Cesium-exchanged heteropolyacid (Cs(x)H3.0-xPW12O40) was impregnated onto activated carbon aerogel (ACA) with a variation of cesium content (X = 2.0, 2.3, 2.5, 2.7, and 3.0) in order to provide acid sites to ACA. Palladium catalysts were then supported on Cs(x)H3.0-xPW12O40-impregnated activated carbon aerogel (Pd/Cs(x)H3.0-xPW12O40/ACA, X = 2.0-3.0) by an incipient wetness impregnation method for use in the decomposition of lignin model compound to aromatics. 4-Phenoxyphenol was used as a lignin model compound for representing 4-O-5 linkage of lignin. In the catalytic decomposition of 4-phenoxyphenol over Pd/Cs(X)H3.0-xPW12O40/ACA, cyclohexanol, benzene, and phenol were mainly produced. Conversion of 4-phenoxyphenol and total yield for main products (cyclohexanol, benzene, and phenol) were closely related to the acidity of Pd/Cs(x)H3.0-xPW12O40/ACA. Conversion of 4-phenoxyphenol and total yield for main products increased with increasing acidity of Pd/Cs(x)H3.0-xPW12O40/ACA. Among the catalysts tested, Pd/Cs2.5H0.5PW12O40/ACA catalyst with the largest acidity showed the highest conversion of 4-phenoxyphenol and total yield for main products. Therefore, it is concluded that acidity of catalysts would be an important factor determining the catalytic performance in the decomposition of 4-phenoxyphenol. PMID:24266173

  11. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    SciTech Connect

    Taylor, D.D.; Hoskinson, R.L.; Kingsford, C.O.; Ball, L.W.

    1994-09-01

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria.

  12. Active Layer and Moisture Measurements for Intensive Site 0 and 1, Barrow, Alaska

    DOE Data Explorer

    John Peterson

    2015-04-17

    These are measurements of Active Layer Thickness collected along several lines beginning in September, 2011 to the present. The data were collected at several time periods along the Site0 L2 Line, the Site1 AB Line, and an ERT Monitoring Line near Area A in Site1.

  13. Fate of iron and polycyclic aromatic hydrocarbons during the remediation of a contaminated soil using iron-activated persulfate: A column study.

    PubMed

    Pardo, F; Santos, A; Romero, A

    2016-10-01

    Remediation of contaminated soils under flow-through conditions is an issue of great interest since it provides a better approach to real case applications than batch experiments. In this work, a column filled with soil, artificially spiked and aged for three months with Phenanthrene (PHE), Anthracene (ANT), Pyrene (PYR) and Benzo(a)pyrene (BaP), was treated for 25days with persulfate (PS) activated by Fe(3+) and nanoparticles of zerovalent iron (nZVI). Effects of type of iron fed into the column (Fe(3+) or nZVI) and nZVI concentration were studied. PS inlet concentration was 0.2mmolcm(-3) and residence time in the column was close to 1.72days. Iron, PS and polycyclic aromatic hydrocarbons (PAHs) concentration, as well as pH, were monitored during treatment. Concentration profiles of iron and PAHs were observed along the column, with higher iron concentrations and higher PAHs removal efficiencies in the closest sections to the column entrance. BaP and ANT were completely depleted regardless the conditions used, but PHE and PYR showed higher resistance to oxidation, achieving near a 90% removal in the closest sections to the injection source in all runs, but decreasing significantly with column length. Besides, natural degradation of ANT resulted in the formation 9.10-anthraquinone (ATQ), an oxy-PAH which showed higher resistance than PHE and PYR. Although higher PAHs removal efficiencies were achieved when nZVI was used as activator, only a moderate improvement was noticed when the highest concentration of nZVI was used as a consequence of radical scavenging by an excess of Fe(2+). Finally, a kinetic model based on runs performed in batch, from a previous work, was able to predict the experimental average concentrations of PAHs in the column when Fe(3+) was used as activator.

  14. Fate of iron and polycyclic aromatic hydrocarbons during the remediation of a contaminated soil using iron-activated persulfate: A column study.

    PubMed

    Pardo, F; Santos, A; Romero, A

    2016-10-01

    Remediation of contaminated soils under flow-through conditions is an issue of great interest since it provides a better approach to real case applications than batch experiments. In this work, a column filled with soil, artificially spiked and aged for three months with Phenanthrene (PHE), Anthracene (ANT), Pyrene (PYR) and Benzo(a)pyrene (BaP), was treated for 25days with persulfate (PS) activated by Fe(3+) and nanoparticles of zerovalent iron (nZVI). Effects of type of iron fed into the column (Fe(3+) or nZVI) and nZVI concentration were studied. PS inlet concentration was 0.2mmolcm(-3) and residence time in the column was close to 1.72days. Iron, PS and polycyclic aromatic hydrocarbons (PAHs) concentration, as well as pH, were monitored during treatment. Concentration profiles of iron and PAHs were observed along the column, with higher iron concentrations and higher PAHs removal efficiencies in the closest sections to the column entrance. BaP and ANT were completely depleted regardless the conditions used, but PHE and PYR showed higher resistance to oxidation, achieving near a 90% removal in the closest sections to the injection source in all runs, but decreasing significantly with column length. Besides, natural degradation of ANT resulted in the formation 9.10-anthraquinone (ATQ), an oxy-PAH which showed higher resistance than PHE and PYR. Although higher PAHs removal efficiencies were achieved when nZVI was used as activator, only a moderate improvement was noticed when the highest concentration of nZVI was used as a consequence of radical scavenging by an excess of Fe(2+). Finally, a kinetic model based on runs performed in batch, from a previous work, was able to predict the experimental average concentrations of PAHs in the column when Fe(3+) was used as activator. PMID:27235898

  15. Aryl hydrocarbon receptor-mediated activity of atmospheric particulate matter from an urban and a rural site in Switzerland

    NASA Astrophysics Data System (ADS)

    Wenger, Daniela; Gerecke, Andreas C.; Heeb, Norbert V.; Hueglin, Christoph; Seiler, Cornelia; Haag, Regula; Naegeli, Hanspeter; Zenobi, Renato

    Atmospheric particulate matter (PM) is an air-suspended mixture of solid and liquid particles that vary in size, shape, and chemical composition. Long-term exposure to elevated concentrations of fine atmospheric particles is considered to pose a health threat to humans and animals. In this context, it has been hypothesized that toxic chemicals such as polycyclic aromatic hydrocarbons (PAHs) play an important role. Some PAHs are known to be carcinogenic and it has been shown that carcinogenic effects of PAHs are mediated by the aryl hydrocarbon receptor (AhR). In this study, PM1 was collected at a rural and an urban traffic site during an intense winter smog period, in which concentration of PM1 often exceeded 50 μg m -3. We applied an in vitro reporter gene assay (DR-CALUX) to detect and quantify PM1-associated chemicals that induce AhR-mediated gene expression. This activity was expressed as CALUX equivalents of 2,3,7,8-tetrachlorodibenzodioxin (PM-TCDD-CEQs). In addition, concentrations of PAHs in the PM1 extracts were determined using gas chromatography/high-resolution mass spectrometry. Concentrations of PM-TCDD-CEQs ranged from 10 to 85 pg m -3 and from 19 to 87 pg m -3 at the urban and rural site, respectively. By the use of known relative potency factors, the measured concentration of a PAH was converted into a PAH-TCDD-CEQ concentration. ΣPAH-TCDD-CEQ and PM-TCDD-CEQ were highly correlated at both sites ( r2 = 0.90 and 0.69). The calculated ΣPAH-TCDD-CEQs explain between 2% and 20% of the measured PM-TCDD-CEQs. Benzo[ k]fluoranthene was the most important PAH causing approximately 60% of the total ΣPAH-TCDD-CEQ activity. In contrast to NO, CO, PM10, and PM1, the concentration of PM-TCDD-CEQs showed no significant difference between the two sites. No indications were found that road traffic emissions caused elevated concentrations of PM-TCDD-CEQs at the urban traffic site.

  16. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine

    PubMed Central

    Stec, Boguslaw

    2012-01-01

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO2. We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O2 and CO2 bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO2 defines an elusive, preactivation complex that contains a metal cation Mg2+ surrounded by three H2O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming. PMID:23112176

  17. Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-09-18

    Catalytic atom maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the "crowdedness" of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å rmsd of the CAM with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these CAMs were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5'-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase rmsd to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  18. Using Catalytic Atom Maps to Predict the Catalytic Functions Present in Enzyme Active Sites

    PubMed Central

    Nosrati, Geoffrey R.; Houk, K. N.

    2012-01-01

    Catalytic Atom Maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the “crowdedness” of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å RMSD of the Catalytic Atom Map with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these Catalytic Atom Maps were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5′-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase RMSD to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  19. Comparative Study of Composition, Antioxidant, and Antimicrobial Activities of Essential Oils of Selected Aromatic Plants from Balkan Peninsula.

    PubMed

    Stanković, Nemanja; Mihajilov-Krstev, Tatjana; Zlatković, Bojan; Matejić, Jelena; Stankov Jovanović, Vesna; Kocić, Branislava; Čomić, Ljiljana

    2016-05-01

    The objective of the present study to perform a comparative analysis of the chemical composition, antioxidant, and antimicrobial activities of the essential oils of plant species Hyssopus officinalis, Achillea grandifolia, Achillea crithmifolia, Tanacetum parthenium, Laserpitium latifolium, and Artemisia absinthium from Balkan Peninsula. The chemical analysis of essential oils was performed by using gas chromatography and gas chromatography-mass spectrometry. Monoterpenes were dominant among the recorded components, with camphor in T. parthenium, A. grandifolia, and A. crithmifolia (51.4, 45.4, and 25.4 %, respectively), 1,8-cineole in H. officinalis, A. grandifolia, and A. crithmifolia (49.1, 16.4, and 14.8 %, respectively), and sabinene in L. latifolium and A. absinthium (47.8 and 21.5 %). The antiradical and antioxidant activities were determined by using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) and 2,2-diphenyl-1-picrylhydrazyl radical scavenging methods. The essential oil of A. grandifolia has shown the highest antioxidant activity [IC50 of 33.575 ± 0.069 mg/mL for 2,2-diphenyl-1-picrylhydrazyl and 2.510 ± 0.036 mg vitamin C/g for the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) assay]. The antimicrobial activity against 16 multiresistant pathogenic bacteria isolated from human source material was tested by the broth microdilution assay. The resulting minimum inhibitory concentration/minimum bactericidal concentration values ranged from 4.72 to 93.2 mg/mL. Therefore, the essential oils of the plant species included in this study may be considered to be prospective natural sources of antimicrobial substances, and may contribute as effective agents in the battle against bacterial multiresistance. PMID:26891001

  20. Comparative Study of Composition, Antioxidant, and Antimicrobial Activities of Essential Oils of Selected Aromatic Plants from Balkan Peninsula.

    PubMed

    Stanković, Nemanja; Mihajilov-Krstev, Tatjana; Zlatković, Bojan; Matejić, Jelena; Stankov Jovanović, Vesna; Kocić, Branislava; Čomić, Ljiljana

    2016-05-01

    The objective of the present study to perform a comparative analysis of the chemical composition, antioxidant, and antimicrobial activities of the essential oils of plant species Hyssopus officinalis, Achillea grandifolia, Achillea crithmifolia, Tanacetum parthenium, Laserpitium latifolium, and Artemisia absinthium from Balkan Peninsula. The chemical analysis of essential oils was performed by using gas chromatography and gas chromatography-mass spectrometry. Monoterpenes were dominant among the recorded components, with camphor in T. parthenium, A. grandifolia, and A. crithmifolia (51.4, 45.4, and 25.4 %, respectively), 1,8-cineole in H. officinalis, A. grandifolia, and A. crithmifolia (49.1, 16.4, and 14.8 %, respectively), and sabinene in L. latifolium and A. absinthium (47.8 and 21.5 %). The antiradical and antioxidant activities were determined by using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) and 2,2-diphenyl-1-picrylhydrazyl radical scavenging methods. The essential oil of A. grandifolia has shown the highest antioxidant activity [IC50 of 33.575 ± 0.069 mg/mL for 2,2-diphenyl-1-picrylhydrazyl and 2.510 ± 0.036 mg vitamin C/g for the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) assay]. The antimicrobial activity against 16 multiresistant pathogenic bacteria isolated from human source material was tested by the broth microdilution assay. The resulting minimum inhibitory concentration/minimum bactericidal concentration values ranged from 4.72 to 93.2 mg/mL. Therefore, the essential oils of the plant species included in this study may be considered to be prospective natural sources of antimicrobial substances, and may contribute as effective agents in the battle against bacterial multiresistance.

  1. Constituents and Pharmacological Activities of Myrcia (Myrtaceae): A Review of an Aromatic and Medicinal Group of Plants

    PubMed Central

    Cascaes, Márcia Moraes; Guilhon, Giselle Maria Skelding Pinheiro; Andrade, Eloisa Helena de Aguiar; Zoghbi, Maria das Graças Bichara; Santos, Lourivaldo da Silva

    2015-01-01

    Myrcia is one of the largest genera of the economically important family Myrtaceae. Some of the species are used in folk medicine, such as a group known as “pedra-hume-caá” or “pedra-ume-caá” or “insulina vegetal” (insulin plant) that it is used for the treatment of diabetes. The species are an important source of essential oils, and most of the chemical studies on Myrcia describe the chemical composition of the essential oils, in which mono- and sesquiterpenes are predominant. The non-volatile compounds isolated from Myrcia are usually flavonoids, tannins, acetophenone derivatives and triterpenes. Anti-inflammatory, antinociceptive, antioxidant, antimicrobial activities have been described to Myrcia essential oils, while hypoglycemic, anti-hemorrhagic and antioxidant activities were attributed to the extracts. Flavonoid glucosides and acetophenone derivatives showed aldose reductase and α-glucosidase inhibition, and could explain the traditional use of Myrcia species to treat diabetes. Antimicrobial and anti-inflammatory are some of the activities observed for other isolated compounds from Myrcia. PMID:26473832

  2. Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome Y

    2011-01-01

    Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

  3. Parameterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2012-12-01

    Thermokarst features are thought to be an important mechanism for landscape change in permafrost-dominated cold regions, but few such features have been incorporated into full featured landscape models. The root of this shortcoming is that historic observations are not detailed enough to parameterize a model, and the models typically do not include the relevant processes for thermal erosion. A new, dynamic thermokarst feature has been identified at the Caribou-Poker Creek Research Watershed (CPCRW) in the boreal forest of Interior Alaska. Located adjacent to a traditional use trail, this feature terminates directly in Caribou Creek. Erosion within the feature is driven predominantly by fluvial interflow. CPCRW is a Long-Term Ecological Research site underlain by varying degrees of relatively warm, discontinuous permafrost. This poster will describe the suite of measurements that have been undertaken to parameterize the ERODE model for this site, including thorough surveys, time lapse- and aerial photography, and 3-D structure from motion algorithms.

  4. Blogs and Social Network Sites as Activity Systems: Exploring Adult Informal Learning Process through Activity Theory Framework

    ERIC Educational Resources Information Center

    Heo, Gyeong Mi; Lee, Romee

    2013-01-01

    This paper uses an Activity Theory framework to explore adult user activities and informal learning processes as reflected in their blogs and social network sites (SNS). Using the assumption that a web-based space is an activity system in which learning occurs, typical features of the components were investigated and each activity system then…

  5. Distribution and Health Risk Assessment of Polycyclic Aromatic Hydrocarbons in Soil from a Typical Contaminated Urban Coking Sites in Shenyang City.

    PubMed

    Hou, Wei; Zhang, Le; Li, Yue; Zhang, Lihong; Li, Shuxian; Ji, Lan; Dan, Su

    2015-12-01

    This study evaluated the level of PAH pollution in typical contaminated coking sites in Shenyang. Sixty surface soil samples were collected from an area of 1.3 × 10(5) m(2) polluted by PAHs. The concentrations, sources and possible health risks of 16 PAHs in the area were analyzed. The average content of Σ16 PAHs was 6.1 × 10(3) mg/kg. In oral intake, benzo(a)pyrene (BaP) presented the largest exposure risk (hazard quotient HQ = 1.17 × 10(-5)), followed by dibenz(a,h)anthracene (DbA) (HQ = 1.14 × 10(-5)). The non-carcinogenic hazard indices and carcinogenic risks of the PAHs were arranged in the order of BaP > DbA > benzo(b)fluoranthene (BbF) > benz(a)anthracene (BaA) > indeno(1,2,3-cd)pyrene (InP) > benzo(k)fluoranthene (BkF) > chrysene (Chr). Bap and DbA were the principal pollution sources, followed by BbF, BaA, InP, BkF and Nap successively. Oral intake was the main route of PAH entry into the human body.

  6. Distribution and Health Risk Assessment of Polycyclic Aromatic Hydrocarbons in Soil from a Typical Contaminated Urban Coking Sites in Shenyang City.

    PubMed

    Hou, Wei; Zhang, Le; Li, Yue; Zhang, Lihong; Li, Shuxian; Ji, Lan; Dan, Su

    2015-12-01

    This study evaluated the level of PAH pollution in typical contaminated coking sites in Shenyang. Sixty surface soil samples were collected from an area of 1.3 × 10(5) m(2) polluted by PAHs. The concentrations, sources and possible health risks of 16 PAHs in the area were analyzed. The average content of Σ16 PAHs was 6.1 × 10(3) mg/kg. In oral intake, benzo(a)pyrene (BaP) presented the largest exposure risk (hazard quotient HQ = 1.17 × 10(-5)), followed by dibenz(a,h)anthracene (DbA) (HQ = 1.14 × 10(-5)). The non-carcinogenic hazard indices and carcinogenic risks of the PAHs were arranged in the order of BaP > DbA > benzo(b)fluoranthene (BbF) > benz(a)anthracene (BaA) > indeno(1,2,3-cd)pyrene (InP) > benzo(k)fluoranthene (BkF) > chrysene (Chr). Bap and DbA were the principal pollution sources, followed by BbF, BaA, InP, BkF and Nap successively. Oral intake was the main route of PAH entry into the human body. PMID:26508427

  7. Molten salt-supported polycondensation of optically active diacid monomers with an aromatic thiazole-bearing diamine using microwave irradiation.

    PubMed

    Mallakpour, Shadpour; Zadehnazari, Amin

    2014-05-01

    Microwave heating was used to prepare optically active thiazole-bearing poly(amide-imide)s. Polymerization reactions were carried out in the molten tetrabutylammonium bromide as a green molten salt medium and triphenyl phosphite as the homogenizer. Structural elucidation of the compounds was performed by Fourier transform infrared and NMR spectroscopic data and elemental analysis results. The polymeric samples were readily soluble in various organic solvents, forming low-colored and flexible thin films via solution casting. They showed high thermal stability with decomposition temperature being above 360 °C. They were assembled randomly in a nanoscale size.

  8. Molten salt-supported polycondensation of optically active diacid monomers with an aromatic thiazole-bearing diamine using microwave irradiation

    PubMed Central

    Mallakpour, Shadpour; Zadehnazari, Amin

    2013-01-01

    Microwave heating was used to prepare optically active thiazole-bearing poly(amide-imide)s. Polymerization reactions were carried out in the molten tetrabutylammonium bromide as a green molten salt medium and triphenyl phosphite as the homogenizer. Structural elucidation of the compounds was performed by Fourier transform infrared and NMR spectroscopic data and elemental analysis results. The polymeric samples were readily soluble in various organic solvents, forming low-colored and flexible thin films via solution casting. They showed high thermal stability with decomposition temperature being above 360 °C. They were assembled randomly in a nanoscale size. PMID:25685498

  9. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    SciTech Connect

    Not Available

    1993-01-27

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation`s energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization`s ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization`s commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans.

  10. Trimerization of aromatic nitriles

    NASA Technical Reports Server (NTRS)

    Hsu, L. C. (Inventor)

    1977-01-01

    Triazine compounds and cross-linked polymer compositions were made by heating aromatic nitriles to a temperature in the range of about 100 C to about 700 C, in the presence of a catalyst or mixture of catalysts. Aromatic nitrile-modified (terminated and/or appended) imide, benzimidazole, imidazopyrrolone, quinoxaline, and other condensation type prepolymers or their precopolymers were made which were trimerized with or without a filler by the aforementioned catalytic trimerization process.

  11. Active Site Structure and Peroxidase Activity of Oxidatively Modified Cytochrome c Species in Complexes with Cardiolipin.

    PubMed

    Capdevila, Daiana A; Oviedo Rouco, Santiago; Tomasina, Florencia; Tortora, Verónica; Demicheli, Verónica; Radi, Rafael; Murgida, Daniel H

    2015-12-29

    We report a resonance Raman and UV-vis characterization of the active site structure of oxidatively modified forms of cytochrome c (Cyt-c) free in solution and in complexes with cardiolipin (CL). The studied post-translational modifications of Cyt-c include methionine sulfoxidation and tyrosine nitration, which lead to altered heme axial ligation and increased peroxidase activity with respect to those of the wild-type protein. In spite of the structural and activity differences between the protein variants free in solution, binding to CL liposomes induces in all cases the formation of a spectroscopically identical bis-His axial coordination conformer that more efficiently promotes lipid peroxidation. The spectroscopic results indicate that the bis-His form is in equilibrium with small amounts of high-spin species, thus suggesting a labile distal His ligand as the basis for the CL-induced increase in enzymatic activity observed for all protein variants. For Cyt-c nitrated at Tyr74 and sulfoxidized at Met80, the measured apparent binding affinities for CL are ∼4 times larger than for wild-type Cyt-c. On the basis of these results, we propose that these post-translational modifications may amplify the pro-apoptotic signal of Cyt-c under oxidative stress conditions at CL concentrations lower than for the unmodified protein.

  12. Identification of ice nucleation active sites on feldspar dust particles.

    PubMed

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-03-19

    Mineral dusts originating from Earth's crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  13. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles

    PubMed Central

    2015-01-01

    Mineral dusts originating from Earth’s crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  14. Highly Active and Specific Tyrosine Ammonia-Lyases from Diverse Origins Enable Enhanced Production of Aromatic Compounds in Bacteria and Saccharomyces cerevisiae

    PubMed Central

    Stahlhut, Steen Gustav; Li, Mingji; Gaspar, Paula; Siedler, Solvej; Förster, Jochen; Maury, Jérôme; Borodina, Irina

    2015-01-01

    Phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. Lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. We therefore identified 22 sequences in silico using synteny information and aiming for sequence divergence. We performed a comparative in vivo study, expressing the genes intracellularly in bacteria and yeast. When produced heterologously, some enzymes resulted in significantly higher production of p-coumaric acid in several different industrially important production organisms. Three novel enzymes were found to have activity exclusively for phenylalanine, including an enzyme from the low-GC Gram-positive bacterium Brevibacillus laterosporus, a bacterial-type enzyme from the amoeba Dictyostelium discoideum, and a phenylalanine ammonia-lyase from the moss Physcomitrella patens (producing 230 μM cinnamic acid per unit of optical density at 600 nm [OD600]) in the medium using Escherichia coli as the heterologous host). Novel tyrosine ammonia-lyases having higher reported substrate specificity than previously characterized enzymes were also identified. Enzymes from Herpetosiphon aurantiacus and Flavobacterium johnsoniae resulted in high production of p-coumaric acid in Escherichia coli (producing 440 μM p-coumaric acid OD600 unit−1 in the medium) and in Lactococcus lactis. The enzymes were also efficient in Saccharomyces cerevisiae, where p-coumaric acid accumulation was improved 5-fold over that in strains expressing previously characterized tyrosine ammonia-lyases. PMID:25911487

  15. Accumulation of halogenated aromatic hydrocarbons and activities of cytochrome P450 and glutathione S-transferase in crabs (Eriocheir japonicus) from Japanese rivers

    SciTech Connect

    Ishizuka, Mayumi; Iwata, Hisato; Kazusaka, Akio; Fujita, Shoichi; Sakiyama, Takanori; Fukushima, Minoru

    1998-08-01

    The hepatopancreases of freshwater crabs (Eriocheir japonicus) collected from three Japanese rivers were analyzed for planar halogenated aromatic hydrocarbons (HAHs), including polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and coplanar polychlorinated biphenyls (PCBs). The hepatic glutathione S-transferase (GST)-dependent enzyme activities in the crab hepatopancreas were also measured to examine their potential as biomarkers for the contaminants. Crabs from the Tone River, which runs through industrial, agricultural, and urban areas, have the highest concentrations of HAHs (4,100 pg/g fat weight), followed by those from the Barato River (2,430--2,970 pg/g fat weight), whereas crabs from the Shiribetsu River were relatively less contaminated (1,350--1,800 pg/g fat weight). Identification and numerous PCDD and PCDF congeners in crabs from the Barato and Shiribetsu Rivers were notably contaminated with 1,3,6,8- and 1,3,7,9-TeCDD congeners, which suggests that a possible source was chlornitrofen, which has been extensively used in paddy fields as a herbicide. Calculation of 2,3,7,8-tetrachlorinated dibenzo-p-dioxin toxic equivalents (TEQs) showed that the causal contaminants of higher TEQs in crabs from the Tone River (94.7 TEQ picograms per gram fat weight) were PCDDs and PCDFs, although the most important contributor to the total TEQs was coplanar PCBs (49.95%). The crab hepatopancreas appeared to have abilities to transfer glutathione to 1-chloro-2,4-nitrobenzene (CDNB) and 3,4-dichloronitrobenzene (DCNB). The crabs with the highest TEQ levels showed the highest GST activities.

  16. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions. PMID:25999343

  17. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions.

  18. Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts.

    PubMed

    Wang, Lu-Cun; Friend, C M; Fushimi, Rebecca; Madix, Robert J

    2016-07-01

    The activation of molecular O2 as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O2 activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O2 dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O2 dissociation is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O2 dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction. PMID:27376884

  19. Aromatic Polyimide Foam

    NASA Technical Reports Server (NTRS)

    Weiser, Erik S. (Inventor); St.Clair, Terry L. (Inventor); Echigo, Yoshiaki (Inventor); Kaneshiro, Hisayasu (Inventor)

    2000-01-01

    A mechanically undensified aromatic polyimide foam is made from an aromatic polyimide precursor solid residuum and has the following combination of properties: a density according to ASTM D-3574A of about 0.5 pounds/cu.ft to about 20 pounds/cu.ft; a compression strength according to ASTM D-3574C of about 1.5 psi to about 1500 psi; and a limiting oxygen index according to ASTM D-2863 of about 35% oxygen to about 75% oxygen at atmospheric pressure. The aromatic polyimide foam has no appreciable solid inorganic contaminants which are residues of inorganic blowing agents. The aromatic polyimide which constitutes the aromatic polyimide foam has a glass transition temperature (Tg) by differential scanning calorimetry of about 235 C to about 400 C; and a thermal stability of 0 to about 1% weight loss at 204 C as determined by thermogravinietric analysis (TGA). The aromatic polyimide foam has utility as foam insulation and as structural foam, for example, for aeronautical, aerospace and maritime applications.

  20. Ultrahigh Gas Storage both at Low and High Pressures in KOH-Activated Carbonized Porous Aromatic Frameworks

    PubMed Central

    Li, Yanqiang; Ben, Teng; Zhang, Bingyao; Fu, Yao; Qiu, Shilun

    2013-01-01

    The carbonized PAF-1 derivatives formed by high-temperature KOH activation showed a unique bimodal microporous structure located at 0.6 nm and 1.2 nm and high surface area. These robust micropores were confirmed by nitrogen sorption experiment and high-resolution transmission electron microscopy (TEM). Carbon dioxide, methane and hydrogen sorption experiments indicated that these novel porous carbon materials have significant gas sorption abilities in both low-pressure and high-pressure environments. Moreover the methane storage ability of K-PAF-1-750 is among the best at 35 bars, and its low-pressure gas adsorption abilities are also comparable to the best porous materials in the world. Combined with excellent physicochemical stability, these materials are very promising for industrial applications such as carbon dioxide capture and high-density clean energy storage. PMID:23939301

  1. Inhibition of the mutagenicity of bay-region diol epoxides of polycyclic aromatic hydrocarbons by naturally occurring plant phenols: Exceptional activity of ellagic acid

    PubMed Central

    Wood, Alexander W.; Huang, Mou-Tuan; Chang, Richard L.; Newmark, Harold L.; Lehr, Roland E.; Yagi, Haruhiko; Sayer, Jane M.; Jerina, Donald M.; Conney, Allan H.

    1982-01-01

    concentrations of ellagic acid are needed to inhibit the mutagenic activity of the chemically less reactive bay-region diol epoxides of benz[a]anthracene, chrysene, and benzo[c]phenanthrene. These studies demonstrate that ellagic acid is a potent antagonist of the adverse biological effects of the ultimate carcinogenic metabolites of several polycyclic aromatic hydrocarbons and suggest that this naturally occurring plant phenol, normally ingested by humans, may inhibit the carcinogenicity of polycyclic aromatic hydrocarbons. PMID:6752950

  2. Diversity of organotrophic bacteria, activity of dehydrogenases and urease as well as seed germination and root growth Lepidium sativum, Sorghum saccharatum and Sinapis alba under the influence of polycyclic aromatic hydrocarbons.

    PubMed

    Lipińska, Aneta; Wyszkowska, Jadwiga; Kucharski, Jan

    2015-12-01

    Polycyclic aromatic hydrocarbons are organic compounds with highly toxic, carcinogenic, and mutagenic properties, which adversely affect the basic biological parameters of the soil, including the count of microorganisms, and the enzymatic activity. In addition to disturbances to the biological activity of the soil, PAHs may also exhibit toxic effects on plants. In view of the above, the study involved testing aimed at the determination of the effects of polycyclic aromatic hydrocarbons in a form of naphthalene, phenanthrene, anthracene and pyrene on the count, colony development (CD) index, ecophysiological (EP) diversity index of organotrophic bacteria, and the activity of soil dehydrogenases and soil urease. Moreover, an attempt was made to determine the soil's resistance based on the activity of the above-listed enzymes, and the effect of polycyclic aromatic hydrocarbons on seed germination and root growth was assessed by Lepidium sativum, Sorghum saccharatum, and Sinapis alba. In addition, the species of bacteria found in a soil subjected to strong pressure of polycyclic aromatic hydrocarbons were isolated. The experiment was performed in a laboratory on samples of loamy sand. Polycyclic aromatic hydrocarbons were introduced into the soil in an amount of 0, 1000, 2000, and 4000 mg kg(-1) of soil dry matter. Germination and growth of cress (L. sativum), white mustard (S. alba), and sweet sorghum (S. saccharatum) were determined using Phytotoxkit tests. It was found that the tested PAHs increased the average colony counts of organotrophic soil bacteria; pyrene did so to the greatest extent (2.2-fold relative to non-contaminated soil), phenanthrene to the smallest extent (1.4-fold relative to non-contaminated soil). None of the PAHs changed the value of the bacterial colony development (CD) index, while anthracene and pyrene increased the value of the eco-physiological (EP) diversity indicator. PAHs lowered the activity of the tested enzymes. The activity of

  3. Diversity of organotrophic bacteria, activity of dehydrogenases and urease as well as seed germination and root growth Lepidium sativum, Sorghum saccharatum and Sinapis alba under the influence of polycyclic aromatic hydrocarbons.

    PubMed

    Lipińska, Aneta; Wyszkowska, Jadwiga; Kucharski, Jan

    2015-12-01

    Polycyclic aromatic hydrocarbons are organic compounds with highly toxic, carcinogenic, and mutagenic properties, which adversely affect the basic biological parameters of the soil, including the count of microorganisms, and the enzymatic activity. In addition to disturbances to the biological activity of the soil, PAHs may also exhibit toxic effects on plants. In view of the above, the study involved testing aimed at the determination of the effects of polycyclic aromatic hydrocarbons in a form of naphthalene, phenanthrene, anthracene and pyrene on the count, colony development (CD) index, ecophysiological (EP) diversity index of organotrophic bacteria, and the activity of soil dehydrogenases and soil urease. Moreover, an attempt was made to determine the soil's resistance based on the activity of the above-listed enzymes, and the effect of polycyclic aromatic hydrocarbons on seed germination and root growth was assessed by Lepidium sativum, Sorghum saccharatum, and Sinapis alba. In addition, the species of bacteria found in a soil subjected to strong pressure of polycyclic aromatic hydrocarbons were isolated. The experiment was performed in a laboratory on samples of loamy sand. Polycyclic aromatic hydrocarbons were introduced into the soil in an amount of 0, 1000, 2000, and 4000 mg kg(-1) of soil dry matter. Germination and growth of cress (L. sativum), white mustard (S. alba), and sweet sorghum (S. saccharatum) were determined using Phytotoxkit tests. It was found that the tested PAHs increased the average colony counts of organotrophic soil bacteria; pyrene did so to the greatest extent (2.2-fold relative to non-contaminated soil), phenanthrene to the smallest extent (1.4-fold relative to non-contaminated soil). None of the PAHs changed the value of the bacterial colony development (CD) index, while anthracene and pyrene increased the value of the eco-physiological (EP) diversity indicator. PAHs lowered the activity of the tested enzymes. The activity of

  4. Impact of salinity and dispersed oil on adsorption of dissolved aromatic hydrocarbons by activated carbon and organoclay.

    PubMed

    Younker, Jessica M; Walsh, Margaret E

    2015-12-15

    Adsorption capacity of phenol and naphthalene by powdered activated carbon (PAC), a commercial organoclay (OC) and a lab synthesized organoclay (BTMA) was studied using batch adsorption experiments under variable feed water quality conditions including single- and multi- solute conditions, fresh water, saline water and oily-and-saline water. Increasing salinity levels was found to reduce adsorption capacity of OC, likely due to destabilization, aggregation and subsequent removal of organoclay from the water column, but did not negatively impact adsorption capacity of PAC or BTMA. Increased dispersed oil concentrations were found to reduce the surface area of all adsorbents. This decreased the adsorption capacity of PAC for both phenol and naphthalene, and reduced BTMA adsorption of phenol, but did not negatively affect naphthalene removals by either organoclay. The presence of naphthalene as a co-solute significantly reduced phenol adsorption by PAC, but had no impact on organoclay adsorption. These results indicated that adsorption by PAC occurred via a surface adsorption mechanism, while organoclay adsorption occurred by hydrophobic or pi electron interactions. In general, PAC was more sensitive to changes in water quality than either of the organoclays evaluated in this study. However, PAC exhibited a higher adsorption capacity for phenol and naphthalene compared to both organoclays even in adverse water quality conditions. PMID:26259095

  5. Possible active site of the sweet-tasting protein thaumatin.

    PubMed

    Slootstra, J W; De Geus, P; Haas, H; Verrips, C T; Meloen, R H

    1995-10-01

    Epitopes on thaumatin and monellin were studied using the PEPSCAN-technology. The antibodies used were raised against thaumatin. Only antibodies that, in an ELISA, both recognized thaumatin and monellin were used in the PEPSCAN-analyses. On thaumatin two major overlapping epitopes were identified. On monellin no epitopes could be identified. The identified epitope region on thaumatin shares structural features with various peptide and protein sweeteners. It contains an aspartame-like site which is formed by Asp21 and Phe80, tips of the two extruding loops KGDAALDAGGR19-29 and CKRFGRPP77-84, which are spatially positioned next to each other. Furthermore, sub-sequences of the KGDAALDAGGR19-29 loop are similar to peptide-sweeteners such as L-Asp-D-Ala-L-Ala-methyl ester and L-Asp-D-Ala-Gly-methyl ester. Since the aspartame-like Asp21-Phe80 site and the peptide-sweetener-like sequences are also not present in non-sweet thaumatin-like proteins it is postulated that the KGDAALDAGGR19-29- and CKRFGRPP77-84 loop contain important sweet-taste determinants. This region has previously not been implicated as a sweet-taste determinant of thaumatin.

  6. Purification of aromatic hydrocarbons via fibrous activated carbon/photocatalytic composite coupled with UV light-emitting diodes.

    PubMed

    Jo, Wan-Kuen

    2013-01-01

    In the present study, the applicability of light-emitting diodes (LEDs) to a fibrous activated carbon (FAC)/titania (TiO2) composite used for the purification of gas-phase benzene, toluene, ethyl benzene and xylene was evaluated. The surface and morphological properties of the FAC and prepared FAC/TiO2 composite were investigated by X-ray diffraction and scanning electron microscopy. The study protocol included two different tests, comparison of FAC and the FAC/TiO2 composite for BTEX removal efficiency and evaluation of the FAC/TiO2 composite for benzene and toluene removal efficiency under differing operation conditions. The time-series ratios obtained with the FAC/TiO2 composite showed longer removal times for all target compounds when compared to those of FAC alone. For both benzene and toluene, the breakthrough time decreased with the stream flow rate, whereas it increased with increasing light intensity under the experimental conditions employed in this study. The breakthrough time of benzene and toluene increased as increasing amounts of TiO2 were coated onto the surface of FAC between 11 and 229 mg-TiO2 (g-FAC)(-1), but decreased as the amount of TiO2 increased to 451 mg (g-FAC)(-1). These findings indicate that the optimal TiO2 weight for the removal process of benzene and toluene via the FAC/TiO2 composite is between 229 and 451 mg-TiO2 (g-FAC)(-1).

  7. Assessment of activation products in the Savannah River Site environment

    SciTech Connect

    Carlton, W.H.; Denham, M.

    1996-07-01

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: {sup 32}P, {sup 51}Cr, {sup 60}C, and {sup 65}Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated.

  8. Ortho-7 bound to the active-site gorge of free and OP-conjugated acetylcholinesterase: cation-π interactions.

    PubMed

    Pathak, Arup Kumar; Bandyopadhyay, Tusar

    2016-01-01

    Despite the immense importance of cation-π interactions prevailing in bispyridinium drug acetylcholinesterase (AChE) complexes, a precise description of cation-π interactions at molecular level has remained elusive. Here, we consider a bispyridinium drug, namely, ortho-7 in three different structures of AChE, with and without complexation with organophosphorus (OP) compounds for detailed investigation using all atom molecular dynamics simulation. By quantum mechanical calculations, Y72, W86, Y124, W286, Y337, and Y341 aromatic residues of the enzyme are investigated for possible cation-π interactions with ortho-7. The cation-π interactions in each of the protein-drug complexes are studied using distance, angle, a suitable functional form of them, and electrostatic criteria. The variation of cation-π functional is remarkably consistent with that of the Columbic variation. It is clearly observed that cation-π interactions for some of the residues in the catalytic active site (CAS) and peripheral anionic site (PAS) of the enzyme are either enhanced or reduced based on the nature of OP conjugation (i.e., nerve gas, tabun or pesticide, fenamiphos) when compared with the OP-free enzyme. The strength of cation-π interaction is strongly dependent on the type OP conjugation. The effect of conjugation at CAS is also seen to influence the cation-π interaction at the PAS region. The variation of cation-π interactions on the type of conjugating OP compounds might be suggestive of a reason as to why wide spectrum drug against any OP poisoning is yet to arrive in the market.

  9. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    PubMed Central

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  10. Characterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2013-12-01

    The goal of this project is to estimate volume loss of soil over time from this site, provide parameterizations on erodibility of ice rich permafrost and serve as a baseline for future landscape evolution simulations. Located in the zone of discontinuous permafrost, the interior region of Alaska (USA) is home to a large quantity of warm, unstable permafrost that is both high in ice content and has soil temperatures near the freezing point. Much of this permafrost maintains a frozen state despite the general warming air temperature trend in the region due to the presence of a thick insulating organic mat and a dense root network in the upper sub-surface of the soil column. At a rapidly evolving thermo-erosion site, located within the Caribou-Poker Creeks Research Watershed (part of the Bonanza Creek LTER) near Chatanika, Alaska (N65.140, W147.570), the protective organic layer and associated plants were disturbed by an adjacent traditional use trail and the shifting of a groundwater spring. These triggers have led to rapid geomorphological change on the landscape as the soil thaws and sediment is transported into the creek at the valley bottom. Since 2006 (approximately the time of initiation), the thermal erosion has grown to 170 meters length, 3 meters max depth, and 15 meters maximum width. This research combines several data sets: DGPS survey, imagery from an extremely low altitude pole-based remote sensing (3 to 5 meters above ground level), and imagery from an Unmanned Aerial System (UAS) at about 60m altitude.

  11. The aromatic stacking interactions between proteins and their macromolecular ligands.

    PubMed

    Rahman, Mohammad Mizanur; Muhseen, Ziyad Tariq; Junaid, Muhammad; Zhang, Houjin

    2015-01-01

    Aromatic stacking interactions arise from the attractive force between the π-electron clouds in the neighboring aromatic groups. The aromatic stacking is common between proteins and small molecules. The stacking interactions at the interfaces of proteins and other macromolecules are relatively rare. However it contributes to a significant portion of the stabilizing forces. In the proteinprotein complexes, aromatic interactions are involved in the protein oligomerization, such as dimer, trimer and tetramer formation. Also, aromatic residues can bind to nanoparticles through stacking interactions which offer them stronger affinity than other residues. These interactions play crucial roles in proteinnanoparticle conjugation. In the protein-nucleotide complexes, the specific recognitions are realized through stacking interactions between aromatic residues and the bases in the nucleotides. Many nucleoproteins use aromatic stacking to recognize binding site on DNA or RNA. Stacking interactions are involved in the process of mismatch repair, strand separation, deadenylation, degradation and RNA cap binding. They are proved to be important for the stability of complexes. The aromatic stacking is also the underlying reasons of many fatal diseases such as Alzheimer, cancer and cardiovascular diseases. The chemicals that can block the stacking interactions could have potential pharmaceutical values. In this review, we summarize recent finding regarding the functions of aromatic stacking interactions in the protein-macromolecule complexes. Our aim is to understand the mechanisms underlying the stacking-mediated complex formation and facilitate the development of drugs and other bio-products.

  12. Aromatic amines and cancer.

    PubMed

    Vineis, P; Pirastu, R

    1997-05-01

    Epidemiological evidence on the relation between aromatic amines and cancer risk is reviewed. In particular, cancer risk in humans resulting from exposure to aromatic amines from occupational sources and tobacco smoking is assessed with reference to ecologic, cohort, and case-control studies. Seven arylamines have been classified by the International Agency for Research on Cancer: benzidine-based dyes and MOCA (4,4'-methylene bis 2-choloroaniline) were considered 'probably' carcinogenic, Group 2A, because of a high level of evidence in experimental animals; two occupational chemicals (2-naphthylamine and benzidine), one drug (Chlornaphazine), and two manufacturing processes (manufacture of auramine and magenta) were included in Group 1 on the basis of 'sufficient' evidence of carcinogenicity in humans. Occupational exposures to aromatic amines explain up to 25 percent of bladder cancers in some areas of Western countries; these estimates might be higher in limited areas of developing countries. Aromatic amines contaminate the ambient air as a component of environmental tobacco smoke. There is increasing evidence that the excess of bladder cancer in smokers is attributable to aromatic amines rather than to other contaminants of tobacco smoke such as polycyclic aromatic hydrocarbons (PAH). A modulating role in the risk of bladder cancer associated with exposure to aromatic amines is played by metabolic polymorphisms, such as the N-acetyltransferase genotype, raising important social and ethical issues. The consistent observation of a difference between men and women in bladder cancer risk, after allowing for known risk factors, suggests consideration of gender-related biological determinants for future investigation.

  13. Molecular Basis for Enzymatic Sulfite Oxidation -- HOW THREE CONSERVED ACTIVE SITE RESIDUES SHAPE ENZYME ACTIVITY

    SciTech Connect

    Bailey, Susan; Rapson, Trevor; Johnson-Winters, Kayunta; Astashkin, Andrei; Enemark, John; Kappler, Ulrike

    2008-11-10

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (~;;60 and 200 s-1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

  14. Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

    PubMed

    Miner, Kyle D; Kurtz, Donald M

    2016-02-16

    HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

  15. Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems.

    PubMed

    Ghanakota, Phani; Carlson, Heather A

    2016-08-25

    Mixed-solvent molecular dynamics (MixMD) is a hotspot-mapping technique that relies on molecular dynamics simulations of proteins in binary solvent mixtures. Previous work on MixMD has established the technique's effectiveness in capturing binding sites of small organic compounds. In this work, we show that MixMD can identify both competitive and allosteric sites on proteins. The MixMD approach embraces full protein flexibility and allows competition between solvent probes and water. Sites preferentially mapped by probe molecules are more likely to be binding hotspots. There are two important requirements for the identification of ligand-binding hotspots: (1) hotspots must be mapped at very high signal-to-noise ratio and (2) the hotspots must be mapped by multiple probe types. We have developed our mapping protocol around acetonitrile, isopropanol, and pyrimidine as probe solvents because they allowed us to capture hydrophilic, hydrophobic, hydrogen-bonding, and aromatic interactions. Charged probes were needed for mapping one target, and we introduce them in this work. In order to demonstrate the robust nature and wide applicability of the technique, a combined total of 5 μs of MixMD was applied across several protein targets known to exhibit allosteric modulation. Most notably, all the protein crystal structures used to initiate our simulations had no allosteric ligands bound, so there was no preorganization of the sites to predispose the simulations to find the allosteric hotspots. The protein test cases were ABL Kinase, Androgen Receptor, CHK1 Kinase, Glucokinase, PDK1 Kinase, Farnesyl Pyrophosphate Synthase, and Protein-Tyrosine Phosphatase 1B. The success of the technique is demonstrated by the fact that the top-four sites solely map the competitive and allosteric sites. Lower-ranked sites consistently map other biologically relevant sites, multimerization interfaces, or crystal-packing interfaces. Lastly, we highlight the importance of including protein

  16. Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole.

    PubMed

    Zhang, Xuwang; Qu, Yuanyuan; Ma, Qiao; Zhang, Zhaojing; Li, Duanxing; Wang, Jingwei; Shen, Wenli; Shen, E; Zhou, Jiti

    2015-01-01

    Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.

  17. Mechanistic quantitative structure-activity relationship model for the photoinduced toxicity of polycyclic aromatic hydrocarbons. 1: Physical model based on chemical kinetics in a two-compartment system

    SciTech Connect

    Krylov, S.N.; Huang, X.D.; Zeiler, L.F.; Dixon, D.G.; Greenberg, B.M.

    1997-11-01

    A quantitative structure-activity relationship model for the photoinduced toxicity of 16 polycyclic aromatic hydrocarbons (PAHs) to duckweed (Lemna gibba) in simulated solar radiation (SSR) was developed. Lemna gibba was chosen for this study because toxicity could be considered in two compartments: water column and leaf tissue. Modeling of photoinduced toxicity was described by photochemical reactions between PAHs and a hypothetical group of endogenous biomolecules (G) required for normal growth, with damage to G by PAHs and/or photomodified PAHs in SSR resulting in impaired growth. The reaction scheme includes photomodification of PAHs, uptake of PAHs into leaves, triplet-state formation of intact PAHs, photosensitization reactions that damage G, and reactions between photomodified PAHs and G. The assumptions used were: the PAH photomodification rate is slower than uptake of chemicals into leaves, the PAH concentration in aqueous solution is nearly constant during a toxicity test, the fluence rate of actinic radiation is lower within leaves than in the aqueous phase, and the toxicity of intact PAHs in the dark is negligible. A series of differential equations describing the reaction kinetics of intact and photomodifed PAHs with G was derived. The resulting equation for PAH toxicity was a function of treatment period, initial PAH concentration, relative absorbance of SSR by each PAH, quantum yield for formation of triplet-state PAH, and rate of PAH photomodification. Data for growth in the presence of intact and photomodified PAHs were used to empirically solve for a photosensitization constant (PSC) and a photomodification constant (PMC) for each of the 16 PAHs tested. For 9 PAHs the PMC dominates and for 7 PAHs the PSC dominates.

  18. Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole

    PubMed Central

    Zhang, Xuwang; Qu, Yuanyuan; Ma, Qiao; Zhang, Zhaojing; Li, Duanxing; Wang, Jingwei; Shen, Wenli; Shen, E; Zhou, Jiti

    2015-01-01

    Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole. PMID:25928424

  19. A rapid and direct method for the determination of active site accessibility in proteins based on ESI-MS and active site titrations.

    PubMed

    O'Farrell, Norah; Kreiner, Michaela; Moore, Barry D; Parker, Marie-Claire

    2006-11-01

    We have developed an electrospray ionisation mass spectrometry (ESI-MS) technique that can be applied to rapidly determine the number of intact active sites in proteins. The methodology relies on inhibiting the protein with an active-site irreversible inhibitor and then using ESI-MS to determine the extent of inhibition. We have applied this methodology to a test system: a serine protease, subtilisin Carlsberg, and monitored the extent of inhibition by phenylmethylsulfonyl fluoride (PMSF), an irreversible serine hydrolase inhibitor as a function of the changes in immobilisation and hydration conditions. Two types of enzyme preparation were investigated, lyophilised enzymes and protein-coated microcrystals (PCMC).

  20. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand.

    PubMed

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins' active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  1. Marine Biology Field Trip Sites. Ocean Related Curriculum Activities.

    ERIC Educational Resources Information Center

    Pauls, John

    The ocean affects all of our lives. Therefore, awareness of and information about the interconnections between humans and oceans are prerequisites to making sound decisions for the future. Project ORCA (Ocean Related Curriculum Activities) has developed interdisciplinary curriculum materials designed to meet the needs of students and teachers…

  2. Endolysosomes Are the Principal Intracellular Sites of Acid Hydrolase Activity.

    PubMed

    Bright, Nicholas A; Davis, Luther J; Luzio, J Paul

    2016-09-12

    The endocytic delivery of macromolecules from the mammalian cell surface for degradation by lysosomal acid hydrolases requires traffic through early endosomes to late endosomes followed by transient (kissing) or complete fusions between late endosomes and lysosomes. Transient or complete fusion results in the formation of endolysosomes, which are hybrid organelles from which lysosomes are re-formed. We have used synthetic membrane-permeable cathepsin substrates, which liberate fluorescent reporters upon proteolytic cleavage, as well as acid phosphatase cytochemistry to identify which endocytic compartments are acid hydrolase active. We found that endolysosomes are the principal organelles in which acid hydrolase substrates are cleaved. Endolysosomes also accumulated acidotropic probes and could be distinguished from terminal storage lysosomes, which were acid hydrolase inactive and did not accumulate acidotropic probes. Using live-cell microscopy, we have demonstrated that fusion events, which form endolysosomes, precede the onset of acid hydrolase activity. By means of sucrose and invertase uptake experiments, we have also shown that acid-hydrolase-active endolysosomes and acid-hydrolase-inactive, terminal storage lysosomes exist in dynamic equilibrium. We conclude that the terminal endocytic compartment is composed of acid-hydrolase-active, acidic endolysosomes and acid hydrolase-inactive, non-acidic, terminal storage lysosomes, which are linked and function in a lysosome regeneration cycle. PMID:27498570

  3. Outside-binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1.

    PubMed

    Tolentino-Lopez, Luis; Segura-Cabrera, Aldo; Reyes-Loyola, Paola; Zimic, Mirko; Quiliano, Miguel; Briz, Veronica; Muñoz-Fernández, Angeles; Rodríguez-Pérez, Mario; Ilizaliturri-Flores, Ian; Correa-Basurto, Jose

    2013-01-01

    The recent occurrence of 2009 influenza A (H1N1) pandemic as well as others has raised concern of a far more dangerous outcome should this virus becomes resistant to current drug therapies. The number of clinical cases that are resistant to oseltamivir (Tamiflu®) is larger than the limited number of neuraminidase (NA) mutations (H275Y, N295S, and I223R) that have been identified at the active site and that are associated to oseltamivir resistance. In this study, we have performed a comparative analysis between a set of NAs that have the most representative mutations located outside the active site. The recently crystallized NA-oseltamivir complex (PDB ID: 3NSS) was used as a wild-type structure. After selecting the target NA sequences, their three-dimensional (3D) structure was built using 3NSS as a template by homology modeling. The 3D NA models were refined by molecular dynamics (MD) simulations. The refined models were used to perform a docking study, using oseltamivir as a ligand. Furthermore, the docking results were refined by free-energy analysis using the MM-PBSA method. The analysis of the MD simulation results showed that the NA models reached convergence during the first 10 ns. Visual inspection and structural measures showed that the mutated NA active sites show structural variations. The docking and MM-PBSA results from the complexes showed different binding modes and free energy values. These results suggest that distant mutations located outside the active site of NA affect its structure and could be considered to be a new source of resistance to oseltamivir, which agrees with reports in the clinical literature.

  4. Active site proton delivery and the lyase activity of human CYP17A1

    SciTech Connect

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G.

    2014-01-03

    equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis.

  5. Identification of inhibitors against the potential ligandable sites in the active cholera toxin.

    PubMed

    Gangopadhyay, Aditi; Datta, Abhijit

    2015-04-01

    The active cholera toxin responsible for the massive loss of water and ions in cholera patients via its ADP ribosylation activity is a heterodimer of the A1 subunit of the bacterial holotoxin and the human cytosolic ARF6 (ADP Ribosylation Factor 6). The active toxin is a potential target for the design of inhibitors against cholera. In this study we identified the potential ligandable sites of the active cholera toxin which can serve as binding sites for drug-like molecules. By employing an energy-based approach to identify ligand binding sites, and comparison with the results of computational solvent mapping, we identified two potential ligandable sites in the active toxin which can be targeted during structure-based drug design against cholera. Based on the probe affinities of the identified ligandable regions, docking-based virtual screening was employed to identify probable inhibitors against these sites. Several indole-based alkaloids and phosphates showed strong interactions to the important residues of the ligandable region at the A1 active site. On the other hand, 26 top scoring hits were identified against the ligandable region at the A1 ARF6 interface which showed strong hydrogen bonding interactions, including guanidines, phosphates, Leucopterin and Aristolochic acid VIa. This study has important implications in the application of hybrid structure-based and ligand-based methods against the identified ligandable sites using the identified inhibitors as reference ligands, for drug design against the active cholera toxin.

  6. Encroachment of Human Activity on Sea Turtle Nesting Sites

    NASA Astrophysics Data System (ADS)

    Ziskin, D.; Aubrecht, C.; Elvidge, C.; Tuttle, B.; Baugh, K.; Ghosh, T.

    2008-12-01

    The encroachment of anthropogenic lighting on sea turtle nesting sites poses a serious threat to the survival of these animals [Nicholas, 2001]. This danger is quantified by combining two established data sets. The first is the Nighttime Lights data produced by the NOAA National Geophysical Data Center [Elvidge et al., 1997]. The second is the Marine Turtle Database produced by the World Conservation Monitoring Centre (WCMC). The technique used to quantify the threat of encroachment is an adaptation of the method described in Aubrecht et al. [2008], which analyzes the stress on coral reef systems by proximity to nighttime lights near the shore. Nighttime lights near beaches have both a direct impact on turtle reproductive success since they disorient hatchlings when they mistake land-based lights for the sky-lit surf [Lorne and Salmon, 2007] and the lights are also a proxy for other anthropogenic threats. The identification of turtle nesting sites with high rates of encroachment will hopefully steer conservation efforts to mitigate their effects [Witherington, 1999]. Aubrecht, C, CD Elvidge, T Longcore, C Rich, J Safran, A Strong, M Eakin, KE Baugh, BT Tuttle, AT Howard, EH Erwin, 2008, A global inventory of coral reef stressors based on satellite observed nighttime lights, Geocarto International, London, England: Taylor and Francis. In press. Elvidge, CD, KE Baugh, EA Kihn, HW Kroehl, ER Davis, 1997, Mapping City Lights with Nighttime Data from the DMSP Operational Linescan System, Photogrammatic Engineering and Remote Sensing, 63:6, pp. 727-734. Lorne, JK, M Salmon, 2007, Effects of exposure to artificial lighting on orientation of hatchling sea turtles on the beach and in the ocean, Endangered Species Research, Vol. 3: 23-30. Nicholas, M, 2001, Light Pollution and Marine Turtle Hatchlings: The Straw that Breaks the Camel's Back?, George Wright Forum, 18:4, p77-82. Witherington, BE, 1999, Reducing Threats To Nesting Habitat, Research and Management Techniques for

  7. The aromatic ene reaction

    PubMed Central

    Niu, Dawen; Hoye, Thomas R.

    2014-01-01

    The ene reaction is a pericyclic process in which an alkene having an allylic hydrogen atom (the ene donor) reacts with a second unsaturated species (the enophile) to form a new product with a transposed π-bond. The aromatic ene reaction, in which the alkene component is embedded in an aromatic ring, has only been reported in a few (four) instances and has proceeded in low yield (≤6%). Here we show efficient aromatic ene reactions in which a thermally generated aryne engages a pendant m-alkylarene substituent to produce a dearomatized isotoluene, itself another versatile but rare reactive intermediate. Our experiments were guided by computational studies that revealed structural features conducive to the aromatic ene process. We proceeded to identify a cascade comprising three reactions: (i) hexadehydro-Diels-Alder (for aryne generation), (ii) intramolecular aromatic ene, and (iii) bimolecular Alder ene. The power of this cascade is evident from the structural complexity of the final products, the considerable scope, and the overall efficiency of these multi-stage, reagent- and byproduct-free, single-pot transformations. PMID:24345944

  8. Reduction of Urease Activity by Interaction with the Flap Covering the Active Site

    PubMed Central

    Macomber, Lee; Minkara, Mona S.; Hausinger, Robert P.; Merz, Kenneth M.

    2015-01-01

    With the increasing appreciation for the human microbiome coupled with the global rise of antibiotic resistant organisms, it is imperative that new methods be developed to specifically target pathogens. To that end, a novel computational approach was devised to identify compounds that reduce the activity of urease, a medically important enzyme of Helicobacter pylori, Proteus mirabilis, and many other microorganisms. Urease contains a flexible loop that covers its active site; Glide was used to identify small molecules predicted to lock this loop in an open conformation. These compounds were screened against the model urease from Klebsiella aerogenes and the natural products epigallocatechin and quercetin were shown to inhibit at low and high micromolar concentrations, respectively. These molecules exhibit a strong time-dependent inactivation of urease that was not due to their oxygen sensitivity. Rather, these compounds appear to inactivate urease by reacting with a specific Cys residue located on the flexible loop. Substitution of this cysteine by alanine in the C319A variant increased the urease resistance to both epigallocatechin and quercetin, as predicted by the computational studies. Protein dynamics are integral to the function of many enzymes; thus, identification of compounds that lock an enzyme into a single conformation presents a useful approach to define potential inhibitors. PMID:25594724

  9. Interrogation of Global Active Site Occupancy of a Fungal Iterative Polyketide Synthase Reveals Strategies for Maintaining Biosynthetic Fidelity

    PubMed Central

    Vagstad, Anna L.; Bumpus, Stefanie B.; Belecki, Katherine; Kelleher, Neil L.; Townsend, Craig A.

    2012-01-01

    Nonreducing iterative polyketide synthases (NR-PKSs) are responsible for assembling the core of fungal aromatic natural products with diverse biological properties. Despite recent advances in the field, many mechanistic details of polyketide assembly by these megasynthases remain unknown. To expand our understanding of substrate loading, polyketide elongation, cyclization, and product release, active site occupancy and product output were explored by Fourier transform mass spectrometry using the norsolorinic acid anthrone-producing polyketide synthase, PksA, from the aflatoxin biosynthetic pathway in Aspergillus parasiticus. Here we report the simultaneous observation of covalent intermediates from all catalytic domains of PksA from in vitro reconstitution reactions. The data provide snapshots of iterative catalysis and reveal an underappreciated editing function for the C-terminal thioesterase domain beyond its recently established synthetic role in Claisen/Dieckmann cyclization and product release. The specificity of thioesterase catalyzed hydrolysis was explored using biosynthetically relevant protein-bound and small molecule acyl substrates, and demonstrated activity against hexanoyl and acetyl, but not malonyl. Processivity of polyketide extension was supported by the inability of a nonhydrolyzable malonyl analog to trap products of intermediate chain lengths and by the detection of only fully extended species observed covalently bound to, and as the predominant products released by, PksA. High occupancy of the malonyl transacylase domain and fast relative rate of malonyl transfer compared to starter unit transfer indicate that rapid loading of extension units onto the carrier domain facilitates efficient chain extension in a manner kinetically favorable to ultimate product formation. PMID:22452347

  10. Spectroscopic definition of the copper active sites in mordenite: selective methane oxidation.

    PubMed

    Vanelderen, Pieter; Snyder, Benjamin E R; Tsai, Ming-Li; Hadt, Ryan G; Vancauwenbergh, Julie; Coussens, Olivier; Schoonheydt, Robert A; Sels, Bert F; Solomon, Edward I

    2015-05-20

    Two distinct [Cu-O-Cu](2+) sites with methane monooxygenase activity are identified in the zeolite Cu-MOR, emphasizing that this Cu-O-Cu active site geometry, having a ∠Cu-O-Cu ∼140°, is particularly formed and stabilized in zeolite topologies. Whereas in ZSM-5 a similar [Cu-O-Cu](2+) active site is located in the intersection of the two 10 membered rings, Cu-MOR provides two distinct local structures, situated in the 8 membered ring windows of the side pockets. Despite their structural similarity, as ascertained by electronic absorption and resonance Raman spectroscopy, the two Cu-O-Cu active sites in Cu-MOR clearly show different kinetic behaviors in selective methane oxidation. This difference in reactivity is too large to be ascribed to subtle differences in the ground states of the Cu-O-Cu sites, indicating the zeolite lattice tunes their reactivity through second-sphere effects. The MOR lattice is therefore functionally analogous to the active site pocket of a metalloenzyme, demonstrating that both the active site and its framework environment contribute to and direct reactivity in transition metal ion-zeolites.

  11. School Pharmacist/School Environmental Hygienic Activities at School Site.

    PubMed

    Muramatsu, Akiyoshi

    2016-01-01

    The "School Health and Safety Act" was enforced in April 2009 in Japan, and "school environmental health standards" were established by the Minister of Education, Culture, Sports, Science and Technology. In Article 24 of the Enforcement Regulations, the duties of the school pharmacist have been clarified; school pharmacists have charged with promoting health activities in schools and carrying out complete and regular checks based on the "school environmental health standards" in order to protect the health of students and staff. In supported of this, the school pharmacist group of Japan Pharmaceutical Association has created and distributed digital video discs (DVDs) on "check methods of school environmental health standards" as support material. We use the DVD to ensure the basic issues that school pharmacists deal with, such as objectives, criteria, and methods for each item to be checked, advice, and post-measures. We conduct various workshops and classes, and set up Q&A committees so that inquiries from members are answered with the help of such activities. In addition, school pharmacists try to improve the knowledge of the school staff on environmental hygiene during their in-service training. They also conduct "drug abuse prevention classes" at school and seek to improve knowledge and recognition of drugs, including "dangerous drugs". PMID:27252053

  12. An Accessory Agonist Binding Site Promotes Activation of α4β2* Nicotinic Acetylcholine Receptors.

    PubMed

    Wang, Jingyi; Kuryatov, Alexander; Sriram, Aarati; Jin, Zhuang; Kamenecka, Theodore M; Kenny, Paul J; Lindstrom, Jon

    2015-05-29

    Neuronal nicotinic acetylcholine receptors containing α4, β2, and sometimes other subunits (α4β2* nAChRs) regulate addictive and other behavioral effects of nicotine. These nAChRs exist in several stoichiometries, typically with two high affinity acetylcholine (ACh) binding sites at the interface of α4 and β2 subunits and a fifth accessory subunit. A third low affinity ACh binding site is formed when this accessory subunit is α4 but not if it is β2. Agonists selective for the accessory ACh site, such as 3-[3-(3-pyridyl)-1,2,4-oxadiazol-5-yl]benzonitrile (NS9283), cannot alone activate a nAChR but can facilitate more efficient activation in combination with agonists at the canonical α4β2 sites. We therefore suggest categorizing agonists according to their site selectivity. NS9283 binds to the accessory ACh binding site; thus it is termed an accessory site-selective agonist. We expressed (α4β2)2 concatamers in Xenopus oocytes with free accessory subunits to obtain defined nAChR stoichiometries and α4/accessory subunit interfaces. We show that α2, α3, α4, and α6 accessory subunits can form binding sites for ACh and NS9283 at interfaces with α4 subunits, but β2 and β4 accessory subunits cannot. To permit selective blockage of the accessory site, α4 threonine 126 located on the minus side of α4 that contributes to the accessory site, but not the α4β2 sites, was mutated to cysteine. Alkylation of this cysteine with a thioreactive reagent blocked activity of ACh and NS9283 at the accessory site. Accessory agonist binding sites are promising drug targets.

  13. Aryl hydrocarbon receptor mediated activities in road dust from a metropolitan area, Hanoi-Vietnam: contribution of polycyclic aromatic hydrocarbons (PAHs) and human risk assessment.

    PubMed

    Tuyen, Le Huu; Tue, Nguyen Minh; Suzuki, Go; Misaki, Kentaro; Viet, Pham Hung; Takahashi, Shin; Tanabe, Shinsuke

    2014-09-01

    Dioxin-Responsive Chemical-Activated LUciferase gene eXpression assay (DR-CALUX) was applied to assess the total toxic activity of the mixture of PAHs and related compounds as well as dioxin-related compounds in road dust from urban areas of Hanoi, Vietnam. Road dust from Hanoi contained significantly higher DR-CALUX activities (3 to 39, mean 20 ng CALUX-TEQ/g dw) than those from a rural site (2 to 13, mean 5 ng CALUX-TEQ/g dw). The total concentrations of 24 major PAHs (Σ24PAHs) in urban road dust (0.1 to 5.5, mean 2.5 μg/g dw) were also 6 times higher than those in rural road dust (0.08 to 1.5, mean 0.4 μg/g dw). Diagnostic ratios of PAHs indicated vehicular engine combustion as the major PAH emission source in both sites. PAHs accounted for 0.8 to 60% (mean 10%) and 2 to 76% (mean 20%) of the measured CALUX-TEQs in road dust for Hanoi the rural site, respectively. Benzo[b]-/benzo[k]fluoranthenes were the major TEQ contributors among PAHs, whereas DRCs contributed <0.1% to CALUX-TEQs for both rural and urban sites. These results suggest TEQ contribution of other aryl hydrocarbon receptor agonists in road dust. Significant PAH concentrations in urban dust indicated high mutagenic and carcinogenic potencies. Estimated results of incremental life time cancer risk (ILCR) indicated that Vietnamese populations, especially those in urban areas such as Hanoi, are potentially exposed to high cancer risk via both dust ingestion and dermal contact. This is the first study on the exposure risk of AhR agonists, including PAHs and DRCs, in urban road dust from a developing country using a combined bio-chemical analytical approach.

  14. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    PubMed

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability.

  15. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    PubMed

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability. PMID:25671686

  16. Magnetic criteria of aromaticity.

    PubMed

    Gershoni-Poranne, Renana; Stanger, Amnon

    2015-09-21

    This review describes the current state of magnetic criteria of aromaticity. The introduction contains the fundamentals of ring currents in aromatic and antiaromatic systems, followed by a brief description of experimental and computational tools: NMR, diamagnetic susceptibility exaltation, current density analyses (CDA) and nucleus independent chemical shifts (NICS). This is followed by more comprehensive chapters: NMR - focusing on the work of R. Mitchell - NICS and CDA - describing the progress and development of the methods to their current state and presenting some examples of representative work. PMID:26035305

  17. Magnetic criteria of aromaticity.

    PubMed

    Gershoni-Poranne, Renana; Stanger, Amnon

    2015-09-21

    This review describes the current state of magnetic criteria of aromaticity. The introduction contains the fundamentals of ring currents in aromatic and antiaromatic systems, followed by a brief description of experimental and computational tools: NMR, diamagnetic susceptibility exaltation, current density analyses (CDA) and nucleus independent chemical shifts (NICS). This is followed by more comprehensive chapters: NMR - focusing on the work of R. Mitchell - NICS and CDA - describing the progress and development of the methods to their current state and presenting some examples of representative work.

  18. Site specific rationale for technical impracticability of active groundwater restoration at a former manufactured gas plant site

    SciTech Connect

    Logan, C.M.; Walden, R.H.; MacFarlane, I.D.

    1995-12-31

    The National Contingency Plan (40 CFR Part 300 ) requires that remedial strategies must, at minimum, protect human health and the environment and meet applicable and relevant or appropriate requirements (ARARs). Where groundwater is impacted, maximum contaminant levels (MCLs) and maximum contaminant level goals (MCLGs) set under the Safe Drinking Water Act are often used as ARARs, whether or not the aquifer is a reasonably anticipated future source of drinking water. The US Environmental Protection Agency now recognizes the difficulty of groundwater restoration at sites where dense nonaqueous phase liquids are present, particularly in certain complex hydrogeological settings (EPA 1993). However, demonstration of impracticability generally does not occur until active remediation (e.g., pump and treat) has been shown to be ineffective. A case study of a former manufactured gas plant (MGP) is used to demonstrate how physical and chemical properties of the aquifer and coal tar, the major waste product from MGP sites, influence the feasibility of active restoration. Field characterization investigations, laboratory studies, and groundwater modeling are integrated into a demonstration following EPA guidelines. Laboratory studies included microbiological characterization and natural biodegradation and suggest that intrinsic bioremediation is occurring at this site. This work will be useful as EPA continues to develop pr