Genomes and Genes
Summary: A group of condensed ring hydrocarbons.
- Pearson J, Dabrowski M, Kung I, Atkins W. The central loop of Escherichia coli glutamine synthetase is flexible and functionally passive. Arch Biochem Biophys. 2005;436:397-405 pubmed
- Lee K, Vermeulen R, Lenters V, Cho S, Strickland P, Kang D. Determinants of urinary 1-hydroxypyrene glucuronide in South Korean children. Int Arch Occup Environ Health. 2009;82:961-8 pubmed publisher..These results support that ETS, frequent grilled fish consumption, and the ambient environment are important predictors of urinary 1-OHPG levels in South Korean children. ..
- Sherrer S, Brown J, Pack L, Jasti V, Fowler J, Basu A, et al. Mechanistic studies of the bypass of a bulky single-base lesion catalyzed by a Y-family DNA polymerase. J Biol Chem. 2009;284:6379-88 pubmed publisher..In contrast, only a large, fast phase was observed during nucleotide incorporation at non-pause sites. Our kinetic studies support a general kinetic mechanism for lesion bypass catalyzed by numerous DNA polymerases. ..
- Han I, Duan X, Zhang L, Yang H, Rhoads G, Wei F, et al. 1-Hydroxypyrene concentrations in first morning voids and 24-h composite urine: intra- and inter-individual comparisons. J Expo Sci Environ Epidemiol. 2008;18:477-85 pubmed..Creatinine adjustments did not significantly improve overall correlations between first morning void and 24-h measurements, but increased total variances for 24-h urines explained by first morning urines in coke workers. ..
- Blahova J, Kruzikova K, Hilscherova K, Grabic R, Halirova J, Jurcikova J, et al. Biliary 1-hydroxypyrene as a biomarker of exposure to polycyclic aromatic hydrocarbons in fish. Neuro Endocrinol Lett. 2008;29:663-8 pubmed..The aim of this study was the assessment of the Svitava and Svratka rivers contamination by polycyclic aromatic hydrocarbons (PAH) using 1-hydroxypyrene (1-OHP) concentrations in fish bile as a biomarker...
- Keller M, Watschinger K, Golderer G, Maglione M, Sarg B, Lindner H, et al. Monitoring of fatty aldehyde dehydrogenase by formation of pyrenedecanoic acid from pyrenedecanal. J Lipid Res. 2010;51:1554-9 pubmed publisher..Thus, monitoring of pyrenedecanoic acid formation from pyrenedecanal by HPLC with fluorescence detection provides a robust and sensitive method for determination of fatty aldehyde dehydrogenase activity. ..
- Wu C, Wang C, Yan L, Yang C. Pyrene excimer nucleic acid probes for biomolecule signaling. J Biomed Nanotechnol. 2009;5:495-504 pubmed
- Colis L, Chakraborti D, Hilario P, McCarty C, Basu A. Synthesis of oligonucleotides containing 2'-deoxyguanosine adducts of nitropyrenes. Nucleosides Nucleotides Nucleic Acids. 2009;28:67-77 pubmed publisher..A total synthetic approach, by contrast, involves several synthetic steps, including Buchwald-Hartwig Pd-catalyzed coupling, but can be used for incorporating both the major and minor adducts in DNA in high yield. ..
- Hoff B, Strandberg E, Ulrich A, Tieleman D, Posten C. 2H-NMR study and molecular dynamics simulation of the location, alignment, and mobility of pyrene in POPC bilayers. Biophys J. 2005;88:1818-27 pubmed..The good agreement can be explained by the fact that the different kind of motions of a pyrene molecule are already averaged within a few nanoseconds, which is the timescale covered by the MD simulation. ..
- Lai C, Liou S, Lin H, Shih T, Tsai P, Chen J, et al. Exposure to traffic exhausts and oxidative DNA damage. Occup Environ Med. 2005;62:216-22 pubmed..372, 95% CI 0.081 to 0.663). Results indicate that exposure to traffic exhausts increases oxidative DNA damage. Urinary 8-OHdG is a promising biomarker of traffic exhaust induced oxidative stress. ..
- Nagatoishi S, Nojima T, Juskowiak B, Takenaka S. A pyrene-labeled G-quadruplex oligonucleotide as a fluorescent probe for potassium ion detection in biological applications. Angew Chem Int Ed Engl. 2005;44:5067-70 pubmed
- Karuppannan S, Chambron J. Supramolecular chemical sensors based on pyrene monomer-excimer dual luminescence. Chem Asian J. 2011;6:964-84 pubmed publisher..This induces a conformational change or the exchange of a component of the system, which is the cause of the luminescence switch effect. ..
- Liu A, Lu W, Wang Z, Chen W, Lu W, Yuan J, et al. Elevated levels of urinary 8-hydroxy-2 -deoxyguanosine, lymphocytic micronuclei, and serum glutathione S-transferase in workers exposed to coke oven emissions. Environ Health Perspect. 2006;114:673-7 pubmed..The consequences of the changes in these biomarkers, such as risk of cancer, warrant further investigations. ..
- Perret F, Nishihara M, Takeuchi T, Futaki S, Lazar A, Coleman A, et al. Anionic fullerenes, calixarenes, coronenes, and pyrenes as activators of oligo/polyarginines in model membranes and live cells. J Am Chem Soc. 2005;127:1114-5 pubmed..Applied to HeLa cells, pyrenebutyrate is shown to significantly increase the uptake of a fluorescently labeled octaarginine in a concentration-dependent manner. ..
- Watt D, Utzat C, Hilario P, Basu A. Mutagenicity of the 1-nitropyrene-DNA adduct N-(deoxyguanosin-8-yl)-1-aminopyrene in mammalian cells. Chem Res Toxicol. 2007;20:1658-64 pubmed..We conclude that C8-AP-dG mutagenesis depends on the type of cell in which it is replicated, the neighboring DNA sequence, and the methylation status of the 5'-C. ..
- Chen B, Hu Y, Zheng L, Wang Q, Zhou Y, Jin T. Urinary 1-hydroxypyrene concentrations in Chinese coke oven workers relative to job category, respirator usage, and cigarette smoking. Am J Ind Med. 2007;50:657-63 pubmed..1). Chinese COWs, especially topside workers and benchmen, are exposed to high levels of PAHs. Urinary 1-OHP concentrations appear to be modulated by respirator usage and BMI in COWs, as well as by smoking in unexposed referents. ..
- Lin Y, Pan C, Chen C, Wu K, Chang Chien G, Ho C, et al. Associations between exposure to polycyclic aromatic hydrocarbons and temporal change of urinary 1-hydroxypyrene levels in Taiwanese coke-oven workers. J Occup Environ Med. 2006;48:930-6 pubmed..We suggest that the pattern of temporal change of urinary 1-OHP levels is different between topside-oven and side-oven workers. ..
- Marczynski B, Pesch B, Wilhelm M, Rossbach B, Preuss R, Hahn J, et al. Occupational exposure to polycyclic aromatic hydrocarbons and DNA damage by industry: a nationwide study in Germany. Arch Toxicol. 2009;83:947-57 pubmed publisher..The type of industry contributed to genotoxic DNA damage and DNA damage was not unequivocally associated to PAH on the individual level most likely due to potential contributions of co-exposures. ..
- Andersson H, Piras E, Demma J, Hellman B, Brittebo E. Low levels of the air pollutant 1-nitropyrene induce DNA damage, increased levels of reactive oxygen species and endoplasmic reticulum stress in human endothelial cells. Toxicology. 2009;262:57-64 pubmed publisher..Our findings suggest that the human blood vessel endothelium is a sensitive target tissue for the major nitro-PAH constituent in diesel exhaust. ..
- Moseley J, Maiti S, Goode B. Formin proteins: purification and measurement of effects on actin assembly. Methods Enzymol. 2006;406:215-34 pubmed..In the last section, we outline fluorometric methods for measuring and quantitatively analyzing the in vitro activities of formins on actin nucleation and processive capping of actin filaments. ..
- Gao Y, Zhu L, Ling W. Application of the partition-limited model for plant uptake of organic chemicals from soil and water. Sci Total Environ. 2005;336:171-82 pubmed..05, n = 10). This investigation substantiated the concept of the partition-limited model and its utility for vegetation-uptake assessment. ..
- Kamangar F, Strickland P, Pourshams A, Malekzadeh R, Boffetta P, Roth M, et al. High exposure to polycyclic aromatic hydrocarbons may contribute to high risk of esophageal cancer in northeastern Iran. Anticancer Res. 2005;25:425-8 pubmed..We conclude that people in northeastern Iran are exposed to widespread and very high levels of PAH, largely from unknown sources, and this may contribute to the high rates of ESCC observed in this area. ..
- Chetiyanukornkul T, Toriba A, Kameda T, Tang N, Hayakawa K. Simultaneous determination of urinary hydroxylated metabolites of naphthalene, fluorene, phenanthrene, fluoranthene and pyrene as multiple biomarkers of exposure to polycyclic aromatic hydrocarbons. Anal Bioanal Chem. 2006;386:712-8 pubmed..The results showed higher urinary concentrations of OHPAHs in rural villagers, consistent with higher respiratory exposure to PAHs. ..
- Fagundes R, Abnet C, Strickland P, Kamangar F, Roth M, Taylor P, et al. Higher urine 1-hydroxy pyrene glucuronide (1-OHPG) is associated with tobacco smoke exposure and drinking maté in healthy subjects from Rio Grande do Sul, Brazil. BMC Cancer. 2006;6:139 pubmed..The increased urine 1-OHPG concentrations associated with maté suggest that contaminants, not just thermal injury, may help explain the increased risk of ESCC previously reported for maté consumption. ..
- Gao Y, Shen Q, Ling W, Ren L. Uptake of polycyclic aromatic hydrocarbons by Trifolium pretense L. from water in the presence of a nonionic surfactant. Chemosphere. 2008;72:636-43 pubmed publisher..Results from this study show promises for the potential efficacy of enhanced phytoremediation in PAH contaminated sites using surfactant amendment...
- Conlon P, Yang C, Wu Y, Chen Y, Martinez K, Kim Y, et al. Pyrene excimer signaling molecular beacons for probing nucleic acids. J Am Chem Soc. 2008;130:336-42 pubmed..The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes. ..
- Leng S, Cheng J, Pan Z, Huang C, Niu Y, Dai Y, et al. Associations between XRCC1 and ERCC2 polymorphisms and DNA damage in peripheral blood lymphocyte among coke oven workers. Biomarkers. 2004;9:395-406 pubmed
- Lai C, Liou S, Shih T, Tsai P, Chen H, Buckley T, et al. Urinary 1-hydroxypyrene-glucuronide as a biomarker of exposure to various vehicle exhausts among highway toll-station workers in Taipei, Taiwan. Arch Environ Health. 2004;59:61-9 pubmed..The authors determined that exposure to various traffic exhausts increased the urinary concentration of 1-OHP-gluc in a dose-response pattern, which suggests that this chemical may be a useful biomarker for exposure to vehicle exhausts. ..
- Filichev V, Pedersen E. Stable and selective formation of hoogsteen-type triplexes and duplexes using twisted intercalating nucleic acids (TINA) prepared via postsynthetic Sonogashira solid-phase coupling reactions. J Am Chem Soc. 2005;127:14849-58 pubmed..0 degrees C at pH 7.2, while the T(m) of unmodified dsDNA was 47.0 degrees C. Experiments with mismatched oligonucleotides, luminescent properties, and potential applications of TINA technology is discussed. ..
- Kim S, Kweon O, Jones R, Freeman J, Edmondson R, Cerniglia C. Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology. J Bacteriol. 2007;189:464-72 pubmed..The results presented here provide a comprehensive picture of pyrene metabolism in M. vanbaalenii PYR-1 and a useful framework for understanding cellular processes involved in PAH degradation. ..
- Cavanagh J, Brown L, Trought K, Kingham S, Epton M. Elevated concentrations of 1-hydroxypyrene in schoolchildren during winter in Christchurch, New Zealand. Sci Total Environ. 2007;374:51-9 pubmed
- Hansen A, Mathiesen L, Pedersen M, Knudsen L. Urinary 1-hydroxypyrene (1-HP) in environmental and occupational studies--a review. Int J Hyg Environ Health. 2008;211:471-503 pubmed publisher..The highest contribution originates from environmental tobacco smoke, but also different country, cooking culture, and behavior influences urinary of 1-HP. ..
- Nakamura M, Fukunaga Y, Sasa K, Ohtoshi Y, Kanaori K, Hayashi H, et al. Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference. Nucleic Acids Res. 2005;33:5887-95 pubmed..Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene-RNA/RNA and the pyrene-DNA/DNA duplexes. ..
- Fiala K, Brown J, Ling H, Kshetry A, Zhang J, Taylor J, et al. Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase. J Mol Biol. 2007;365:590-602 pubmed publisher..This unprecedented base-stacking pattern can be applied to subsequent blunt-end additions only if all incorporated dAMPs are extrahelical, leading to predominantly single non-templated dATP incorporation...
- Patel A, Khumsupan P, Narayanaswami V. Pyrene fluorescence analysis offers new insights into the conformation of the lipoprotein-binding domain of human apolipoprotein E. Biochemistry. 2010;49:1766-75 pubmed publisher..This study presents the possibility of employing pyrene fluorophores as powerful new alternatives to obtain conformational information of proteins at physiologically relevant concentrations. ..
- Wang M, Chen Y, Chen S, Chang Chien S, Sunkara S. Phytoremediation of pyrene contaminated soils amended with compost and planted with ryegrass and alfalfa. Chemosphere. 2012;87:217-25 pubmed publisher..It was thus suggested that the interactions among the consortia of plant root exudates, microorganisms, and amended compost in rhizosphere soils could facilitate bioavailability of pyrene and subsequently enhance its dissipation. ..
- Wei J, Huang G, Zhu L, Zhao S, An C, Fan Y. Enhanced aqueous solubility of naphthalene and pyrene by binary and ternary Gemini cationic and conventional nonionic surfactants. Chemosphere. 2012;89:1347-53 pubmed publisher..Certainly, the solubilization abilities of the selected surfactants not only depend on their structure and mixing effect but also associate with solubilizing microenvironment and chemical nature of organic solutes. ..
- Kuramitz H, Sazawa K, Nanayama Y, Hata N, Taguchi S, Sugawara K, et al. Electrochemical genotoxicity assay based on a SOS/umu test using hydrodynamic voltammetry in a droplet. Sensors (Basel). 2012;12:17414-32 pubmed publisher..The genotoxicity of tested chemicals with a high hydrophobicity such as 1,8-DNP and 1-NP were decreased substantially with the presence of 1 g?L-1 sediment. This was not observed in the case of genotoxins with a low log K(ow) value. ..
- Aotake T, Tanimoto H, Hotta H, Kuzuhara D, Okujima T, Uno H, et al. In situ preparation of highly fluorescent pyrene-dyes from non-luminous precursors upon photoirradiation. Chem Commun (Camb). 2013;49:3661-3 pubmed publisher..99. ..
- Wei F, Nie G, Zhou B, Wang L, Ma Y, Peng S, et al. Association between Chinese cooking oil fumes and sleep quality among a middle-aged Chinese population. Environ Pollut. 2017;227:543-551 pubmed publisher..30, 95% CIÂ =Â 1.31-4.05). The results indicated that exposure to COFs from Chinese household cooking may be a risk factor for poor sleep quality among middle-aged Chinese population. ..
- Danyluk H, Shum L, Zandberg W. A Rapid Procedure for the Purification of 8-Aminopyrene Trisulfonate (APTS)-Labeled Glycans for Capillary Electrophoresis (CE)-Based Enzyme Assays. Methods Mol Biol. 2017;1588:223-236 pubmed publisher..This chapter describes a FACE/SPE procedure ideal for preparing glycans for capillary electrophoresis (CE)-based enzyme assays, as well as for the purification of rare, commercially unavailable glycans from tissue culture samples. ..
- Saima B, Khan A, Nisa R, Mahmood T, Ayub K. Theoretical insights into thermal cyclophanediene to dihydropyrene electrocyclic reactions; a comparative study of Woodward Hoffmann allowed and forbidden reactions. J Mol Model. 2016;22:81 pubmed publisher..We also believe that this is the first study of its type, where W-H allowed and forbidden reactions are compared on a similar set of molecules, and compared for electronic effect through substituents. ..
- Fowler M, Siddique B, Duhamel J. Effect of sequence on the ionization behavior of a series of amphiphilic polypeptides. Langmuir. 2013;29:4451-9 pubmed publisher..Together, these experiments provide a complete description of how pH affects the behavior of a series of unique amphiphilic polypeptides designed with a well-defined sequence. ..
- Hallett A, White N, Wu W, Cui X, Horton P, Coles S, et al. Enhanced photooxidation sensitizers: the first examples of cyclometalated pyrene complexes of iridium(III). Chem Commun (Camb). 2012;48:10838-40 pubmed publisher..The iridium(III) cyclometalation of alkylated pyrene-benzimidazole ligands proceeds in an unprecedented manner. The resultant complexes display remarkably enhanced photooxidation capabilities using 1,5-dihydroxynaphthalene as a substrate. ..
- Reddy E, Banote R, Chatti K, Kulkarni P, Rajadurai M. Selective multicolour imaging of zebrafish muscle fibres by using fluorescent organic nanoparticles. Chembiochem. 2012;13:1889-94 pubmed publisher..This study demonstrates for the first time the possibility of using FONs for in vivo, whole-body, fluorescence imaging of zebrafish. ..
- Zhang X, Kah M, Jonker M, Hofmann T. Dispersion state and humic acids concentration-dependent sorption of pyrene to carbon nanotubes. Environ Sci Technol. 2012;46:7166-73 pubmed publisher..The present results contribute to an improved understanding of the sorption behavior of CNTs in both natural and wastewater systems. ..
- Wu S, Zhang H, Zhao S, Wang J, Li H, Chen J. Biomarker responses of earthworms (Eisenia fetida) exposured to phenanthrene and pyrene both singly and combined in microcosms. Chemosphere. 2012;87:285-93 pubmed publisher..5 (Phe)+100 (Pyr) mg kg(-1) soils. Phe and Pyr synergistically decreased sperm count and NRRT, but antagonistically caused changes in antioxidant enzyme activities to disrupt the detoxification functions and inhibit earthworm growth. ..
- Niko Y, Kawauchi S, Otsu S, Tokumaru K, Konishi G. Fluorescence enhancement of pyrene chromophores induced by alkyl groups through ?-? conjugation: systematic synthesis of primary, secondary, and tertiary alkylated pyrenes at the 1, 3, 6, and 8 positions and their photophysical properties. J Org Chem. 2013;78:3196-207 pubmed publisher..In other words, they can be used to develop new photofunctional materials. ..
- Zhang Y, Pignatello J, Tao S. Bioaccessibility of nitro- and oxy-PAHs in fuel soot assessed by an in vitro digestive model with absorptive sink. Environ Pollut. 2016;218:901-908 pubmed publisher..Consistent with earlier experiments on a wider range of PAHs, the results suggest that a major determinant of bioaccessibility is the distribution of chemical between nonlabile and labile states in the original solid. ..