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Journal articles on the topic 'Aromatic reconstructions'
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1
Burdelnaya, N., Yu Golubeva, and Dmitry Bushnev. "Hydrocarbons-biomarkers and palynological characteristics of peat of the Mezen-Vychegda plain." Vestnik of geosciences, no. 10 (December 7, 2022): 11–22. http://dx.doi.org/10.19110/geov.2022.10.2.
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The peat from the Cherny Yar section at the Vychegda river was studied by a complex of palynological and geochemical methods. We determined that among the aliphatic hydrocarbons of bitumen, the maximum concentrations were characteristic for odd n-alkanes with a predominance of C27-C31 homologues, as well as 18-norabietane. Aromatic hydrocarbons are mainly represented by structures formed during the fossilization of diterpenoids and triterpenoids of higher vegetation. Among the aromatic diterpenoids, there are 18-norabieta-8,11,13-triene, 18-norsimonellite and retene, which are markers of conifers, as well as 18-norabietane of the aliphatic fraction. Among the aromatic triterpenoids, numerous transformation products of compounds with the carbon skeleton of lupan, oleanan, and ursane, characteristic of angiosperms, have been identified. For example, dinorolean(ursa)-1,3,5(10),13(18)-tetraene, dinorolean(ursa)-1,3,5(10)-triene, pentanoroleana-1,3,5(10), 6,8,11,13,17(18)-octaene and others. The data on the composition of hydrocarbons confirm the palynological data about the presence of coniferous and hardwood pollen in the composition of peat. The change in the composition of hydrocarbons along the section confirms the change in the species composition of vegetation in the study area, diagnosed by microfossils. The comparison of the composition of peat biomarker hydrocarbons with palynological data revealed their consistency with each other and possibility of conjugated use of these methods in paleogeographic reconstructions.
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Krock, Kevin A., and Charles L. Wilkins. "Determination of Minimum Identifiable Quantities for Target Analysis of Semivolatile Organic Compounds." Applied Spectroscopy 46, no. 11 (November 1992): 1621–24. http://dx.doi.org/10.1366/0003702924926925.
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Thirty-five semivolatile compounds from the phenolic, chlorinated hydrocarbon, and polynuclear aromatic hydrocarbon classes are analyzed with the use of lightpipe-based gas chromatography/infrared spectrometry in order to determine the minimum identifiable quantities (MIQ) as defined in the U.S. Environmental Protection Agency Method 8410. MIQs for all compounds studied are in the range of 1 to 20 nanograms. The present results represent an improvement of about an order of magnitude over those reported earlier in U.S. EPA studies. An important factor in achieving this improvement is the use of selected wavelength chromatogram reconstructions for locating high-noise chromatogram data files. These data suggest that target analysis of complex semivolatile environmental organic samples is achievable by lightpipe GC/FT-IR.
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Culp, Tyler E., Yue-xiao Shen, Michael Geitner, Mou Paul, Abhishek Roy, Michael J. Behr, Steve Rosenberg, Junsi Gu, Manish Kumar, and Enrique D. Gomez. "Electron tomography reveals details of the internal microstructure of desalination membranes." Proceedings of the National Academy of Sciences 115, no. 35 (August 13, 2018): 8694–99. http://dx.doi.org/10.1073/pnas.1804708115.
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As water availability becomes a growing challenge in various regions throughout the world, desalination and wastewater reclamation through technologies such as reverse osmosis (RO) are becoming more important. Nevertheless, many open questions remain regarding the internal structure of thin-film composite RO membranes. In this work, fully aromatic polyamide films that serve as the active layer of state-of-the-art water filtration membranes were investigated using high-angle annular dark-field scanning transmission electron microscopy tomography. Reconstructions of the 3D morphology reveal intricate aspects of the complex microstructure not visible from 2D projections. We find that internal voids of the active layer of compressed commercial membranes account for less than 0.2% of the total polymer volume, contrary to previously reported values that are two orders of magnitude higher. Measurements of the local variation in polyamide density from electron tomography reveal that the polymer density is highest at the permeable surface for the two membranes tested and establish the significance of surface area on RO membrane transport properties. The same type of analyses could provide explanations for different flux variations with surface area for other types of membranes where the density is distributed differently. Thus, 3D reconstructions and quantitative analyses will be crucial to characterize the complex morphology of polymeric membranes used in next-generation water-purification membranes.
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Durán-Viseras, Ana, David J. Castro, José Carlos Reina, Victoria Béjar, and Fernando Martínez-Checa. "Taxogenomic and Metabolic Insights into Marinobacterium ramblicola sp. nov., a New Slightly Halophilic Bacterium Isolated from Rambla Salada, Murcia." Microorganisms 9, no. 8 (August 3, 2021): 1654. http://dx.doi.org/10.3390/microorganisms9081654.
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A Gram-negative, motile, rod-shaped bacteria, designated D7T, was isolated by using the dilution-to-extinction method, from a soil sample taken from Rambla Salada (Murcia, Spain). Growth of strain D7T was observed at 15–40 °C (optimum, 37 °C), pH 5–9 (optimum, 7) and 0–7.5% (w/v) NaCl (optimum, 3%). It is facultatively anaerobic. Phylogenetic analysis based on 16S rRNA gene sequence showed it belongs to the genus Marinobacterium. The in silico DDH and ANI against closest Marinobacterium relatives support its placement as a new species within this genus. The major fatty acids of strain D7T were C16:0, summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω7c/C18:1 ω6c). The polar lipid profile consists of phosphatidylethanolamine, phosphatidylglycerol and two uncharacterized lipids. Ubiquinone 8 was the unique isoprenoid quinone detected. The DNA G + C content was 59.2 mol%. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic characterization, strain D7T (= CECT 9818T = LMG 31312T) represents a novel species of the genus Marinobacterium for which the name Marinobacterium ramblicola sp. nov. is proposed. Genome-based metabolic reconstructions of strain D7T suggested a heterotrophic and chemolitotrophic lifestyle, as well as the capacity to biosynthetize and catabolize compatible solutes, and to degrade hydrocarbon aromatic compounds.
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Ardenghi, Nicolò, David J. Harning, Jonathan H. Raberg, Brooke R. Holman, Thorvaldur Thordarson, Áslaug Geirsdóttir, Gifford H. Miller, and Julio Sepúlveda. "A Holocene history of climate, fire, landscape evolution, and human activity in northeastern Iceland." Climate of the Past 20, no. 4 (May 2, 2024): 1087–123. http://dx.doi.org/10.5194/cp-20-1087-2024.
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Abstract. Paleoclimate reconstructions across Iceland provide a template for past changes in climate across the northern North Atlantic, a crucial region due to its position relative to the global northward heat transport system and its vulnerability to climate change. The roles of orbitally driven summer cooling, volcanism, and human impact as triggers of local environmental changes in the Holocene of Iceland remain debated. While there are indications that human impact may have reduced environmental resilience during late Holocene summer cooling, it is still difficult to resolve to what extent human and natural factors affected Iceland's late Holocene landscape instability. Here, we present a continuous Holocene fire record of northeastern Iceland from proxies archived in Stóra Viðarvatn sediment. We use pyrogenic polycyclic aromatic hydrocarbons (pyroPAHs) to trace shifts in fire regimes, paired with continuous biomarker and bulk geochemical records of soil erosion, lake productivity, and human presence. The molecular composition of pyroPAHs and a wind pattern reconstruction indicate a naturally driven fire signal that is mostly regional. Generally low fire frequency during most of the Holocene significantly increased at 3 ka and again after 1.5 ka BP before known human settlement in Iceland. We propose that shifts in vegetation type caused by cooling summers over the past 3 kyr, in addition to changes in atmospheric circulation, such as shifts in North Atlantic Oscillation (NAO) regime, led to increased aridity and biomass flammability. Our results show no evidence of faecal biomarkers associated with human activity during or after human colonisation in the 9th century CE. Instead, faecal biomarkers follow the pattern described by erosional proxies, pointing toward a negligible human presence and/or a diluted signal in the lake's catchment. However, low post-colonisation levels of pyroPAHs, in contrast to an increasing flux of erosional bulk proxies, suggest that farming and animal husbandry may have suppressed fire frequency by reducing the spread and flammability of fire-prone vegetation (e.g. heathlands). Overall, our results describe a fire frequency heavily influenced by long-term changes in climate through the Holocene. They also suggest that human colonisation had contrasting effects on the local environment by lowering its resilience to soil erosion while increasing its resilience to fire.
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Kurth, Julia M., Huub J. M. Op den Camp, and Cornelia U. Welte. "Several ways one goal—methanogenesis from unconventional substrates." Applied Microbiology and Biotechnology 104, no. 16 (June 15, 2020): 6839–54. http://dx.doi.org/10.1007/s00253-020-10724-7.
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Abstract Methane is the second most important greenhouse gas on earth. It is produced by methanogenic archaea, which play an important role in the global carbon cycle. Three main methanogenesis pathways are known: in the hydrogenotrophic pathway H2 and carbon dioxide are used for methane production, whereas in the methylotrophic pathway small methylated carbon compounds like methanol and methylated amines are used. In the aceticlastic pathway, acetate is disproportionated to methane and carbon dioxide. However, next to these conventional substrates, further methanogenic substrates and pathways have been discovered. Several phylogenetically distinct methanogenic lineages (Methanosphaera, Methanimicrococcus, Methanomassiliicoccus, Methanonatronarchaeum) have evolved hydrogen-dependent methylotrophic methanogenesis without the ability to perform either hydrogenotrophic or methylotrophic methanogenesis. Genome analysis of the deep branching Methanonatronarchaeum revealed an interesting membrane-bound hydrogenase complex affiliated with the hardly described class 4 g of multisubunit hydrogenases possibly providing reducing equivalents for anabolism. Furthermore, methylated sulfur compounds such as methanethiol, dimethyl sulfide, and methylmercaptopropionate were described to be converted into adapted methylotrophic methanogenesis pathways of Methanosarcinales strains. Moreover, recently it has been shown that the methanogen Methermicoccus shengliensis can use methoxylated aromatic compounds in methanogenesis. Also, tertiary amines like choline (N,N,N-trimethylethanolamine) or betaine (N,N,N-trimethylglycine) have been described as substrates for methane production in Methanococcoides and Methanolobus strains. This review article will provide in-depth information on genome-guided metabolic reconstructions, physiology, and biochemistry of these unusual methanogenesis pathways. Key points • Newly discovered methanogenic substrates and pathways are reviewed for the first time. • The review provides an in-depth analysis of unusual methanogenesis pathways. • The hydrogenase complex of the deep branching Methanonatronarchaeum is analyzed.
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Hisham, Nur Faiqah, and Nor Syazwani Zainal Abidin. "Sedimentology and Paleodepositional Environment of the Early-Middle Miocene Tanjong Formation, Southeast Sabah: Evidence from Bulk Geochemistry and Palynology Analyses." Minerals 13, no. 4 (March 30, 2023): 494. http://dx.doi.org/10.3390/min13040494.
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Eight stratigraphic sections from well-exposed outcrops of the Early to Middle Miocene Tanjong Formation in the Kalabakan area, southeast Sabah, were investigated using an integrated approach, in which a comprehensive sedimentological facies analysis was linked with bulk geochemistry and palynological analyses. The integration of facies analysis, elemental CHNS, Fourier-transform infrared spectroscopy (FTIR), and palynological data provided a refined evaluation of the origin of organic matter (OM) and the reconstruction of the paleodepositional model. Seven facies associations were classified in the studied Tanjong Formation from 12 lithofacies components, interpreted as environments ranging from fluvial-deltaic to shallow marine: FA1—Floodplain, FA2—Fluvial channel, FA3—Coastal peat mires, FA4—Tidal flat, FA5—Delta front, FA6—Mouth bar, and FA7—Upper shoreface. Evaluation of the C/N ratio ranged between 4 and 48, and the total sulfur content ranged from 0.5 to 3. Elemental CHNS analysis suggests that the organic matter extracted from the coal and mudstone originated from terrestrial plants and fresh marine plankton. Accordingly, the three most prevalent FTIR spectra from the coal and mudstone samples were the OH- functional group stretching, the absorption spectrum of aromatic C=C stretching, and aromatic in-plane/out-of-plane C-H bending. Terrestrially derived organic matter within the examined samples was further validated by the predominance of aromatic compounds, and the palynological analysis indicated a back-mangrove freshwater pollen assemblage and a lower coastal plain setting proximal to the marine environment. The integrated findings from this research are vital in reconstructing a paleodepositional environment model that will improve the predictability of the petroleum system mechanisms and the future hydrocarbon potential for conventional petroleum exploration.
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Vilniškis, Rokas, and Rasa Vaiškūnaitė. "Complex Contamination Research and Hazard Assessment of the Waste of the Wooden Railway Sleeper." Baltic Journal of Road and Bridge Engineering 13, no. 4 (December 21, 2018): 385–403. http://dx.doi.org/10.7250/bjrbe.2018-13.424.
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Before being put to use, wooden railway sleepers are impregnated with creosote to increase their longevity and protect them from any adverse environmental impact. Creosote consists of a number of chemical substances, and some of those substances, namely, the polycyclic aromatic hydrocarbons, phenolic compounds and heterocyclic aromatic compounds, are potent carcinogens. Apart from polycyclic aromatic hydrocarbons and phenolic compounds, during their use, sleepers are mostly contaminated with heavy metals and petroleum products. Upon railway reconstruction, wooden railway sleepers become the waste, which must be handled by the current legislation of the European Union. After determining the concentration of contaminants with laboratory research, it is possible to identify their hazard level and classify them as hazardous or non-hazardous waste. After conducting laboratory research on the waste of wooden railway sleeper analysed, they are classified as hazardous waste.
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Fazlyyyakhmatov, M. G., I. N. Shamanov, B. V. Sakharov, N. M. Khasanova, M. A. Varfolomeev, G. G. Samosorov, and M. O. Pastukhov. "Determination of the Aromatics Content in Mineral Oils by LF NMR." Uchenye Zapiski Kazanskogo Universiteta. Seriya Estestvennye Nauki 165, no. 2 (2023): 322–39. http://dx.doi.org/10.26907/2542-064x.2023.2.322-339.
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Molecular group composition analysis of mineral oils is helpful to predict the performance of a future lubricant and to assess the compatibility of plasticizer oil with rubbers. The method of pulsed low-frequency NMR relaxation was used to determine the molecular group composition of 11 mineral oil samples, and the ratio of aromatic and non-aromatic hydrocarbons in them was calculated. NMR measurements were performed on a Chromatec-Proton 20M NMR analyzer with a 1H resonance frequency of 20 MHz. The method used consists in recording free induction decay signals, reconstructing the total signal amplitude, estimating the relative signal amplitude per unit mass of the sample, and calculating the proportion of aromatic hydrocarbons in the sample. The results were compared with those obtained by the standard chromatographic method. A high degree of correlation (R2 = 0.99) was observed between the results.
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Kim, Se Hyeuk, Yun Hee Park, Claudia Schmidt-Dannert, and Pyung Cheon Lee. "Redesign, Reconstruction, and Directed Extension of the Brevibacterium linens C40 Carotenoid Pathway in Escherichia coli." Applied and Environmental Microbiology 76, no. 15 (June 4, 2010): 5199–206. http://dx.doi.org/10.1128/aem.00263-10.
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ABSTRACT In this study, the carotenoid biosynthetic pathways of Brevibacterium linens DSMZ 20426 were reconstructed, redesigned, and extended with additional carotenoid-modifying enzymes of other sources in a heterologous host Escherichia coli. The modular lycopene pathway synthesized an unexpected carotenoid structure, 3,4-didehydrolycopene, as well as lycopene. Extension of the novel 3,4-didehydrolycopene pathway with the mutant Pantoea lycopene cyclase CrtY2 and the Rhodobacter spheroidene monooxygenase CrtA generated monocyclic torulene and acyclic oxocarotenoids, respectively. The reconstructed β-carotene pathway synthesized an unexpected 7,8-dihydro-β-carotene in addition to β-carotene. Extension of the β-carotene pathway with the B. linens β-ring desaturase CrtU and Pantoea β-carotene hydroxylase CrtZ generated asymmetric carotenoid agelaxanthin A, which had one aromatic ring at the one end of carotene backbone and one hydroxyl group at the other end, as well as aromatic carotenoid isorenieratene and dihydroxy carotenoid zeaxanthin. These results demonstrate that reconstruction of the biosynthetic pathways and extension with promiscuous enzymes in a heterologous host holds promise as a rational strategy for generating structurally diverse compounds that are hardly accessible in nature.
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Kong, Sher-Rine, Masanobu Yamamoto, Hasrizal Shaari, Ryoma Hayashi, Osamu Seki, Norhayati Mohd Tahir, Muhammad Fais Fadzil, and Abdullah Sulaiman. "The significance of pyrogenic polycyclic aromatic hydrocarbons in Borneo peat core for the reconstruction of fire history." PLOS ONE 16, no. 9 (September 8, 2021): e0256853. http://dx.doi.org/10.1371/journal.pone.0256853.
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The reconstruction of fire history is essential to understand the palaeoclimate and human history. Polycyclic aromatic hydrocarbons (PAHs) have been extensively used as a fire marker. In this work, the distribution of PAHs in Borneo peat archives was investigated to understand how PAHs reflect the palaeo-fire activity. In total, 52 peat samples were analysed from a Borneo peat core for the PAH analysis. Pyrogenic PAHs consist of 2–7 aromatic rings, some of which have methyl and ethyl groups. The results reveal that the concentration of pyrogenic PAHs fluctuated with the core depth. Compared to low-molecular-weight (LMW) PAHs, the high-molecular-weight (HMW) PAHs had a more similar depth variation to the charcoal abundance. This finding also suggests that the HMW PAHs were mainly formed at a local fire near the study area, while the LMW PAHs could be transported from remote locations.
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Aarssen, B. G. K. van, R. Alexander, and R. I. Kagi. "RECONSTRUCTING THE GEOLOGICAL HISTORY OF AUSTRALIAN CRUDE OILS USING AROMATIC HYDROCARBONS." APPEA Journal 40, no. 1 (2000): 283. http://dx.doi.org/10.1071/aj99015.
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The distributions of methylated naphthalenes in crude oils carry within them detailed information regarding the geological history of the oils. The effects of thermal stress, mixing, biodegradation and migration contamination all leave recognisable imprints, which can be deconvoluted. An extended suite of crude oils from several locations in Australia was analysed for their methylated naphthalene content. It was shown that three ratios of selected isomers, each reflecting the same underlying sedimentary reactions, are linearly related to each other when thermal stress has been the only factor controlling the distribution of methylated naphthalenes. This internal consistency allows for an assessment of maturity independent of source, age and location of the crude oil. When the relationships between the three ratios are not linear, secondary processes such as mixing, biodegradation or migration contamination have affected the crude oil. Close examination of the distribution of methylated naphthalenes can reveal the extent to which either of these processes has affected the oil.
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Kim, So-Jeong, Soo-Je Park, Man-Young Jung, Jong-Geol Kim, Eugene L. Madsen, and Sung-Keun Rhee. "An Uncultivated Nitrate-Reducing Member of the Genus Herminiimonas Degrades Toluene." Applied and Environmental Microbiology 80, no. 10 (March 14, 2014): 3233–43. http://dx.doi.org/10.1128/aem.03975-13.
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ABSTRACTStable isotope probing (SIP) is a cultivation-free methodology that provides information about the identity of microorganisms participating in assimilatory processes in complex communities. In this study, aHerminiimonas-related bacterium was identified as the dominant member of a denitrifying microcosm fed [13C]toluene. The genome of the uncultivated toluene-degrading bacterium was obtained by applying pyrosequencing to the heavy DNA fraction. The draft genome comprised ∼3.8 Mb, in 131 assembled contigs. Metabolic reconstruction of aromatic hydrocarbon (toluene, benzoate,p-cresol, 4-hydroxybenzoate, phenylacetate, and cyclohexane carboxylate) degradation indicated that the bacterium might specialize in anaerobic hydrocarbon degradation. This characteristic is novel for the orderBurkholderialeswithin the classBetaproteobacteria. Under aerobic conditions, the benzoate oxidation gene cluster (BOX) system is likely involved in the degradation of benzoate via benzoyl coenzyme A. Many putative genes for aromatic hydrocarbon degradation were closely related to those in theRhodocyclaceae(particularlyAromatoleum aromaticumEbN1) with respect to organization and sequence similarity. Putative mobile genetic elements associated with these catabolic genes were highly abundant, suggesting gene acquisition byHerminiimonasvia horizontal gene transfer.
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Huang, Haiping, Hong Zhang, Zheng Li, and Mei Liu. "Thermal Maturation Regime Revisited in the Dongying Depression, Bohai Bay Basin, East China." Geofluids 2021 (September 24, 2021): 1–17. http://dx.doi.org/10.1155/2021/6020850.
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To the accurate reconstruction of the hydrocarbon generation history in the Dongying Depression, Bohai Bay Basin, East China, core samples of the Eocene Shahejie Formation from 3 shale oil boreholes were analyzed using organic petrology and organic geochemistry methods. The shales are enriched in organic matter with good to excellent hydrocarbon generation potential. The maturity indicated by measured vitrinite reflectance (%Ro) falls in the range of 0.5–0.9% and increases with burial depth in each well. Changes in biomarker and aromatic hydrocarbon isomer distributions and biomarker concentrations are also unequivocally correlated with the thermal maturity of the source rocks. Maturity/depth relationships for hopanes, steranes, and aromatic hydrocarbons, constructed from core data indicate different well locations, have different thermal regimes. A systematic variability of maturity with geographical position along the depression has been illustrated, which is a dependence on the distance to the Tanlu Fault. Higher thermal gradient at the southern side of the Dongying Depression results in the same maturity level at shallower depth compared to the northern side. The significant regional thermal regime change from south to north in the Dongying Depression may exert an important impact on the timing of hydrocarbon maturation and expulsion at different locations. Different exploration strategies should be employed accordingly.
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Xu, Pan, Xiaoxiao Chen, Kai Li, Rong Meng, and Yuewu Pu. "Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network." International Journal of Environmental Research and Public Health 19, no. 19 (September 23, 2022): 12039. http://dx.doi.org/10.3390/ijerph191912039.
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Polycyclic aromatic hydrocarbons are a widespread organic pollutant worldwide. In this study, a highly efficient phenanthrene (PHE)-degrading microbial community was enriched from oil extraction soil, which could degrade 500 mg/L PHE within 4 days. Using 16S rRNA sequencing, the dominant bacteria in this community at the phylum level were found to be Proteobacteria, Actinobacteria, and Firmicutes. Metagenomic annotation of genes revealed the metabolic pathways and the contribution of different bacteria to the degradation process. Pseudomonadaceae contributed multiple functional genes in the degradation process. This study revealed the functional genes, metabolic pathways, and microbial interactions of the microbial community, which are expected to provide guidance for practical management.
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dos Santos Melo-Nascimento, Amanda Oliveira, Brena Mota Moitinho Sant´Anna, Carolyne Caetano Gonçalves, Giovanna Santos, Eliane Noronha, Nádia Parachin, Milton Ricardo de Abreu Roque, and Thiago Bruce. "Complete genome reveals genetic repertoire and potential metabolic strategies involved in lignin degradation by environmental ligninolytic Klebsiella variicola P1CD1." PLOS ONE 15, no. 12 (December 22, 2020): e0243739. http://dx.doi.org/10.1371/journal.pone.0243739.
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Lignin is a recalcitrant macromolecule formed by three alcohols (monolignols) predominantly connected by β-aryl ether linkages and is one of the most abundant organic macromolecules in the biosphere. However, the role played by environmental bacteria in lignin degradation is still not entirely understood. In this study, we identified an environmental Klebsiella strain isolated from sediment collected from an altitudinal region in a unique Brazilian biome called Caatinga. This organism can also grow in the presence of kraft lignin as a sole source of carbon and aromatic compounds. We performed whole-genome sequencing and conducted an extensive genome-based metabolic reconstruction to reveal the potential mechanisms used by the bacterium Klebsiella variicola P1CD1 for lignin utilization as a carbon source. We identified 262 genes associated with lignin-modifying enzymes (LMEs) and lignin-degrading auxiliary enzymes (LDAs) required for lignin and aromatic compound degradation. The presence of one DyP (Dye-decolorizing Peroxidase) gene suggests the ability of P1CD1 strain to access phenolic and nonphenolic structures of lignin molecules, resulting in the production of catechol and protocatechuate (via vanillin or syringate) along the peripheral pathways of lignin degradation. K. variicola P1CD1 uses aldehyde-alcohol dehydrogenase to perform direct conversion of vanillin to protocatechol. The upper funneling pathways are linked to the central pathways of the protocatechuate/catechol catabolic branches via β-ketoadipate pathways, connecting the more abundant catabolized aromatic compounds with essential cellular functions, such as energy cellular and biomass production (i.e., via acetyl-CoA formation). The combination of phenotypic and genomic approaches revealed the potential dissimilatory and assimilatory ability of K. variicola P1CD1 to perform base-catalyzed lignin degradation, acting on high- and low-molecular-weight lignin fragments. These findings will be relevant for developing metabolic models to predict the ligninolytic mechanism used by environmental bacteria and shedding light on the flux of carbon in the soil.
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Zhao, Jian-Kang, Xiao-Ming Li, Guo-Min Ai, Ye Deng, Shuang-Jiang Liu, and Cheng-Ying Jiang. "Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil." Journal of Hazardous Materials 318 (November 2016): 90–98. http://dx.doi.org/10.1016/j.jhazmat.2016.06.055.
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McInerney, Michael J., Lars Rohlin, Housna Mouttaki, UnMi Kim, Rebecca S. Krupp, Luis Rios-Hernandez, Jessica Sieber, et al. "The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth." Proceedings of the National Academy of Sciences 104, no. 18 (April 18, 2007): 7600–7605. http://dx.doi.org/10.1073/pnas.0610456104.
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Biochemically, the syntrophic bacteria constitute the missing link in our understanding of anaerobic flow of carbon in the biosphere. The completed genome sequence of Syntrophus aciditrophicus SB, a model fatty acid- and aromatic acid-degrading syntrophic bacterium, provides a glimpse of the composition and architecture of the electron transfer and energy-transducing systems needed to exist on marginal energy economies of a syntrophic lifestyle. The genome contains 3,179,300 base pairs and 3,169 genes where 1,618 genes were assigned putative functions. Metabolic reconstruction of the gene inventory revealed that most biosynthetic pathways of a typical Gram-negative microbe were present. A distinctive feature of syntrophic metabolism is the need for reverse electron transport; the presence of a unique Rnf-type ion-translocating electron transfer complex, menaquinone, and membrane-bound Fe-S proteins with associated heterodisulfide reductase domains suggests mechanisms to accomplish this task. Previously undescribed approaches to degrade fatty and aromatic acids, including multiple AMP-forming CoA ligases and acyl-CoA synthetases seem to be present as ways to form and dissipate ion gradients by using a sodium-based energy strategy. Thus, S. aciditrophicus, although nutritionally self-sufficient, seems to be a syntrophic specialist with limited fermentative and respiratory metabolism. Genomic analysis confirms the S. aciditrophicus metabolic and regulatory commitment to a nonconventional mode of life compared with our prevailing understanding of microbiology.
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Blank, P. N., A. A. Barnett, T. A. Ronnebaum, K. E. Alderfer, B. N. Gillott, D. W. Christianson, and J. A. Himmelberger. "Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota." Acta Crystallographica Section D Structural Biology 76, no. 6 (May 29, 2020): 542–57. http://dx.doi.org/10.1107/s2059798320004878.
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Archaea are uniquely adapted to thrive in harsh environments, and one of these adaptations involves the archaeal membrane lipids, which are characterized by their isoprenoid alkyl chains connected via ether linkages to glycerol 1-phosphate. The membrane lipids of the thermophilic and acidophilic euryarchaeota Thermoplasma volcanium are exclusively glycerol dibiphytanyl glycerol tetraethers. The first committed step in the biosynthetic pathway of these archaeal lipids is the formation of the ether linkage between glycerol 1-phosphate and geranylgeranyl diphosphate, and is catalyzed by the enzyme geranylgeranylglyceryl phosphate synthase (GGGPS). The 1.72 Å resolution crystal structure of GGGPS from T. volcanium (TvGGGPS) in complex with glycerol and sulfate is reported here. The crystal structure reveals TvGGGPS to be a dimer, which is consistent with the absence of the aromatic anchor residue in helix α5a that is required for hexamerization in other GGGPS homologs; the hexameric quaternary structure in GGGPS is thought to provide thermostability. A phylogenetic analysis of the Euryarchaeota and a parallel ancestral state reconstruction investigated the relationship between optimal growth temperature and the ancestral sequences. The presence of an aromatic anchor residue is not explained by temperature as an ecological parameter. An examination of the active site of the TvGGGPS dimer revealed that it may be able to accommodate longer isoprenoid substrates, supporting an alternative pathway of isoprenoid membrane-lipid synthesis.
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Li, Wei, Chen Fang, Ying Wei Ai, Dong Yu, Chuan Ren Li, Zhi Jin Fan, and Yu Hong Xiao. "Difference between Organic Materials of Distinct Slope Soils in Hilly Area of Sichuan Province, China." Advanced Materials Research 726-731 (August 2013): 1287–91. http://dx.doi.org/10.4028/www.scientific.net/amr.726-731.1287.
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Organic materials in soils mainly consist of alkanes, esters, aromatic compounds and plant secondary metabolites, but they are different from one another in material type and quantity, depending on the types of slopes. This paper conducts a comparitive study on soils from slopes along the Suining-Chongqing Railway. Preparing soil samples from the rocky slope, the cultivated and uncultivated slopes by using ultrasonic methods, we measured the organic materials with a chromatograph mass spectrometer (QP2100). The results show that the number and types of organic materials decrease from the cultivated slopes to uncultivated slopes and then to rocky slopes. No contaminant appears in artificial soils on rocky slopes, but it is found in natural soils. Hence, it can be concluded that the reconstruction of soils on engineering slopes is beneficial not only for ecological restoration, but also for the prevention of pollution.
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Wang, Bin, Shuai Wu, Chenggao Li, and Weiyu Cao. "Evolution mechanism of cyclized structure of PAN-based pre-oxidized fiber during low temperature carbonization process." Materials Research Express 8, no. 11 (November 1, 2021): 115602. http://dx.doi.org/10.1088/2053-1591/ac3587.
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Abstract The low temperature carbonization process is an important stage to realize the structural transition from the organic cyclized structure of PAN based pre-oxidized fiber to the inorganic pseudo-graphite structure of the ultimate carbon fiber. In the present paper, the evolution mechanism of cyclized structure and aggregation structure of PAN stabilized fiber during low temperature carbonization was studied by means of TGA, 13C-NMR, XRD, XPS and Raman. The results indicated that when the heat-treated temperature was lower than 450 °C, the mainly chemical reactions were the dehydrogenation and pyrolysis reactions in acyclic linear molecular chain or partial cyclized structure. At this stage, the growth of cyclized structure was not obvious. While the original ordered structure was destroyed gradually and the internal stress increased significantly. It induced the cyclized structure to be further oriented. When the temperature was higher than 450 °C, the polycondensation and reconstruction in aromatic heterocyclic structure was more important. The early aromatic heterocycles had many different structural scales, poor homogeneity and many defects in the heterocycles. At this stage, a new pseudo-graphite crystalline structure gradually formed and the d-spacing of graphite layer decreased slightly and crystallites size increased slowly with the increase of heat-treated temperature. When the temperature was higher than 550 °C, the pseudo-graphite base structure gradually formed. The d-spacing were further reduced slightly, and the crystallites size increased slowly. A new ordered basis structure was gradually developed into carbon fiber.
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Pérez-Pantoja, Danilo, Rodrigo De la Iglesia, Dietmar H. Pieper, and Bernardo González. "Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacteriumCupriavidus necatorJMP134." FEMS Microbiology Reviews 32, no. 5 (August 2008): 736–94. http://dx.doi.org/10.1111/j.1574-6976.2008.00122.x.
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Canto-Encalada, Gabriela, Diego Tec-Campos, Juan D. Tibocha-Bonilla, Karsten Zengler, Alejandro Zepeda, and Cristal Zuñiga. "Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds." PLOS Computational Biology 18, no. 2 (February 2, 2022): e1009828. http://dx.doi.org/10.1371/journal.pcbi.1009828.
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The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N. europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N. europaea, iGC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.
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Daugherty, Matthew, Veronika Vonstein, Ross Overbeek, and Andrei Osterman. "Archaeal Shikimate Kinase, a New Member of the GHMP-Kinase Family." Journal of Bacteriology 183, no. 1 (January 1, 2001): 292–300. http://dx.doi.org/10.1128/jb.183.1.292-300.2001.
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ABSTRACT Shikimate kinase (EC 2.7.1.71 ) is a committed enzyme in the seven-step biosynthesis of chorismate, a major precursor of aromatic amino acids and many other aromatic compounds. Genes for all enzymes of the chorismate pathway except shikimate kinase are found in archaeal genomes by sequence homology to their bacterial counterparts. In this study, a conserved archaeal gene (gi‖1500322 in Methanococcus jannaschii) was identified as the best candidate for the missing shikimate kinase gene by the analysis of chromosomal clustering of chorismate biosynthetic genes. The encoded hypothetical protein, with no sequence similarity to bacterial and eukaryotic shikimate kinases, is distantly related to homoserine kinases (EC 2.7.1.39 ) of the GHMP-kinase superfamily. The latter functionality in M. jannaschii is assigned to another gene (gi‖1591748), in agreement with sequence similarity and chromosomal clustering analysis. Both archaeal proteins, overexpressed in Escherichia coliand purified to homogeneity, displayed activity of the predicted type, with steady-state kinetic parameters similar to those of the corresponding bacterial kinases:K m,shikimate = 414 ± 33 μM,K m,ATP = 48 ± 4 μM, andk cat = 57 ± 2 s−1 for the predicted shikimate kinase andK m,homoserine = 188 ± 37 μM,K m,ATP = 101 ± 7 μM, andk cat = 28 ± 1 s−1 for the homoserine kinase. No overlapping activity could be detected between shikimate kinase and homoserine kinase, both revealing a >1,000-fold preference for their own specific substrates. The case of archaeal shikimate kinase illustrates the efficacy of techniques based on reconstruction of metabolism from genomic data and analysis of gene clustering on chromosomes in finding missing genes.
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Wang, Shuangshuang, Jie Zhang, Yan Zhang, Liwei Wang, Zhongxue Sun, and Hailing Wang. "Review on Source Profiles of Volatile Organic Compounds (VOCs) in Typical Industries in China." Atmosphere 14, no. 5 (May 17, 2023): 878. http://dx.doi.org/10.3390/atmos14050878.
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The source profile of volatile organic compounds (VOCs) is essential for establishing reactivity- and toxicity-based emission inventories and developing effective air pollution control strategies. In this paper, the establishment of VOC source profiles and the VOC emission characteristics are reviewed in the petrochemical, solvent use, and chemical industries, and the most up-to-date profiles of the three industries in China are compiled via necessary adjustment and reconstruction of the test data from the literature. Alkanes dominated and OVOCs were often neglected in the overall petrochemical industry and refined processes. They accounted for 60.6% and 3.2% in the merged profiles. Aromatics and OVOCs dominated in the industrial solvent use industry. OVOCs were the most prevalent in the printing and dyeing industries, furniture manufacturing industries, and automobile coating process, whereas aromatics were major contributors of the total VOCs in metal surface coating, shipping coating, and other surface coating industries in the merged profiles. A wide range of products and limited profile studies were obtained in chemical industry, and the compositions of VOCs varied significantly in the production of 30 products in the merged profile. The future research directions of VOC source profiles are discussed, mainly focusing on the sampling, establishment, and evaluation of VOC profiles.
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Mitchell, Robert F., Ann M. Ray, Lawrence M. Hanks, and Jocelyn G. Millar. "The Common Natural Products (S)-α-Terpineol and (E)-2-Hexenol are Important Pheromone Components of Megacyllene antennata (Coleoptera: Cerambycidae)." Environmental Entomology 47, no. 6 (August 21, 2018): 1547–52. http://dx.doi.org/10.1093/ee/nvy126.
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Abstract We report here the pheromone of Megacyllene antennata (White) (Coleoptera: Cerambycidae), a species native to southwestern North America whose larvae feed in woody tissues of mesquite (Prosopis species; Fabaceae). Adult males sex-specifically produced a blend of eight common natural products, including the monoterpene alcohol (S)-α-terpineol; the monoterpenes (S)-limonene and terpinolene; the aromatic alcohols (R)-1-phenylethanol and 2-phenylethanol; and (E)-2-hexenol, (E)-2-hexenal, and 1-hexanol. Individual males produced the components in varying amounts, but (S)-α-terpineol and (E)-2-hexenal were always present and together constituted the majority of the blend. A synthetic reconstruction of the complete blend attracted both males and females of M. antennata during field bioassays, as did all subsets of the blend that included (S)-α-terpineol and (E)-2-hexenol. Adults were most strongly attracted to blends of the latter two compounds when in ratios approaching parity. Neither of the compounds were present in the bouquet of volatiles emitted by host plants of the larvae.
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Lim, Hee Jun, Sung Mi Yun, Kim Gillan, and Han Seung Kim. "Analysis of Contaminants Found from Soils in the Abandoned Railroad Sites." Advanced Materials Research 1073-1076 (December 2014): 541–44. http://dx.doi.org/10.4028/www.scientific.net/amr.1073-1076.541.
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Recently, reconstruction of abandoned railroad stations and railroad beds are increasingly taking place in Korea. Soil remediation is necessary for the eco-friendly development. Soil found in abandoned railroad sites typically contaminated with heavy oils, which are low volatile petroleum products and less decomposable in nature. The objective of this study is to analyze those contaminants and contamination levels of the soils collected from an abandoned railroad bed located in Seoul, Korea. Heavy oils were extracted from contaminated soils using an organic solvent mixture of methanol and dichloromethane (1:2, v/v). Extracted solvent were analyzed qualitatively by Fourier transform infrared spectroscopy (FT-IR) and qualitatively using high performance liquid chromatography. It was found that the abandoned railroad bed soil was mainly contaminated by heavy oils such as bunker C oil, which was confirmed by FT-IR spectra of petroleum oil products such as gasoline, diesel, kerosene, JP-8, bunker C oil, and lubricants. Benzo [a] antracene was found from the contaminated soil and its level was as high as 11.45 mg/kg, and other polycyclic aromatic hydrocarbons were trivial.
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Feng, Xiaoyuan, and Peng Xing. "Genomics of Yoonia sp. Isolates (Family Roseobacteraceae) from Lake Zhangnai on the Tibetan Plateau." Microorganisms 11, no. 11 (November 20, 2023): 2817. http://dx.doi.org/10.3390/microorganisms11112817.
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Understanding the genomic differentiation between marine and non-marine aquatic microbes remains a compelling question in ecology. While previous research has identified several lacustrine lineages within the predominantly marine Roseobacteraceae family, limited genomic data have constrained our understanding of their ecological adaptation mechanisms. In this study, we isolated four novel Yoonia strains from a brackish lake on the Tibetan Plateau. These strains have diverged from their marine counterparts within the same genus, indicating a recent habitat transition event from marine to non-marine environments. Metabolic comparisons and ancestral genomic reconstructions in a phylogenetic framework reveal metabolic shifts in salinity adaptation, compound transport, aromatics degradation, DNA repair, and restriction systems. These findings not only corroborate the metabolic changes commonly observed in other non-marine Roseobacters but also unveil unique adaptations, likely reflecting the localized metabolic changes in responses to Tibetan Plateau environments. Collectively, our study expands the known genomic diversity of non-marine Roseobacteraceae lineages and enhances our understanding of microbial adaptations to lacustrine ecosystems.
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Shu, Suxun, Guofu Chen, Jiaming Yan, Ziqing Li, Weili Shen, Kai Gong, and Yi Luo. "Combined Use of Polyurethane Prepolymer and Aromatic Oil in Physicochemical Rejuvenation of Aged SBS Modified Bitumen for Performance Recovery." Polymers 15, no. 5 (February 23, 2023): 1120. http://dx.doi.org/10.3390/polym15051120.
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The high-quality reutilization of waste styrene–butadiene–styrene copolymer (SBS) modified asphalt mixtures is a difficult issue in the field of highways today, and the main reason is that conventional rejuvenation technology fails to achieve the effective rejuvenation of aged SBS in binder, causing significant deterioration in the high-temperature performance of the rejuvenated mixture. In view of this, this study proposed a physicochemical rejuvenation process using a reactive single-component polyurethane (PU) prepolymer as the repairing substance for structural reconstruction and aromatic oil (AO) as a common rejuvenator used to supplement the lost light fractions of asphalt molecules in aged SBSmB, according to the characteristics of oxidative degradation products of SBS. The joint rejuvenation of aged SBS modified bitumen (aSBSmB) by PU and AO was investigated based on Fourier transform infrared Spectroscopy, Brookfield rotational viscosity, linear amplitude sweep, and dynamic shear rheometer tests. The results show that 3 wt% PU can completely react with the oxidation degradation products of SBS and rebuild its structure, while AO mainly acted as an inert component to increase the content of aromatic components, thereby reasonably adjusting the compatibility of chemical components of aSBSmB. Compared with the PU reaction-rejuvenated binder, the 3 wt% PU/10 wt% AO rejuvenated binder had a lower high-temperature viscosity for better workability. The chemical reaction between PU and SBS degradation products dominated in the high-temperature stability of rejuvenated SBSmB and had a negative impact on its fatigue resistance, while the joint rejuvenation of 3 wt% PU and 10 wt% AO not only gave a better high-temperature property to aged SBSmB but could also have the capacity to improve its fatigue resistance. Compared to virgin SBSmB, PU/AO rejuvenated SBSmB has comparative low-temperature viscoelastic behavior characteristics and a much better resistance to medium-high-temperature elastic deformation.
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Foan, L., C. Sablayrolles, D. Elustondo, E. Lasheras, L. González, A. Ederra, V. Simon, and J. M. Santamaría. "Reconstructing historical trends of polycyclic aromatic hydrocarbon deposition in a remote area of Spain using herbarium moss material." Atmospheric Environment 44, no. 26 (August 2010): 3207–14. http://dx.doi.org/10.1016/j.atmosenv.2010.05.019.
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Gattiglia, Gabriele, Eleonora Rattighieri, Eleonora Clò, Francesca Anichini, Antonio Campus, Marta Rossi, Mauro Buonincontri, and Anna Maria Mercuri. "Palynology of Gardens and Archaeobotany for the Environmental Reconstruction of the Charterhouse of Calci-Pisa in Tuscany (Central Italy)." Quaternary 6, no. 3 (August 8, 2023): 45. http://dx.doi.org/10.3390/quat6030045.
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In central Italy, the Charterhouse of Calci hosts the Natural History Museum of the University of Pisa. This monumental monastery was founded in 1366 by Carthusian monks. The Charterhouse has experienced various transformations over the centuries, until its abandonment in the 1970s. Since 2018, interdisciplinary archaeological research focused on the monks’ gardens (and particularly: the Prior’s, the Apothecary’s, and the Master’s garden) and the green spaces outside the cloister walls, consisting of courtyards and orchards, to determine the individual (gardens) and collective (green spaces and surrounding woods) practices adopted by Carthusians. Palynology and archaeobotany have allowed to reconstruct the plant biodiversity, with flowers and ornamental, aromatic, and medicinal herbs that grew in the gardens, as well as the management of local hilly woods and agricultural practices, including the cultivation of fruit trees, such as chestnut, olive tree, almond tree, and grapevine. Our research has been based on a solid theoretical approach, interpreting archaeological and archaeobotanical data in relation to the intricate network of human and non-human connections. Gardens are seen as a co-creation made together by human and non-human agencies, and their diachronic transformation is read as an expression of personalities of the monks, feelings, and connections with nature and divinity.
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Zhao, Guangyao, Minglei Yang, and Feng Qian. "Study on the Domain of Parameters in the Stochastic Reconstruction Method." Processes 10, no. 4 (March 30, 2022): 669. http://dx.doi.org/10.3390/pr10040669.
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In the stochastic reconstruction of petroleum fractions, the domain configuration for parameters is of great significance to the performance of the model in terms of accuracy and convergence. Based on the stochastic reconstruction model of gas oils, this work investigates the influence of different domains on the simulating accuracy, the convergence rate and the ability to predict detailed composition. In this paper, the parameters to be optimized in the model include histogram distributions and gamma distributions, which are used to represent the structural attributes. In each histogram distribution, the parameters are real numbers between zero and one that should increase progressively. The mean and shape parameters are used as the tuning parameters for gamma distribution. As for the mean, the lower and upper boundaries are configured as fixed values that depend on the predefined values of the structural attributes. For the shape parameter, multiple cases are considered for its upper boundary, which is set to 5, 10, 20, 50 and 100, respectively. The lower boundary is set to 0 or 1, depending on the structural attribute. The results indicate that the simulating accuracy of the stochastic reconstruction model improves with the increase of the upper boundary for the shape parameter. When the upper boundary of each shape parameter is 20, the simulating accuracy is better than that when the upper boundary is 5 and 10, and close to that when the upper boundary is 50 and 100. The detailed group-type analysis is involved in the model to predict the distributions of mass fraction in chemical families against the carbon number. The results show that the predicted distributions in normal paraffins, isoparaffins, naphthenes, and aromatics are closest to the experimental distributions when the upper boundary is 20 and 50. When the upper boundary is 5 and 10, the predicted distributions in normal paraffins and isoparaffins are lower and broader than the experimental distributions. On the contrary, the predicted distributions in normal paraffins and isoparaffins are higher when the upper boundary is 100. By studying the effects of different domains on the results of the stochastic reconstruction model, a better molecular characterization of petroleum fractions can be achieved.
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Startsev, Viktor, Nikolay Gorbach, Anton Mazur, Anatoly Prokushkin, Lyudmila Karpenko, and Alexey Dymov. "Macrocharcoal Signals in Histosols Reveal Wildfire History of Vast Western Siberian Forest-Peatland Complexes." Plants 11, no. 24 (December 12, 2022): 3478. http://dx.doi.org/10.3390/plants11243478.
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Fires are a naturally cyclical factor regulating ecosystems’ function and forming new postfire ecosystems. Peat soils are unique archives that store information about ecological and climatic changes and the history of past fires during the Holocene. The paper presents a reconstruction of the dynamics of fires in the subzone of the middle taiga of Western Siberia in the Holocene. Data on fires were obtained based on the results of a study of the content of macroscopic coal particles and radiocarbon dating. The effect of fires on soil organic matter (SOM) was estimated using 13C NMR spectroscopy and the content of polyaromatic hydrocarbons (PAHs). It is shown that throughout the Holocene, the peatlands studied were prone to fires. The conducted analyses show that the maximum content of charcoal particles is observed in the Atlantic (~9100–5800 cal. B.P.) and Subatlantic (~3100 cal. B.P. to the present) periods. The high correlation dependence of the content of coals with the content of PAHs (r = 0.56, p < 0.05) and aromatic structures of SOM (r = 0.61, p < 0.05) in peat horizons is shown, which can characterize these parameters as a reliable marker of pyrogenesis.
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Yasir, Muhammad, A. K. Qureshi, S. Srinivasan, R. Ullah, F. Bibi, M. Rehan, S. B. Khan, and E. I. Azhar. "Domination of Filamentous Anoxygenic Phototrophic Bacteria and Prediction of Metabolic Pathways in Microbial Mats from the Hot Springs of Al Aridhah." Folia Biologica 66, no. 1 (2020): 24–35. http://dx.doi.org/10.14712/fb2020066010024.
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Microbial mats in hot springs form a dynamic ecosystem and support the growth of diverse communities with broad-ranging metabolic capacity. In this study, we used 16S rRNA gene amplicon sequencing to analyse microbial communities in mat samples from two hot springs in Al Aridhah, Saudi Arabia. Putative metabolic pathways of the microbial communities were identified using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). Filamentous anoxygenic phototrophic bacteria associated with phylum Chloroflexi were abundant (> 50 %) in both hot springs at 48 °C. Chloroflexi were mainly represented by taxa Chloroflexus followed by Roseiflexus. Cyanobacteria of genus Arthrospira constituted 3.4 % of microbial mats. Heterotrophic microorganisms were mainly represented by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Archaea were detected at a lower relative abundance (< 1 %). Metabolic pathways associated with membrane transport, carbon fixation, methane metabolism, amino acid biosynthesis, and degradation of aromatic compounds were commonly found in microbial mats of both hot springs. In addition, pathways for production of secondary metabolites and antimicrobial compounds were predicted to be present in microbial mats. In conclusion, microbial communities in the hot springs of Al Aridhah were composed of diverse bacteria, with taxa of Chloroflexus being dominant.
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UNNES, Sudarmin, Woro SUMARNI, Skunda DILIAROSTA, and Isabela RAMADANTY. "THE RECONSTRUCTION OF SCIENTIFIC KNOWLEDGE ABOUT BAJAKAH KALALAWIT (UNCARIA GAMBIR ROXB) BIOACTIVITY AS ETHNOMEDICINE." Periódico Tchê Química 17, no. 35 (July 20, 2020): 524–35. http://dx.doi.org/10.52571/ptq.v17.n35.2020.44_unnes_pgs_524_535.pdf.
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Indonesia has more than 25.000-30.000 plant species. The Indonesia tropical forest is a huge source for secondary metabolite compounds that are beneficial for health and life. One of the treasures is Bajakah (Uncaria gambir roxb), a plant endemic to Borneo that has been hereditarily believed to cure tumors and cancers. This research belongs to an educational study that reconstructed scientific knowledge about secondary metabolite compounds' bioactivities of Bajakah as ethnomedicine and aimed at reestablishing scientific research on bioactivities of Bajakah for cancer and tumor medication. The wood and root of Bajakah Kalalawit of the National Conservation Forest, Samarinda, Indonesia, were taken as the sample. The root and wood powder was isolated and extracted for their secondary metabolite compounds using water, ethanol + water, and ethanol + hexane as the solvents. The resulted isolates were tested for the phytochemical, structure, and bioactivity towards Bacillus subtilis and Escherichia coli (E.Colli). The results were supported by structure tests with FTIR spectroscopy, which showed the appearance of uptake of functional groups for hydroxyl, carbonyl, and aromatics that corresponded to secondary metabolite molecules. The analysis of the obtained data concluded that the Bajakah root and the wood extract contain the inhibitory activity of cancer cells and tumors because they contain compounds of secondary metabolites, including terpenes, phenols, alkaloids, and flavonoids. The secondary metabolite compounds from the Bajakah isolates were able to inhibit the activity of Bacillus subtilis and Escherichia coli (E.Colli).
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Li, Chaocan, Xiaopeng Zhang, Xuqin Wang, Xinbo Zhang, Shigang Liu, Ting Yuan, Weigui Qu, and Youjun Zhang. "Distribution Characteristics and Potential Risks of Polycyclic Aromatic Hydrocarbon (PAH) Pollution at a Typical Industrial Legacy Site in Tianjin, North China." Land 11, no. 10 (October 15, 2022): 1806. http://dx.doi.org/10.3390/land11101806.
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Polycyclic aromatic hydrocarbon (PAH) pollution in the soil of industrial legacy sites is a prominent problem when reusing urban land. To estimate the potential risks of PAHs, this study investigated 16 priority PAHs in the soil at different depths in a typical decommissioned industrial site in Tianjin. PAH concentrations were determined via gas chromatography-(tandem) quadrupole mass spectrometry. Incremental lifetime cancer risk (ILCR) assessment was applied to assess the potential risks to the population after land reconstruction. The total concentrations of PAHs in the soil at different depths ranged from 38.3 ng·g−1 to 1782.5 ng·g−1, which were below the risk control standard for soil contamination of development land (GB 36600-2018). Low-ring (two-three ring) PAHs exhibit a dominant component, and the variations in PAH compositions were closely related to the former production units and soil properties. Compared to silty clay layers, PAHs tended to accumulate in the permeable miscellaneous fill layers. Incremental lifetime cancer risk assessment values associated with different exposure pathways for children, adolescents, and adults were calculated. The results showed potential carcinogenic risks for people of varying ages in this area, but they were still acceptable. In general, this legacy site can meet the demands of sustainable land development.
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Yelwa, Nura Abdulmumini, Khairul Azlan Mustapha, Mimonitu Opuwari, and Azharuddin Abd Aziz. "Biomarkers, stable carbon isotope, and trace element distribution of source rocks in the Orange Basin, South Africa: implications for paleoenvironmental reconstruction, provenance, and tectonic setting." Journal of Petroleum Exploration and Production Technology 12, no. 2 (November 27, 2021): 307–39. http://dx.doi.org/10.1007/s13202-021-01317-9.
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AbstractAptian to Campanian sediments from the Western offshore to Central Orange Basin were studied by integrating molecular geochemistry, inorganic and isotopic studies to recognize their geochemical characteristics via the reconstruction of the Orange basin’s paleoweathering, paleosalinity, paleovegetation, paleoclimate, and tectonic records. Molecular analyses of both aliphatic and aromatic compounds reveal an input dominantly from a marine source. The source rocks accumulated in a reduced, anoxic, saline water column. Based on various biomarker proxies and vitrinite reflectance data, some samples are thermally mature to produce petroleum, while others are not. According to the V/Ni ratio, samples from the Orange Basin in South Africa are mainly anoxic, with only a few samples ranging from suboxic to anoxic. This is congruent with biomarker and isotope analyses that further indicate the presence of marine-derived source rocks with some terrestrial remains generating hydrocarbons. The investigated sediments are made up of intermediate igneous rocks that have undergone moderate chemical weathering. Geochemical figures on tectonic setting discriminant function diagrams revealed a continental rift of passive margin settings. As a result, the extrapolated crustal processes are directly analogous to the genesis and evolution of the Orange Basin, demonstrating Gondwana’s breaking up and the opening of the Atlantic Ocean Margin.
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Papale, Maria, Carmen Rizzo, Gabriella Caruso, Rosabruna La Ferla, Giovanna Maimone, Angelina Lo Giudice, Maurizio Azzaro, and Mauro Guglielmin. "First Insights into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land." Diversity 13, no. 7 (July 15, 2021): 323. http://dx.doi.org/10.3390/d13070323.
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Different polar environments (lakes and glaciers), also in Antarctica, encapsulate brine pools characterized by a unique combination of extreme conditions, mainly in terms of high salinity and low temperature. Since 2014, we have been focusing our attention on the microbiology of brine pockets from three lakes in the Northern Victoria Land (NVL), lying in the Tarn Flat (TF) and Boulder Clay (BC) areas. The microbial communities have been analyzed for community structure by next generation sequencing, extracellular enzyme activities, metabolic potentials, and microbial abundances. In this study, we aim at reconsidering all available data to analyze the influence exerted by environmental parameters on the community composition and activities. Additionally, the prediction of metabolic functions was attempted by the phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) tool, highlighting that prokaryotic communities were presumably involved in methane metabolism, aromatic compound biodegradation, and organic compound (proteins, polysaccharides, and phosphates) decomposition. The analyzed cryoenvironments were different in terms of prokaryotic diversity, abundance, and retrieved metabolic pathways. By the analysis of DNA sequences, common operational taxonomic units ranged from 2.2% to 22.0%. The bacterial community was dominated by Bacteroidetes. In both BC and TF brines, sequences of the most thermally tolerant and methanogenic Archaea were detected, some of them related to hyperthermophiles.
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Anugrah, Indah Rizki, and Kartimi Kartimi. "Local Wisdom-based Contextual Learning as Embedded-STEM approach in High School Chemistry." IJIS Edu : Indonesian Journal of Integrated Science Education 4, no. 1 (January 11, 2022): 1. http://dx.doi.org/10.29300/ijisedu.v4i1.5783.
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The application of STEM in Indonesia can be made through an embedded approach using the social, cultural and technological contexts encountered by students daily. This study aimed to reconstruct the context of Cirebon local wisdom, i.e. batik, to be used as a context for embedded STEM chemistry learning in high school. This research used a qualitative method by choosing the Model of Educational Reconstruction (MER) as the research framework. In this study, observations were made on the batik-making process, a literature review to explore the batik context's chemical perspective, and interviews to obtain information about students' preconceptions about batik. The findings indicated that the essential components of batik (fabric, wax, and dye) and the process of batik making were inextricably linked to chemical processes. According to the literature review, the context of batik is connected to several high school chemistry concepts, including organic chemistry (particularly regarding aromatic derivatives and polymers), electromagnetic radiation, chemical bonds, acid-base, oxidation and reduction, and stoichiometry. Meanwhile, it is known from student interviews that students' preconceptions about the scientific content of batik and related chemical concepts remain clearly distinguishable from their correct scientific conceptions. However, students expressed a favourable attitude toward the possibility of incorporating batik into chemistry instruction
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Perchat, Nadia, Pierre-Loïc Saaidi, Ekaterina Darii, Christine Pellé, Jean-Louis Petit, Marielle Besnard-Gonnet, Véronique de Berardinis, et al. "Elucidation of the trigonelline degradation pathway reveals previously undescribed enzymes and metabolites." Proceedings of the National Academy of Sciences 115, no. 19 (April 23, 2018): E4358—E4367. http://dx.doi.org/10.1073/pnas.1722368115.
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Trigonelline (TG;N-methylnicotinate) is a ubiquitous osmolyte. Although it is known that it can be degraded, the enzymes and metabolites have not been described so far. In this work, we challenged the laboratory model soil-borne, gram-negative bacteriumAcinetobacter baylyiADP1 (ADP1) for its ability to grow on TG and we identified a cluster of catabolic, transporter, and regulatory genes. We dissected the pathway to the level of enzymes and metabolites, and proceeded to in vitro reconstruction of the complete pathway by six purified proteins. The four enzymatic steps that lead from TG to methylamine and succinate are described, and the structures of previously undescribed metabolites are provided. Unlike many aromatic compounds that undergo hydroxylation prior to ring cleavage, the first step of TG catabolism proceeds through direct cleavage of the C5–C6 bound, catalyzed by a flavin-dependent, two-component oxygenase, which yields (Z)-2-((N-methylformamido)methylene)-5-hydroxy-butyrolactone (MFMB). MFMB is then oxidized into (E)-2-((N-methylformamido) methylene) succinate (MFMS), which is split up by a hydrolase into carbon dioxide, methylamine, formic acid, and succinate semialdehyde (SSA). SSA eventually fuels up the TCA by means of an SSA dehydrogenase, assisted by a Conserved Hypothetical Protein. The cluster is conserved across marine, soil, and plant-associated bacteria. This emphasizes the role of TG as a ubiquitous nutrient for which an efficient microbial catabolic toolbox is available.
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Callegaro, Alice, Dario Battistel, Natalie M. Kehrwald, Felipe Matsubara Pereira, Torben Kirchgeorg, Maria del Carmen Villoslada Hidalgo, Broxton W. Bird, and Carlo Barbante. "Fire, vegetation, and Holocene climate in a southeastern Tibetan lake: a multi-biomarker reconstruction from Paru Co." Climate of the Past 14, no. 10 (October 23, 2018): 1543–63. http://dx.doi.org/10.5194/cp-14-1543-2018.
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Abstract. The fire history of the Tibetan Plateau over centennial to millennial timescales is not well known. Recent ice core studies reconstruct fire history over the past few decades but do not extend through the Holocene. Lacustrine sedimentary cores, however, can provide continuous records of local environmental change on millennial scales during the Holocene through the accumulation and preservation of specific organic molecular biomarkers. To reconstruct Holocene fire events and vegetation changes occurring on the southeastern Tibetan Plateau and the surrounding areas, we used a multi-proxy approach, investigating multiple biomarkers preserved in core sediment samples retrieved from Paru Co, a small lake located in the Nyainqentanglha Mountains (29∘47′45.6′′ N, 92∘21′07.2′′ E; 4845 m a.s.l.). Biomarkers include n-alkanes as indicators of vegetation, polycyclic aromatic hydrocarbons (PAHs) as combustion proxies, fecal sterols and stanols (FeSts) as indicators of the presence of humans or grazing animals, and finally monosaccharide anhydrides (MAs) as specific markers of vegetation burning processes. Insolation changes and the associated influence on the Indian summer monsoon (ISM) affect the vegetation distribution and fire types recorded in Paru Co throughout the Holocene. The early Holocene (10.7–7.5 cal kyr BP) n-alkane ratios demonstrate oscillations between grass and conifer communities, resulting in respective smouldering fires represented by levoglucosan peaks, and high-temperature fires represented by high-molecular-weight PAHs. Forest cover increases with a strengthened ISM, where coincident high levoglucosan to mannosan (L ∕ M) ratios are consistent with conifer burning. The decrease in the ISM at 4.2 cal kyr BP corresponds with the expansion of regional civilizations, although the lack of human FeSts above the method detection limits excludes local anthropogenic influence on fire and vegetation changes. The late Holocene is characterized by a relatively shallow lake surrounded by grassland, where all biomarkers other than PAHs display only minor variations. The sum of PAHs steadily increases throughout the late Holocene, suggesting a net increase in local to regional combustion that is separate from vegetation and climate change.
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Forero-Rodríguez, Johanna, Johannes Zimmermann, Jan Taubenheim, Natalia Arias-Rodríguez, Juan David Caicedo-Narvaez, Lena Best, Cindy V. Mendieta, et al. "Changes in Bacterial Gut Composition in Parkinson’s Disease and Their Metabolic Contribution to Disease Development: A Gut Community Reconstruction Approach." Microorganisms 12, no. 2 (February 4, 2024): 325. http://dx.doi.org/10.3390/microorganisms12020325.
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Parkinson’s disease (PD) is a chronic and progressive neurodegenerative disease with the major symptoms comprising loss of movement coordination (motor dysfunction) and non-motor dysfunction, including gastrointestinal symptoms. Alterations in the gut microbiota composition have been reported in PD patients vs. controls. However, it is still unclear how these compositional changes contribute to disease etiology and progression. Furthermore, most of the available studies have focused on European, Asian, and North American cohorts, but the microbiomes of PD patients in Latin America have not been characterized. To address this problem, we obtained fecal samples from Colombian participants (n = 25 controls, n = 25 PD idiopathic cases) to characterize the taxonomical community changes during disease via 16S rRNA gene sequencing. An analysis of differential composition, diversity, and personalized computational modeling was carried out, given the fecal bacterial composition and diet of each participant. We found three metabolites that differed in dietary habits between PD patients and controls: carbohydrates, trans fatty acids, and potassium. We identified six genera that changed significantly in their relative abundance between PD patients and controls, belonging to the families Lachnospiraceae, Lactobacillaceae, Verrucomicrobioaceae, Peptostreptococcaceae, and Streptococcaceae. Furthermore, personalized metabolic modeling of the gut microbiome revealed changes in the predicted production of seven metabolites (Indole, tryptophan, fructose, phenylacetic acid, myristic acid, 3-Methyl-2-oxovaleric acid, and N-Acetylneuraminic acid). These metabolites are associated with the metabolism of aromatic amino acids and their consumption in the diet. Therefore, this research suggests that each individual’s diet and intestinal composition could affect host metabolism. Furthermore, these findings open the door to the study of microbiome–host interactions and allow us to contribute to personalized medicine.
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S. V., Pyshiev, Lipko Yu. V., Shlyakhova A. O., and Korchak B. A. "THE OBTAINING AND STUDYING OF THE COMPOSITION OF CAR TIRE BASED LIQUID PYROLYSIS PRODUCTS." Journal of Coal Chemistry 1 (2022): 21–28. http://dx.doi.org/10.31081/1681-309x-2022-0-1-21-28.
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The actual problem of the accumulation of used car tires in the environment has been considered and rational ways of its solving have been proposed. The "traditional" (thermal) method has been considered, the essence of which lies in the following technological operations: theextraction of metal parts from the tires, the grinding of the obtaining rubber material and its heating to high temperatures without air access. The result products of the pyrolysis of used car tires are gas, liquid fraction and carbon black. To carry out the process of pyrolysis of used car tires, a basic technological scheme of the process has been proposed, which was implemented on a pilot scale. The main product is liquid pyrolysis products of used car tires, the mass yield of which is about 35 %. In order to search a further rational use of liquid pyrolysis products of used car tires, a number of their physicochemical properties and fractional composition have been analysed, and their hydrocarbon composition has been determined. Comparison of the characteristics of liquid pyrolysis products of used car tires with the requirements of regulatory documents for commercial fuels allowed to assert that these materials cannot be used as a component of boiler fuel. The main reason for this conclusion is the low flash point in the open crucible. After the removing of gasoline fractions from the liquid products of pyrolysis of used car tires (boiling temperature 200 °C), the resulting residue (boiling temperature > 200 °C) met the requirements of DSTU 4058-2001 for fuel oils of grades "40" and "100". This fact allows to use such a material as a component of boiler fuel. The possibility of using gasoline fractions as components of commercial gasoline is analyzed. The revealed high content of aromatic compounds and a relatively high content of unsaturated hydrocarbons in the composition of the fractions (fr. with a boiling interval of 140–200 °C and fr. with initial boiling point of 140 °C) are unacceptable for gasoline fractions. Establishing effective and simple methods for reducing the content of aromatic and unsaturated compounds without significant reconstruction of the installation will be the goal of further research. Key words: used car tires, pyrolysis, liquid pyrolysis products, chromatography, boiler fuel, gasoline fractions. Corresponding author S. V. Pyshiev, e-mail: gajva@polynet.lviv.ua
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Kerou, Melina, Pierre Offre, Luis Valledor, Sophie S. Abby, Michael Melcher, Matthias Nagler, Wolfram Weckwerth, and Christa Schleper. "Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers." Proceedings of the National Academy of Sciences 113, no. 49 (November 18, 2016): E7937—E7946. http://dx.doi.org/10.1073/pnas.1601212113.
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Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile “Ca. Nitrosotalea devanaterra” revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and “Ca. Nitrosopelagicus brevis” proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs.
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Hanami, Hitoshi, and Tsuyoshi Ishigaki. "Reconstruction of Star Formation and AGNs Activities in Galaxies Classified with the Balmer Break, 1.6 μm Bump and PAH Features up to z ≃2." Proceedings of the International Astronomical Union 6, S277 (December 2010): 182–85. http://dx.doi.org/10.1017/s1743921311022733.
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AbstractWe have studied the star-forming and AGN activity of massive galaxies in the redshift range z = 0.4−2, which are detected in a deep survey field using the AKARI and Subaru telescopes toward the North Ecliptic Pole (NEP). The multi-wavelength survey allows us to select Mid-InfraRed (MIR) bright populations as Luminous InfraRed Galaxies (LIRGs) with L(IR) ≃ 1010–11 L⊙, which can be also sub-classified into Balmer Break Galaxies (BBGs) and Infra-Red (IR) Bump Galaxies (IRBGs). AKARI/IRC multiband photometry can distinguish their star-forming/AGN activity for LIRGs with/without the Polycyclic-Aromatic Hydrocarbon (PAH) emission bands at 6.2, 7.7 and 11.3 μm, and estimate the Star Formation Rate (SFR) from their total emitting InfraRed (IR) luminosities for star-formings and the emissions from dusty torus for AGNs. The results are summarised as below: 1) The rest-frame 7.7 μm luminosity is still a good tracer of the total IR (tIR) luminosity, as the PAH emission dominates for star-forming galaxies even up to z ≃ 2, 2) Rest-frame 5μm Luminosities may trace emissions from dusty torus of AGN in the LIRGs, 3) SFR of Starburst-AGN LIRGs (s/a-LIRGs) tends to quench at z < 0.8 more rapidly than that of Starburst dominated LIRGs (sb-LIRGs), 4) Intrinsic Stellar populations in the s/a-LIRGs show redder colours than those in the sb-LIRGs. These results suggest that Super Massive Black Holes (SMBH) could already have grown to ≃ 3 × 108M⊙ in the agn-LIRGs, with ≃ 1011L⊙ at z > 1.2, and the growth of SMBH tends to follow the star-forming activities around z = 1–2.
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Vigneron, Adrien, Perrine Cruaud, Frederic Ducellier, Ian M. Head, and Nicolas Tsesmetzis. "Syntrophic Hydrocarbon Degradation in a Decommissioned Off-Shore Subsea Oil Storage Structure." Microorganisms 9, no. 2 (February 11, 2021): 356. http://dx.doi.org/10.3390/microorganisms9020356.
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Over the last decade, metagenomic studies have revealed the impact of oil production on the microbial ecology of petroleum reservoirs. However, despite their fundamental roles in bioremediation of hydrocarbons, biocorrosion, biofouling and hydrogen sulfide production, oil field and oil production infrastructure microbiomes are poorly explored. Understanding of microbial activities within oil production facilities is therefore crucial for environmental risk mitigation, most notably during decommissioning. The analysis of the planktonic microbial community from the aqueous phase of a subsea oil-storage structure was conducted. This concrete structure was part of the production platform of the Brent oil field (North Sea), which is currently undergoing decommissioning. Quantification and sequencing of microbial 16S rRNA genes, metagenomic analysis and reconstruction of metagenome assembled genomes (MAGs) revealed a unique microbiome, strongly dominated by organisms related to Dethiosulfatibacter and Cloacimonadetes. Consistent with the hydrocarbon content in the aqueous phase of the structure, a strong potential for degradation of low molecular weight aromatic hydrocarbons was apparent in the microbial community. These degradation pathways were associated with taxonomically diverse microorganisms, including the predominant Dethiosulfatibacter and Cloacimonadetes lineages, expanding the list of potential hydrocarbon degraders. Genes associated with direct and indirect interspecies exchanges (multiheme type-C cytochromes, hydrogenases and formate/acetate metabolism) were widespread in the community, suggesting potential syntrophic hydrocarbon degradation processes in the system. Our results illustrate the importance of genomic data for informing decommissioning strategies in marine environments and reveal that hydrocarbon-degrading community composition and metabolisms in man-made marine structures might differ markedly from natural hydrocarbon-rich marine environments.
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Ayuso-Fernández, Iván, Jorge Rencoret, Ana Gutiérrez, Francisco Javier Ruiz-Dueñas, and Angel T. Martínez. "Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants." Proceedings of the National Academy of Sciences 116, no. 36 (August 19, 2019): 17900–17905. http://dx.doi.org/10.1073/pnas.1905040116.
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A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated here by resurrecting ancestral fungal peroxidases, after sequence reconstruction from genomes of extant white-rot Polyporales, and evaluating their oxidative attack on the lignin polymer by state-of-the-art analytical techniques. Rapid stopped-flow estimation of the transient-state constants for the 2 successive one-electron transfers from lignin to the peroxide-activated enzyme (k2app and k3app) showed a progressive increase during peroxidase evolution (up to 50-fold higher values for the rate-limiting k3app). The above agreed with 2-dimensional NMR analyses during steady-state treatments of hardwood lignin, showing that its degradation (estimated from the normalized aromatic signals of lignin units compared with a control) and syringyl-to-guaiacyl ratio increased with the enzyme evolutionary distance from the first peroxidase ancestor. More interestingly, the stopped-flow estimations of electron transfer rates also showed how the most recent peroxidase ancestors that already incorporated the exposed tryptophan into their molecular structure (as well as the extant lignin peroxidase) were comparatively more efficient at oxidizing hardwood (angiosperm) lignin, while the most ancestral “tryptophanless” enzymes were more efficient at abstracting electrons from softwood (conifer) lignin. A time calibration of the ancestry of Polyporales peroxidases localized the appearance of the first peroxidase with a solvent-exposed catalytic tryptophan to 194 ± 70 Mya, coincident with the diversification of angiosperm plants characterized by the appearance of dimethoxylated syringyl lignin units.
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Hooker, Jerry J., Pim F. Van Bergen, Ros L. Singer, Margaret E. Collinson, Jan W. De Leeuw, and Tim P. Jones. "Reconstruction of Tertiary palaeoenvironments using a combination of molecular and conventional palaeobiology." Paleontological Society Special Publications 6 (1992): 134. http://dx.doi.org/10.1017/s2475262200006948.
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The Bembridge Limestone Formation (BLF), Late Eocene of Headon Hill, Isle of Wight, England, contains a diverse array of mammals (around 50 spp.) distributed through 10 levels. Its lower part (“lower fauna”) marks the appearance of a significant number of species, genera and one family unknown from earlier English Late Eocene strata. Towards the top of the BLF there is a reversion to faunas (“upper fauna”) more typical of the underlying Headon Hill Formation. This represents their last appearance in England. The succeeding Bembridge Marls Member fauna is similar to that in the lower part of the BLF. These changes are provincial in scale and may be climate induced (reflecting a slight warming followed by terminal Eocene cooling). Superimposed on these changes are smaller-scale more frequent fluctuations linked to alternating marl and black mud lithologies which may represent local habitat changes. In order to obtain overall understanding of the environment of deposition and taphonomic bias influencing these mammalian assemblages an integrated multidisciplinary study is being undertaken.Plant macrofossils are unfortunately extremely rare in this sequence. Those few which are present typify the fresh-water marsh vegetation widespread in the Late Eocene/Early Oligocene of England. In contrast mammalian faunas indicate more wooded conditions. Seeds like those of the modern free-floating fresh-water plant Stratiotes occur in three levels. However, they are poorly-preserved. The chemical composition of the seed coat as revealed by flash pyrolysis gas chromatography indicates a very simple polyphenol macromolecule probably resulting from transformations of more complex polyphenols in well-preserved Stratiotes seeds.Determinable palynomorphs are very rare and largely restricted to the part of the sequence which contains the “upper fauna”. They suggest a tranquil fresh-water depositional setting as do several molluscs and charophytes. Palynomorphs also include fungal remains, fern spores and a few tree pollen, the latter possibly from regional vegetation. However, the bulk of the palynological organic matter consists of brown structureless organic matter (SOM), resin-like particles and “platy kerogen”. In the lower beds, pale shelly muds with potamidids and corbiculids lack mammals and contain palynological organic matter dominated by resin-like particles and with abundant pyrite. These beds probably reflect brackish influence, the loss of which largely coincides with the reappearance of abundant mammals (“lower fauna”), occurrence of Stratiotes and of charophytes. Resin-like particles remain dominant in the palynological organic matter. “Platy kerogen” dominates three units including that containing the first occurrence of the “upper fauna”. Subsequently resin-like particles again dominate. Brown SOM is scattered throughout but is well represented in two units one of which contains “lower fauna” the other “upper fauna”.Variations in palynological organic matter are reflected in the chemical composition of residues studied. Results from five black muds show that samples which mainly contain resin-like particles are dominated by n-alkanes and n-alk-1-enes in their pyrolysates. However, there is no indication of known resin chemical signatures. This indicates that the organic matter in these residues is mainly derived from cuticles (cutan) and/or cell wall remains (algaenan) of fresh-water algae. Samples containing “platy kerogen” and brown SOM are dominated by aromatics and phenols in their pyrolysates indicating an origin from woody materials. Work in progress on stable isotope analyses of the residues may further clarify the nature of the organic input.
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Babynin, E. V., and I. A. Degtyareva. "Possibilities of using information resources In bioremediation." Proceedings of Universities. Applied Chemistry and Biotechnology 11, no. 3 (October 7, 2021): 372–83. http://dx.doi.org/10.21285/2227-2925-2021-11-3-372-383.
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Abstract: Bioremediation using microorganisms has a number of advantages over physical and chemical methods of water, soil and atmosphere purification. Microorganisms have a wide range of metabolic capabilities that enable them to convert, modify and utilize toxic pollutants for energy and biomass production. This article shows their participation in the decomposition of various industrial wastes, such as dyes, hydrocarbons, chlorinated aromatic compounds and pesticides, among others. Although the use of microorganisms is an environmentally friendly and promising way of solving environmental threats, many factors affect the effectiveness of bioremediation, such as the chemical nature of pollutants, their accessibility to microorganisms, the physical and chemical characteristics of the environment, as well as the interaction of the destructive organisms with each other. The search for new effective strains or the creation of superdestructors using genetic and protein engineering methods proves to be crucial under current circumstances. This task can be solved using such “tools” as genomics, proteomics, transcriptomics and metabolomics. These technologies require the integration of a huge amount of data, which cannot be achieved without the use of bioinformatics. Bioinformatics is used in microbial bioremediation in different ways: analysis of genome sequencing data, identification of protein-coding genes, comparative analysis to identify the function of unknown genes, automatic reconstruction and comparison of metabolic pathways, and study of protein–protein and protein–DNA interactions to understand regulatory mechanisms. This review aims to highlight various resources that store information about possible pathways of microbial metabolism involved in the biodegradation of petroleum products. The use of such information resources can become a starting point for many studies in bioremediation.
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Nabhan, Gary Paul. "Aromas Emanating from the Driest of Places." Gastronomica 14, no. 1 (2014): 44–50. http://dx.doi.org/10.1525/gfc.2014.14.1.44.
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This chapter interweaves the author's personal journey, which begins in the deserts of Arabia, with a reconstruction of the beginnings of the Semitic peoples and the etymologic origins of the words for aromatics and spices. It also describes the properties and uses of frankincense. The book from which this chapter is taken—the author's Cumin, Camels, and Caravans: A Spice Odyssey (University of California Press, 2014)—is the first to relate the spice trade to culinary and ecological imperialism and to demonstrate the indelible mark that Semitic peoples had in managing the spice trade not only in Eurasia, Africa, and Arabia but in the Americas and Caribbean as well. It demonstrates that globalization did not begin in 1492, as recently argued by several scholars, but grew out of intercontinental spice trading practices, principles, and ethics over 3,500 years. Sephardic Jews and Muslim Arabs, Berbers and Persians, all played a disproportionately large role in setting the ground rules for globalization. Phoenicians, Nabateans, Arabized Jews, Sogdians, and Minaeans prehistorically played similar roles in its earliest development. A unique aspect of the book is the linguistic tracking of recipes and terms for spices to reveal routes of cultural diffusion worldwide. The text is accompanied by recipes the author has gathered during his travels, as well as a “cabinet” of profiles describing the history and characteristics of many of the world's most popular and sought-after spices.