Advances of structure, function, and catalytic mechanism of methyl-coenzyme M reductase / 生物工程学报

Methanogens are unique microorganisms for methane production and the main contributor of the biogenic methane in atmosphere. Methyl-coenzyme M reductase (Mcr) catalyzes the last step of methane production in methanogenesis and the first step of methane activation in anaerobic oxidation of methane. The genes encoding this enzyme are highly conserved and are widely used as a marker in the identification and phylogenetic study of archaea. There has been a longstanding interest in its unique cofactor F430 and the underpinning mechanisms of enzymatic cleavage of alkane C-H bond. The recent breakthroughs of high-resolution protein and catalytic-transition-state structures further advanced the structure-function study of Mcr. In particular, the recent discovery of methyl-coenzyme M reductase-like (Mcr-like) enzymes that activates the anaerobic degradation of non-methane alkanes has attracted much interest in the molecular mechanisms of C-H activation without oxygen. This review summarized the advances on function-structure-mechanism study of Mcr/Mcr-like enzymes. Additionally, future directions in anaerobic oxidation of alkanes and greenhouse-gas control using Mcr/Mcr-like enzymes were proposed.

Isolation and characterization of hydrocarbon-degrading bacteria from gas station leaking-contaminated groundwater in the Southern Amazon, Brazil / Isolamento e caracterização de bactérias degradadoras de hidrocarbonetos de água subterrânea contaminada por vazamentos em posto de combustível no sul da Amazônia, Brasil

Abstract Twenty-three hydrocarbon-degrading bacteria strains were isolated from gas station leaking-contaminated groundwater located in the Southern Amazon, Brazil. Based on hydrocarbon (diesel, hexadecane, benzene, toluene and xylene) degradation ability, two strains were selected for further study. The amplification and sequencing of the 16S rRNA gene showed that these two strains belonged to the genus Bacillus (Bacillus sp. L26 and Bacillus sp. L30). GC-MS analysis showed that strain L30 was the most effective in degrading n-alkane (C10-C27) from diesel after 7 days of cultivation in mineral medium. Both strains produced biosurfactants and showed emulsification activity, specially the strain L30. Alkane hydroxylase gene (group III), which is important for alkane biodegradation, was present in strains. As a result, this study indicated that these bacteria could have promising applications in hydrocarbon bioremediation.

Resumo Vinte e três linhagens bacterianas degradadoras de hidrocarbonetos foram isoladas de água subterrânea contaminada por vazamento em posto de combustível no sul da Amazônia, Brasil. Com base na habilidade de degradar hidrocarbonetos (diesel, hexadecano, benzeno, tolueno e xileno), duas linhagens foram selecionadas para estudos posteriores. A amplificação e sequenciamento do gene 16S rRNA demonstrou que essas linhagens pertencem ao gênero Bacillus (Bacillus sp. L26 and Bacillus sp. L30). Análises de GC-MS mostraram que a linhagem L30 foi mais eficiente em degradar n-alcanos (C10-C27) presentes no diesel, após 7 dias de cultivo em meio mineral. Ambas as linhagens produziram biossurfactantes e apresentaram atividade emulsificante, especialmente a linhagem L30. O gene alcano hidroxilase (grupo III), o qual é importante para degradação de alcanos, foram detectados nas linhagens. Como resultado, este estudo indicou que essas linhagens bacterianas podem ser promissoras se aplicadas em processos de biorremediação.

Influence of Halogenated Hydroxyl-Alkanes Inhalation Anesthetic on the Determination of Ethanol Content in Blood / 法医学杂志

Objective To study the influence of halogenated hydroxyl-alkanes inhalation anesthetic on the determination of ethanol content in blood. Methods Halogenated hydroxyl-alkanes were analyzed by headspace gas chromatography with double column confirmatory detection method. The influence of halogenated hydroxyl-alkanes on determination of ethanol content in blood sample by headspace gas chromatography was explored under the different detection conditions of KB-BAC1/ KB-BAC2 and J&W DB-ALC1/DB-ALC2 gas chromatographic column. Results The retention time of sevoflurane and enflurane was similar to that of ethanol and tert butanol respectively when using the J&W DB-ALC1/DB-ALC2 gas chromatographic column, and interfered with the detection of ethanol content in blood; only J&W DB-ALC1 gas chromatographic column can separate the sevoflurane and ethanol components, so as to eliminate their influence on the detection of ethanol content in blood. When using KB-BAC1/KB-BAC2 gas chromatographic column, the retention time of sevoflurane, isoflurane and ethanol is similar, especially that of sevoflurane and ethanol, and sevoflurane obviously interferes with the determination of ethanol content in blood. Conclusion Halogenated hydroxy-alkanes interfere with determination of ethanol content in blood by headspace gas chromatography. The interference can be discriminated effectively by choosing the suitable chromatographic column and double column confirmatory detection.

Isolation and characterization of hydrocarbon-degrading bacteria from gas station leaking-contaminated groundwater in the Southern Amazon, Brazil

Abstract Twenty-three hydrocarbon-degrading bacteria strains were isolated from gas station leaking-contaminated groundwater located in the Southern Amazon, Brazil. Based on hydrocarbon (diesel, hexadecane, benzene, toluene and xylene) degradation ability, two strains were selected for further study. The amplification and sequencing of the 16S rRNA gene showed that these two strains belonged to the genus Bacillus (Bacillus sp. L26 and Bacillus sp. L30). GC-MS analysis showed that strain L30 was the most effective in degrading n-alkane (C10-C27) from diesel after 7 days of cultivation in mineral medium. Both strains produced biosurfactants and showed emulsification activity, specially the strain L30. Alkane hydroxylase gene (group III), which is important for alkane biodegradation, was present in strains. As a result, this study indicated that these bacteria could have promising applications in hydrocarbon bioremediation.

Resumo Vinte e três linhagens bacterianas degradadoras de hidrocarbonetos foram isoladas de água subterrânea contaminada por vazamento em posto de combustível no sul da Amazônia, Brasil. Com base na habilidade de degradar hidrocarbonetos (diesel, hexadecano, benzeno, tolueno e xileno), duas linhagens foram selecionadas para estudos posteriores. A amplificação e sequenciamento do gene 16S rRNA demonstrou que essas linhagens pertencem ao gênero Bacillus (Bacillus sp. L26 and Bacillus sp. L30). Análises de GC-MS mostraram que a linhagem L30 foi mais eficiente em degradar n-alcanos (C10-C27) presentes no diesel, após 7 dias de cultivo em meio mineral. Ambas as linhagens produziram biossurfactantes e apresentaram atividade emulsificante, especialmente a linhagem L30. O gene alcano hidroxilase (grupo III), o qual é importante para degradação de alcanos, foram detectados nas linhagens. Como resultado, este estudo indicou que essas linhagens bacterianas podem ser promissoras se aplicadas em processos de biorremediação.

GC-MS Analysis of N-alkanes in Artemisia Argyi of Different Storage Periods / 上海针灸杂志

Objective To explore the mechanisms of Artemisia argyi burning and moxibustion photo-thermal effect.Methods N-alkanes were obtained by gradient solvent extraction and silica gel column chromatography elution from 1, 3 and 5 years’ Artemisia argyi produced in QiChun, Hubei and analyzed by gas chromatography mass spectrometry (GC-MS).Results The n-alkane contents of 1, 3 and 5 years’ Artemisia argyi were 318.65, 528.23 and 394.20μg/g, respectively. A total of seventeen kinds of n-alkanes were detected from the Artemisia argyi of three kinds of years. The 31 carbon alkane content was highest in all of them. Because N-alkanes affect the temperature and stability of Artemisia argyi burning, it may be the material basis for explaining “worrying seven years’ diseases seek 3 years’ Artemisia argyi”.

Establishment of Analysis Method for Detection of Petroleum Degrading Genes AlkB and Nah in Contaminated Soil and Its Application / 分析化学

SYBR Green I Real Time-qPCR method was developed to quantify the numbers of copyies of AlkB ( alkanes degradation gene) and Nah ( naphthalene dioxygenase degradation gene) functional degradation gene corresponding to alkanes and aromatic hydrocarbons degradation. Two pairs of primers AlkBf/AlkBr and Nahf/Nahr were designed for AlkB and Nah amplification respectively, according to the nucleotide sequences of related degradation microorganisms published in GenBank. The purified recovery products of traditional PCR were combined with pEASY-T1 vectors and transformed in competent cells to amplify. The recombinant plasmids were extracted and used as positive templates to create standard curve through gradient dilution. The conditions for the real time PCR were as the follows: the final concentration of forward and reverse primers were 0. 2 μmol/L, 2×TransStart Top Green qPCR SuperMix, and the annealing temperatures of AlkB and Nah PCR were 50℃ and 57℃, respectively. The method showed a sensitivity of 100 times higher than that of the traditional PCR method and good repeatability. The numbers of copies of AlkB in three functional regions of an oilfield indicated that oil producing zone with serious oil pollution had the highest AlkB copy numbers, and residential zone with lighter oil pollution had the lowest AlkB copy numbers. Nah degradation gene distribution was more uniform.

Patterns of leaf epicuticular waxes in species of Clusia: taxonomical implications

El género Clusia L. (Clusiaceae) comprende unas 300 especies que ocurren desde México y el sur de EEUU hasta Bolivia y el sur de Brasil. Entre ellas se incluyen árboles y arbustos, hemiepifitas, epifitas y lianas. El análisis taxonómico del género se dificulta por la pobre preservación de las flores al ser secadas. Este trabajo explora la composición de ceras epicuticulares para caracterizar especies mediante marcadores químicos. Se analizó la composición del extracto obtenido de seis especies mediante lavado de la superficie foliar con hexano. Las especies pudieron separarse en base a la proporción de alcanos, >90% del total en Clusia rosea, C. orthoneura y C. minor, a la presencia de los triterpenos a-amirina y lupeol en C. multiflora, y de friedelina y taraxerol, conjuntamente con C33 y C35 en C. grandiflora y C. schomburgkiana. Los resultados sugieren que la proporción de alcanos y triterpenoides de ceras epicuticulares tiene importancia taxonómica y puede ser utilizada para separar especies o secciones infragenéricas.

The genus Clusia L. (Clusiaceae) encompasses ca. 300 species and occurs from southern USA and Mexico, to southern Brazil and Bolivia. It includes free-standing trees and shrubs, hemiepiphytes, epiphytes, and lianas. Taxonomic analysis of this genus is difficult because of the poor preservation of floral material after drying. This work explores the composition of epicuticular waxes in order to allow characterization, at the species level, using chemical markers. The six species analyzed could be separated using the relative quantity of hexane-soluble compounds extractable from the leaf surface, which amount to >90% in Clusia rosea, C. orthoneura, and C. minor, the presence of the triterpenes a-amyrin and lupeol in C. multiflora, and of friedelin and taraxerol, together with C33 and C35, in C. grandiflora and C. schomburgkiana. The results suggest that the relative proportions of alkanes and triterpenoids in epicuticular waxes may have taxonomic significance for separating species or infrageneric sections.

O gênero Clusia L. (Clusiaceae) compreende umas 300 espécies que ocorrem desde México e o sul dos EE.UU. até Bolívia e o sul do Brasil. Entre elas se incluem árvores e arbustos, hemiepífitas, epífitas e lianas. A análise taxonômica do gênero se dificulta pela pobre preservação das flores ao ser secadas. Este trabalho explora a composição de ceras epicuticulares para caracterizar espécies mediante marcadores químicos. Se analisou a composição do extrato obtido de seis espécies mediante lavado da superfície foliar com hexano. As espécies puderam separar-se em base à proporção de alcanos, >90% do total em Clusia rosea, C. orthoneura e C. minor, à presença dos triterpenos a-amirina e lupeol em C. multiflora, e de friedelina e taraxerol, conjuntamente com C33 e C35 em C. grandiflora e C. schomburgkiana. Os resultados sugerem que a proporção de alcanos e triterpenóides de ceras epicuticulares tem importância taxonômica e pode ser utilizada para separar espécies ou seções infragenéricas.

Uptake of volatile n-alkanes by Pseudomonas PG-I.

Using a bacterial species Pseudomonas PG-1, evidence has been obtained which indicates that uptake of n-pentane to n-octane by microbial cells takes place primarily from the gas phase either directly or via the aqueous phase. Specific growth rate increased along with the increase in substrate concentration but above the alkane concentration of 0·3% by volume, specific growth rate decreased indicating substrate inhibition of growth. In the case of less volatile alkanes, n-nonane and n-decane, substrate transfer is predominantly through substrate solubilization system elaborated by the cells. EDTA, a strong inhibitor of hydrocarbon solubilization by the cells, inhibited growth on these two alkanes but had negligible effect on growth on n-pentane to n-octane.