-
FEMS Microbiology Letters Mar 2011The genetic background of long-chain n-alkane degradation was investigated in detail in strain E1, a member of the genetically unexplored Dietzia genus. A suicide vector...
The genetic background of long-chain n-alkane degradation was investigated in detail in strain E1, a member of the genetically unexplored Dietzia genus. A suicide vector carrying a 518-bp alkB fragment was site-specifically integrated into the E1 chromosome, and the full alkB, as well as its chromosomal environment was sequenced after plasmid rescue experiments. Four out of the nine putative genes were strongly induced by long-chain n-alkanes in wild-type E1. ORF4 encoded a natural fusion protein consisting of an integral membrane alkane hydroxylase and a rubredoxin domain. The significance of the alkB-rub gene in n-alkane degradation was investigated in phenotypic tests, and the disruption mutant strain exhibited severely impaired growth on n-C(20) alkane carbon source. The mutation was successfully complemented with the expression of intact AlkB-Rub protein, the full-length form of which was detected by simultaneous immunoblotting. The presented data furnish the first experimental evidence of the in vivo existence of an AlkB-Rub natural fusion protein, which plays a major role in long-chain n-alkane degradation.
Topics: Actinomycetales; Alkanes; Amino Acid Sequence; Bacterial Proteins; Biodegradation, Environmental; Cytochrome P-450 CYP4A; Molecular Sequence Data; Sequence Alignment
PubMed: 21204932
DOI: 10.1111/j.1574-6968.2010.02198.x -
Applied and Environmental Microbiology Jun 1982Torulopsis bombicola produces extracellular sophorolipids when it is grown on water-insoluble alkanes. Sophorolipids and related model compounds, which were not...
Torulopsis bombicola produces extracellular sophorolipids when it is grown on water-insoluble alkanes. Sophorolipids and related model compounds, which were not themselves used for growth, were found to stimulate markedly the growth of T. bombicola on alkanes. This stimulatory effect was restricted to growth on C10 to C20 alkanes, whereas no significantly influence was observed for growth on fatty alcohols, fatty acids, glucose, or glycerol. The nonionic methyl ester of the glycolipid supported the greatest cell yield. However, a number of synthetic nonionic surfactants were unable to replace the glycolipid. When organisms were grown on hexadecane, stimulation of growth by sophorolipids was observed almost exclusively with strains of Torulopsis yeasts. In contrast, the growth of other typical alkane-utilizing yeasts, such as candida and Pichia strains, was inhibited or not affected. It appears that sophorolipids are involved in alkane dissimilation by T. bombicola through an undetermined mechanism.
Topics: Alkanes; Candida; Culture Media; Glycolipids; Kinetics
PubMed: 7201782
DOI: 10.1128/aem.43.6.1278-1283.1982 -
Journal of Chromatography. A Oct 2012In this study, the retention factors (logk) of 44 polar neutral compounds were measured using hydrophilic interaction chromatography (HILIC). This retention parameter...
In this study, the retention factors (logk) of 44 polar neutral compounds were measured using hydrophilic interaction chromatography (HILIC). This retention parameter was compared with experimental logPalk obtained by a traditional method (shake-flask) or with the calculated logPalk for the most hydrophilic compounds. A good correlation was obtained between logk90 (measured with a mobile phase containing 90% acetonitrile) and logPalk. In contrast, no correlation was obtained between the retention factor and logPoct. This method could thus represent an advantageous alternative and reliable method to characterise the lipophilicity of polar compounds in an alkane/water system by chromatography, providing an important insight in (Q)SAR studies to predict drug permeation through numerous biorelevant membranes.
Topics: Acetonitriles; Alkanes; Chromatography, Liquid; Hydrophobic and Hydrophilic Interactions; Linear Models; Organic Chemicals; Water
PubMed: 22995195
DOI: 10.1016/j.chroma.2012.08.094 -
The Science of the Total Environment Dec 2018Plant-derived lipid molecular proxies can provide insight into present-day soil carbon input and to what extent organic carbon is degraded within soil. To explore...
Plant-derived lipid molecular proxies can provide insight into present-day soil carbon input and to what extent organic carbon is degraded within soil. To explore whether soil characteristics of 'primary' (i.e., native grasslands above the historic treeline) and 'secondary' (i.e., human-modified grasslands below the historic treeline) grasslands reflect recent and/or past vegetation input we compared lipid characteristics in modern vegetation and soil from 30 locations around the historic treeline (1150 m) in Central Otago, New Zealand. At each location the dominant plant species and the mineral topsoil (0-10 cm) were analyzed for a range of n-alkane and n-fatty acid proxies. Grass/herbs and trees differed in their total n-alkane concentration (88.9 vs 232.6 μg/g plant dry weight), even-over-odd predominance (EOP, 10.2 vs 18.3) and n-C/n-C ratio (2.2 vs 6.4). Soil samples under all plant growth forms had considerably lower n-alkane and n-fatty concentrations than the corresponding plant samples. Soil under grass/herbs had lower (4.1) odd-over-even predominance (OEP) values compared to soil under trees (10.1) indicating that lipid degradation under grass/herbs cover was higher. Principle component analysis demonstrated that soil lipid characteristics reflected the current vegetation cover. Principal component analysis also revealed a separation between 'primary' and 'secondary' grasslands. However, further evaluations are required to confirm the validity of lipid proxies in reconstructing the vegetation history of secondary grasslands.
Topics: Alkanes; Fatty Acids; Grassland; Humans; New Zealand; Plants; Poaceae; Soil
PubMed: 30248875
DOI: 10.1016/j.scitotenv.2018.07.105 -
Journal of Molecular Graphics &... Jun 2017The structural and thermal properties of the passivated gold nanoparticles were explored employing molecular dynamics simulation for the different surface coverage...
The structural and thermal properties of the passivated gold nanoparticles were explored employing molecular dynamics simulation for the different surface coverage densities of the self-assembled monolayer (SAM) of alkane thiol. The structural properties of the monolayer protected gold nanoparticles such us overall shape, organization and conformation of the capping alkane thiol chains were found to be influenced by the capping density. The structural order of the thiol capped gold nanoparticles enhances with the increase in the surface coverage density. The specific heat capacity of the alkane thiol capped gold nanoparticles was found to increase linearly with the thiol coverage density. This may be attributed to the enhancement in the lattice vibrational energy. The present simulation results suggest, that the structural and thermal properties of the alkane thiol capped gold nanoparticles may be modified by the suitable selection of the SAM coverage density.
Topics: Alkanes; Computer Simulation; Gold; Metal Nanoparticles; Models, Molecular; Organometallic Compounds; Sulfhydryl Compounds; Thermodynamics
PubMed: 28499270
DOI: 10.1016/j.jmgm.2017.03.023 -
Proceedings of the National Academy of... Nov 2010Fast time-resolved infrared spectroscopic measurements have allowed precise determination of the rates of activation of alkanes by Cp'Rh(CO) (Cp(') = η(5)-C(5)H(5) or...
Fast time-resolved infrared spectroscopic measurements have allowed precise determination of the rates of activation of alkanes by Cp'Rh(CO) (Cp(') = η(5)-C(5)H(5) or η(5)-C(5)Me(5)). We have monitored the kinetics of C─H activation in solution at room temperature and determined how the change in rate of oxidative cleavage varies from methane to decane. The lifetime of CpRh(CO)(alkane) shows a nearly linear behavior with respect to the length of the alkane chain, whereas the related Cp*Rh(CO)(alkane) has clear oscillatory behavior upon changing the alkane. Coupled cluster and density functional theory calculations on these complexes, transition states, and intermediates provide the insight into the mechanism and barriers in order to develop a kinetic simulation of the experimental results. The observed behavior is a subtle interplay between the rates of activation and migration. Unexpectedly, the calculations predict that the most rapid process in these Cp'Rh(CO)(alkane) systems is the 1,3-migration along the alkane chain. The linear behavior in the observed lifetime of CpRh(CO)(alkane) results from a mechanism in which the next most rapid process is the activation of primary C─H bonds (─CH(3) groups), while the third key step in this system is 1,2-migration with a slightly slower rate. The oscillatory behavior in the lifetime of Cp*Rh(CO)(alkane) with respect to the alkane's chain length follows from subtle interplay between more rapid migrations and less rapid primary C─H activation, with respect to CpRh(CO)(alkane), especially when the CH(3) group is near a gauche turn. This interplay results in the activation being controlled by the percentage of alkane conformers.
Topics: Acetates; Acetic Anhydrides; Alkanes; Crystallography, X-Ray; Kinetics; Models, Molecular; Molecular Structure; Organometallic Compounds; Rhodium; Spectrum Analysis
PubMed: 21048088
DOI: 10.1073/pnas.1001249107 -
Journal of the American Chemical Society May 2012A cylindrical capsule provides an environment for straight-chain alkanes that can properly fill the space through extended or compressed conformations. The encapsulation...
A cylindrical capsule provides an environment for straight-chain alkanes that can properly fill the space through extended or compressed conformations. The encapsulation rates of a series of alkanes were examined and found to be dependent on guest length: the rates of uptake are C(9) > C(10) > C(11), while complex stability is in the reverse order, C(11) > C(10) > C(9). Direct competition experiments, pairwise or between all 3 alkanes, maintain this order as the longer alkanes sequentially displace the shorter ones. The distribution of species with time provides a clock for this complex system, which combines elements of self-sorting phenomena and dynamic combinatorial chemistry. The clock can be stopped by replacing the alkanes with the superior guest 4,4'-dimethylazobenzene, then restarted by irradiation.
Topics: Alkanes; Capsules; Dimerization; Ethers, Cyclic; Kinetics; Models, Molecular; Molecular Conformation; Resorcinols; Thermodynamics
PubMed: 22548529
DOI: 10.1021/ja302669y -
Chemistry & Biodiversity Sep 2018The n-alkane composition in the leaf cuticular waxes of natural populations of Bosnian pine (Pinus heldreichii), Austrian pine (P. nigra), and Macedonian pine...
The n-alkane composition in the leaf cuticular waxes of natural populations of Bosnian pine (Pinus heldreichii), Austrian pine (P. nigra), and Macedonian pine (P. peuce) was compared for the first time. The range of n-alkanes was wider in P. nigra (C - C ) than in P. heldreichii and P. peuce (C - C ). Species also diverged in abundance and range of dominant n-alkanes (P. heldreichii: C , C , and C ; P. nigra: C , C , C , and C ; P. peuce: C , C , C , and C ). Multivariate statistical analyses (PCA, DA, and CA) generally pointed out separation of populations of P. nigra from populations of P. heldreichii and P. peuce (which were, to a greater or lesser extent, separated too). However, position of these species on the basis of n-alkane composition was in accordance neither with infrageneric classification nor with recent molecular and terpene investigations.
Topics: Alkanes; Gas Chromatography-Mass Spectrometry; Multivariate Analysis; Pinus; Principal Component Analysis; Species Specificity
PubMed: 29989350
DOI: 10.1002/cbdv.201800161 -
Current Microbiology Jul 2015Cyanobacteria possess the unique capacity to produce alkane. In this study, effects of nitrogen deficiency and salt stress on biosynthesis of alkanes were investigated...
Cyanobacteria possess the unique capacity to produce alkane. In this study, effects of nitrogen deficiency and salt stress on biosynthesis of alkanes were investigated in three kinds of cyanobacteria. Intracellular alkane accumulation was increased in nitrogen-fixing cyanobacterium Anabaena sp. PCC7120, but decreased in non-diazotrophic cyanobacterium Synechococcus elongatus PCC7942 and constant in a halotolerant cyanobacterium Aphanothece halophytica under nitrogen-deficient condition. We also found that salt stress increased alkane accumulation in Anabaena sp. PCC7120 and A. halophytica. The expression levels of two alkane synthetic genes were not upregulated significantly under nitrogen deficiency or salt stress in Anabaena sp. PCC7120. The transformant Anabaena sp. PCC7120 cells with additional alkane synthetic gene set from A. halophytica increased intracellular alkane accumulation level compared to control cells. These results provide a prospect to improve bioproduction of alkanes in nitrogen-fixing halotolerant cyanobacteria via abiotic stresses and genetic engineering.
Topics: Alkanes; Cyanobacteria; Metabolic Engineering; Metabolic Networks and Pathways; Nitrogen; Osmotic Pressure; Salts; Stress, Physiological
PubMed: 25971893
DOI: 10.1007/s00284-015-0833-7 -
Biodegradation Dec 2007A Monte Carlo model was developed to characterize the molecular composition of polychlorinated alkane mixtures. The model is based upon a simulation of the free-radical...
A Monte Carlo model was developed to characterize the molecular composition of polychlorinated alkane mixtures. The model is based upon a simulation of the free-radical chlorination process by which polychlorinated alkane mixtures are produced industrially from n-alkanes. In the model, the free-radical chlorination reaction was simulated by randomly selecting a position on a partially converted alkane molecule for target by chlorine free-radical attack. The relative reactivities of the hydrogen atoms on the alkane chain towards chlorine free-radical substitution were either determined experimentally or extrapolated from experimental results and incorporated into the model. The result of the simulation is the prediction of the detailed molecular composition of any PCA mixture. Good agreement was found when comparing the distribution of molecules predicted by the model to analytically determined distributions of real PCA mixtures. Results from the model were then coupled with rules describing the action of biological enzymes to estimate the upper limit possible for the aerobic biodegradation of PCA mixtures.
Topics: Alkanes; Carbon; Hydrocarbons, Chlorinated; Hydrogen; Models, Chemical; Monte Carlo Method; Reproducibility of Results
PubMed: 17237980
DOI: 10.1007/s10532-007-9099-5