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Sample records for alkane chain length

  1. Heterogeneity of Alkane Chain Length in Freshwater and Marine Cyanobacteria

    PubMed Central

    Shakeel, Tabinda; Fatma, Zia; Fatma, Tasneem; Yazdani, Syed Shams

    2015-01-01

    The potential utilization of cyanobacteria for the biological production of alkanes represents an exceptional system for the next generation of biofuels. Here, we analyzed a diverse group of freshwater and marine cyanobacterial isolates from Indian culture collections for their ability to produce both alkanes and alkenes. Among the 50 cyanobacterial isolates screened, 32 isolates; 14 freshwater and 18 marine isolates; produced predominantly alkanes. The GC-MS/MS profiles revealed a higher percentage of pentadecane and heptadecane production for marine and freshwater strains, respectively. Oscillatoria species were found to be the highest producers of alkanes. Among the freshwater isolates, Oscillatoria CCC305 produced the maximum alkane level with 0.43 μg/mg dry cell weight, while Oscillatoria formosa BDU30603 was the highest producer among the marine isolates with 0.13 μg/mg dry cell weight. Culturing these strains under different media compositions showed that the alkane chain length was not influenced by the growth medium but was rather an inherent property of the strains. Analysis of the cellular fatty acid content indicated the presence of predominantly C16 chain length fatty acids in marine strains, while the proportion of C18 chain length fatty acids increased in the majority of freshwater strains. These results correlated with alkane chain length specificity of marine and freshwater isolates indicating that alkane chain lengths may be primarily determined by the fatty acid synthesis pathway. Moreover, the phylogenetic analysis showed clustering of pentadecane-producing marine strains that was distinct from heptadecane-producing freshwater strains strongly suggesting a close association between alkane chain length and the cyanobacteria habitat. PMID:25853127

  2. Chain length dependence of the thermodynamic properties of linear and cyclic alkanes and polymers.

    PubMed

    Huang, Dinghai; Simon, Sindee L; McKenna, Gregory B

    2005-02-22

    The specific heat capacity was measured with step-scan differential scanning calorimetry for linear alkanes from pentane (C(5)H(12)) to nonadecane (C(19)H(40)), for several cyclic alkanes, for linear and cyclic polyethylenes, and for a linear and a cyclic polystyrene. For the linear alkanes, the specific heat capacity in the equilibrium liquid state decreases as chain length increases; above a carbon number N of 10 (decane) the specific heat asymptotes to a constant value. For the cyclic alkanes, the heat capacity in the equilibrium liquid state is lower than that of the corresponding linear chains and increases with increasing chain length. At high enough molecular weights, the heat capacities of cyclic and linear molecules are expected to be equal, and this is found to be the case for the polyethylenes and polystyrenes studied. In addition, the thermal properties of the solid-liquid and the solid-solid transitions are examined for the linear and cyclic alkanes; solid-solid transitions are observed only in the odd-numbered alkanes. The thermal expansion coefficients and the specific volumes of the linear and cyclic alkanes are also calculated from literature data and compared with the trends in the specific heats.

  3. Molecular mobility depending on chain length and thermally induced molecular motion of n-alkane/urea inclusion compounds

    NASA Astrophysics Data System (ADS)

    Nakaoki, Takahiko; Nagano, Hiromasa; Yanagida, Toshinori

    2004-08-01

    Solid-state high resolution 13C NMR was used to analyze the end group conformation and molecular mobility of n-alkanes in a urea host as a function of the carbon number of the n-alkane. It was shown that the chemical shift of the inner methylenes could be interpreted by the γ- gauche effect. Of further interest is our finding that the chemical shift of 3-methylene is independent of both chain length and temperature, a result indicating that the torsional rotation of the bond ω 3 between the 4-methylene and 5-methylene carbons is so inhibited that there is little gauche conformation. The chemical shift of the inner methylenes indicated a different tendency between the even- and the odd-numbered n-alkanes. The fact that the signals of the even-numbered n-alkanes were observed at a comparatively more upfield location than those of the odd-numbered ones indicated that the even-numbered n-alkane had a higher molecular mobility and tended to adopt a more gauche conformation. The decomposition temperature obtained by thermal analysis also suggested a difference between the even- and odd-numbered n-alkanes. The decomposition temperature of the even-numbered n-alkane/urea inclusion compounds was a little lower than that of the odd-numbered ones, a disparity corresponding to the higher molecular mobility of the n-alkane in the urea host. The spin-lattice relaxation time ( T1C) increased with increasing chain length for chains with less than the 14 carbon atoms but reached a constant value for all longer chains. This result is completely different from that for the n-alkane crystal, which gave a longer T1C depending on the chain length, and can be explained by a reduced intermolecular interaction between the n-alkane and the urea host. Clearly, T1C measurements can be applied to confirm the formation of inclusion compounds. However, the different T1C values between the methyl, 2-, 3-, and inner methylene carbons indicates that the n-alkane molecule does not rotate so fast

  4. Biodegradation of variable-chain-length alkanes at low temperatures by a psychrotrophic Rhodococcus sp.

    SciTech Connect

    Whyte, L.G.; Hawari, J.; Zhou, E.; Bourbonniere, L.; Greer, C.W.; Inniss, W.E.

    1998-07-01

    The psychrotroph Rhodococcus sp. strain Q15 was examined for its ability to degrade individual n-alkanes and diesel fuel at low temperatures, and its alkane catabolic pathway was investigated by biochemical and genetic techniques. At 0 and 5 C, Q15 mineralized the short-chain alkanes dodecane and hexadecane to a greater extent than that observed for the long-chain alkanes octacosane and dotriacontane. Q15 utilized a broad range of aliphatics (C{sub 10} to C{sub 21} alkanes, branched alkanes, and a substituted cyclohexane) present in diesel fuel at 5 C. Mineralization of hexadecane at 5 C was significantly greater in both hydrocarbon-contaminated and pristine soil microcosms seeded with Q15 cells than in uninoculated control soil microcosms. The detection of hexadecane and dodecane metabolic intermediates (1-hexadecanol and 2-hexadecanol and 1-do-decanol and 2-dodecanone, respectively) by solid-phase microextraction-gas chromatography-mass spectrometry and the utilization of potential metabolic intermediates indicated that Q15 oxidizes alkanes by both the terminal oxidation pathway and the subterminal oxidation pathway. Genetic characterization by PCR and nucleotide sequence analysis indicated that Q15 possesses an aliphatic aldehyde dehydrogenase gene highly homologous to the Rhodococcus erythropolis thcA gene. Rhodococcus sp. strain Q15 possessed two large plasmids of approximately 90 and 115 kb (shown to mediate Cd resistance) which were not required for alkane mineralization, although the 90-kb plasmid enhanced mineralization of some alkanes and growth on diesel oil at both 5 and 25 C.

  5. Biodegradation of Variable-Chain-Length Alkanes at Low Temperatures by a Psychrotrophic Rhodococcus sp.

    PubMed Central

    Whyte, Lyle G.; Hawari, Jalal; Zhou, Edward; Bourbonnière, Luc; Inniss, William E.; Greer, Charles W.

    1998-01-01

    The psychrotroph Rhodococcus sp. strain Q15 was examined for its ability to degrade individual n-alkanes and diesel fuel at low temperatures, and its alkane catabolic pathway was investigated by biochemical and genetic techniques. At 0 and 5°C, Q15 mineralized the short-chain alkanes dodecane and hexadecane to a greater extent than that observed for the long-chain alkanes octacosane and dotriacontane. Q15 utilized a broad range of aliphatics (C10 to C21 alkanes, branched alkanes, and a substituted cyclohexane) present in diesel fuel at 5°C. Mineralization of hexadecane at 5°C was significantly greater in both hydrocarbon-contaminated and pristine soil microcosms seeded with Q15 cells than in uninoculated control soil microcosms. The detection of hexadecane and dodecane metabolic intermediates (1-hexadecanol and 2-hexadecanol and 1-dodecanol and 2-dodecanone, respectively) by solid-phase microextraction–gas chromatography-mass spectrometry and the utilization of potential metabolic intermediates indicated that Q15 oxidizes alkanes by both the terminal oxidation pathway and the subterminal oxidation pathway. Genetic characterization by PCR and nucleotide sequence analysis indicated that Q15 possesses an aliphatic aldehyde dehydrogenase gene highly homologous to the Rhodococcus erythropolis thcA gene. Rhodococcus sp. strain Q15 possessed two large plasmids of approximately 90 and 115 kb (shown to mediate Cd resistance) which were not required for alkane mineralization, although the 90-kb plasmid enhanced mineralization of some alkanes and growth on diesel oil at both 5 and 25°C. PMID:9647833

  6. Biodegradation of variable-chain-length n-alkanes in Rhodococcus opacus R7 and the involvement of an alkane hydroxylase system in the metabolism

    PubMed Central

    2014-01-01

    Rhodococcus opacus R7 is a Gram-positive bacterium isolated from a polycyclic aromatic hydrocarbon contaminated soil for its versatile metabolism; indeed the strain is able to grow on naphthalene, o-xylene, and several long- and medium-chain n-alkanes. In this work we determined the degradation of n-alkanes in Rhodococcus opacus R7 in presence of n-dodecane (C12), n-hexadecane (C16), n-eicosane (C20), n-tetracosane (C24) and the metabolic pathway in presence of C12. The consumption rate of C12 was 88%, of C16 was 69%, of C20 was 51% and of C24 it was 78%. The decrement of the degradation rate seems to be correlated to the length of the aliphatic chain of these hydrocarbons. On the basis of the metabolic intermediates determined by the R7 growth on C12, our data indicated that R. opacus R7 metabolizes medium-chain n-alkanes by the primary alcohol formation. This represents a difference in comparison with other Rhodococcus strains, in which a mixture of the two alcohols was observed. By GC-MSD analysis we also identified the monocarboxylic acid, confirming the terminal oxidation. Moreover, the alkB gene cluster from R. opacus R7 was isolated and its involvement in the n-alkane degradation system was investigated by the cloning of this genomic region into a shuttle-vector E. coli-Rhodococcus to evaluate the alkane hydroxylase activity. Our results showed an increased biodegradation of C12 in the recombinant strain R. erythropolis AP (pTipQT1-alkR7) in comparison with the wild type strain R. erythropolis AP. These data supported the involvement of the alkB gene cluster in the n-alkane degradation in the R7 strain. PMID:25401074

  7. Biodegradation of variable-chain-length n-alkanes in Rhodococcus opacus R7 and the involvement of an alkane hydroxylase system in the metabolism.

    PubMed

    Zampolli, Jessica; Collina, Elena; Lasagni, Marina; Di Gennaro, Patrizia

    2014-01-01

    Rhodococcus opacus R7 is a Gram-positive bacterium isolated from a polycyclic aromatic hydrocarbon contaminated soil for its versatile metabolism; indeed the strain is able to grow on naphthalene, o-xylene, and several long- and medium-chain n-alkanes. In this work we determined the degradation of n-alkanes in Rhodococcus opacus R7 in presence of n-dodecane (C12), n-hexadecane (C16), n-eicosane (C20), n-tetracosane (C24) and the metabolic pathway in presence of C12. The consumption rate of C12 was 88%, of C16 was 69%, of C20 was 51% and of C24 it was 78%. The decrement of the degradation rate seems to be correlated to the length of the aliphatic chain of these hydrocarbons. On the basis of the metabolic intermediates determined by the R7 growth on C12, our data indicated that R. opacus R7 metabolizes medium-chain n-alkanes by the primary alcohol formation. This represents a difference in comparison with other Rhodococcus strains, in which a mixture of the two alcohols was observed. By GC-MSD analysis we also identified the monocarboxylic acid, confirming the terminal oxidation. Moreover, the alkB gene cluster from R. opacus R7 was isolated and its involvement in the n-alkane degradation system was investigated by the cloning of this genomic region into a shuttle-vector E. coli-Rhodococcus to evaluate the alkane hydroxylase activity. Our results showed an increased biodegradation of C12 in the recombinant strain R. erythropolis AP (pTipQT1-alkR7) in comparison with the wild type strain R. erythropolis AP. These data supported the involvement of the alkB gene cluster in the n-alkane degradation in the R7 strain.

  8. Effects of chain length, chlorination degree, and structure on the octanol-water partition coefficients of polychlorinated n-alkanes.

    PubMed

    Hilger, Bettina; Fromme, Hermann; Völkel, Wolfgang; Coelhan, Mehmet

    2011-04-01

    Log octanol-water partition coefficients (log Kow) of 40 synthesized polychlorinated n-alkanes (PCAs) with different chlorination degrees were determined using reversed-phase high performance liquid chromatography (RP-HPLC). In addition, log Kow values of a technical mixture namely Cereclor 63L as well as 15 individual in house synthesized C10, C11, and C12 chloroalkanes with known chlorine positions were estimated. Based on these results, the effects of chain length, chlorination degree, and structure were explored. The estimated log Kow values ranged from 4.10 (polychlorinated n-decanes with 50.2% chlorine content) to 11.34 (polychlorinated n-octacosanes with 54.8% chlorine content) for PCAs and from 3.82 (1,2,5,6,9,10-hexachlorodecane) to 7.75 (1,1,1,3,9,11,11,11-octachlorododecane) for the individual chloroalkanes studied. The results showed that log Kow value was influenced linearly at a given chlorine content by chain length, while a polynominal effect was observed in dependence on the chlorination degree of an alkane chain. Chlorine substitution pattern influenced markedly the log Kow value of chloroalkanes.

  9. Enthalpy difference between conformations of normal alkanes: effects of basis set and chain length on intramolecular basis set superposition error

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.

    2011-03-01

    The quantum chemistry of conformation equilibrium is a field where great accuracy (better than 100 cal mol-1) is needed because the energy difference between molecular conformers rarely exceeds 1000-3000 cal mol-1. The conformation equilibrium of straight-chain (normal) alkanes is of particular interest and importance for modern chemistry. In this paper, an extra error source for high-quality ab initio (first principles) and DFT calculations of the conformation equilibrium of normal alkanes, namely the intramolecular basis set superposition error (BSSE), is discussed. In contrast to out-of-plane vibrations in benzene molecules, diffuse functions on carbon and hydrogen atoms were found to greatly reduce the relative BSSE of n-alkanes. The corrections due to the intramolecular BSSE were found to be almost identical for the MP2, MP4, and CCSD(T) levels of theory. Their cancelation is expected when CCSD(T)/CBS (CBS, complete basis set) energies are evaluated by addition schemes. For larger normal alkanes (N > 12), the magnitude of the BSSE correction was found to be up to three times larger than the relative stability of the conformer; in this case, the basis set superposition error led to a two orders of magnitude difference in conformer abundance. No error cancelation due to the basis set superposition was found. A comparison with amino acid, peptide, and protein data was provided.

  10. Adsorption of linear alkanes on Cu(111): Temperature and chain-length dependence of the softened vibrational mode

    NASA Astrophysics Data System (ADS)

    Fosser, Kari A.; Kang, Joo H.; Nuzzo, Ralph G.; Wöll, Christof

    2007-05-01

    The vibrational spectra of linear alkanes, with lengths ranging from n-propane to n-octane, were examined on a copper surface by reflection-absorption infrared spectroscopy. The appearance and frequency of the "soft mode," a feature routinely seen in studies of saturated hydrocarbons adsorbed on metals, were examined and compared between the different adsorbates. The frequency of the mode was found to be dependent on both the number of methylene units of each alkane as well as specific aspects of the order of the monolayer phase. Studies of monolayer coverages at different temperatures provide insights into the nature of the two-dimensional (2D) melting transitions of these adlayer structures, ones that can be inferred from observed shifts in the soft vibrational modes appearing in the C-H stretching region of the infrared spectrum. These studies support recently reported hypotheses as to the origins of such soft modes: the metal-hydrogen interactions that mediate them and the dynamics that underlay their pronounced temperature dependencies. The present data strongly support a model for the 2D to one-dimensional order-order phase transition arising via a continuous rather than discrete first-order process.

  11. The long-chain alkane metabolism network of Alcanivorax dieselolei.

    PubMed

    Wang, Wanpeng; Shao, Zongze

    2014-12-12

    Alkane-degrading bacteria are ubiquitous in marine environments, but little is known about how alkane degradation is regulated. Here we investigate alkane sensing, chemotaxis, signal transduction, uptake and pathway regulation in Alcanivorax dieselolei. The outer membrane protein OmpS detects the presence of alkanes and triggers the expression of an alkane chemotaxis complex. The coupling protein CheW2 of the chemotaxis complex, which is induced only by long-chain (LC) alkanes, sends signals to trigger the expression of Cyo, which participates in modulating the expression of the negative regulator protein AlmR. This change in turn leads to the expression of ompT1 and almA, which drive the selective uptake and hydroxylation of LC alkanes, respectively. AlmA is confirmed as a hydroxylase of LC alkanes. Additional factors responsible for the metabolism of medium-chain-length alkanes are also identified, including CheW1, OmpT1 and OmpT2. These results provide new insights into alkane metabolism pathways from alkane sensing to degradation.

  12. Length-dependent nucleation mechanisms rule the vaporization of n-alkanes

    NASA Astrophysics Data System (ADS)

    Zahn, Dirk

    2008-12-01

    The liquid → vapor transition of a series of n-alkanes is explored by means of molecular dynamics simulations. From the comparison of the vaporization of methane, pentane and decane we elaborate the dependence of the nucleation mechanisms on the chain length. While the boiling of methane may be characterized as 'ideal' vapor bubble nucleation and growth, our studies related to pentane and decane reveal an increasing importance of liquid droplets acting as intermediates of the vaporization process. With increasing chain length the investigated n-alkanes were found to avoid the formation of large liquid-vapor interfaces by following a different nucleation mechanism.

  13. Evolution of an alkane-inducible biosensor for increased responsiveness to short-chain alkanes.

    PubMed

    Reed, Ben; Blazeck, John; Alper, Hal

    2012-04-15

    Synthetic alkane-inducible biosensors have applications as detectors for environmental hydrocarbon contamination and as novel inducible expression systems with low-cost inducers. Here, we have assembled and evolved an alkane-responsive biosensor with a fluorescence output signal in Escherichia coli by utilizing regulatory machinery from Pseudomonas putida's alkane metabolism. Within our system, the transcriptional regulator, AlkSp, is activated by the presence of alkanes and binds to the P(alkB) promoter, stimulating transcription of a Green Fluorescent Protein reporter. Through two successive rounds of directed evolution via error prone PCR and fluorescence activated cell sorting, we isolated alkS mutants enabling up to a 5 fold increase in fluorescence output signal in response to short-chain alkanes such as hexane and pentane. Further characterization of selected mutants demonstrated altered responsiveness to a wide range of linear alkanes (pentane to dodecane). Sequence analysis highlighted the S470T mutation as a likely candidate responsible for increased effectiveness of the AlkS protein for short-chain alkanes. This work represents the first evolution of a synthetic biosensor system for alkanes.

  14. Long-chain alkane production by the yeast Saccharomyces cerevisiae.

    PubMed

    Buijs, Nicolaas A; Zhou, Yongjin J; Siewers, Verena; Nielsen, Jens

    2015-06-01

    In the past decade industrial-scale production of renewable transportation biofuels has been developed as an alternative to fossil fuels, with ethanol as the most prominent biofuel and yeast as the production organism of choice. However, ethanol is a less efficient substitute fuel for heavy-duty and maritime transportation as well as aviation due to its low energy density. Therefore, new types of biofuels, such as alkanes, are being developed that can be used as drop-in fuels and can substitute gasoline, diesel, and kerosene. Here, we describe for the first time the heterologous biosynthesis of long-chain alkanes by the yeast Saccharomyces cerevisiae. We show that elimination of the hexadecenal dehydrogenase Hfd1 and expression of a redox system are essential for alkane biosynthesis in yeast. Deletion of HFD1 together with expression of an alkane biosynthesis pathway resulted in the production of the alkanes tridecane, pentadecane, and heptadecane. Our study provides a proof of principle for producing long-chain alkanes in the industrial workhorse S. cerevisiae, which was so far limited to bacteria. We anticipate that these findings will be a key factor for further yeast engineering to enable industrial production of alkane based drop-in biofuels, which can allow the biofuel industry to diversify beyond bioethanol.

  15. DITERMINAL OXIDATION OF LONG-CHAIN ALKANES BY BACTERIA1

    PubMed Central

    Kester, A. S.; Foster, J. W.

    1963-01-01

    Kester, A. S. (The University of Texas, Austin) and J. W. Foster. Diterminal oxidation of long-chain alkanes by bacteria. J. Bacteriol. 85:859–869. 1963.—A corynebacterial organism capable of growing in mineral salts with individual pure alkanes as carbon sources produces a series of acids from the C10-C14 alkanes. They have been isolated in pure form and identified as monoic, ω-hydroxy monoic, and dioic acids containing the same number of carbon atoms as the substrate alkane. Oxidation took place at both terminal methyl groups—“diterminal oxidation.” Appropriate labeling experiments indicate that omega oxidation of fatty acids occurs in this organism and that an oxygenation with O2 occurs. Images PMID:14044955

  16. Length dependence of the thermal conductance of alkane-based single-molecule junctions: An ab initio study

    NASA Astrophysics Data System (ADS)

    Klöckner, J. C.; Bürkle, M.; Cuevas, J. C.; Pauly, F.

    2016-11-01

    Motivated by recent experiments, we present here a systematic ab initio study of the length dependence of the thermal conductance of single-molecule junctions. We make use of a combination of density functional theory with nonequilibrium Green's function techniques to investigate the length dependence of the phonon transport in single-alkane chains, contacted with gold electrodes via both thiol and amine anchoring groups. Additionally, we study the effect of the substitution of the hydrogen atoms in the alkane chains by heavier fluorine atoms to form polytetrafluoroethylenes. Our results demonstrate that (i) the room-temperature thermal conductance is fairly length independent for chains with more than 5 methylene units and (ii) the efficiency of the thermal transport is strongly influenced by the strength of the phononic metal-molecule coupling. Our study sheds light on the phonon transport in molecular junctions, and it provides clear guidelines for the design of molecular junctions for thermal management.

  17. Two novel alkane hydroxylase-rubredoxin fusion genes isolated from a Dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation.

    PubMed

    Nie, Yong; Liang, Jieliang; Fang, Hui; Tang, Yue-Qin; Wu, Xiao-Lei

    2011-10-01

    Two alkane hydroxylase-rubredoxin fusion gene homologs (alkW1 and alkW2) were cloned from a Dietzia strain, designated DQ12-45-1b, which can grow on crude oil and n-alkanes ranging in length from 6 to 40 carbon atoms as sole carbon sources. Both AlkW1 and AlkW2 have an integral-membrane alkane monooxygenase (AlkB) conserved domain and a rubredoxin (Rd) conserved domain which are fused together. Phylogenetic analysis showed that these two AlkB-fused Rd domains formed a novel third cluster with all the Rds from the alkane hydroxylase-rubredoxin fusion gene clusters in Gram-positive bacteria and that this third cluster was distant from the known AlkG1- and AlkG2-type Rds. Expression of the alkW1 gene in DQ12-45-1b was induced when cells were grown on C(8) to C(32) n-alkanes as sole carbon sources, but expression of the alkW2 gene was not detected. Functional heterologous expression in an alkB deletion mutant of Pseudomonas fluorescens KOB2Δ1 suggested the alkW1 could restore the growth of KOB2Δ1 on C(14) and C(16) n-alkanes and induce faster growth on C(18) to C(32) n-alkanes than alkW1ΔRd, the Rd domain deletion mutant gene of alkW1, which also caused faster growth than KOB2Δ1 itself. In addition, the artificial fusion of AlkB from the Gram-negative P. fluorescens CHA0 and the Rds from both Gram-negative P. fluorescens CHA0 and Gram-positive Dietzia sp. DQ12-45-1b significantly increased the degradation of C(32) alkane compared to that seen with AlkB itself. In conclusion, the alkW1 gene cloned from Dietzia species encoded an alkane hydroxylase which increased growth on and degradation of n-alkanes up to C(32) in length, with its fused rubredoxin domain being necessary to maintain the functions. In addition, the fusion of alkane hydroxylase and rubredoxin genes from both Gram-positive and -negative bacteria can increase the degradation of long-chain n-alkanes (such as C(32)) in the Gram-negative bacterium.

  18. Characterization of the medium- and long-chain n-alkanes degrading Pseudomonas aeruginosa strain SJTD-1 and its alkane hydroxylase genes.

    PubMed

    Liu, Huan; Xu, Jing; Liang, Rubing; Liu, Jianhua

    2014-01-01

    A gram-negative aliphatic hydrocarbon-degrading bacterium SJTD-1 isolated from oil-contaminated soil was identified as Pseudomonas aeruginosa by comparative analyses of the 16S rRNA sequence, phenotype, and physiological features. SJTD-1 could efficiently mineralize medium- and long-chain n-alkanes (C12-C30) as its sole carbon source within seven days, showing the most optimal growth on n-hexadecane, followed by n-octadecane, and n-eicosane. In 36 h, 500 mg/L of tetradecane, hexadecane, and octadecane were transformed completely; and 2 g/L n-hexadecane was degraded to undetectable levels within 72 h. Two putative alkane-degrading genes (gene 3623 and gene 4712) were characterized and our results indicated that their gene products were rate-limiting enzymes involved in the synergetic catabolism of C12-C16 alkanes. On the basis of bioinformatics and transcriptional analysis, two P450 monooxygenases, along with a putative AlmA-like oxygenase, were examined. Genetically defective mutants lacking the characteristic alkane hydroxylase failed to degrade n-octadecane, thereby suggesting a different catalytic mechanism for the microbial transformation of alkanes with chain lengths over C18.

  19. Ligand chain length conveys thermochromism.

    PubMed

    Ganguly, Mainak; Panigrahi, Sudipa; Chandrakumar, K R S; Sasmal, Anup Kumar; Pal, Anjali; Pal, Tarasankar

    2014-08-14

    Thermochromic properties of a series of non-ionic copper compounds have been reported. Herein, we demonstrate that Cu(II) ion with straight-chain primary amine (A) and alpha-linolenic (fatty acid, AL) co-jointly exhibit thermochromic properties. In the current case, we determined that thermochromism becomes ligand chain length-dependent and at least one of the ligands (A or AL) must be long chain. Thermochromism is attributed to a balanced competition between the fatty acids and amines for the copper(II) centre. The structure-property relationship of the non-ionic copper compounds Cu(AL)2(A)2 has been substantiated by various physical measurements along with detailed theoretical studies based on time-dependent density functional theory. It is presumed from our results that the compound would be a useful material for temperature-sensor applications.

  20. Mass dependence of the activation enthalpy and entropy of unentangled linear alkane chains.

    PubMed

    Jeong, Cheol; Douglas, Jack F

    2015-10-14

    The mass scaling of the self-diffusion coefficient D of polymers in the liquid state, D ∼ M(β), is one of the most basic characteristics of these complex fluids. Although traditional theories such as the Rouse and reptation models of unentangled and entangled polymer melts, respectively, predict that β is constant, this exponent for alkanes has been estimated experimentally to vary from -1.8 to -2.7 upon cooling. Significantly, β changes with temperature T under conditions where the chains are not entangled and at temperatures far above the glass transition temperature Tg where dynamic heterogeneity does not complicate the description of the liquid dynamics. Based on atomistic molecular dynamics simulations on unentangled linear alkanes in the melt, we find that the variation of β with T can be directly attributed to the dependence of the enthalpy ΔHa and entropy ΔSa of activation on the number of alkane backbone carbon atoms, n. In addition, we find a sharp change in the melt dynamics near a "critical" chain length, n ≈ 17. A close examination of this phenomenon indicates that a "buckling transition" from rod-like to coiled chain configurations occurs at this characteristic chain length and distinct entropy-enthalpy compensation relations, ΔSa ∝ ΔHa, hold on either side of this polymer conformational transition. We conclude that the activation free energy parameters exert a significant influence on the dynamics of polymer melts that is not anticipated by either the Rouse and reptation models. In addition to changes of ΔHa and ΔSa with M, we expect changes in these free energy parameters to be crucial for understanding the dynamics of polymer blends, nanocomposites, and confined polymers because of changes of the fluid free energy by interfacial interactions and geometrical confinement.

  1. Mass dependence of the activation enthalpy and entropy of unentangled linear alkane chains

    SciTech Connect

    Jeong, Cheol; Douglas, Jack F.

    2015-10-14

    The mass scaling of the self-diffusion coefficient D of polymers in the liquid state, D ∼ M{sup β}, is one of the most basic characteristics of these complex fluids. Although traditional theories such as the Rouse and reptation models of unentangled and entangled polymer melts, respectively, predict that β is constant, this exponent for alkanes has been estimated experimentally to vary from −1.8 to −2.7 upon cooling. Significantly, β changes with temperature T under conditions where the chains are not entangled and at temperatures far above the glass transition temperature T{sub g} where dynamic heterogeneity does not complicate the description of the liquid dynamics. Based on atomistic molecular dynamics simulations on unentangled linear alkanes in the melt, we find that the variation of β with T can be directly attributed to the dependence of the enthalpy ΔH{sub a} and entropy ΔS{sub a} of activation on the number of alkane backbone carbon atoms, n. In addition, we find a sharp change in the melt dynamics near a “critical” chain length, n ≈ 17. A close examination of this phenomenon indicates that a “buckling transition” from rod-like to coiled chain configurations occurs at this characteristic chain length and distinct entropy-enthalpy compensation relations, ΔS{sub a} ∝ ΔH{sub a}, hold on either side of this polymer conformational transition. We conclude that the activation free energy parameters exert a significant influence on the dynamics of polymer melts that is not anticipated by either the Rouse and reptation models. In addition to changes of ΔH{sub a} and ΔS{sub a} with M, we expect changes in these free energy parameters to be crucial for understanding the dynamics of polymer blends, nanocomposites, and confined polymers because of changes of the fluid free energy by interfacial interactions and geometrical confinement.

  2. Evaluating the potential of long chain n-alkanes and n-carboxylic acids as biomarkers for past vegetation

    NASA Astrophysics Data System (ADS)

    Lanny, Verena; Zech, Roland; Eglinton, Timothy

    2014-05-01

    Leaf waxes, such as long chain n-alkanes and n-carboxylic acids, may have a great potential for the reconstruction of past environmental and climate conditions (e.g. (Zech R. et al., 2013). While n-C27 and n-C29 alkanes often predominantly occur in trees and shrubs, n-C31 and n-C33 are more abundant in grasses and herbs. However, little is known about chain-length distributions of n-carboxylic acids, and very few studies have systematically investigated leaf waxes in top soils. We analyzed n-alkanes and n-carboxylic acids in ~100 litter and topsoil samples from Southern Germany to Sweden. Our results show that sites under deciduous trees often contain a lot of C27 n-alkanes and C28 n-carboxylic acids. Coniferous sites are characterized by dominance in n-alkanes C29 and C31 and have relatively high concentrations of n-carboxylic acids C22 and C24. Grass sites show a Cmax at C31 for n-alkanes and at C24 or C26 for n-carboxylic acids. Differences in homologue patterns are most pronounced in the litter samples, but are well preserved also in the topsoils (0-3 cm depth, a little less in the lower topsoils from 3-10 cm). Our results illustrate the potential of combining n-alkane and n-carboxylic acid analyses for paleo-vegetation reconstructions, yet indicate that the degree of degradation may have to be taken into consideration (Zech M. et al., 2013). References: Zech, M. et al. (2013) Quat. Int. 296, 108-116. Zech, R. et al. (2013) Palaeo3, 387, 165-175.

  3. Using the alkanes and long-chain alcohols of plant cuticular wax to estimate diet composition and the intakes of mixed forages in sheep consuming a known amount of alkane-labelled supplement.

    PubMed

    Dove, H; Charmley, E

    2008-10-01

    In a feeding trial with 24 sheep, we used the alkanes, long-chain alcohols (LCOH) or both of these plant wax markers, to estimate the diet composition of animals offered diets comprising alkane-labelled cottonseed meal (CSM) together with up to four forages. The diets used were: Diet 1 subterranean clover (Trifolium subterraneum); Diet 2 subterranean clover + phalaris (Phalaris aquatica); Diet 3 subterranean clover, phalaris + annual ryegrass (Lolium rigidum); and Diet 4 subterranean clover, phalaris, annual ryegrass + wheat straw (Triticum aestivum). Estimates of diet composition were made following correction of faecal alkane or LCOH concentrations for incomplete faecal recovery, using recovery estimates derived from individual animals, mean recoveries for a given dietary treatment or grand mean recoveries. Estimated dietary proportions of CSM and known intakes of CSM were used to estimate forage intake. The LCOH concentrations of the diet components were much higher than their alkane concentrations, especially for phalaris. Multivariate analyses showed that the discriminatory information provided by the LCOH was additional to that provided by the alkanes, and that a combination of (LCOH + alkanes) discriminated better between diet components than either class of marker alone. Faecal recoveries of LCOH increased with increasing carbon-chain length; there were no differences in recovery attributable to diet. The most accurate estimates of diet composition were obtained with the combination of (LCOH + alkanes). Estimates of diet composition based on LCOH alone were not as good as alkanes alone, due to the high correlation between the LCOH profiles of phalaris and ryegrass. Total grass content of the diet was very accurately estimated using LCOH. Diet composition estimates provided estimates of whole-diet digestibility, which did not differ from the measured values. Trends in the accuracy of forage intake estimates reflected those found with diet composition and

  4. Reprint of "Stable hydrogen and carbon isotopic compositions of long-chain (C21-C33) n-alkanes and n-alkenes in insects"

    NASA Astrophysics Data System (ADS)

    Chikaraishi, Yoshito; Kaneko, Masanori; Ohkouchi, Naohiko

    2013-06-01

    We report the molecular and stable isotopic (δD and δ13C) compositions of long-chain n-alkanes in common insects including the cabbage butterfly, swallowtail, wasp, hornet, grasshopper, and ladybug. Insect n-alkanes are potential candidates of the contamination of soil and sedimentary n-alkanes that are believed to be derived from vascular plant waxes. Long-chain n-alkanes (range C21-33; maximum C23-C29) are found to be abundant in the insects (31-781 μg/dry g), with a carbon preference index (CPI) of 5.1-31.5 and an average chain length (ACL) of 24.9-29.3. The isotopic compositions (mean ± 1σ, n = 33) of the n-alkanes are -195 ± 16‰ for hydrogen and -30.6 ± 2.4‰ for carbon. The insect n-alkanes are depleted in D by approximately 30-40‰ compared with wax n-alkanes from C3 (-155 ± 25‰) and C4 vascular plants (-167 ± 13‰), whereas their δ13C values fall between those of C3 (-36.2 ± 2.4‰) and C4 plants (-20.3 ± 2.4‰). Thus, the contribution of insect-derived n-alkanes to soil and sediment could potentially shift δD records of n-alkanes toward more negative values and potentially muddle the assumed original C3/C4 balance in the δ13C records of the soil and sedimentary n-alkanes. n-Alkenes are also found in three insects (swallowtail, wasp and hornet). They are more depleted in D relative to the same carbon numbered n-alkanes (δDn-alkene - δDn-alkane = -17 ± 16‰), but the δ13C values are almost identical to those of the n-alkanes (δ13Cn-alkene - δ13Cn-alkane = 0.1 ± 0.2‰). These results suggest that these n-alkenes are desaturated products of the same carbon numbered n-alkanes.

  5. Stable hydrogen and carbon isotopic compositions of long-chain (C21-C33) n-alkanes and n-alkenes in insects

    NASA Astrophysics Data System (ADS)

    Chikaraishi, Yoshito; Kaneko, Masanori; Ohkouchi, Naohiko

    2012-10-01

    We report the molecular and stable isotopic (δD and δ13C) compositions of long-chain n-alkanes in common insects including the cabbage butterfly, swallowtail, wasp, hornet, grasshopper, and ladybug. Insect n-alkanes are potential candidates of the contamination of soil and sedimentary n-alkanes that are believed to be derived from vascular plant waxes. Long-chain n-alkanes (range C21-33; maximum C23-C29) are found to be abundant in the insects (31-781 μg/dry g), with a carbon preference index (CPI) of 5.1-31.5 and an average chain length (ACL) of 24.9-29.3. The isotopic compositions (mean ± 1σ, n = 33) of the n-alkanes are -195 ± 16‰ for hydrogen and -30.6 ± 2.4‰ for carbon. The insect n-alkanes are depleted in D by approximately 30-40‰ compared with wax n-alkanes from C3 (-155 ± 25‰) and C4 vascular plants (-167 ± 13‰), whereas their δ13C values fall between those of C3 (-36.2 ± 2.4‰) and C4 plants (-20.3 ± 2.4‰). Thus, the contribution of insect-derived n-alkanes to soil and sediment could potentially shift δD records of n-alkanes toward more negative values and potentially muddle the assumed original C3/C4 balance in the δ13C records of the soil and sedimentary n-alkanes. n-Alkenes are also found in three insects (swallowtail, wasp and hornet). They are more depleted in D relative to the same carbon numbered n-alkanes (δDn-alkene - δDn-alkane = -17 ± 16‰), but the δ13C values are almost identical to those of the n-alkanes (δ13Cn-alkene - δ13Cn-alkane = 0.1 ± 0.2‰). These results suggest that these n-alkenes are desaturated products of the same carbon numbered n-alkanes.

  6. Geomicrobiological linkages between short-chain alkane consumption and sulfate reduction rates in seep sediments

    PubMed Central

    Bose, Arpita; Rogers, Daniel R.; Adams, Melissa M.; Joye, Samantha B.; Girguis, Peter R.

    2013-01-01

    Marine hydrocarbon seeps are ecosystems that are rich in methane, and, in some cases, short-chain (C2–C5) and longer alkanes. C2–C4 alkanes such as ethane, propane, and butane can be significant components of seeping fluids. Some sulfate-reducing microbes oxidize short-chain alkanes anaerobically, and may play an important role in both the competition for sulfate and the local carbon budget. To better understand the anaerobic oxidation of short-chain n-alkanes coupled with sulfate-reduction, hydrocarbon-rich sediments from the Gulf of Mexico (GoM) were amended with artificial, sulfate-replete seawater and one of four n-alkanes (C1–C4) then incubated under strict anaerobic conditions. Measured rates of alkane oxidation and sulfate reduction closely follow stoichiometric predictions that assume the complete oxidation of alkanes to CO2 (though other sinks for alkane carbon likely exist). Changes in the δ13C of all the alkanes in the reactors show enrichment over the course of the incubation, with the C3 and C4 incubations showing the greatest enrichment (4.4 and 4.5‰, respectively). The concurrent depletion in the δ13C of dissolved inorganic carbon (DIC) implies a transfer of carbon from the alkane to the DIC pool (−3.5 and −6.7‰ for C3 and C4 incubations, respectively). Microbial community analyses reveal that certain members of the class Deltaproteobacteria are selectively enriched as the incubations degrade C1–C4 alkanes. Phylogenetic analyses indicate that distinct phylotypes are enriched in the ethane reactors, while phylotypes in the propane and butane reactors align with previously identified C3–C4 alkane-oxidizing sulfate-reducers. These data further constrain the potential influence of alkane oxidation on sulfate reduction rates (SRRs) in cold hydrocarbon-rich sediments, provide insight into their contribution to local carbon cycling, and illustrate the extent to which short-chain alkanes can serve as electron donors and govern microbial

  7. Geomicrobiological linkages between short-chain alkane consumption and sulfate reduction rates in seep sediments.

    PubMed

    Bose, Arpita; Rogers, Daniel R; Adams, Melissa M; Joye, Samantha B; Girguis, Peter R

    2013-01-01

    Marine hydrocarbon seeps are ecosystems that are rich in methane, and, in some cases, short-chain (C2-C5) and longer alkanes. C2-C4 alkanes such as ethane, propane, and butane can be significant components of seeping fluids. Some sulfate-reducing microbes oxidize short-chain alkanes anaerobically, and may play an important role in both the competition for sulfate and the local carbon budget. To better understand the anaerobic oxidation of short-chain n-alkanes coupled with sulfate-reduction, hydrocarbon-rich sediments from the Gulf of Mexico (GoM) were amended with artificial, sulfate-replete seawater and one of four n-alkanes (C1-C4) then incubated under strict anaerobic conditions. Measured rates of alkane oxidation and sulfate reduction closely follow stoichiometric predictions that assume the complete oxidation of alkanes to CO2 (though other sinks for alkane carbon likely exist). Changes in the δ(13)C of all the alkanes in the reactors show enrichment over the course of the incubation, with the C3 and C4 incubations showing the greatest enrichment (4.4 and 4.5‰, respectively). The concurrent depletion in the δ(13)C of dissolved inorganic carbon (DIC) implies a transfer of carbon from the alkane to the DIC pool (-3.5 and -6.7‰ for C3 and C4 incubations, respectively). Microbial community analyses reveal that certain members of the class Deltaproteobacteria are selectively enriched as the incubations degrade C1-C4 alkanes. Phylogenetic analyses indicate that distinct phylotypes are enriched in the ethane reactors, while phylotypes in the propane and butane reactors align with previously identified C3-C4 alkane-oxidizing sulfate-reducers. These data further constrain the potential influence of alkane oxidation on sulfate reduction rates (SRRs) in cold hydrocarbon-rich sediments, provide insight into their contribution to local carbon cycling, and illustrate the extent to which short-chain alkanes can serve as electron donors and govern microbial community

  8. Estimating organic chain length through sound velocity measurements.

    PubMed

    Povey, Malcolm J W; Stec, Zoe; Hindle, Scott A; Kennedy, John D; Taylor, Richard G

    2005-02-01

    The ability to measure the length of polymers while monitoring their production is evidently extremely valuable, but is also a useful tool for chemical identification purposes at other times, e.g. the analysis of waste water. A study of the relationship between velocity of sound and chain length has been carried out. Initial studies were performed on two model systems; a series of pure liquid n-alkanes (pentane to hexadecane) and 1-alcohols (methanol to 1-dodecanol). This study was extended to look at an industrially significant system of dimethylsiloxanes 200 fluid (L2, 0.65 cSt) to 200 fluid (5000 cSt). Corresponding density data have been taken from the literature and the adiabatic compressibility determined. The measured adiabatic compressibility has been compared with two molecular models of wound velocity, the Schaaffs model and a development of the Urick equation. The Urick equation approach is based on a determination of the compressibility of the methylene or siloxane repeat units which make up the chains in these linear molecules. We show that the Urick equation approach accurately predicts sound velocity and compressibility for the higher members of each series, whilst the Schaaffs approach fails for the 1-alcohols. We suggest that this is because of the influence of the hydroxyl end group through hydrogen bonding with methylene groups within the chain. This interaction modifies the derived compressibility of the methylene groups, so reducing their compressibility relative to that of the n-alkanes. The technique described provides valuable new insights into end-group, intermolecular and intra-molecular interactions in liquid linear-chain molecules. From this detailed analysis of the mechanisms involved, a model is derived. This model can give very precise estimations of the composition of a pure liquid. In the case of mixtures of polymers, it is necessary to use the modified Urick equation and then, in addition, the concentration dependence of both the

  9. Gene Structures and Regulation of the Alkane Hydroxylase Complex in Acinetobacter sp. Strain M-1

    PubMed Central

    Tani, Akio; Ishige, Takeru; Sakai, Yasuyoshi; Kato, Nobuo

    2001-01-01

    In the long-chain n-alkane degrader Acinetobacter sp. strain M-1, two alkane hydroxylase complexes are switched by controlling the expression of two n-alkane hydroxylase-encoding genes in response to the chain length of n-alkanes, while rubredoxin and rubredoxin ruductase are encoded by a single gene and expressed constitutively. PMID:11160120

  10. Reconstitution of plant alkane biosynthesis in yeast demonstrates that Arabidopsis ECERIFERUM1 and ECERIFERUM3 are core components of a very-long-chain alkane synthesis complex.

    PubMed

    Bernard, Amélie; Domergue, Frédéric; Pascal, Stéphanie; Jetter, Reinhard; Renne, Charlotte; Faure, Jean-Denis; Haslam, Richard P; Napier, Johnathan A; Lessire, René; Joubès, Jérôme

    2012-07-01

    In land plants, very-long-chain (VLC) alkanes are major components of cuticular waxes that cover aerial organs, mainly acting as a waterproof barrier to prevent nonstomatal water loss. Although thoroughly investigated, plant alkane synthesis remains largely undiscovered. The Arabidopsis thaliana ECERIFERUM1 (CER1) protein has been recognized as an essential element of wax alkane synthesis; nevertheless, its function remains elusive. In this study, a screen for CER1 physical interaction partners was performed. The screen revealed that CER1 interacts with the wax-associated protein ECERIFERUM3 (CER3) and endoplasmic reticulum-localized cytochrome b5 isoforms (CYTB5s). The functional relevance of these interactions was assayed through an iterative approach using yeast as a heterologous expression system. In a yeast strain manipulated to produce VLC acyl-CoAs, a strict CER1 and CER3 coexpression resulted in VLC alkane synthesis. The additional presence of CYTB5s was found to enhance CER1/CER3 alkane production. Site-directed mutagenesis showed that CER1 His clusters are essential for alkane synthesis, whereas those of CER3 are not, suggesting that CYTB5s are specific CER1 cofactors. Collectively, our study reports the identification of plant alkane synthesis enzymatic components and supports a new model for alkane production in which CER1 interacts with both CER3 and CYTB5 to catalyze the redox-dependent synthesis of VLC alkanes from VLC acyl-CoAs.

  11. Electrical communication between glucose oxidase and different ferrocenylalkanethiol chain lengths

    SciTech Connect

    Rubin, S.; Bar, G.; Cutts, R.W.; Zawodzinski, T.A. Jr.; Chow, J.T.; Ferraris, J.P.

    1995-12-31

    We describe the factors affecting the electron transfer process between the different components of a self-assembled mixed monolayer. The system is comprised of mixed monolayers containing aminoalkanethiols (AMATs) and ferrocenylakanethiols (FATs) of variable chain lengths. We study the effects of different ratio of the two mixed monolayer components on the permeability of the monolayer toward a Ru(NH{sub 3}{sub 6}Cl{sub 3} redox probe. In order to study the electrical communication between the enzyme and the mediator molecules, the enzyme glucose oxidase (GOx) was attached to the AMAT sites to create a biosensor device. The relative efficiency of a biosensor of each chain-length combination of FAT and AMAT was examined. In light of this comparison, we consider the critical factors for efficient electron transfer between the ferrocene mediator and the GOx redox active site immobilized as part of the surface-confined system. We find that the biosensor response is greatest when the enzyme and the FATs are attached to the surface with different alkane chain lengths. We also find strong evidence for the existence of domains of FAT and AMAT in the mixed monolayer system.

  12. Biochemistry of Short-Chain Alkanes (Tissue-Specific Biosynthesis of n-Heptane in Pinus jeffreyi).

    PubMed Central

    Savage, T. J.; Hamilton, B. S.; Croteau, R.

    1996-01-01

    Short-chain (C7-C11) alkanes accumulate as the volatile component of oleoresin (pitch) in several pine species native to western North America. To establish the tissue most amenable for use in detailed studies of short-chain alkane biosynthesis, we examined the tissue specificity of alkane accumulation and biosynthesis in Pinus jeffreyi Grev. & Balf. Short-chain alkane accumulation was highly tissue specific in both 2-year-old saplings and mature trees; heart-wood xylem accumulated alkanes up to 7.1 mg g-1 dry weight, whereas needles and other young green tissue contained oleoresin with monoterpenoid, rather than paraffinic, volatiles. These tissue-specific differences in oleoresin composition appear to be a result of tissue-specific rates of alkane and monoterpene biosynthesis; incubation of xylem tissue with [14C]sucrose resulted in accumulation of radiolabel in alkanes but not monoterpenes, whereas incubation of foliar tissue with 14CO2 resulted in the accumulation of radiolabel in monoterpenes but not alkanes. Furthermore, incubation of xylem sections with [14C]acetate resulted in incorporation of radiolabel into alkanes at rates up to 1.7 nmol h-1 g-1 fresh weight, a rate that exceeds most biosynthetic rates reported with other plant systems for the incorporation of this basic precursor into natural products. This suggests that P. jeffreyi may provide a suitable model for elucidating the enzymology and molecular biology of short-chain alkane biosynthesis. PMID:12226177

  13. Biochemistry of Short-Chain Alkanes (Tissue-Specific Biosynthesis of n-Heptane in Pinus jeffreyi).

    PubMed

    Savage, T. J.; Hamilton, B. S.; Croteau, R.

    1996-01-01

    Short-chain (C7-C11) alkanes accumulate as the volatile component of oleoresin (pitch) in several pine species native to western North America. To establish the tissue most amenable for use in detailed studies of short-chain alkane biosynthesis, we examined the tissue specificity of alkane accumulation and biosynthesis in Pinus jeffreyi Grev. & Balf. Short-chain alkane accumulation was highly tissue specific in both 2-year-old saplings and mature trees; heart-wood xylem accumulated alkanes up to 7.1 mg g-1 dry weight, whereas needles and other young green tissue contained oleoresin with monoterpenoid, rather than paraffinic, volatiles. These tissue-specific differences in oleoresin composition appear to be a result of tissue-specific rates of alkane and monoterpene biosynthesis; incubation of xylem tissue with [14C]sucrose resulted in accumulation of radiolabel in alkanes but not monoterpenes, whereas incubation of foliar tissue with 14CO2 resulted in the accumulation of radiolabel in monoterpenes but not alkanes. Furthermore, incubation of xylem sections with [14C]acetate resulted in incorporation of radiolabel into alkanes at rates up to 1.7 nmol h-1 g-1 fresh weight, a rate that exceeds most biosynthetic rates reported with other plant systems for the incorporation of this basic precursor into natural products. This suggests that P. jeffreyi may provide a suitable model for elucidating the enzymology and molecular biology of short-chain alkane biosynthesis.

  14. Activated aluminum oxide selectively retaining long chain n-alkanes. Part I, description of the retention properties.

    PubMed

    Fiselier, Katell; Fiorini, Dennis; Grob, Koni

    2009-02-16

    Aluminum oxide activated by heating to 350-400 degrees C retains n-alkanes with more than about 20 carbon atoms, whereas iso-alkanes largely pass the column non-retained. Retention of n-alkanes is strong with n-pentane or n-hexane as mobile phase, but weak or negligible with cyclohexane or iso-octane. It is strongly reduced with increasing column temperature. Even small amounts of polar components, such as modifiers or impurities in the mobile phase, cause the retention of n-alkanes to irreversibly collapse. Since n-alkanes are not more polar than iso-alkanes and long chain n-alkanes not more polar than those of shorter chains, retention by a mechanism based on steric properties is assumed. The sensitivity to deactivation by polar components indicates that polar components and n-alkanes are retained by the same sites. The capacity for retaining n-alkanes is low, with the effect that the retention of n-alkanes depends on the load with retained paraffins. These retention properties are useful for the pre-separation of hydrocarbons in the context of the analysis of mineral oil paraffins in foodstuffs and tissue, where plant n-alkanes, typically ranging from C(23) to C(33), may severely disturb the analysis (subject of Part II).

  15. Distribution, activity and function of short-chain alkane degrading phylotypes in hydrothermal vent sediments

    NASA Astrophysics Data System (ADS)

    Adams, M. M.; Joye, S. B.; Hoarfrost, A.; Girguis, P. R.

    2012-12-01

    Global geochemical analyses suggest that C2-C4 short chain alkanes are a common component of the utilizable carbon pool in deep-sea sediments worldwide and have been found in diverse ecosystems. From a thermodynamic standpoint, the anaerobic microbial oxidation of these aliphatic hydrocarbons is more energetically yielding than the anaerobic oxidation of methane (AOM). Therefore, the preferential degradation of these hydrocarbons may compete with AOM for the use of oxidants such as sulfate, or other potential oxidants. Such processes could influence the fate of methane in the deep-sea. Sulfate-reducing bacteria (SRB) from hydrocarbon seep sediments of the Gulf of Mexico and Guaymas Basin have previously been enriched that anaerobically oxidize short chain alkanes to generate CO2 with the preferential utilization of 12C-enriched alkanes (Kniemeyer et al. 2007). Different temperature regimens along with multiple substrates were tested and a pure culture (deemed BuS5) was isolated from mesophilic enrichments with propane or n-butane as the sole carbon source. Through comparative sequence analysis, strain BuS5 was determined to cluster with the metabolically diverse Desulfosarcina / Desulfococcus cluster, which also contains the SRB found in consortia with anaerobic, methane-oxidizing archaea in seep sediments. Enrichments from a terrestrial, low temperature sulfidic hydrocarbon seep also corroborated that propane degradation occurred with most bacterial phylotypes surveyed belonging to the Deltaproteobacteria, particularly Desulfobacteraceae (Savage et al. 2011). To date, no microbes capable of ethane oxidation or anaerobic C2-C4 alkane oxidation at thermophilic temperature have been isolated. The sediment-covered, hydrothermal vent systems found at Middle Valley (Juan de Fuca Ridge, eastern Pacific Ocean) are a prime environment for investigating mesophilic to thermophilic anaerobic oxidation of short-chain alkanes, given the elevated temperatures and dissolved

  16. Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin.

    PubMed

    Dowell, Frederick; Cardman, Zena; Dasarathy, Srishti; Kellermann, Matthias Y; Lipp, Julius S; Ruff, S Emil; Biddle, Jennifer F; McKay, Luke J; MacGregor, Barbara J; Lloyd, Karen G; Albert, Daniel B; Mendlovitz, Howard; Hinrichs, Kai-Uwe; Teske, Andreas

    2016-01-01

    The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico), are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, hot sediments (above 60°C) covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed "Mat Mound") were characterized by porewater geochemistry of methane, C2-C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas, and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates.

  17. Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin

    PubMed Central

    Dowell, Frederick; Cardman, Zena; Dasarathy, Srishti; Kellermann, Matthias Y.; Lipp, Julius S.; Ruff, S. Emil; Biddle, Jennifer F.; McKay, Luke J.; MacGregor, Barbara J.; Lloyd, Karen G.; Albert, Daniel B.; Mendlovitz, Howard; Hinrichs, Kai-Uwe; Teske, Andreas

    2016-01-01

    The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico), are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, hot sediments (above 60°C) covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed “Mat Mound”) were characterized by porewater geochemistry of methane, C2–C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas, and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates. PMID:26858698

  18. Scaling of the viscosity of the Lennard-Jones chain fluid model, argon, and some normal alkanes.

    PubMed

    Galliero, Guillaume; Boned, Christian; Fernández, Josefa

    2011-02-14

    In this work, we have tested the efficiency of two scaling approaches aiming at relating shear viscosity to a single thermodynamic quantity in dense fluids, namely the excess entropy and the thermodynamic scaling methods. Using accurate databases, we have applied these approaches first to a model fluid, the flexible Lennard-Jones chain fluid (from the monomer to the hexadecamer), then to real fluids, such as argon and normal alkanes. To enlarge noticeably the range of thermodynamics conditions for which these scaling methods are applicable, we have shown that the use of the residual viscosity instead of the total viscosity is preferable in the scaling procedures. It has been found that both approaches, using the adequate scaling, are suitable for the Lennard-Jones chain fluid model for a wide range of thermodynamic conditions whatever the chain length when scaling law exponents and prefactors are adjusted for each chain length. Furthermore, these results were found to be well respected by the corresponding real fluids.

  19. Conversion of raw lignocellulosic biomass into branched long-chain alkanes through three tandem steps.

    PubMed

    Li, Chunrui; Ding, Daqian; Xia, Qineng; Liu, Xiaohui; Wang, Yanqin

    2016-07-07

    Synthesis of branched long-chain alkanes from renewable biomass has attracted intensive interest in recent years, but the feedstock for this synthesis is restricted to platform chemicals. Here, we develop an effective and energy-efficient process to convert raw lignocellulosic biomass (e.g., corncob) into branched diesel-range alkanes through three tandem steps for the first time. Furfural and isopropyl levulinate (LA ester) were prepared from hemicellulose and cellulose fractions of corncob in toluene/water biphasic system with added isopropanol, which was followed by double aldol condensation of furfural with LA ester into C15 oxygenates and the final hydrodeoxygenation of C15 oxygenates into branched long-chain alkanes. The core point of this tandem process is the addition of isopropanol in the first step, which enables the spontaneous transfer of levulinic acid (LA) into the toluene phase in the form of LA ester through esterification, resulting in LA ester co-existing with furfural in the same phase, which is the basis for double aldol condensation in the toluene phase. Moreover, the acidic aqueous phase and toluene can be reused and the residues, including lignin and humins in aqueous phase, can be separated and carbonized to porous carbon materials.

  20. Long chain n-alkanes and their carbon isotopes in lichen species from western Hubei Province: implication for geological records

    NASA Astrophysics Data System (ADS)

    Huang, Xianyu; Xue, Jiantao; Guo, Shouyu

    2012-03-01

    Five coticolous lichen samples were collected from western Hubei Province of China to analyze the long chain n-alkanes and their carbon isotope compositions. The n-alkanes range in carbon number from C17 to C33 with strong odd-over-even predominance between C21 and C33. Lichens are dominated by n-C29 in the samples of Dajiuhu, Shennongjia Mountain, but by both n-C23 and n-C29 at Qizimei Mountain. This difference may result from the different environmental conditions in these two sites. The δ 13C values of long chain n-alkanes in lichen samples show the signature of C3 plants. Based on compoundspecific carbon isotopic values and previous results, we state that alkane homologs >C23 mainly originate from the symbiotic fungi, while symbiotic algae only contribute trace amount of long chain alkanes. Of great interesting is the occurrence of long chain 3-methylalkanes in the Qizimei samples. These anteiso compounds range from C24 to C32, displaying obvious even-over-odd predominance. This study reveals that the association of long chain 3-methylalkanes with n-C23 alkane might be used as proxies to reconstruct the paleoecological implications of lichens in Earth history.

  1. Leaf waxes in riparian trees: hydrogen isotopes, concentrations, and chain-length patterns

    NASA Astrophysics Data System (ADS)

    Tipple, B. J.; Ehleringer, J.; Doman, C.; Khachaturyan, S.

    2011-12-01

    The stable hydrogen isotope ratios of epicuticular leaf wax n-alkanes record aspects of a plant's ecophysiological conditions. However, it remains unclear as to whether n-alkane hydrogen isotope values (δ2H) directly reflect environmental water (source water or tissue water) or environmental water in combination with a biochemical fractionation. Furthermore, it is uncertain if leaf n-alkane δ2H values reflect a single time interval during leaf expansion or if n-alkane δ2H values record the combination of inputs throughout the entire lifespan of a leaf. These different possibilities will influence how leaf wax biomarkers are interpreted in both ecological and environmental reconstruction contexts. To address these issues, we sampled leaves/buds, stems, and water sources of five common western U.S. riparian species under natural field conditions throughout the growing season. Riparian species were selected because the input water source is most likely to be nearly constant through the growing season. We found that species in this study demonstrated marked and systematic variations in n-alkane concentration, average chain length, and δ2H values. Intraspecific patterns were consistent: average chain lengths and δ2H values increased from bud opening through full leaf expansion with little variation during the remainder of the sampling interval, while leaf-wax concentration as a fraction of total biomass increased throughout the growing season. These data imply that leaf-wax δ2H values reflect multiple periods of wax growth and that the leaf wax is continually produced throughout a leaf's lifespan.

  2. Anaerobic biodegradation of longer-chain n-alkanes coupled to methane production in oil sands tailings.

    PubMed

    Siddique, Tariq; Penner, Tara; Semple, Kathleen; Foght, Julia M

    2011-07-01

    Extraction of bitumen from mined oil sands ores produces enormous volumes of tailings that are stored in settling basins (current inventory ≥ 840 million m(3)). Our previous studies revealed that certain hydrocarbons (short-chain n-alkanes [C(6)-C(10)] and monoaromatics [toluene, o-xylene, m-xylene]) in residual naphtha entrained in the tailings are biodegraded to CH(4) by a consortium of microorganisms. Here we show that higher molecular weight n-alkanes (C(14), C(16), and C(18)) are also degraded under methanogenic conditions in oil sands tailings, albeit after a lengthy lag (~180 d) before the onset of methanogenesis. Gas chromatographic analyses showed that the longer-chain n-alkanes each added at ~400 mg L(-1) were completely degraded by the resident microorganisms within ~440 d at ~20 °C. 16S rRNA gene sequence analysis of clone libraries implied that the predominant pathway of longer-chain n-alkane metabolism in tailings is through syntrophic oxidation of n-alkanes coupled with CO(2) reduction to CH(4). These studies demonstrating methanogenic biodegradation of longer-chain n-alkanes by microbes native to oil sands tailings may be important for effective management of tailings and greenhouse gas emissions from tailings ponds.

  3. n-Alkane adsorption to polar silica surfaces.

    PubMed

    Brindza, Michael R; Ding, Feng; Fourkas, John T; Walker, Robert A

    2010-03-21

    The structures of medium-length n-alkane species (C(8)-C(11)) adsorbed to a hydrophilic silica/vapor interface were examined using vibrational sum frequency spectroscopy. Experiments sampling out-of-plane orientation show a clear pattern in vibrational band intensities that implies chains having primarily all-trans conformations lying flat along the interface. Further analysis shows that the methylene groups of the alkane chains have their local symmetry axes directed into and away from the surface. Spectra acquired under different polarization conditions interlock to reinforce this picture of interfacial structure and organization. Variation in signal intensities with chain length suggests that correlation between adsorbed monomers weakens with increasing chain length. This result stands in contrast with alkane behavior at neat liquid/vapor interfaces where longer length alkanes show considerably more surface induced ordering than short chain alkanes.

  4. Self-diffusion in molecular liquids: Medium-chain n-alkanes and coenzyme Q10 studied by quasielastic neutron scattering

    NASA Astrophysics Data System (ADS)

    Smuda, Christoph; Busch, Sebastian; Gemmecker, Gerd; Unruh, Tobias

    2008-07-01

    A systematic time-of-flight quasielastic neutron scattering (TOF-QENS) study on diffusion of n-alkanes in a melt is presented for the first time. As another example of a medium-chain molecule, coenzyme Q10 is investigated in the same way. The data were evaluated both in the frequency and in the time domain. TOF-QENS data can be satisfactorily described by different models, and it turned out that the determined diffusion coefficients are largely independent of the applied model. The derived diffusion coefficients are compared with values measured by pulsed-field gradient nuclear magnetic resonance (PFG-NMR). With increasing chain length, an increasing difference between the TOF-QENS diffusion coefficient and the PFG-NMR diffusion coefficient is observed. This discrepancy in the diffusion coefficients is most likely due to a change of the diffusion mechanism on a nanometer length scale for molecules of medium-chain length.

  5. Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity

    PubMed Central

    Adams, Melissa M.; Hoarfrost, Adrienne L.; Bose, Arpita; Joye, Samantha B.; Girguis, Peter R.

    2013-01-01

    Short-chain alkanes play a substantial role in carbon and sulfur cycling at hydrocarbon-rich environments globally, yet few studies have examined the metabolism of ethane (C2), propane (C3), and butane (C4) in anoxic sediments in contrast to methane (C1). In hydrothermal vent systems, short-chain alkanes are formed over relatively short geological time scales via thermogenic processes and often exist at high concentrations. The sediment-covered hydrothermal vent systems at Middle Valley (MV, Juan de Fuca Ridge) are an ideal site for investigating the anaerobic oxidation of C1–C4 alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these metalliferous sediments. We examined whether MV microbial communities oxidized C1–C4 alkanes under mesophilic to thermophilic sulfate-reducing conditions. Here we present data from discrete temperature (25, 55, and 75°C) anaerobic batch reactor incubations of MV sediments supplemented with individual alkanes. Co-registered alkane consumption and sulfate reduction (SR) measurements provide clear evidence for C1–C4 alkane oxidation linked to SR over time and across temperatures. In these anaerobic batch reactor sediments, 16S ribosomal RNA pyrosequencing revealed that Deltaproteobacteria, particularly a novel sulfate-reducing lineage, were the likely phylotypes mediating the oxidation of C2–C4 alkanes. Maximum C1–C4 alkane oxidation rates occurred at 55°C, which reflects the mid-core sediment temperature profile and corroborates previous studies of rate maxima for the anaerobic oxidation of methane (AOM). Of the alkanes investigated, C3 was oxidized at the highest rate over time, then C4, C2, and C1, respectively. The implications of these results are discussed with respect to the potential competition between the anaerobic oxidation of C2–C4alkanes with AOM for available oxidants and the influence on the fate of C1 derived from these hydrothermal systems. PMID:23717305

  6. Multiple alkane hydroxylase systems in a marine alkane degrader, Alcanivorax dieselolei B-5.

    PubMed

    Liu, Chenli; Wang, Wanpeng; Wu, Yehui; Zhou, Zhongwen; Lai, Qiliang; Shao, Zongze

    2011-05-01

    Alcanivorax dieselolei strain B-5 is a marine bacterium that can utilize a broad range of n-alkanes (C(5) -C(36) ) as sole carbon source. However, the mechanisms responsible for this trait remain to be established. Here we report on the characterization of four alkane hydroxylases from A. dieselolei, including two homologues of AlkB (AlkB1 and AlkB2), a CYP153 homologue (P450), as well as an AlmA-like (AlmA) alkane hydroxylase. Heterologous expression of alkB1, alkB2, p450 and almA in Pseudomonas putida GPo12 (pGEc47ΔB) or P. fluorescens KOB2Δ1 verified their functions in alkane oxidation. Quantitative real-time RT-PCR analysis showed that these genes could be induced by alkanes ranging from C(8) to C(36) . Notably, the expression of the p450 and almA genes was only upregulated in the presence of medium-chain (C(8) -C(16) ) or long-chain (C(22) -C(36) ) n-alkanes, respectively; while alkB1 and alkB2 responded to both medium- and long-chain n-alkanes (C(12) -C(26) ). Moreover, branched alkanes (pristane and phytane) significantly elevated alkB1 and almA expression levels. Our findings demonstrate that the multiple alkane hydroxylase systems ensure the utilization of substrates of a broad chain length range.

  7. Additional chain-branching pathways in the low-temperature oxidation of branched alkanes

    DOE PAGES

    Wang, Zhandong; Zhang, Lidong; Moshammer, Kai; ...

    2015-12-31

    Chain-branching reactions represent a general motif in chemistry, encountered in atmospheric chemistry, combustion, polymerization, and photochemistry; the nature and amount of radicals generated by chain-branching are decisive for the reaction progress, its energy signature, and the time towards its completion. In this study, experimental evidence for two new types of chain-branching reactions is presented, based upon detection of highly oxidized multifunctional molecules (HOM) formed during the gas-phase low-temperature oxidation of a branched alkane under conditions relevant to combustion. The oxidation of 2,5-dimethylhexane (DMH) in a jet-stirred reactor (JSR) was studied using synchrotron vacuum ultra-violet photoionization molecular beam mass spectrometry (SVUV-PI-MBMS).more » Specifically, species with four and five oxygen atoms were probed, having molecular formulas of C8H14O4 (e.g., diketo-hydroperoxide/keto-hydroperoxy cyclic ether) and C8H16O5 (e.g., keto-dihydroperoxide/dihydroperoxy cyclic ether), respectively. The formation of C8H16O5 species involves alternative isomerization of OOQOOH radicals via intramolecular H-atom migration, followed by third O2 addition, intramolecular isomerization, and OH release; C8H14O4 species are proposed to result from subsequent reactions of C8H16O5 species. The mechanistic pathways involving these species are related to those proposed as a source of low-volatility highly oxygenated species in Earth's troposphere. At the higher temperatures relevant to auto-ignition, they can result in a net increase of hydroxyl radical production, so these are additional radical chain-branching pathways for ignition. Furthermore, the results presented herein extend the conceptual basis of reaction mechanisms used to predict the reaction behavior of ignition, and have implications on atmospheric gas-phase chemistry and the oxidative stability of organic substances.« less

  8. Identification of In-Chain-Functionalized Compounds and Methyl-Branched Alkanes in Cuticular Waxes of Triticum aestivum cv. Bethlehem

    PubMed Central

    Racovita, Radu C.; Jetter, Reinhard

    2016-01-01

    In this work, cuticular waxes from flag leaf blades and peduncles of Triticum aestivum cv. Bethlehem were investigated in search for novel wax compounds. Seven wax compound classes were detected that had previously not been reported, and their structures were elucidated using gas chromatography-mass spectrometry of various derivatives. Six of the classes were identified as series of homologs differing by two methylene units, while the seventh was a homologous series with homologs with single methylene unit differences. In the waxes of flag leaf blades, secondary alcohols (predominantly C27 and C33), primary/secondary diols (predominantly C28) and esters of primary/secondary diols (predominantly C50, combining C28 diol with C22 acid) were found, all sharing similar secondary hydroxyl group positions at and around C-12 or ω-12. 7- and 8-hydroxy-2-alkanol esters (predominantly C35), 7- and 8-oxo-2-alkanol esters (predominantly C35), and 4-alkylbutan-4-olides (predominantly C28) were found both in flag leaf and peduncle wax mixtures. Finally, a series of even- and odd-numbered alkane homologs was identified in both leaf and peduncle waxes, with an internal methyl branch preferentially on C-11 and C-13 of homologs with even total carbon number and on C-12 of odd-numbered homologs. Biosynthetic pathways are suggested for all compounds, based on common structural features and matching chain length profiles with other wheat wax compound classes. PMID:27820857

  9. RNAi silencing of a cytochrome P450 monooxygenase disrupts the ability of a filamentous fungus, Graphium sp. to grow on short-chain gaseous alkanes and ethers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Graphium sp. (ATCC 58400), a filamentous fungus, is one of the few eukaryotes that grows on short-chain alkanes and ethers. In this study, we investigated the genetic underpinnings that enable this fungus to catalyze the first step in the alkane and ether oxidation pathway. A gene, CYP52L1, was iden...

  10. Ecosystem size determines food-chain length in lakes.

    PubMed

    Post, D M; Pace, M L; Hairston, N G

    2000-06-29

    Food-chain length is an important characteristic of ecological communities: it influences community structure, ecosystem functions and contaminant concentrations in top predators. Since Elton first noted that food-chain length was variable among natural systems, ecologists have considered many explanatory hypotheses, but few are supported by empirical evidence. Here we test three hypotheses that predict food-chain length to be determined by productivity alone (productivity hypothesis), ecosystem size alone (ecosystem-size hypothesis) or a combination of productivity and ecosystem size (productive-space hypothesis). The productivity and productive-space hypotheses propose that food-chain length should increase with increasing resource availability; however, the productivity hypothesis does not include ecosystem size as a determinant of resource availability. The ecosystem-size hypothesis is based on the relationship between ecosystem size and species diversity, habitat availability and habitat heterogeneity. We find that food-chain length increases with ecosystem size, but that the length of the food chain is not related to productivity. Our results support the hypothesis that ecosystem size, and not resource availability, determines food-chain length in these natural ecosystems.

  11. Structure and phase transitions of monolayers of intermediate-length n-alkanes on graphite studied by neutron diffraction and molecular dynamics simulation.

    PubMed

    Diama, A; Matthies, B; Herwig, K W; Hansen, F Y; Criswell, L; Mo, H; Bai, M; Taub, H

    2009-08-28

    We present evidence from neutron diffraction measurements and molecular dynamics (MD) simulations of three different monolayer phases of the intermediate-length alkanes tetracosane (n-C(24)H(50) denoted as C24) and dotriacontane (n-C(32)H(66) denoted as C32) adsorbed on a graphite basal-plane surface. Our measurements indicate that the two monolayer films differ principally in the transition temperatures between phases. At the lowest temperatures, both C24 and C32 form a crystalline monolayer phase with a rectangular-centered (RC) structure. The two sublattices of the RC structure each consists of parallel rows of molecules in their all-trans conformation aligned with their long axis parallel to the surface and forming so-called lamellas of width approximately equal to the all-trans length of the molecule. The RC structure is uniaxially commensurate with the graphite surface in its [110] direction such that the distance between molecular rows in a lamella is 4.26 A=sqrt[3a(g)], where a(g)=2.46 A is the lattice constant of the graphite basal plane. Molecules in adjacent rows of a lamella alternate in orientation between the carbon skeletal plane being parallel and perpendicular to the graphite surface. Upon heating, the crystalline monolayers transform to a "smectic" phase in which the inter-row spacing within a lamella expands by approximately 10% and the molecules are predominantly oriented with the carbon skeletal plane parallel to the graphite surface. In the smectic phase, the MD simulations show evidence of broadening of the lamella boundaries as a result of molecules diffusing parallel to their long axis. At still higher temperatures, they indicate that the introduction of gauche defects into the alkane chains drives a melting transition to a monolayer fluid phase as reported previously.

  12. Additional chain-branching pathways in the low-temperature oxidation of branched alkanes

    SciTech Connect

    Wang, Zhandong; Zhang, Lidong; Moshammer, Kai; Popolan-Vaida, Denisia M.; Shankar, Vijai Shankar Bhavani; Lucassen, Arnas; Hemken, Christian; Taatjes, Craig A.; Leone, Stephen R.; Kohse-Hoinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Sarathy, S. Mani

    2015-12-31

    Chain-branching reactions represent a general motif in chemistry, encountered in atmospheric chemistry, combustion, polymerization, and photochemistry; the nature and amount of radicals generated by chain-branching are decisive for the reaction progress, its energy signature, and the time towards its completion. In this study, experimental evidence for two new types of chain-branching reactions is presented, based upon detection of highly oxidized multifunctional molecules (HOM) formed during the gas-phase low-temperature oxidation of a branched alkane under conditions relevant to combustion. The oxidation of 2,5-dimethylhexane (DMH) in a jet-stirred reactor (JSR) was studied using synchrotron vacuum ultra-violet photoionization molecular beam mass spectrometry (SVUV-PI-MBMS). Specifically, species with four and five oxygen atoms were probed, having molecular formulas of C8H14O4 (e.g., diketo-hydroperoxide/keto-hydroperoxy cyclic ether) and C8H16O5 (e.g., keto-dihydroperoxide/dihydroperoxy cyclic ether), respectively. The formation of C8H16O5 species involves alternative isomerization of OOQOOH radicals via intramolecular H-atom migration, followed by third O2 addition, intramolecular isomerization, and OH release; C8H14O4 species are proposed to result from subsequent reactions of C8H16O5 species. The mechanistic pathways involving these species are related to those proposed as a source of low-volatility highly oxygenated species in Earth's troposphere. At the higher temperatures relevant to auto-ignition, they can result in a net increase of hydroxyl radical production, so these are additional radical chain-branching pathways for ignition. Furthermore, the results presented herein extend the conceptual basis of reaction mechanisms used to predict the reaction behavior of ignition, and have

  13. Overexpression of Arabidopsis ECERIFERUM1 Promotes Wax Very-Long-Chain Alkane Biosynthesis and Influences Plant Response to Biotic and Abiotic Stresses1[W

    PubMed Central

    Bourdenx, Brice; Bernard, Amélie; Domergue, Frédéric; Pascal, Stéphanie; Léger, Amandine; Roby, Dominique; Pervent, Marjorie; Vile, Denis; Haslam, Richard P.; Napier, Johnathan A.; Lessire, René; Joubès, Jérôme

    2011-01-01

    Land plant aerial organs are covered by a hydrophobic layer called the cuticle that serves as a waterproof barrier protecting plants against desiccation, ultraviolet radiation, and pathogens. Cuticle consists of a cutin matrix as well as cuticular waxes in which very-long-chain (VLC) alkanes are the major components, representing up to 70% of the total wax content in Arabidopsis (Arabidopsis thaliana) leaves. However, despite its major involvement in cuticle formation, the alkane-forming pathway is still largely unknown. To address this deficiency, we report here the characterization of the Arabidopsis ECERIFERUM1 (CER1) gene predicted to encode an enzyme involved in alkane biosynthesis. Analysis of CER1 expression showed that CER1 is specifically expressed in the epidermis of aerial organs and coexpressed with other genes of the alkane-forming pathway. Modification of CER1 expression in transgenic plants specifically affects VLC alkane biosynthesis: waxes of TDNA insertional mutant alleles are devoid of VLC alkanes and derivatives, whereas CER1 overexpression dramatically increases the production of the odd-carbon-numbered alkanes together with a substantial accumulation of iso-branched alkanes. We also showed that CER1 expression is induced by osmotic stresses and regulated by abscisic acid. Furthermore, CER1-overexpressing plants showed reduced cuticle permeability together with reduced soil water deficit susceptibility. However, CER1 overexpression increased susceptibility to bacterial and fungal pathogens. Taken together, these results demonstrate that CER1 controls alkane biosynthesis and is highly linked to responses to biotic and abiotic stresses. PMID:21386033

  14. Overexpression of Arabidopsis ECERIFERUM1 promotes wax very-long-chain alkane biosynthesis and influences plant response to biotic and abiotic stresses.

    PubMed

    Bourdenx, Brice; Bernard, Amélie; Domergue, Frédéric; Pascal, Stéphanie; Léger, Amandine; Roby, Dominique; Pervent, Marjorie; Vile, Denis; Haslam, Richard P; Napier, Johnathan A; Lessire, René; Joubès, Jérôme

    2011-05-01

    Land plant aerial organs are covered by a hydrophobic layer called the cuticle that serves as a waterproof barrier protecting plants against desiccation, ultraviolet radiation, and pathogens. Cuticle consists of a cutin matrix as well as cuticular waxes in which very-long-chain (VLC) alkanes are the major components, representing up to 70% of the total wax content in Arabidopsis (Arabidopsis thaliana) leaves. However, despite its major involvement in cuticle formation, the alkane-forming pathway is still largely unknown. To address this deficiency, we report here the characterization of the Arabidopsis ECERIFERUM1 (CER1) gene predicted to encode an enzyme involved in alkane biosynthesis. Analysis of CER1 expression showed that CER1 is specifically expressed in the epidermis of aerial organs and coexpressed with other genes of the alkane-forming pathway. Modification of CER1 expression in transgenic plants specifically affects VLC alkane biosynthesis: waxes of TDNA insertional mutant alleles are devoid of VLC alkanes and derivatives, whereas CER1 overexpression dramatically increases the production of the odd-carbon-numbered alkanes together with a substantial accumulation of iso-branched alkanes. We also showed that CER1 expression is induced by osmotic stresses and regulated by abscisic acid. Furthermore, CER1-overexpressing plants showed reduced cuticle permeability together with reduced soil water deficit susceptibility. However, CER1 overexpression increased susceptibility to bacterial and fungal pathogens. Taken together, these results demonstrate that CER1 controls alkane biosynthesis and is highly linked to responses to biotic and abiotic stresses.

  15. Alkane oxidation with porphyrins and metal complexes thereof having haloalkyl side chains

    DOEpatents

    Wijesekera, T.; Lyons, J.E.; Ellis, P.E. Jr.; Bhinde, M.V.

    1998-06-23

    Transition metal complexes of meso-haloalkylporphyrins are disclosed, wherein the haloalkyl groups contain 2 to 8 carbon atoms have been found to be highly effective catalysts for oxidation of alkanes and for the decomposition of hydroperoxides. 7 figs.

  16. Alkane oxidation with porphyrins and metal complexes thereof having haloalkyl side chains

    DOEpatents

    Wijesekera, Tilak; Lyons, James E.; Ellis, Jr., Paul E.; Bhinde, Manoj V.

    1998-01-01

    Transition metal complexes of meso-haloalkylporphyrins, wherein the haloalkyl groups contain 2 to 8 carbon atoms have been found to be highly effective catalysts for oxidation of alkanes and for the decomposition of hydroperoxides.

  17. Constraints on food chain length arising from regional metacommunity dynamics.

    PubMed

    Calcagno, Vincent; Massol, François; Mouquet, Nicolas; Jarne, Philippe; David, Patrice

    2011-10-22

    Classical ecological theory has proposed several determinants of food chain length, but the role of metacommunity dynamics has not yet been fully considered. By modelling patchy predator-prey metacommunities with extinction-colonization dynamics, we identify two distinct constraints on food chain length. First, finite colonization rates limit predator occupancy to a subset of prey-occupied sites. Second, intrinsic extinction rates accumulate along trophic chains. We show how both processes concur to decrease maximal and average food chain length in metacommunities. This decrease is mitigated if predators track their prey during colonization (habitat selection) and can be reinforced by top-down control of prey vital rates (especially extinction). Moreover, top-down control of colonization and habitat selection can interact to produce a counterintuitive positive relationship between perturbation rate and food chain length. Our results show how novel limits to food chain length emerge in spatially structured communities. We discuss the connections between these constraints and the ones commonly discussed, and suggest ways to test for metacommunity effects in food webs.

  18. RNAi silencing of a cytochrome P450 monoxygenase disrupts the ability of a filamentous fungus, Graphium sp., to grow on short-chain gaseous alkanes and ethers.

    PubMed

    Trippe, Kristin M; Wolpert, Thomas J; Hyman, Michael R; Ciuffetti, Lynda M

    2014-02-01

    Graphium sp. (ATCC 58400), a filamentous fungus, is one of the few eukaryotes that grows on short-chain alkanes and ethers. In this study, we investigated the genetic underpinnings that enable this fungus to catalyze the first step in the alkane and ether oxidation pathway. A gene, CYP52L1, was identified, cloned and functionally characterized as an alkane-oxidizing cytochrome P450 (GSPALK1). Analysis of CYP52L1 suggests that it is a member of the CYP52 cytochrome P450 family, which is comprised of medium- and long-chain alkane-oxidizing enzymes found in yeasts. However, phylogenetic analysis of GSPALK1 with other CYP52 members suggests they are not closely related. Post-transcriptional ds-RNA-mediated gene silencing of CYP52L1 severely reduced the ability of this fungus to oxidize alkanes and ethers, however, downstream metabolic steps in these pathways were unaffected. Collectively, the results of this study suggest that GSPALK1 is the enzyme that catalyzes the initial oxidation of alkanes and ethers but is not involved in the later steps of alkane or ether metabolism.

  19. Quantification of chemotaxis-related alkane accumulation in Acinetobacter baylyi using Raman microspectroscopy.

    PubMed

    Li, Hanbing; L Martin, Francis Luke; Zhang, Dayi

    2017-03-03

    Alkanes are one of the most widespread contaminants in the natural environment, primarily as a consequence of biological synthesis and oil spills. Many indigenous microbes metabolize alkanes, and the chemotaxis and accumulation in some strains has been identified. For the first time, we apply Raman microspectroscopy to identify such chemotaxis-related affinity, and quantify the alkane concentrations via spectral alterations. Raman spectral alterations were only found for the alkane chemo-attractant bacteria Acinetobacter baylyi ADP1, not for Pseudomonas fluorescence, which exhibits limited chemotaxis towards alkane. The significant alterations were attributed to the strong chemotactic ability of A. baylyi enhancing the affinity and accumulation of alkane molecules on cell membranes or cellular internalization. Spectral fingerprints of A. baylyi significantly altered after 1-h exposure to pure alkanes (dodecane or tetradecane) and alkane mixtures (mineral oil or crude oil), but not monocyclic aromatic hydrocarbons (MAHs) or polycyclic aromatic hydrocarbons (PAHs). A semi-log linear regression relationship between Raman spectral alterations and alkane concentrations showed its feasibility in quantifying alkane concentration in environmental samples. Pure alkanes or alkane mixtures exhibited different limits of detection and regression slopes, indicating that the chemotaxis-related alkane accumulation in A. baylyi is dependent on the carbon chain length. This work provides a novel biospectroscopy approach to characterize the chemotaxis-related alkane bioaccumulation, and has immense potential for fast and high-throughput screening bacterial chemotaxis.

  20. Utilization of n-Alkanes by Cladosporium resinae

    PubMed Central

    Teh, J. S.; Lee, K. H.

    1973-01-01

    Four different isolates of Cladosporium resinae from Australian soils were tested for their ability to utilize liquid n-alkanes ranging from n-hexane to n-octadecane under standard conditions. The isolates were unable to make use of n-hexane, n-heptane, and n-octane for growth. In fact, these hydrocarbons, particularly n-hexane, exerted an inhibitory effect on spore germination and mycelial growth. All higher n-alkanes from n-nonane to n-octadecane were assimilated by the fungus, although only limited growth occurred on n-nonane and n-decane. The long chain n-alkanes (C14 to C18) supported good growth of all isolates, but there was no obvious correlation between cell yields and chain lengths of these n-alkanes. Variation in growth responses to individual n-alkane among the different isolates was also observed. The cause of this variation is unknown. PMID:4735447

  1. Sodium montmorillonite silylation: unexpected effect of the aminosilane chain length.

    PubMed

    Piscitelli, Filomena; Posocco, Paola; Toth, Radovan; Fermeglia, Maurizio; Pricl, Sabrina; Mensitieri, Giuseppe; Lavorgna, Marino

    2010-11-01

    In this work, the silylation of sodium montmorillonite (Na-MMT) was performed in glycerol using 3-aminopropyltriethoxysilane, N-(2-aminoethyl)-3-aminopropyltrimethoxysilane and 3-[2-(2-aminoethylamino)ethylamino]-propyl-trimethoxysilane. The effects on the d-spacing of sodium montmorillonite (Na-MMT) upon reaction with three aminosilanes of different chain length were studied in details by combining experimental and computational techniques. Infrared spectroscopy was used to monitor the grafting process, while the degree of grafting was calculated using thermogravimetric analysis. X-ray diffraction experiments were carried out to evaluate the shift of the (0 0 1) basal spacing. It was found that the degree of silylation of Na-MMT increases with increasing the length of the aminosilane organic moieties, the overall aminosilane concentration, and temperature. The same beneficial effects were observed on the silicate d-spacing, as its value increases with increasing silane concentration and reaction temperature. Remarkably, however, increasing the length of the organic chains in the silane modifiers resulted in decreasing values of the Na-MMT interlayer distance. A rationale for this behavior is proposed on the basis of atomistic molecular dynamics simulation evidences.

  2. Short-chain alkane cycling in deep Gulf of Mexico cold-seep sediments

    NASA Astrophysics Data System (ADS)

    Sibert, R.; Joye, S. B.; Hunter, K.

    2015-12-01

    Mixtures of light hydrocarbon gases are common in deep Gulf of Mexico cold-seep sediments, and are typically dissolved in pore fluids, adsorbed to sediment particles, trapped in methane ice, or as free gas. The dominant component in these natural gas mixtures is usually methane (>80% C1), but ethane (C2) and propane (C3) are nearly always present in trace amounts (<1% total). The processes that control the concentration and isotopic signature of these gases in sediments are well explained for methane, but the controls for C2/C3 cycling are still a relative mystery. Methane production proceeds in deep anoxic sediments by either 1) thermocatalytic cracking of fossil organic matter, or 2) as a direct product of microbial metabolism, i.e. methanogenesis. In surface sediments, it appears that both microbial consumption and chemical deposition of methane (i.e. as methane clathrate) ensures that >95% of the methane produced at depth never reaches the water column. Production of C1 and C2 in deep-sea sediments has been historically attributed only to thermocatalytic processes, though limited data suggests production of C2/C3 compounds through the activity of archaea at depth. Furthermore, carbon isotopic data on ethane and propane from deep cores of Gulf of Mexico sediments suggest alkanogenesis at >3 m depth in the sediment column and alkane oxidation in uppermost oxidant-rich sediments. Additional studies have also isolated microorganisms capable of oxidizing ethane and propane in the laboratory, but field studies of microbial-driven dynamics of C2/C3 gases in cold-seep sediments are rare. Here, we present the results of a series of incubation experiments using sediment slurries culled from surface sediments from one of the most prolific natural oil and gas seeps in the Gulf of Mexico. Rates of alkane oxidation were measured under a variety of conditions to assess the surface-driven microbial controls on C2/C3 cycling in cold-seep environments. Such microbial processes

  3. Effects of quaternary ammonium chain length on antibacterial bonding agents.

    PubMed

    Li, F; Weir, M D; Xu, H H K

    2013-10-01

    The objectives of this study were to synthesize new quaternary ammonium methacrylates (QAMs) with systematically varied alkyl chain lengths (CL) and to investigate, for the first time, the CL effects on antibacterial efficacy, cytotoxicity, and dentin bond strength of bonding agents. QAMs were synthesized with CL of 3 to 18 and incorporated into Scotchbond Multi-Purpose (SBMP) bonding agent. The cured resins were inoculated with Streptococcus mutans. Bacterial early attachment was investigated at 4 hrs. Biofilm colony-forming units (CFU) were measured after 2 days. With CL increasing from 3 to 16, the minimum inhibitory concentration and minimum bactericidal concentration were decreased by 5 orders of magnitude. Incorporating QAMs into SBMP reduced bacterial early attachment, with the least colonization at CL = 16. Biofilm CFU for CL = 16 was 4 log lower than SBMP control (p < .05). All groups had similar dentin bond strengths (p > .1). The new antibacterial materials had fibroblast/odontoblast viability similar to that of commercial controls. In conclusion, increasing the chain length of new QAMs in bonding agents greatly increased the antibacterial efficacy. A reduction in Streptococcus mutans biofilm CFU by 4 log could be achieved, without compromising bond strength and cytotoxicity. New QAM-containing bonding agents are promising for a wide range of restorations to inhibit biofilms.

  4. Effects of Quaternary Ammonium Chain Length on Antibacterial Bonding Agents

    PubMed Central

    Li, F.; Weir, M.D.; Xu, H.H.K.

    2013-01-01

    The objectives of this study were to synthesize new quaternary ammonium methacrylates (QAMs) with systematically varied alkyl chain lengths (CL) and to investigate, for the first time, the CL effects on antibacterial efficacy, cytotoxicity, and dentin bond strength of bonding agents. QAMs were synthesized with CL of 3 to 18 and incorporated into Scotchbond Multi-Purpose (SBMP) bonding agent. The cured resins were inoculated with Streptococcus mutans. Bacterial early attachment was investigated at 4 hrs. Biofilm colony-forming units (CFU) were measured after 2 days. With CL increasing from 3 to 16, the minimum inhibitory concentration and minimum bactericidal concentration were decreased by 5 orders of magnitude. Incorporating QAMs into SBMP reduced bacterial early attachment, with the least colonization at CL = 16. Biofilm CFU for CL = 16 was 4 log lower than SBMP control (p < .05). All groups had similar dentin bond strengths (p > .1). The new antibacterial materials had fibroblast/odontoblast viability similar to that of commercial controls. In conclusion, increasing the chain length of new QAMs in bonding agents greatly increased the antibacterial efficacy. A reduction in Streptococcus mutans biofilm CFU by 4 log could be achieved, without compromising bond strength and cytotoxicity. New QAM-containing bonding agents are promising for a wide range of restorations to inhibit biofilms. PMID:23958761

  5. Diversity of flavin-binding monooxygenase genes (almA) in marine bacteria capable of degradation long-chain alkanes.

    PubMed

    Wang, Wanpeng; Shao, Zongze

    2012-06-01

    Many bacteria have been reported as degraders of long-chain (LC) n-alkanes, but the mechanism is poorly understood. Flavin-binding monooxygenase (AlmA) was recently found to be involved in LC-alkane degradation in bacteria of the Acinetobacter and Alcanivorax genera. However, the diversity of this gene and the role it plays in other bacteria remains unclear. In this study, we surveyed the diversity of almA in marine bacteria and in bacteria found in oil-enrichment communities. To identify the presence of this gene, a pair of degenerate PCR primers were was designed based on conserved motifs of the almA gene sequences in public databases. Using this approach, we identified diverse almA genes in the hydrocarbon-degrading bacteria and in bacterial communities from the surface seawater of the Xiamen coastal area, the South China Sea, the Indian Ocean, and the Atlantic Ocean. As a result, almA was positively detected in 35 isolates belonging to four genera, and a total of 39 different almA sequences were obtained. Five isolates were confirmed to harbor two to three almA genes. From the Xiamen coastal area and the Atlantic Ocean oil-enrichment communities, a total of 60 different almA sequences were obtained. These sequences mainly formed two clusters in the phylogenetic tree, named Class I and Class II, and these shared 45-56% identity at the amino acid level. Class I contained 11 sequences from bacteria represented by the Salinisphaera and Parvibaculum genera. Class II was larger and more diverse, and it was composed of 88 sequences from Proteobacteria, Gram-negative bacteria, and the enriched bacterial communities. These communities were represented by the Alcanivorax and Marinobacter genera, which are the two most popular genera hosting the almA gene. AlmA was also detected across a wide geographical range, as determined by the origin of the bacterial host. Our results demonstrate the diversity of almA and confirm its high rate of occurrence in hydrocarbon

  6. Adsorption of alkyltrimethylammonium bromides at water/alkane interfaces: competitive adsorption of alkanes and surfactants.

    PubMed

    Fainerman, V B; Mucic, N; Pradines, V; Aksenenko, E V; Miller, R

    2013-11-12

    The adsorption of members of the homologous series of alkyl trimethylammonium bromides (C(n)TAB) is studied at water/alkane interfaces by drop profile analysis tensiometry. The results are discussed in terms of a competitive adsorption process of alkane and surfactant molecules. A thermodynamic model, derived originally for the adsorption of surfactant mixtures, is adapted such that it describes a competitive adsorption of the surfactant molecules from the aqueous phase and alkane molecules from the oil phase. This new model involves the interspecies attraction coefficient, which mutually increases the adsorption activities of the alkane and C(n)TAB. The effects of the alkyl chain length n of C(n)TABs and the influence of the number of C atoms in the alkane chain are discussed, and the physical quantities are compared to those determined at the aqueous solution/air interface. The new theoretical model for aqueous solution/oil interfaces is also compared to a theory that does not consider the adsorption of alkane. The proposed new model demonstrates good agreement with the experimental data.

  7. Expanding the product profile of a microbial alkane biosynthetic pathway.

    PubMed

    Harger, Matthew; Zheng, Lei; Moon, Austin; Ager, Casey; An, Ju Hye; Choe, Chris; Lai, Yi-Ling; Mo, Benjamin; Zong, David; Smith, Matthew D; Egbert, Robert G; Mills, Jeremy H; Baker, David; Pultz, Ingrid Swanson; Siegel, Justin B

    2013-01-18

    Microbially produced alkanes are a new class of biofuels that closely match the chemical composition of petroleum-based fuels. Alkanes can be generated from the fatty acid biosynthetic pathway by the reduction of acyl-ACPs followed by decarbonylation of the resulting aldehydes. A current limitation of this pathway is the restricted product profile, which consists of n-alkanes of 13, 15, and 17 carbons in length. To expand the product profile, we incorporated a new part, FabH2 from Bacillus subtilis , an enzyme known to have a broader specificity profile for fatty acid initiation than the native FabH of Escherichia coli . When provided with the appropriate substrate, the addition of FabH2 resulted in an altered alkane product profile in which significant levels of n-alkanes of 14 and 16 carbons in length are produced. The production of even chain length alkanes represents initial steps toward the expansion of this recently discovered microbial alkane production pathway to synthesize complex fuels. This work was conceived and performed as part of the 2011 University of Washington international Genetically Engineered Machines (iGEM) project.

  8. An emulsion of sulfoquinovosylacylglycerol with long-chain alkanes increases its permeability to tumor cells.

    PubMed

    Aoki, Satoko; Ohta, Keisuke; Matsumoto, Kenjiro; Sakai, Hideki; Abe, Masahiko; Miura, Masahiko; Sugawara, Fumio; Sakaguchi, Kengo

    2006-01-01

    The alpha-anomer form of sulfoquinovosyl-monoacylglycerol with a saturated C18 fatty acid (alpha-SQMG-C(18:0)) is a natural sulfolipid that is a clinically promising antitumor agent. It forms vesicles, micelles or an emulsion in water, depending on several physicochemical conditions. The type of aggregate formed appears to strongly influence the bioactivity level. Thus, we investigated the nature of the aggregates in relation to their bioactivities. The structure of the alpha-SQMG-C(18:0) assembly was greatly affected by the type of additive used in the preparation. Emulsification with ethanol and n-decane might be more effective at inhibiting tumor cell growth than the micelle or vesicle preparations. alpha-SQMG-C(18:0) formed an "emulsion-like-aggregate" in ethanol containing an n-decane concentration in the range of 1.03-103 mM: . These ethanol/n-alkane/alpha-SQMG-C(18:0) aggregates inhibited cell growth in a dose-dependent manner, under optimum conditions (i.e., ethanol containing 103 mM: of n-decane or n-dodecane dispersed in phosphate-buffered saline or culture medium). Based on these data, we discuss the relationship between the molecular action of and antitumor activity by alpha-SQMG-C(18:0).

  9. Microwave-assisted extraction versus Soxhlet extraction for the analysis of short-chain chlorinated alkanes in sediments.

    PubMed

    Parera, J; Santos, F J; Galceran, M T

    2004-08-13

    Microwave-assisted extraction (MAE) was evaluated as a possible alternative to Soxhlet extraction for analysing short-chain chlorinated alkanes (commonly called short-chain chlorinated paraffins, SCCPs) in river sediment samples, using gas chromatography coupled to negative chemical ionisation mass spectrometry. For MAE optimisation, several extraction parameters such as solvent extraction mixture, extraction time and extraction temperature were studied. Maximum extraction efficiencies for SCCPs (90%) and for 12 polychlorinated biphenyl (PCB) congeners (91-95%) were achieved using 5 g of sediment sample, 30 ml of n-hexane-acetone (1:1, v/v) as solvent extraction, and 15 min and 115 degrees C of extraction time and temperature, respectively. Activated Florisil was used to clean-up the extracts, allowing highly selective separation of SCCPs from other organic contaminants such as PCBs. MAE was compared with a conventional extraction technique such as Soxhlet and good agreement in the results was obtained. Quality parameters of the optimised MAE method such as run-to-run (R.S.D. 7%) and day-to-day precision (R.S.D. 9%) were determined using spiked river sediment samples, with LODs of 1.5 ng g(-1). This method was successfully applied to the analysis of SCCPs in river sediment samples at concentrations below the ng g(-1) level. O 2004 Elsevier B.V. All rights reserved.

  10. Melting of linear alkanes between swollen elastomers and solid substrates.

    PubMed

    Nanjundiah, Kumar; Dhinojwala, Ali

    2013-10-01

    We have measured the melting and freezing behavior of linear alkanes confined between cross-linked poly(dimethylsiloxane) (PDMS) elastomers and solid sapphire substrates. Small molecules are often used as lubricants to reduce friction or as plasticizers, but very little is directly known about the migration or changes in physical properties of these small molecules at interfaces, particularly the changes in transition temperatures upon confinement. Our previous studies highlighted striking differences between the crystal structure of confined and unconfined pentadecane crystals in contact with sapphire substrates. Here, we have used surface-sensitive infrared-visible sum-frequency-generation spectroscopy (SFG) to study the melting temperatures (Tm) of alkanes in nanometer thick interfacial regions between swollen PDMS elastomers in contact with sapphire substrate. We find that confined alkanes show depression in Tm compared to the melting temperature of unconfined bulk alkanes. The depression in Tm is a function of chain length, and these differences were smallest for shorter alkanes and largest for 19 unit long alkanes. In comparison, the DSC results for swollen PDMS elastomer show a broad distribution of melting points corresponding to different sizes of crystals formed within the network. The Tm for confined alkanes has been modeled using the combination of Flory-Rehner and Gibbs-Thomson models, and the depression in Tm is related to the thickness of the confined alkanes. These findings have important implications in understanding friction and adhesion of soft elastomeric materials and also the effects of confinement between two solid materials.

  11. Utilization of n-alkanes by a newly isolated strain of Acinetobacter venetianus: the role of two AlkB-type alkane hydroxylases.

    PubMed

    Throne-Holst, Mimmi; Markussen, Sidsel; Winnberg, Asgeir; Ellingsen, Trond E; Kotlar, Hans-Kristian; Zotchev, Sergey B

    2006-09-01

    A bacterial strain capable of utilizing n-alkanes with chain lengths ranging from decane (C10H22) to tetracontane (C40H82) as a sole carbon source was isolated using a system for screening microorganisms able to grow on paraffin (mixed long-chain n-alkanes). The isolate, identified according to its 16S rRNA sequence as Acinetobacter venetianus, was designated A. venetianus 6A2. Two DNA fragments encoding parts of AlkB-type alkane hydroxylase homologues, designated alkMa and alkMb, were polymerase chain reaction-amplified from the genome of A. venetianus 6A2. To study the roles of these two alkM paralogues in n-alkane utilization in A. venetianus 6A2, we constructed alkMa, alkMb, and alkMa/alkMb disruption mutants. Studies on the growth patterns of the disruption mutants using n-alkanes with different chain lengths as sole carbon source demonstrated central roles for the alkMa and alkMb genes in utilization of C10 to C18 n-alkanes. Comparative analysis of these patterns also suggested different substrate preferences for AlkMa and AlkMb in n-alkane utilization. Because both single and double mutants were able to grow on n-alkanes with chain lengths of C20 and longer, we concluded that yet another enzyme(s) for the utilization of these n-alkanes must exist in A. venetianus 6A2.

  12. Topological analysis of polymeric melts: Chain-length effects and fast-converging estimators for entanglement length

    NASA Astrophysics Data System (ADS)

    Hoy, Robert S.; Foteinopoulou, Katerina; Kröger, Martin

    2009-09-01

    Primitive path analyses of entanglements are performed over a wide range of chain lengths for both bead spring and atomistic polyethylene polymer melts. Estimators for the entanglement length Ne which operate on results for a single chain length N are shown to produce systematic O(1/N) errors. The mathematical roots of these errors are identified as (a) treating chain ends as entanglements and (b) neglecting non-Gaussian corrections to chain and primitive path dimensions. The prefactors for the O(1/N) errors may be large; in general their magnitude depends both on the polymer model and the method used to obtain primitive paths. We propose, derive, and test new estimators which eliminate these systematic errors using information obtainable from the variation in entanglement characteristics with chain length. The new estimators produce accurate results for Ne from marginally entangled systems. Formulas based on direct enumeration of entanglements appear to converge faster and are simpler to apply.

  13. Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds.

    PubMed

    Shahimin, Mohd Faidz Mohamad; Foght, Julia M; Siddique, Tariq

    2016-05-15

    Oil sands tailings ponds harbor diverse anaerobic microbial communities capable of methanogenic biodegradation of solvent hydrocarbons entrained in the tailings. Mature fine tailings (MFT) from two operators (Albian and CNRL) that use different extraction solvents were incubated with mixtures of either two (n-pentane and n-hexane) or four (n-pentane, n-hexane, n-octane and n-decane) n-alkanes under methanogenic conditions for ~600 d. Microbes in Albian MFT began methane production by ~80 d, achieving complete depletion of n-pentane and n-hexane in the two-alkane mixture and their preferential biodegradation in the four-alkane mixture. Microbes in CNRL MFT preferentially metabolized n-octane and n-decane in the four-alkane mixture after a ~80 d lag but exhibited a lag of ~360 d before commencing biodegradation of n-pentane and n-hexane in the two-alkane mixture. 16S rRNA gene pyrosequencing revealed Peptococcaceae members as key bacterial n-alkane degraders in all treatments except CNRL MFT amended with the four-alkane mixture, in which Anaerolineaceae, Desulfobacteraceae (Desulfobacterium) and Syntrophaceae (Smithella) dominated during n-octane and n-decane biodegradation. Anaerolineaceae sequences increased only in cultures amended with the four-alkane mixture and only during n-octane and n-decane biodegradation. The dominant methanogens were acetoclastic Methanosaetaceae. These results highlight preferential n-alkane biodegradation by microbes in oil sands tailings from different producers, with implications for tailings management and reclamation.

  14. Infrared Spectroscopic Investigation on CH Bond Acidity in Cationic Alkanes

    NASA Astrophysics Data System (ADS)

    Matsuda, Yoshiyuki; Xie, Min; Fujii, Asuka

    2016-06-01

    We have demonstrated large enhancements of CH bond acidities in alcohol, ether, and amine cations through infrared predissociation spectroscopy based on the vacuum ultraviolet photoionization detection. In this study, we investigate for the cationic alkanes (pentane, hexane, and heptane) with different alkyl chain lengths. The σ electrons are ejected in the ionization of alkanes, while nonbonding electrons are ejected in ionization of alcohols, ethers, and amines. Nevertheless, the acidity enhancements of CH in these cationic alkanes have also been demonstrated by infrared spectroscopy. The correlations of their CH bond acidities with the alkyl chain lengths as well as the mechanisms of their acidity enhancements will be discussed by comparison of infrared spectra and theoretical calculations.

  15. On the inclusion of alkanes into the monolayer of aliphatic alcohols at the water/alkane vapor interface: a quantum chemical approach.

    PubMed

    Vysotsky, Yuri B; Fomina, Elena S; Belyaeva, Elena A; Fainerman, Valentin B; Vollhardt, Dieter

    2013-02-14

    In the framework of the quantum chemical semiempirical PM3 method thermodynamic and structural parameters of the formation and clusterization of aliphatic alcohols C(n)H(2n+1)OH (n(OH) = 8-16) at 298 K at the water/alkane vapor C(n)H(2n+2), (n(CH(3)) = 6-16) interface were calculated. The dependencies of enthalpy, entropy and Gibbs' energy of clusterization per one monomer molecule of 2D films on the alkyl chain length of corresponding alcohols and alkanes, the molar fraction of alkanes in the monolayers and the immersion degree of alcohol molecules into the water phase were shown to be linear or stepwise. The threshold of spontaneous clusterization of aliphatic alcohols at the water/alkane vapor interface was 10-11 carbon atoms at 298 K which is in line with experimental data at the air/water interface. It is shown that the presence of alkane vapor does not influence the process of alcohol monolayer formation. The structure of these monolayers is analogous to those obtained at the air/water interface in agreement with experimental data. The inclusion of alkane molecules into the amphiphilic monolayer at the water/alkane vapor interface is possible for amphiphiles with the spontaneous clusterization threshold at the air/water interface (n(s)(0)) of at least 16 methylene units in the alkyl chain, and it does not depend on the molar fraction of alkanes in the corresponding monolayer. The inclusion of alkanes from the vapor phase into the amphiphilic monolayer also requires that the difference between the alkyl chain lengths of alcohols and alkanes is not larger than n(s)(0) - 15 and n(s)(0) - 14 for the 2D film 1 and 2D film 2, respectively.

  16. Antibacterial effect of phosphates and polyphosphates with different chain length.

    PubMed

    Lorencová, Eva; Vltavská, Pavlína; Budinský, Pavel; Koutný, Marek

    2012-01-01

    The aim of this study was to monitor the antibacterial effect of seven phosphate salts on selected strains of Gram-negative and Gram-positive bacteria, which could be considered responsible for food-borne diseases (Bacillus cereus, Bacillus subtilis, Enterococcus faecalis, Micrococcus luteus, Staphylococcus aureus, Citrobacter freundii, Escherichia coli, Proteus mirabilis, Salmonella enterica ser. Enteritidis and Pseudomonas aeruginosa). For these purposes, phosphates differing in chain length were used. The tested concentrations were in the range of 0.1-2.0% (wt v(-1)) applied at the model conditions. In the majority of cases the visible inhibitory effect on the growth of observed microorganisms could be seen. Due to the chemical structure of salts and their dissociation both the pH values of cultivation broth and similarly the growth characteristics of bacterial strains were affected. The inhibition of above mentioned bacteria was apparently supported by this dissociation. Phosphates obviously made the development of most Gram-positive bacteria impossible. Especially Micrococcus luteus was extremely sensitive to the presence of these substances. On the other hand, Gram-negative bacteria seemed to be resistant to the phosphate incidence. The exemption clause from the tested salts was represented by a high alkaline trisodium phosphate. It should be pointed out that generally the most significant antibacterial effects were shown by polyphosphates HEXA68 and HEXA70, trisodium phosphate undecahydrate, tetrasodium pyrophosphate and finally trisodium phosphate. By comparing the inhibitory effects of various phosphate salts can be concluded that the antibacterial activity was not determined only by the condensation degree but there was also proved the dependence on pH values.

  17. Variation in n-Alkane Distributions of Modern Plants: Questioning Applications of n-Alkanes in Chemotaxonomy and Paleoecology

    NASA Astrophysics Data System (ADS)

    Bush, R. T.; McInerney, F. A.

    2010-12-01

    Long chain n-alkanes (n-C21 to n-C37) are synthesized as part of the epicuticular leaf wax of terrestrial plants and are among the most recognizable and widely used plant biomarkers. n-Alkane distributions have been utilized in previous studies on modern plant chemotaxonomy, testing whether taxa can be identified based on characteristic n-alkane profiles. Dominant n-alkanes (e.g. n-C27 or n-C31) have also been ascribed to major plant groups (e.g. trees or grasses respectively) and have been used in paleoecology studies to reconstruct fluctuations in plant functional types. However, many of these studies have been based on relatively few modern plant data; with the wealth of modern n-alkane studies, a more comprehensive analysis of n-alkanes in modern plants is now possible and can inform the usefulness of n-alkane distributions as paleoecological indicators. The work presented here is a combination of measurements made using plant leaves collected from the Chicago Botanic Garden and a compilation of published literature data from six continents. We categorized plants by type: angiosperms, gymnosperms, woody plants, forbs, grasses, ferns and pteridophytes, and mosses. We then quantified n-alkane distribution parameters such as carbon preference index (CPI), average chain length (ACL), and dispersion (a measure of the spread of the profile over multiple chain lengths) and used these to compare plant groups. Among all plants, one of the emergent correlations is a decrease in dispersion with increasing CPI. Within and among plant groups, n-alkane distributions show a very large range of variation, and the results show little or no correspondence between broad plant groups and a single dominant n-alkane or a ratio of n-alkanes. These findings are true both when data from six continents are combined and when plants from a given region are compared (North America). We also compared the n-alkane distributions of woody angiosperms, woody gymnosperms, and grasses with one

  18. Surface vibrational structure at alkane liquid/vapor interfaces.

    PubMed

    Esenturk, Okan; Walker, Robert A

    2006-11-07

    Broadband vibrational sum frequency spectroscopy (VSFS) has been used to examine the surface structure of alkane liquid/vapor interfaces. The alkanes range in length from n-nonane (C(9)H(20)) to n-heptadecane (C(17)H(36)), and all liquids except heptadecane are studied at temperatures well above their bulk (and surface) freezing temperatures. Intensities of vibrational bands in the CH stretching region acquired under different polarization conditions show systematic, chain length dependent changes. Data provide clear evidence of methyl group segregation at the liquid/vapor interface, but two different models of alkane chain structure can predict chain length dependent changes in band intensities. Each model leads to a different interpretation of the extent to which different chain segments contribute to the anisotropic interfacial region. One model postulates that changes in vibrational band intensities arise solely from a reduced surface coverage of methyl groups as alkane chain length increases. The additional methylene groups at the surface must be randomly distributed and make no net contribution to the observed VSF spectra. The second model considers a simple statistical distribution of methyl and methylene groups populating a three dimensional, interfacial lattice. This statistical picture implies that the VSF signal arises from a region extending several functional groups into the bulk liquid, and that the growing fraction of methylene groups in longer chain alkanes bears responsibility for the observed spectral changes. The data and resulting interpretations provide clear benchmarks for emerging theories of molecular structure and organization at liquid surfaces, especially for liquids lacking strong polar ordering.

  19. The roles of productivity and ecosystem size in determining food chain length in tropical terrestrial ecosystems.

    PubMed

    Young, Hillary S; McCauley, Douglas J; Dunbar, Robert B; Hutson, Michael S; Ter-Kuile, Ana Miller; Dirzo, Rodolfo

    2013-03-01

    Many different drivers, including productivity, ecosystem size, and disturbance, have been considered to explain natural variation in the length of food chains. Much remains unknown about the role of these various drivers in determining food chain length, and particularly about the mechanisms by which they may operate in terrestrial ecosystems, which have quite different ecological constraints than aquatic environments, where most food chain length studies have been thus far conducted. In this study, we tested the relative importance of ecosystem size and productivity in influencing food chain length in a terrestrial setting. We determined that (1) there is no effect of ecosystem size or productive space on food chain length; (2) rather, food chain length increases strongly and linearly with productivity; and (3) the observed changes in food chain length are likely achieved through a combination of changes in predator size, predator behavior, and consumer diversity along gradients in productivity. These results lend new insight into the mechanisms by which productivity can drive changes in food chain length, point to potential for systematic differences in the drivers of food web structure between terrestrial and aquatic systems, and challenge us to consider how ecological context may control the drivers that shape food chain length.

  20. Characterization of a CYP153 alkane hydroxylase gene in a Gram-positive Dietzia sp. DQ12-45-1b and its "team role" with alkW1 in alkane degradation.

    PubMed

    Nie, Yong; Liang, Jie-Liang; Fang, Hui; Tang, Yue-Qin; Wu, Xiao-Lei

    2014-01-01

    CYP153 and AlkB-like hydroxylases were recently discovered in Gram-positive alkane-degrading bacteria. However, it is unclear whether they cooperate with each other in alkane degradation as they do in Gram-negative bacteria. In this paper, we cloned the CYP153 gene from a representative Gram-positive alkane-degrading bacterium, Dietzia sp. DQ12-45-1b. The CYP153 gene transcription in Dietzia sp. DQ12-45-1b and heterologous expression in alkB gene knockout mutant strain Pseudomonas fluorescens KOB2∆1 both confirmed the functions of CYP153 on C6-C10 n-alkanes degradation, but not on longer chain-length n-alkanes. In addition, substrate-binding analysis of the purified CYP153 protein revealed different substrate affinities to C6-C16 n-alkanes, confirming n-alkanes binding to CYP153 protein. Along with AlkW1, an AlkB-like alkane hydroxylase in Dietzia sp. DQ12-45-1b, a teamwork pattern was found in n-alkane degradation, i.e. CYP153 was responsible for hydroxylating n-alkanes shorter than C10 while AlkW1 was responsible for those longer than C14. Further sequence analysis suggested that the high horizontal gene transfer (HGT) potential of CYP153 genes may be universal in Gram-positive alkane-degrading actinomycetes that contain both alkB and CYP153 genes.

  1. MR Elastography Studies of the 3D Force Chain Structure in Dense Granular Media: Distribution of Chain Lengths

    NASA Astrophysics Data System (ADS)

    Sanfratello, L.; Fukushima, E.

    2009-06-01

    We recently developed a novel extension of MR Elastograpy (MRE) to image the force chain structure within a dense 3D quasi-static granular assembly. Subsequently, computer codes and algorithms to determine the distribution of the force chain lengths, where a chain is taken to be a relatively straight section between branching points, were developed. Similar tools were used previously to analyze 2D photoelastic data and now have been expanded to analyze our most current 3D MRE force chain data. These investigations reveal that the distribution of the chain lengths in 3D decays exponentially, as was observed in 2D. The exponential decay of the length distribution is consistent with DEM simulation results of Peters, et al. We conclude that the decay length of this distribution is a meaningful quantitative measure that characterizes granular assemblies.

  2. Regulation of alkane oxidation in Pseudomonas putida.

    PubMed Central

    Grund, A; Shapiro, J; Fennewald, M; Bacha, P; Leahy, J; Markbreiter, K; Nieder, M; Toepfer, M

    1975-01-01

    We have studied the appearance of whole-cell oxidizing activity for n-alkanes and their oxidation products in strains of Pseudomonas putida carrying the OCT plasmid. Our results indicate that the OCT plasmid codes for inducible alkane-hydroxylating and primary alcohol-dehydrogenating activities and that the chromosome codes for constitutive oxidizing activities for primary alcohols, aliphatic aldehydes, and fatty acids. Mutant isolation confirms the presence of an alcohol dehydrogenase locus on the OCT plasmid and indicated the presence of multiple alcohol and aldehyde dehydrogenase loci on the P. putida chromosome. Induction tests with various compounds indicate that inducer recognition has specificity for chain length and can be affected by the degree of oxidation of the carbon chain. Some inducers are neither growth nor respiration substrates. Growth tests with and without a gratuitous inducer indicate that undecane is not a growth substrate because it does not induce alkane hydroxylase activity. Using a growth test for determining induction of the plasmid alcohol dehydrogenase it is possible to show that heptane induces this activity in hydroxylase-negative mutants. This suggests that unoxidized alkane molecules are the physiological inducers of both plasmid activities. PMID:1150626

  3. Adaptation of the hydrocarbonoclastic bacterium Alcanivorax borkumensis SK2 to alkanes and toxic organic compounds: a physiological and transcriptomic approach.

    PubMed

    Naether, Daniela J; Slawtschew, Slavtscho; Stasik, Sebastian; Engel, Maria; Olzog, Martin; Wick, Lukas Y; Timmis, Kenneth N; Heipieper, Hermann J

    2013-07-01

    The marine hydrocarbonoclastic bacterium Alcanivorax borkumensis is able to degrade mixtures of n-alkanes as they occur in marine oil spills. However, investigations of growth behavior and physiology of these bacteria when cultivated with n-alkanes of different chain lengths (C6 to C30) as the substrates are still lacking. Growth rates increased with increasing alkane chain length up to a maximum between C12 and C19, with no evident difference between even- and odd-numbered chain lengths, before decreasing with chain lengths greater than C19. Surface hydrophobicity of alkane-grown cells, assessed by determination of the water contact angles, showed a similar pattern, with maximum values associated with growth rates on alkanes with chain lengths between C11 and C19 and significantly lower values for cells grown on pyruvate. A. borkumensis was found to incorporate and modify the fatty acid intermediates generated by the corresponding n-alkane degradation pathway. Cells grown on distinct n-alkanes proved that A. borkumensis is able to not only incorporate but also modify fatty acid intermediates derived from the alkane degradation pathway. Comparing cells grown on pyruvate with those cultivated on hexadecane in terms of their tolerance toward two groups of toxic organic compounds, chlorophenols and alkanols, representing intensely studied organic compounds, revealed similar tolerances toward chlorophenols, whereas the toxicities of different n-alkanols were significantly reduced when hexadecane was used as a carbon source. As one adaptive mechanism of A. borkumensis to these toxic organic solvents, the activity of cis-trans isomerization of unsaturated fatty acids was proven. These findings could be verified by a detailed transcriptomic comparison between cultures grown on hexadecane and pyruvate and including solvent stress caused by the addition of 1-octanol as the most toxic intermediate of n-alkane degradation.

  4. Understanding the factors affecting the activation of alkane by Cp'Rh(CO)2 (Cp' = Cp or Cp*).

    PubMed

    George, Michael W; Hall, Michael B; Jina, Omar S; Portius, Peter; Sun, Xue-Zhong; Towrie, Michael; Wu, Hong; Yang, Xinzheng; Zaric, Snezana D

    2010-11-23

    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.

  5. Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus

    PubMed Central

    Khelifi, Nadia; Amin Ali, Oulfat; Roche, Philippe; Grossi, Vincent; Brochier-Armanet, Céline; Valette, Odile; Ollivier, Bernard; Dolla, Alain; Hirschler-Réa, Agnès

    2014-01-01

    The thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain VC-16 (DSM 4304), which is known to oxidize fatty acids and n-alkenes, was shown to oxidize saturated hydrocarbons (n-alkanes in the range C10–C21) with thiosulfate or sulfate as a terminal electron acceptor. The amount of n-hexadecane degradation observed was in stoichiometric agreement with the theoretically expected amount of thiosulfate reduction. One of the pathways used by anaerobic microorganisms to activate alkanes is addition to fumarate that involves alkylsuccinate synthase as a key enzyme. A search for genes encoding homologous enzymes in A. fulgidus identified the pflD gene (locus-tag AF1449) that was previously annotated as a pyruvate formate lyase. A phylogenetic analysis revealed that this gene is of bacterial origin and was likely acquired by A. fulgidus from a bacterial donor through a horizontal gene transfer. Based on three-dimensional modeling of the corresponding protein and molecular dynamic simulations, we hypothesize an alkylsuccinate synthase activity for this gene product. The pflD gene expression was upregulated during the growth of A. fulgidus on an n-alkane (C16) compared with growth on a fatty acid. Our results suggest that anaerobic alkane degradation in A. fulgidus may involve the gene pflD in alkane activation through addition to fumarate. These findings highlight the possible importance of hydrocarbon oxidation at high temperatures by A. fulgidus in hydrothermal vents and the deep biosphere. PMID:24763368

  6. Dietary accumulation and quantitative structure-activity relationships for depuration and biotransformation of short (C{sub 10}), medium (C{sub 14}), and long (C{sub 18}) carbon-chain polychlorinated alkanes by juvenile rainbow trout (Oncorhynchus mykiss)

    SciTech Connect

    Fisk, A.T.; Tomy, G.T.; Cymbalisty, C.D.; Muir, D.C.G.

    2000-06-01

    Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to three [{sup 14}C]-polychlorinated alkanes at nominal concentrations of 1.5 and 15 {micro}g/g for 40 d, followed by 160 d of clean food, to measure bioaccumulation parameters and biotransformation. These PCSs are identical in carbon-chain length and chlorine content to industrial chlorinated paraffin products, although their method of synthesis differs from that of chlorinated paraffin products. Half-lives ranged from 26 to 91 d, biomagnification factors ranged from 0.9 to 2.8, and both exhibited increasing trends with increasing carbon-chain length. Data from this work and others on PCAs were used to determine biotransformation rates and to examine quantitative structure-activity relationships for bioaccumulation and biotransformation. Quantitative structure-activity relationships developed for half-life and biomagnification factor showed positive linear relationships with the number of carbon atoms, or chlorine atoms, of total carbon and chlorine atoms, and log K{sub ow}. The PCA biotransformation rates (per day) ranged from -0.00028 to 8.4 and exhibited negative relationships with the number of carbon atoms, of chlorine atoms, of total carbon and chlorine atoms, and log K{sub ow}. Results suggest that PCAs with a total number of carbon and chlorine atoms between 22 and 30 are slowly, or are not, biotransformed in juvenile rainbow trout. Increasing carbon-chain length and chlorine content result in greater bioaccumulation of PCAs by reducing partition-based (i.e., diffusion) and metabolic (i.e., biotransformation) elimination processes. High bioaccumulation potential and low biotransformation rates of medium (C{sub 14--18}) and long (C{sub 18--30}) carbon-chain PCAs and highly chlorinated PCAs indicate that information is needed regarding the environmental concentrations of these PCAs in aquatic food chains.

  7. Interfacial properties of semifluorinated alkane diblock copolymers

    NASA Astrophysics Data System (ADS)

    Pierce, Flint; Tsige, Mesfin; Borodin, Oleg; Perahia, Dvora; Grest, Gary S.

    2008-06-01

    The liquid-vapor interfacial properties of semifluorinated linear alkane diblock copolymers of the form F3C(CF2)n-1(CH2)m-1CH3 are studied by fully atomistic molecular dynamics simulations. The chemical composition and the conformation of the molecules at the interface are identified and correlated with the interfacial energies. A modified form of the Optimized Parameter for Liquid Simulation All-Atom (OPLS-AA) force field of Jorgensen and co-workers [J. Am. Chem. Soc. 106, 6638 (1984); 118, 11225 (1996); J. Phys. Chem. A 105, 4118 (2001)], which includes specific dihedral terms for H-F blocks-and corrections to the H-F nonbonded interaction, is used together with a new version of the exp-6 force field developed in this work. Both force fields yield good agreement with the available experimental liquid density and surface tension data as well as each other over significant temperature ranges and for a variety of chain lengths and compositions. The interfacial regions of semifluorinated alkanes are found to be rich in fluorinated groups compared to hydrogenated groups, an effect that decreases with increasing temperature but is independent of the fractional length of the fluorinated segments. The proliferation of fluorine at the surface substantially lowers the surface tension of the diblock copolymers, yielding values near those of perfluorinated alkanes and distinct from those of protonated alkanes of the same chain length. With decreasing temperatures within the liquid state, chains are found to preferentially align perpendicular to the interface, as previously seen.

  8. An experimental disturbance alters fish size structure but not food chain length in streams.

    PubMed

    Walters, Annika W; Post, David M

    2008-12-01

    Streams experience frequent natural disturbance and are undergoing considerable anthropogenic disturbance due to dam construction and water diversion. Disturbance is known to impact community structure, but its effect on food chain length is still a matter of considerable debate. Theoretical models show that longer food chains are less resilient to disturbance, so food chain length is predicted to be shorter following a disturbance event. Here we experimentally test the effect of disturbance on food chain length in streams by diverting stream flow. We found that our experimental low-flow disturbance did not alter food chain length. We did see an effect on body-size structure in our food webs suggesting that food chain length may be an insensitive indicator of disturbance. We suggest that habitat heterogeneity and food web complexity buffer the effect of disturbance on food chain length. The theoretical predictions of disturbance on food chain length are only likely to be seen in homogeneous systems that closely approximate the linear food chains the models are based upon.

  9. Effects of carbon atom parity and alkyl side chain length on the crystallization and morphology of biscarbamates, a set of model compounds for polyurethanes.

    PubMed

    Khan, Mostofa Kamal; Sundararajan, Pudupadi R

    2011-07-14

    Solid state morphology and crystallization behavior of a homologous series of biscarbamate molecules having varying alkyl side chain lengths with different carbon atom parity were investigated. These are model compounds for polyurethanes. We synthesized a set of biscarbamates with double hydrogen bonding motifs separated by a (CH(2))(6) spacer and with alkyl side chains of various lengths ranging from C(3) to C(18) at the ends. Thermal analysis showed an odd-even alternation in their melting temperatures and heats of fusion, with the odd number of carbon atoms in the side chain having higher melting temperatures and heats of fusion than the even numbered ones, in contrast to the case of n-alkanes. The effect of carbon atom parity in the alkyl side chains on the spherulite size, spherulite growth rate, and isothermal crystallization kinetics was studied. Although the spherulite size increases with the alkyl side chain length, the maximum is seen at an intermediate length and not with a short or long alkyl chain for both the odd and even series. Along this series of molecules, a maximum in spherulite size, spherulite growth rate, and rate of crystallization is seen for C(7)C(6) (odd series) and C(8)C(6) (even series) biscarbamates. There is a significant difference in spherulite size with respect to carbon atom parity in the alkyl side chains as well as sample preparation protocol. Hence the length of the alkyl side chain, carbon atom parity in the alkyl side chains, and the sample preparation protocol (i.e., quenching versus slow cooling) play an important role in the morphology of these molecules. We rationalize this behavior with the relative contributions of hydrogen bonding and van der Waals forces as discerned from IR spectroscopy. While the van der Waals interaction increases with the alkyl side chain length in this series, the hydrogen bond contribution remains invariant. The rate of crystallization follows the trend seen with the spherulitic growth. The

  10. Palladium Catalysts for Fatty Acid Deoxygenation: Influence of the Support and Fatty Acid Chain Length on Decarboxylation Kinetics

    SciTech Connect

    Ford, JP; Immer, JG; Lamb, HH

    2012-03-29

    Supported metal catalysts containing 5 wt% Pd on silica, alumina, and activated carbon were evaluated for liquid-phase deoxygenation of stearic (octadecanoic), lauric (dodecanoic), and capric (decanoic) acids under 5 % H-2 at 300 A degrees C and 15 atm. On-line quadrupole mass spectrometry (QMS) was used to measure CO + CO2 yield, CO2 selectivity, H-2 consumption, and initial decarboxylation rate. Post-reaction analysis of liquid products by gas chromatography was used to determine n-alkane yields. The Pd/C catalyst was highly active and selective for stearic acid (SA) decarboxylation under these conditions. In contrast, SA deoxygenation over Pd/SiO2 occurred primarily via decarbonylation and at a much slower rate. Pd/Al2O3 exhibited high initial SA decarboxylation activity but deactivated under the test conditions. Similar CO2 selectivity patterns among the catalysts were observed for deoxygenation of lauric and capric acids; however, the initial decarboxylation rates tended to be lower for these substrates. The influence of alkyl chain length on deoxygenation kinetics was investigated for a homologous series of C-10-C-18 fatty acids using the Pd/C catalyst. As fatty acid carbon number decreases, reaction time and H-2 consumption increase, and CO2 selectivity and initial decarboxylation rate decrease. The increase in initial decarboxylation rates for longer chain fatty acids is attributed to their greater propensity for adsorption on the activated carbon support.

  11. Novel long-chain anteiso-alkanes and anteiso-alkanoic acids in Antarctic rocks colonized by living and fossil cryptoendolithic microorganisms.

    PubMed

    Matsumoto, G I; Friedmann, E I; Watanuki, K; Ocampo-Friedmann, R

    1992-01-01

    Saponified extracts of rock samples colonized by cryptoendolithic microbial communities from the McMurdo Dry Valleys of Southern Victoria Land, Antarctica, were separated into hydrocarbon and fatty acid fractions by silica gel column chromatography. Hydrocarbons and methyl esters of fatty acids were analyzed by capillary gas chromatography-mass spectrometry. Unusually, a suite of long-chain anteiso-alkanes (a-C20 to a-C30) and anteiso-alkanoic acids (a-C20 to a-C30) were detected in many samples, together with straight-chain, branched and/or cyclic and acyclic isoprenoid compounds. These novel compounds are probably derived from unidentified heterotrophic bacteria or symbiotic processes in a unique microbial community in the Antarctic cold desert and suggest the occurrence of a special biosynthetic pathway. Long-chain anteiso-alkanes are probably formed through microbial decarboxylation of corresponding anteiso-alkanoic acids. They may serve as new biomarkers in environmental and geochemical studies.

  12. Novel long-chain anteiso-alkanes and anteiso-alkanoic acids in Antarctic rocks colonized by living and fossil cryptoendolithic microorganisms

    NASA Technical Reports Server (NTRS)

    Matsumoto, G. I.; Friedmann, E. I.; Watanuki, K.; Ocampo-Friedmann, R.

    1992-01-01

    Saponified extracts of rock samples colonized by cryptoendolithic microbial communities from the McMurdo Dry Valleys of Southern Victoria Land, Antarctica, were separated into hydrocarbon and fatty acid fractions by silica gel column chromatography. Hydrocarbons and methyl esters of fatty acids were analyzed by capillary gas chromatography-mass spectrometry. Unusually, a suite of long-chain anteiso-alkanes (a-C20 to a-C30) and anteiso-alkanoic acids (a-C20 to a-C30) were detected in many samples, together with straight-chain, branched and/or cyclic and acyclic isoprenoid compounds. These novel compounds are probably derived from unidentified heterotrophic bacteria or symbiotic processes in a unique microbial community in the Antarctic cold desert and suggest the occurrence of a special biosynthetic pathway. Long-chain anteiso-alkanes are probably formed through microbial decarboxylation of corresponding anteiso-alkanoic acids. They may serve as new biomarkers in environmental and geochemical studies.

  13. Vibrational Spectroscopic Study of Imidazolium Dicationic Ionic Liquids: Effect of Cation Alkyl Chain Length

    NASA Astrophysics Data System (ADS)

    Moumene, T.; Belarbi, E. H.; Haddad, B.; Villemin, D.; Abbas, O.; Khelifa, B.; Bresson, S.

    2016-05-01

    Two new dicationic ionic liquids were synthesized: bis-methyl imidazolium methylidene hexafluorophosphate [M(CH2)IM2 +][2PF 6 - ] and bis-methyl imidazolium propylidene hexafluorophosphate [M(CH2)3IM2 +][2PF 6 - ]. Their structures were identified by H, C, P, F NMR, FTIR/ATR, and FT-Raman spectroscopies in order to study the effect of cation alkyl chain length on vibration behaviors. Several changes were recorded, which were related to alkyl chain length. A frequency shift was observed in some modes while others remained insensitive. A greater number of peaks was found in the FTIR/ATR spectra and the FT-Raman spectra with increasing alkyl chain length, which indicated that chain length influences the N-C connection twisting. More peaks with strong intensity appeared for longer alkyl chain lengths.

  14. Modular and selective biosynthesis of gasoline-range alkanes.

    PubMed

    Sheppard, Micah J; Kunjapur, Aditya M; Prather, Kristala L J

    2016-01-01

    Typical renewable liquid fuel alternatives to gasoline are not entirely compatible with current infrastructure. We have engineered Escherichia coli to selectively produce alkanes found in gasoline (propane, butane, pentane, heptane, and nonane) from renewable substrates such as glucose or glycerol. Our modular pathway framework achieves carbon-chain extension by two different mechanisms. A fatty acid synthesis route is used to generate longer chains heptane and nonane, while a more energy efficient alternative, reverse-β-oxidation, is used for synthesis of propane, butane, and pentane. We demonstrate that both upstream (thiolase) and intermediate (thioesterase) reactions can act as control points for chain-length specificity. Specific free fatty acids are subsequently converted to alkanes using a broad-specificity carboxylic acid reductase and a cyanobacterial aldehyde decarbonylase (AD). The selectivity obtained by different module pairings provides a foundation for tuning alkane product distribution for desired fuel properties. Alternate ADs that have greater activity on shorter substrates improve observed alkane titer. However, even in an engineered host strain that significantly reduces endogenous conversion of aldehyde intermediates to alcohol byproducts, AD activity is observed to be limiting for all chain lengths. Given these insights, we discuss guiding principles for pathway selection and potential opportunities for pathway improvement.

  15. Driven polymer translocation through a cylindrical nanochannel: interplay between the channel length and the chain length

    NASA Astrophysics Data System (ADS)

    Yong, Huaisong; Wang, Yilin; Yuan, Shichen; Xu, Bi; Luo, Kaifu

    Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation through a nanochannel embedded in two dimensions under an applied external field. We examine the translocation time for various ratio of the channel length $L$ to the polymer length $N$. For short channels $L\\ll N$, the translocation time $\\tau \\sim N^{1+\

  16. Alkyl chain length dependence of the field-effect mobility in novel anthracene derivatives.

    PubMed

    Back, Jang Yeol; An, Tae Kyu; Cheon, Ye Rim; Cha, Hyojung; Jang, Jaeyoung; Kim, Yebyeol; Baek, Yonghwa; Chung, Dae Sung; Kwon, Soon-Ki; Park, Chan Eon; Kim, Yun-Hi

    2015-01-14

    We report six asymmetric alkylated anthracene-based molecules with different alkyl side chain lengths for use in organic field-effect transistors (OFETs). Alkyl side chains can potentially improve the solubility and processability of anthracene derivatives. The crystallinity and charge mobility of the anthracene derivatives may be improved by optimizing the side chain length. The highest field-effect mobility of the devices prepared here was 0.55 cm(2)/(V s), for 2-(p-pentylphenylethynyl)anthracene (PPEA). The moderate side chain length appeared to be optimal for promoting self-organization among asymmetric anthracene derivatives in OFETs, and was certainly better than the short or long alkyl side chain lengths, as confirmed by X-ray diffraction measurements.

  17. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir.

    PubMed

    Feng, Lu; Wang, Wei; Cheng, Jiansong; Ren, Yi; Zhao, Guang; Gao, Chunxu; Tang, Yun; Liu, Xueqian; Han, Weiqing; Peng, Xia; Liu, Rulin; Wang, Lei

    2007-03-27

    The complete genome sequence of Geobacillus thermodenitrificans NG80-2, a thermophilic bacillus isolated from a deep oil reservoir in Northern China, consists of a 3,550,319-bp chromosome and a 57,693-bp plasmid. The genome reveals that NG80-2 is well equipped for adaptation into a wide variety of environmental niches, including oil reservoirs, by possessing genes for utilization of a broad range of energy sources, genes encoding various transporters for efficient nutrient uptake and detoxification, and genes for a flexible respiration system including an aerobic branch comprising five terminal oxidases and an anaerobic branch comprising a complete denitrification pathway for quick response to dissolved oxygen fluctuation. The identification of a nitrous oxide reductase gene has not been previously described in Gram-positive bacteria. The proteome further reveals the presence of a long-chain alkane degradation pathway; and the function of the key enzyme in the pathway, the long-chain alkane monooxygenase LadA, is confirmed by in vivo and in vitro experiments. The thermophilic soluble monomeric LadA is an ideal candidate for treatment of environmental oil pollutions and biosynthesis of complex molecules.

  18. Hyaluronan derivatives: Alkyl chain length boosts viscoelastic behavior to depolymerization.

    PubMed

    Pavan, Mauro; Galesso, Devis; Menon, Giampaolo; Renier, Davide; Guarise, Cristian

    2013-09-12

    Five amide derivatives of Hyaluronic Acid (HA) were synthesized with C8, C12, C15, C16 and C18 linear alkyl-amines. These polymers (Hyadd) were tested against thermal, oxidative and hyaluronidase degradation by means of rheological experiments and SEC analysis and compared to non-modified HA. First of all, no free hexadecylamine was detected in the treated samples, meaning that under these stressing conditions only cleavage of glycosidic bonds occurs. Then, viscoelastic properties were assessed during thermal degradation and their variation as a function of time was expressed by means of a decay constant k(G'): while no significant difference in the decrease rate was observed between Hyadd-C8 and Hyadd-C12, a marked stabilization of viscoelastic properties during thermal treatment was detected for Hyadd-C15, Hyadd-C16 and Hyadd-C18. On the other hand, no difference was observed between the MW decrease rate (kMW decay constant) of HA and Hyadd-C12 to-C18; the depolymerization takes place on the backbone of the polymers independently whether they are derivatized or not, but longer alkyl chains lead to higher viscoelasticity in the depolymerized products. Finally, both oxidative and enzymatic degradation were carried out analyzing the changes in elastic modulus and in dynamic viscosity: once again, the amide side chain came out with similar behavior to chemical cross-linked HA (HBC) and with improved performances respect to linear HA in terms of preservation of viscoelasticity after chain depolymerization.

  19. The role of ceramide chain length distribution on the barrier properties of the skin lipid membranes.

    PubMed

    Mojumdar, E H; Kariman, Z; van Kerckhove, L; Gooris, G S; Bouwstra, J A

    2014-10-01

    The skin barrier function is provided by the stratum corneum (SC). The lipids in the SC are composed of three lipid classes: ceramides (CERs), cholesterol (CHOL) and free fatty acids (FFAs) which form two crystalline lamellar structures. In the present study, we investigate the effect of CER chain length distribution on the barrier properties of model lipid membranes mimicking the lipid composition and organization of SC. The membranes were prepared with either isolated pig CERs (PCERs) or synthetic CERs. While PCERs have a wide chain length distribution, the synthetic CERs are quite uniform in chain length. The barrier properties were examined by means of permeation studies using hydrocortisone as a model drug. Our studies revealed a reduced barrier in lipid membranes prepared with PCERs compared to synthetic CERs. Additional studies revealed that a wider chain length distribution of PCERs results in an enhanced hexagonal packing and increased conformational disordering of the lipid tails compared to synthetic CERs, while the lamellar phases did not change. This demonstrates that the chain length distribution affects the lipid barrier by reducing the lipid ordering and density within the lipid lamellae. In subsequent studies, the effect of increased levels of FFAs or CERs with a long acyl chain in the PCERs membranes was also studied. These changes in lipid composition enhanced the level of orthorhombic packing, reduced the conformational disordering and increased the barrier of the lipid membranes. In conclusion, the CER chain length distribution is an important key factor for maintaining a proper barrier.

  20. Thiolases of Escherichia coli: purification and chain length specificities.

    PubMed Central

    Feigenbaum, J; Schulz, H

    1975-01-01

    The presence of only one thiolase (EC 2.3.1.9) in wild-type Escherichia coli induced for enzymes of beta oxidation was demonstrated. A different thiolase was shown to be present in a mutant constitutive for the enzymes of butyrate degradation. The two thiolases were purified to near homogeneity by a simple two-step procedure and were found to be associated with different proteins as shown by gel electrophoresis. The thiolase isolated from induced wild-type Escherichia coli cell was active on beta-ketoacyl-coenzyme A derivatives containing 4 to 16 carbons, but exhibited optimal activity with medium-chain substrates. In contrast, the thiolase isolated from the constitutive mutant was shown to be specific for acetoacetyl-coenzyme A. PMID:236278

  1. On the partitioning of benzene between water and n-alkanes

    NASA Astrophysics Data System (ADS)

    Graziano, Giuseppe

    2010-02-01

    The magnitude of the work of cavity creation increases with the n-alkane chain-length due to the volume packing density increase, in line with expectations based on correlations with surface tension, cohesive energy density, and the inverse of isothermal compressibility. Also the magnitude of the Gibbs energy gain to turn on benzene-alkane attractive interactions increases with the n-alkane chain-length, but to a lesser extent than the work of cavity creation, thus benzene solubility, under Ben-Naim standard conditions, slightly decreases on lengthening the alkyl chain, in line with experimental data. It is unjustified to apply a Flory-Huggins correction to the Ben-Naim standard Gibbs energy of transfer.

  2. A molecule that detects the length of DNA by using chain fluctuations

    NASA Astrophysics Data System (ADS)

    Iwasa, Kuni H.; Florescu, Ana Maria

    2016-05-01

    A class of nucleosome remodelling motors translocates the nucleosomes, to which they are attached, towards the middle of the DNA chain in the presence of ATP during in vitro experiments. This biological activity is likely based on a physical mechanism for detecting and comparing the lengths of the flanking polymer chains. Here we propose that a pivoting mode of DNA fluctuations near the surface of the nucleosome coupled with a binding reaction with a DNA binding site of the motor provides a physical basis for length detection. Since the mean frequency of the fluctuations is higher for a shorter chain than a longer one due to its lower drag coefficient, a shorter chain has a higher rate of receptor binding, which triggers the ATP-dependent activity of the remodelling motor. The dimerisation of these units allows the motor to compare the length of the flanking DNA chains, enabling the translocation of the nucleosome towards the centre of the DNA.

  3. Effects of odd-even side chain length of alkyl-substituted diphenylbithiophenes on first monolayer thin film packing structure.

    PubMed

    Akkerman, Hylke B; Mannsfeld, Stefan C B; Kaushik, Ananth P; Verploegen, Eric; Burnier, Luc; Zoombelt, Arjan P; Saathoff, Jonathan D; Hong, Sanghyun; Atahan-Evrenk, Sule; Liu, Xueliang; Aspuru-Guzik, Alán; Toney, Michael F; Clancy, Paulette; Bao, Zhenan

    2013-07-31

    Because of their preferential two-dimensional layer-by-layer growth in thin films, 5,5'bis(4-alkylphenyl)-2,2'-bithiophenes (P2TPs) are model compounds for studying the effects of systematic chemical structure variations on thin-film structure and morphology, which in turn, impact the charge transport in organic field-effect transistors. For the first time, we observed, by grazing incidence X-ray diffraction (GIXD), a strong change in molecular tilt angle in a monolayer of P2TP, depending on whether the alkyl chain on the P2TP molecules was of odd or even length. The monolayers were deposited on densely packed ultrasmooth self-assembled alkane silane modified SiO2 surfaces. Our work shows that a subtle change in molecular structure can have a significant impact on the molecular packing structure in thin film, which in turn, will have a strong impact on charge transport of organic semiconductors. This was verified by quantum-chemical calculations that predict a corresponding odd-even effect in the strength of the intermolecular electronic coupling.

  4. Singular eigenstates in the even(odd) length Heisenberg spin chain

    NASA Astrophysics Data System (ADS)

    Ranjan Giri, Pulak; Deguchi, Tetsuo

    2015-05-01

    We study the implications of the regularization for the singular solutions on the even(odd) length spin-1/2 XXX chains in some specific down-spin sectors. In particular, the analytic expressions of the Bethe eigenstates for three down-spin sector have been obtained along with their numerical forms in some fixed length chains. For an even-length chain if the singular solutions \\{{{λ }α }\\} are invariant under the sign changes of their rapidities \\{{{λ }α }\\}=\\{-{{λ }α }\\}, then the Bethe ansatz equations are reduced to a system of (M-2)/2((M-3)/2) equations in an even (odd) down-spin sector. For an odd N length chain in the three down-spin sector, it has been analytically shown that there exist singular solutions in any finite length of the spin chain of the form N=3(2k+1) with k=1,2,3,\\cdots . It is also shown that there exist no singular solutions in the four down-spin sector for some odd-length spin-1/2 XXX chains.

  5. Long-Chain Aldehyde Dehydrogenase That Participates in n-Alkane Utilization and Wax Ester Synthesis in Acinetobacter sp. Strain M-1

    PubMed Central

    Ishige, Takeru; Tani, Akio; Sakai, Yasuyoshi; Kato, Nobuo

    2000-01-01

    A long-chain aldehyde dehydrogenase, Ald1, was found in a soluble fraction of Acinetobacter sp. strain M-1 cells grown on n-hexadecane as a sole carbon source. The gene (ald1) was cloned from the chromosomal DNA of the bacterium. The open reading frame of ald1 was 1,512 bp long, corresponding to a protein of 503 amino acid residues (molecular mass, 55,496 Da), and the deduced amino acid sequence showed high similarity to those of various aldehyde dehydrogenases. The ald1 gene was stably expressed in Escherichia coli, and the gene product (recombinant Ald1 [rAld1]) was purified to apparent homogeneity by gel electrophoresis. rAld1 showed enzyme activity toward n-alkanals (C4 to C14), with a preference for longer carbon chains within the tested range; the highest activity was obtained with tetradecanal. The ald1 gene was disrupted by homologous recombination on the Acinetobacter genome. Although the ald1 disruptant (ald1Δ) strain still had the ability to grow on n-hexadecane to some extent, its aldehyde dehydrogenase activity toward n-tetradecanal was reduced to half the level of the wild-type strain. Under nitrogen-limiting conditions, the accumulation of intracellular wax esters in the ald1Δ strain became much lower than that in the wild-type strain. These and other results imply that a soluble long-chain aldehyde dehydrogenase indeed plays important roles both in growth on n-alkane and in wax ester formation in Acinetobacter sp. strain M-1. PMID:10919810

  6. Certain Chemical Substances Containing Varying Carbon Chain Lengths (Alkyl Ranges Using the Cx-y Notation) on the TSCA Inventory

    EPA Pesticide Factsheets

    This paper explains the conventions that are applied to certain listings of chemical substances containing ranges of alkyl chain lengths (i.e., carbon chains of varying lengths) for chemical substances on the Toxic Substances Control Act (TSCA)

  7. Bulk and Compound-Specific Isotope Analysis of Long-Chain, n-alkanes From a 85-kyr Core From Lake Peten Itza, Guatemala

    NASA Astrophysics Data System (ADS)

    Mays, J. L.; Brenner, M.; Bush, M. B.; Correa, A.; Curtis, J. H.; Hodell, D. A.

    2007-12-01

    Drill cores obtained from Lake Petén Itzá, Guatemala, contain a ~85-kyr record of terrestrial climate from lowland Central America. Variations in sediment lithology suggest rapid changes in precipitation during the last glacial and deglacial periods. Previous work in nearby Lake Quexil demonstrated the utility of using the carbon isotopic compositions of leaf wax n-alkanes to infer changes in terrestrial vegetation (Huang et al., 2001). Here we report carbon isotopes of bulk organic and long-chain n-alkanes in 60 samples to reconstruct changes in the relative proportion of C3 and C4 biomass in the watershed under changing climate and atmospheric CO2 conditions during the past 85 kyrs. Compound-specific carbon isotope results are compared directly with pollen analysis from the same samples. Huang, Y., F.A. Street-Perrott, S.E. Metcalfe, M. Brenner, M. Moreland, and K.H. Freeman. 2001. Climate change as the dominant control on glacial-interglacial variations in C3 and C4 plant abundance. Science 293:1647-1651.

  8. Evaluation of Microbial Diversity in Wetland through Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP)

    DTIC Science & Technology

    2006-06-01

    MICROBIAL DIVERSITY IN WETLANDS THROUGH POLYMERASE CHAIN REACTION ( PCR ) AND RESTRICTION FRAGMENT LENGTH POLYMORPHISM ( RFLP ) THESIS Presented to the...MICROBIAL DIVERSITY IN WETLANDS THROUGH POLYMERASE CHAIN REACTION ( PCR ) AND RESTRICTION FRAGMENT LENGTH POLYMORPHISM ( RFLP ) Gregory K. Joseph, B.A...AFIT/GES/ENV/06J-02 EVALUATION OF MICROBIAL DIVERSITY IN WETLANDS THROUGH POLYMERASE CHAIN REACTION ( PCR ) AND RESTRICTION FRAGMENT LENGTH

  9. Effect of the chain length on the thermal and analytical properties of laterally biforked nematogens.

    PubMed

    Dahmane, Mohamed; Athman, Fatiha; Sebih, Saïd; Guermouche, Moulay-Hassane; Bayle, Jean-Pierre; Boudah, Soulimane

    2010-10-15

    Three laterally substituted liquid crystals were synthesized in order to investigate the effect of a lateral biforked chain on the thermal and analytical properties. The mesogenic molecules have the same core containing four aromatic rings connected by two ester and one diazo linkages, they differ by the length of one chain within the lateral biforked substituent. The phase transition temperatures were obtained by polarized light microscopy and differential scanning calorimetry (DSC). The clearing temperature and the nematic range decrease with increasing length of the lateral biforked chain. The stationary phases derived from these nematogens provide excellent resolution of various classes of compounds, including aromatic hydrocarbons (AH), substituted benzenes, polycyclic aromatic hydrocarbons (PAH), phenols and volatile organic compounds (VOC) present in the essential oils. The selectivities of the stationary phases were found to decrease according to the length of the side chain.

  10. Application of headspace solid-phase microextraction followed by gas chromatography-mass spectrometry to determine short-chain alkane monocarboxylic acids in aqueous samples.

    PubMed

    Banel, Anna; Wasielewska, Marta; Zygmunt, Bogdan

    2011-03-01

    In this study, a procedure was developed to determine short-chain alkane monocarboxylic acids (SCMAs) in aqueous samples using headspace solid-phase microextraction (HS-SPME) followed by gas chromatography (GC) coupled with mass spectrometry (MS). A Stabilwax-DA capillary column (30 m × 0.32-mm inner diameter, 0.50-μm film thickness) was used for GC separation and a 60-μm poly(ethylene glycol) fiber was used to isolate SCMAs from water and introduce them into the gas chromatograph. Parameters of HS-SPME, analyte desorption, and GC-MS analysis were selected and an analytical procedure was proposed. Limits of quantitation were on the order of about 0.2 mg L(-1). As an example of the application of the procedure, SCAMs were determined in municipal wastewater at different steps of treatment.

  11. Cloning and expression of three ladA-type alkane monooxygenase genes from an extremely thermophilic alkane-degrading bacterium Geobacillus thermoleovorans B23.

    PubMed

    Boonmak, Chanita; Takahashi, Yasunori; Morikawa, Masaaki

    2014-05-01

    An extremely thermophilic bacterium, Geobacillus thermoleovorans B23, is capable of degrading a broad range of alkanes (with carbon chain lengths ranging between C11 and C32) at 70 °C. Whole-genome sequence analysis revealed that unlike most alkane-degrading bacteria, strain B23 does not possess an alkB-type alkane monooxygenase gene. Instead, it possesses a cluster of three ladA-type genes, ladAαB23, ladAβB23, and ladB B23, on its chromosome, whose protein products share significant amino acid sequence identities, 49.8, 34.4, and 22.7 %, respectively, with that of ladA alkane monooxygenase gene found on a plasmid of Geobacillus thermodetrificans NG 80-2. Each of the three genes, ladAαB23, ladAβB23, and ladB B23, was heterologously expressed individually in an alkB1 deletion mutant strain, Pseudomonas fluorescens KOB2Δ1. It was found that all three genes were functional in P. fluorescens KOB2Δ1, and partially restored alkane degradation activity. In this study, we suggest that G. thermoleovorans B23 utilizes multiple LadA-type alkane monooxygenases for the degradation of a broad range of alkanes.

  12. Interaction between n-Alkane Chains:  Applicability of the Empirically Corrected Density Functional Theory for Van der Waals Complexes.

    PubMed

    Goursot, Annick; Mineva, Tzonka; Kevorkyants, Ruslan; Talbi, Dahbia

    2007-05-01

    The geometries, interaction energies, and vibrational frequencies of a series of n-alkane dimers up to dodecane have been calculated using density functional theory (DFT) augmented with an empirical dispersion energy term (DFT-D). The results obtained from this method for ethane to hexane dimers are compared with those provided by the MP2 level of theory and the combined Gaussian-3 approach with CCSD(T) being the highest correlation method [G3(CCSD(T))]. Two types of dimer isomers have been studied. The most stable isomers have the two carbon chains in parallel planes, whereas the second ones have the two carbon chains in the same plane. Butane is found to be the shortest carbon chain to form dimers with similar properties, that is, a constant average distance between the monomer carbon skeletons, a similar increment per CH2 unit for the dimer interaction energy, and comparable dimer symmetric stretching frequencies. The values and trends obtained from the DFT-D approach agree very well with those obtained from MP2 for the geometries and vibrational frequencies and from the G3(CCSD(T)) method for the energies, validating the use of DFT-D for the study of large hydrocarbon complexes.

  13. Regulation of chain length in two diatoms as a growth-fragmentation process

    NASA Astrophysics Data System (ADS)

    Gherardi, Marco; Amato, Alberto; Bouly, Jean-Pierre; Cheminant, Soizic; Ferrante, Maria Immacolata; d'Alcalá, Maurizio Ribera; Iudicone, Daniele; Falciatore, Angela; Cosentino Lagomarsino, Marco

    2016-08-01

    Chain formation in diatoms is relevant because of several aspects of their adaptation to the ecosystem. However, the tools to quantify the regulation of their assemblage and infer specific mechanisms in a laboratory setting are scarce. To address this problem, we define an approach based on a statistical physics model of chain growth and separation in combination with experimental evaluation of chain-length distributions. Applying this combined analysis to data from Chaetoceros decipiens and Phaeodactylum tricornutum, we find that cells of the first species control chain separation, likely through a cell-to-cell communication process, while the second species only modulates the separation rate. These results promote quantitative methods for characterizing chain formation in several chain-forming species and in diatoms in particular.

  14. Understanding the factors affecting the activation of alkane by Cp′Rh(CO)2 (Cp′ = Cp or Cp*)

    PubMed Central

    George, Michael W.; Hall, Michael B.; Jina, Omar S.; Portius, Peter; Sun, Xue-Zhong; Towrie, Michael; Wu, Hong; Yang, Xinzheng; Zarić, Snežana D.

    2010-01-01

    Fast time-resolved infrared spectroscopic measurements have allowed precise determination of the rates of activation of alkanes by Cp′Rh(CO) (Cp′ = η5-C5H5 or η5-C5Me5). 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 (─CH3 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 CH3 group is near a gauche turn. This interplay results in the activation being controlled by the percentage of alkane conformers. PMID:21048088

  15. Distribution of alkB genes within n-alkane-degrading bacteria.

    PubMed

    Vomberg, A; Klinner, U

    2000-08-01

    Fifty-four bacterial strains belonging to 37 species were tested for their ability to assimilate short chain and/or medium chain liquid n-alkanes. A gene probe derived from the alkB gene of Pseudomonas oleovorans ATCC 29347 was utilized in hybridization experiments. Results of Southern hybridization of PCR-amplificates were compared with those of colony hybridization and dot blot hybridization. Strongest signals were received only from Gram-negative bacteria growing solely with short n-alkanes (C10). Hybridization results with soil isolates growing with n-alkanes of different chain lengths suggested as well that alkB genes seem to be widespread only in solely short-chain n-alkane-degrading pseudomonads. PCR products of Rhodococcus sp., Nocardioides sp., Gordona sp. and Sphingomonas sp. growing additionally or solely with medium-chain n-alkane as hexadecane had only few sequence identity with alkB though hybridizing with the gene probe. The derived amino acid sequence of the alkB-amplificate of Pseudomonas aureofaciens showed high homology (95%) with AlkB from Ps. oleovorans. alkB gene disruptants were not able to grow with decane.

  16. Spectroscopic study on interaction between three cationic surfactants with different alkyl chain lengths and DNA.

    PubMed

    Guo, Lili; Zhang, Zhaohong; Qiao, Heng; Liu, Miao; Shen, Manli; Yuan, Tianxin; Chen, Jing; Dionysiou, Dionysios D

    2015-01-01

    In this study, the interaction between cationic surfactants with different alkyl chain lengths, such as hexyltrimethyl ammonium bromide (HTAB), dodecyltrimethyl ammonium bromide (DTAB) and cetyltrimethyl ammonium bromide (CTAB), and DNA was investigated by UV-vis spectroscopy, fluorescence spectroscopy and viscosity techniques. The results showed that these three cationic surfactants with different hydrocarbon chain lengths could all interact with DNA. Their binding modes were estimated and their interaction strength was compared. In addition, the effects of the surfactant, NaCl and phosphate ion concentrations on the interaction were reviewed. It is wished that this work would provide some valuable references to investigate the influence of cationic surfactants with different alkyl chain lengths on DNA.

  17. Signal recognition particle-ribosome binding is sensitive to nascent chain length.

    PubMed

    Noriega, Thomas R; Tsai, Albert; Elvekrog, Margaret M; Petrov, Alexey; Neher, Saskia B; Chen, Jin; Bradshaw, Niels; Puglisi, Joseph D; Walter, Peter

    2014-07-11

    The signal recognition particle (SRP) directs ribosome-nascent chain complexes (RNCs) displaying signal sequences to protein translocation channels in the plasma membrane of prokaryotes and endoplasmic reticulum of eukaryotes. It was initially proposed that SRP binds the signal sequence when it emerges from an RNC and that successful binding becomes impaired as translation extends the nascent chain, moving the signal sequence away from SRP on the ribosomal surface. Later studies drew this simple model into question, proposing that SRP binding is unaffected by nascent chain length. Here, we reinvestigate this issue using two novel and independent fluorescence resonance energy transfer assays. We show that the arrival and dissociation rates of SRP binding to RNCs vary according to nascent chain length, resulting in the highest affinity shortly after a functional signal sequence emerges from the ribosome. Moreover, we show that SRP binds RNCs in multiple and interconverting conformations, and that conversely, RNCs exist in two conformations distinguished by SRP interaction kinetics.

  18. Effect of n-alkanes on lipid bilayers depending on headgroups.

    PubMed

    Hishida, Mafumi; Endo, Asami; Nakazawa, Koyomi; Yamamura, Yasuhisa; Saito, Kazuya

    2015-05-01

    Phase behavior and structural properties were examined for phospholipid bilayers having different headgroups (DMPC, DMPS and DMPE) with added n-alkanes to study effect of flexible additives. Change in the temperatures of main transition of the lipid/alkane mixtures against the length of added alkanes depends largely on the headgroup. Theoretical analysis of the change of the temperature of transition indicates that the headgroup dependence is dominantly originated in the strong dependence of total enthalpy on the headgroups. The results of X-ray diffraction show that the enthalpic stabilization due to enhanced packing of acyl chains of the lipid by alkanes in the gel phase causes the headgroup-dependent change in the phase transition behavior. The enhanced packing in the gel phase also leads to easy emergence of the subgel phase with very short relaxation time at room temperature in the DMPE-based bilayers.

  19. Effects of alkyl chain length on properties of 1-alkyl-3-methylimidazolium fluorohydrogenate ionic liquid crystals.

    PubMed

    Xu, Fei; Matsumoto, Kazuhiko; Hagiwara, Rika

    2010-11-15

    A series of 1-alkyl-3-methylimidazolium fluorohydrogenate salts (C(x)MIm(FH)(2)F, x=8, 10, 12, 14, 16, and 18) have been characterized by thermal analysis, polarized optical microscopy, IR spectroscopy, X-ray diffraction, and anisotropic ionic conductivity measurements. Liquid crystalline mesophases with a smectic A interdigitated bilayer structure are observed from C(10) to C(18), showing a fan-like or focal conic texture. The temperature range of the mesophase increases with the increase in the alkyl chain length (from 10.1 °C for C(10)MIm(FH)(2)F to 123.1 °C for C(18)MIm(FH)(2)F). The distance between the two layers in the smectic structure gradually increases with increasing alkyl chain length and decreases with increasing temperature. Conductivity parallel to the smectic layers is around 10 mS cm(-1) regardless of the alkyl chain length, whereas that perpendicular to the smectic layers decreases with increasing alkyl chain length because of the thicker insulating sheet with the longer alkyl chain.

  20. Fat-free plain yogurt manufactured with inulins of various chain lengths and Lactobacillus acidophilus.

    PubMed

    Aryana, K J; Plauche, S; Rao, R M; McGrew, P; Shah, N P

    2007-04-01

    Inulin is a prebiotic food ingredient that increases the activity of Lactobacillus acidophilus, increases calcium absorption, and is a good source of dietary fiber. The objective was to determine the effect of short, medium, and long chain inulins on the physicochemical, sensory, and microbiological characteristics of fat-free plain yogurt containing L. acidophilus. Inulins of short (P95), medium (GR), and long (HP) chain lengths were incorporated at 1.5% w/w of the yogurt mix. Viscosity, pH, syneresis, sensory properties (flavor, body and texture, and appearance and color), L. acidophilus counts, and color (L*, a*, and b*) of yogurts were determined at 1, 11, and 22 d after yogurt manufacture. The P95 containing yogurt had a significantly lower pH than the remaining yogurts, higher flavor scores than the yogurt containing HP, and comparable flavor scores with the control. The yogurts containing HP had less syneresis than the control and a better body and texture than the remaining yogurts. Yogurts containing prebiotics of different chain lengths had comparable L. acidophilus counts with each other but higher counts than the control. However, inulins of various chain lengths did not affect viscosity, color, and product appearance. Chain length of prebiotics affected some quality attributes of probiotic yogurts.

  1. Contact-line friction of liquid drops on self-assembled monolayers: chain-length effects.

    PubMed

    Voué, M; Rioboo, R; Adao, M H; Conti, J; Bondar, A I; Ivanov, D A; Blake, T D; De Coninck, J

    2007-04-24

    The static and dynamic wetting properties of self-assembled alkanethiol monolayers of increasing chain length were studied. The molecular-kinetic theory of wetting was used to interpret the dynamic contact angle data and evaluate the contact-line friction on the microscopic scale. Although the surfaces had a similar static wettability, the coefficient of contact-line friction zeta0 increased linearly with alkyl chain length. This result supports the hypothesis of energy dissipation due to a local deformation of the nanometer-thick layer at the contact line.

  2. Chain Length Dependence of Energies of Electron and Triplet Polarons in Oligofluorenes

    DOE PAGES

    Chen, Hung Cheng; Sreearunothai, Paiboon; Cook, Andrew R.; ...

    2017-03-01

    Bimolecular equilibria measured the one-electron reduction potentials and triplet free energies (ΔG°T) of oligo(9,9-dihexyl)fluorenes and a polymer with lengths of n = 1–10 and 57 repeat units. We can accurately measure one-electron potentials electrochemically only for the shorter oligomers. Starting at n = 1 the free energies change rapidly with increasing length and become constant for lengths longer than the delocalization length. Both the reduction potentials and triplet energies can be understood as the sum of a free energy for a fixed polaron and a positional entropy. Furthermore, the positional entropy increases gradually with length beyond the delocalization length duemore » to the possible occupation sites of the charge or the triplet exciton. Our results reinforce the view that charges and triplet excitons in conjugated chains exist as polarons and find that positional entropy can replace a popular empirical model of the energetics.« less

  3. Light, nutrients, and food-chain length constrain planktonic energy transfer efficiency across multiple trophic levels.

    PubMed

    Dickman, Elizabeth M; Newell, Jennifer M; González, María J; Vanni, Michael J

    2008-11-25

    The efficiency of energy transfer through food chains [food chain efficiency (FCE)] is an important ecosystem function. It has been hypothesized that FCE across multiple trophic levels is constrained by the efficiency at which herbivores use plant energy, which depends on plant nutritional quality. Furthermore, the number of trophic levels may also constrain FCE, because herbivores are less efficient in using plant production when they are constrained by carnivores. These hypotheses have not been tested experimentally in food chains with 3 or more trophic levels. In a field experiment manipulating light, nutrients, and food-chain length, we show that FCE is constrained by algal food quality and food-chain length. FCE across 3 trophic levels (phytoplankton to carnivorous fish) was highest under low light and high nutrients, where algal quality was best as indicated by taxonomic composition and nutrient stoichiometry. In 3-level systems, FCE was constrained by the efficiency at which both herbivores and carnivores converted food into production; a strong nutrient effect on carnivore efficiency suggests a carryover effect of algal quality across 3 trophic levels. Energy transfer efficiency from algae to herbivores was also higher in 2-level systems (without carnivores) than in 3-level systems. Our results support the hypothesis that FCE is strongly constrained by light, nutrients, and food-chain length and suggest that carryover effects across multiple trophic levels are important. Because many environmental perturbations affect light, nutrients, and food-chain length, and many ecological services are mediated by FCE, it will be important to apply these findings to various ecosystem types.

  4. Photoionization of alkylphenothiazines in vesicles: Effects of the alkyl chain length and the vesicle surface charge

    SciTech Connect

    Sakaguchi, Masato; Hu, Ming; Kevan, L. )

    1990-01-25

    The photoionization of alkylphenothiazine (AP = alkylphenothiazine) in vesicles were observed by electron spin resonance (ESR) and electron spin echo modulation (ESEM) methods. Alkylphenothiazine derivatives including sodium 10-methylphenothiazinesulfonate (C{sub 1}PSO{sub 3}Na), sodium 10-dodecylphenothiazinesulfonate (C{sub 12}PSO{sub 3}Na), sodium 3-(10{prime}-phenothiazinyl)propane-1-sulfonate (PC{sub 3}SO{sub 3}Na), sodium 6-(10{prime}-phenothiazinyl)hexane-1-sulfonate (PC{sub 6}SO{sub 3}Na), and sodium 12-(10{prime}-phenothiazinyl)dodecane-1-sulfonate (PC{sub 12}SO{sub 3} Na) were synthesized and used to study the effects of the alkyl chain length, the position of the sulfonate group, and the vesicle surface charge on the photoionization. A single ESR spectrum due to the alkylphenothiazine cation radicals (AP{sup +}) was observed from rapidly frozen AP in dioctadecyldimethylammonium chloride (DODAC) or dihexadecyl phosphate (DHP) vesicles photoirradiated for 10 min with {lambda} > 300 nm. In DODAC vesicles with a positive surface charge, the photoionization yield of PC{sub 12}SO{sub 3}Na with a sulfonate group at the dodecyl chain end is higher than that of C{sub 12}PSO{sub 3}Na with a sulfonate group on the phenothiazine ring. The photoionization yields of AP having the sulfonate group at the alkyl chain end in DODAC vesicles increase with decreasing alkyl chain length. The highest photoionization yield was obtained from PC{sub 3}SO{sub 3}Na, which has the shortest alkyl chain in this study and has the sulfonate group at the end of the propyl chain. The photoionization yield of AP in DHP vesicles with a negative surface charge was not changed by added alkyl chains or the position of the sulfonate group in AP. The results are discussed in terms of the alkyl chain length, the position of the sulfonate group, and the vesicle surface charge.

  5. Engineering Saccharomyces cerevisiae to produce odd chain-length fatty alcohols.

    PubMed

    Jin, Zhu; Wong, Adison; Foo, Jee Loon; Ng, Joey; Cao, Ying-Xiu; Chang, Matthew Wook; Yuan, Ying-Jin

    2016-04-01

    Fatty aldehydes and alcohols are valuable precursors used in the industrial manufacturing of a myriad of specialty products. Herein, we demonstrate the de novo production of odd chain-length fatty aldehydes and fatty alcohols in Saccharomyces cerevisiae by expressing a novel biosynthetic pathway involving cytosolic thioesterase, rice α-dioxygenase and endogenous aldehyde reductases. We attained production titers of ∼20 mg/l fatty aldehydes and ∼20 mg/l fatty alcohols in shake flask cultures after 48 and 60 h respectively without extensive fine-tuning of metabolic fluxes. In contrast to prior studies which relied on bi-functional fatty acyl-CoA reductase to produce even chain-length fatty alcohols, our biosynthetic route exploits α-oxidation reaction to produce odd chain-length fatty aldehyde intermediates without using NAD(P)H cofactor, thereby conserving cellular resource during the overall synthesis of odd chain-length fatty alcohols. The biosynthetic pathway presented in this study has the potential to enable sustainable and efficient synthesis of fatty acid-derived chemicals from processed biomass.

  6. Modification of eucalyptus pulp fiber using silane coupling agents with aliphatic side chains of different length

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this work was to evaluate the effect of three silane coupling agents with different aliphatic chain lengths on the hydrophobicity of eucalyptus pulp fiber. The three silanes coupling agents used (isobutyltrimethoxysilane, methyltrimethoxysilane, and n-octyltriethoxysilane [OTES]) we...

  7. PWA-diureasils organic-inorganic hybrids. Photochromism and effect of the organic chain length

    NASA Astrophysics Data System (ADS)

    Obara, P. A.; Sarmento, V. H. V.; Ribeiro, S. J. L.; Nalin, M.; Molina, C.

    2015-08-01

    Di-ureasil organic-inorganic hybrids have been used together with Phosphotungstic acid (PWA- H3PW12O40) in the preparation of new photochromic materials. PWA was incorporated in different relative concentrations in di-ureasils displaying different organic chain lengths. The structure and photochromic behaviour of these novel material were investigated by means of infrared (FTIR), photoluminescence (PL) and Ultraviolet-Visible (UV-Vis) spectroscopies and Small Angle X-ray Scattering (SAXS) technique as a function of PWA content and also of the polymer chain length. Eu3+ has been incorporated as probe ion. For the short polymer chains, europium and PWA keggin structures are located close to oxygen in the ether type of the polyoxides segments and for the long polymer chain carbonyl groups of the urea units were observed to contribute in the coordination. Moreover, the photochromic effect was followed by UV-Vis measurements which showed that in both hybrid families changing from colorless to blue after UV exposure, and the bleaching process, depend directly on the polymer chain length and the nature of the sites where PWA are coordinated in the matrix.

  8. Laboratory evolution of a soluble, self-sufficient, highly active alkane hydroxylase.

    PubMed

    Glieder, Anton; Farinas, Edgardo T; Arnold, Frances H

    2002-11-01

    We have converted cytochrome P450 BM-3 from Bacillus megaterium (P450 BM-3), a medium-chain (C12-C18) fatty acid monooxygenase, into a highly efficient catalyst for the conversion of alkanes to alcohols. The evolved P450 BM-3 exhibits higher turnover rates than any reported biocatalyst for the selective oxidation of hydrocarbons of small to medium chain length (C3-C8). Unlike naturally occurring alkane hydroxylases, the best known of which are the large complexes of methane monooxygenase (MMO) and membrane-associated non-heme iron alkane monooxygenase (AlkB), the evolved enzyme is monomeric, soluble, and requires no additional proteins for catalysis. The evolved alkane hydroxylase was found to be even more active on fatty acids than wild-type BM-3, which was already one of the most efficient fatty acid monooxgenases known. A broad range of substrates including the gaseous alkane propane induces the low to high spin shift that activates the enzyme. This catalyst for alkane hydroxylation at room temperature opens new opportunities for clean, selective hydrocarbon activation for chemical synthesis and bioremediation.

  9. Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds.

    PubMed

    Bastolla, U; Demetrius, Lloyd

    2005-09-01

    Stability of the native state is an essential requirement in protein evolution and design. Here we investigated the interplay between chain length and stability constraints using a simple model of protein folding and a statistical study of the Protein Data Bank. We distinguish two types of stability of the native state: with respect to the unfolded state (unfolding stability) and with respect to misfolded configurations (misfolding stability). Several contributions to stability are evaluated and their correlations are disentangled through principal components analysis, with the following main results. (1) We show that longer proteins can fulfil more easily the requirements of unfolding and misfolding stability, because they have a higher number of native interactions per residue. Consistently, in longer proteins native interactions are weaker and they are less optimized with respect to non-native interactions. (2) Stability against misfolding is negatively correlated with the strength of native interactions, which is related to hydrophobicity. Hence there is a trade-off between unfolding and misfolding stability. This trade-off is influenced by protein length: less hydrophobic sequences are observed in very long proteins. (3) The number of disulfide bonds is positively correlated with the deficit of free energy stabilizing the native state. Chain length and the number of disulfide bonds per residue are negatively correlated in proteins with short chains and uncorrelated in proteins with long chains. (4) The number of salt bridges per residue and per native contact increases with chain length. We interpret these observations as an indication that the constraints imposed by unfolding stability are less demanding in long proteins and they are further reduced by the competing requirement for stability against misfolding. In particular, disulfide bonds appear to be positively selected in short proteins, whereas they evolve in an effectively neutral way in long proteins.

  10. Chain-length heterogeneity allows for the assembly of fatty acid vesicles in dilute solutions.

    PubMed

    Budin, Itay; Prwyes, Noam; Zhang, Na; Szostak, Jack W

    2014-10-07

    A requirement for concentrated and chemically homogeneous pools of molecular building blocks would severely restrict plausible scenarios for the origin of life. In the case of membrane self-assembly, models of prebiotic lipid synthesis yield primarily short, single-chain amphiphiles that can form bilayer vesicles only at very high concentrations. These high critical aggregation concentrations (cacs) pose significant obstacles for the self-assembly of single-chain lipid membranes. Here, we examine membrane self-assembly in mixtures of fatty acids with varying chain lengths, an expected feature of any abiotic lipid synthesis. We derive theoretical predictions for the cac of mixtures by adapting thermodynamic models developed for the analogous phenomenon of mixed micelle self-assembly. We then use several complementary methods to characterize aggregation experimentally, and find cac values in close agreement with our theoretical predictions. These measurements establish that the cac of fatty acid mixtures is dramatically lowered by minor fractions of long-chain species, thereby providing a plausible route for protocell membrane assembly. Using an NMR-based approach to monitor aggregation of isotopically labeled samples, we demonstrate the incorporation of individual components into mixed vesicles. These experiments suggest that vesicles assembled in dilute, mixed solutions are depleted of the shorter-chain-length lipid species, a finding that carries implications for the composition of primitive cell membranes.

  11. Altered ceramide acyl chain length and ceramide synthase gene expression in Parkinson’s disease.

    PubMed

    Abbott, Sarah K; Li, Hongyun; Muñoz, Sonia Sanz; Knoch, Bianca; Batterham, Marijka; Murphy, Karen E; Halliday, Glenda M; Garner, Brett

    2014-04-01

    Genetic studies have provided increasing evidence that ceramide homeostasis plays a role in neurodegenerative diseases including Parkinson’s disease (PD). It is known that the relative amounts of different ceramide molecular species, as defined by their fatty acyl chain length, regulate ceramide function in lipid membranes and in signaling pathways. In the present study we used a comprehensive sphingolipidomic case-control approach to determine the effects of PD on ceramide composition in postmortem brain tissue from the anterior cingulate cortex (a region with significant PD pathology) and the occipital cortex (spared in PD), also assessing mRNA expression of the major ceramide synthase genes that regulate ceramide acyl chain composition in the same tissue using quantitative PCR. In PD anterior cingulate cortex but not occipital cortex, total ceramide and sphingomyelin levels were reduced from control levels by 53% (P < 0.001) and 42% (P < 0.001), respectively. Of the 13 ceramide and 15 sphingomyelin molecular lipid species identified and quantified, there was a significant shift in the ceramide acyl chain composition toward shorter acyl chain length in the PD anterior cingulate cortex. This PD-associated change in ceramide acyl chain composition was accompanied by an upregulation of ceramide synthase-1 gene expression, which we consider may represent a response to reduced ceramide levels. These data suggest a significant shift in ceramide function in lipid membranes and signaling pathways occurs in regions with PD pathology. Identifying the regulatory mechanisms precipitating this change may provide novel targets for future therapeutics.

  12. Influence of chain length and double bond on the aqueous behavior of choline carboxylate soaps.

    PubMed

    Rengstl, Doris; Diat, Olivier; Klein, Regina; Kunz, Werner

    2013-02-26

    In preceding studies, we demonstrated that choline carboxylates ChC(m) with alkyl chain lengths of m = 12 - 18 are highly water-soluble (for m = 12, soluble up to 93 wt % soap and 0 °C). In addition, choline soaps are featured by an extraordinary lyotropic phase behavior. With decreasing water concentration, the following phases were found: micellar phase (L(1)), discontinuous cubic phase (I(1)' and I(1)"), hexagonal phase (H(1)), bicontinuous cubic phase (V(1)), and lamellar phase (L(α)). The present work is also focused on the lyotropic phase behavior of choline soaps but with shorter alkyl chains or different alkyl chain properties. We have investigated the aqueous phase behavior of choline soaps with C(8) and C(10) chain-lengths (choline octanoate and choline decanoate) and with a C(18) chain-length with a cis-double bond (choline oleate). We found that choline decanoate follows the lyotropic phase behavior of the longer-chain homologues mentioned above. Choline octanoate in water shows no discontinuous cubic phases, but an extended, isotropic micellar solution phase. In addition, choline octanoate is at the limit between a surfactant and a hydrotrope. The double bond in choline oleate leads also to a better solubility in water and a decrease of the solubilization temperature. It also influences the Gaussian curvature of the aggregates which results in a loss of discontinuous cubic phases in the binary phase diagram. The different lyotropic mesophases were identified by the penetration scan technique with polarizing light microscope and visual observations. To clarify the structural behavior small (SAXS) and wide (WAXS) angle X-ray scattering were performed. To further characterize the extended, isotropic micellar solution phase in the binary phase diagram of choline octanoate viscosity and conductivity measurements were also carried out.

  13. Whole-cell bacterial bioreporter for actively searching and sensing of alkanes and oil spills.

    PubMed

    Zhang, Dayi; He, Yi; Wang, Yun; Wang, Hui; Wu, Lin; Aries, Eric; Huang, Wei E

    2012-01-01

    Acinetobacter baylyi ADP1 was found to tolerate seawater and have a special ability of adhering to an oil-water interface of 10-80 µm emulsified mineral and crude oil droplets. These properties make ADP1 an ideal bacterial chassis for constructing bioreporters that are able to actively search and sense oil spill in water and soils. Acinetobacter baylyi bioreporter ADPWH_alk was developed and applied to the detection of alkanes and alkenes in water, seawater and soils. Bioreporter ADPWH_alk was able to detect a broad range of alkanes and alkenes with carbon chain length from C7 to C36. So far, ADPWH_alk is the only bioreporter that is able to detect alkane with carbon chain length greater than C18. This bioreporter responded to the alkanes in about 30 min and it was independent to the cell growth phase because of two point mutations in alkM promoter recognized by alkane regulatory protein ALKR. ADPWH_alk was applied to detect mineral oil, Brent, Chestnut and Sirri crude oils in water and seawater in the range 0.1-100 mg l(-1), showing that the bioreporter oil detection was semi-quantitative. This study demonstrates that ADPWH_alk is a rapid, sensitive and semi-quantitative bioreporter that can be useful for environmental monitoring and assessment of oil spills in seawater and soils.

  14. CYP153A6, a Soluble P450 Oxygenase Catalyzing Terminal-Alkane Hydroxylation

    PubMed Central

    Funhoff, Enrico G.; Bauer, Ulrich; García-Rubio, Inés; Witholt, Bernard; van Beilen, Jan B.

    2006-01-01

    The first and key step in alkane metabolism is the terminal hydroxylation of alkanes to 1-alkanols, a reaction catalyzed by a family of integral-membrane diiron enzymes related to Pseudomonas putida GPo1 AlkB, by a diverse group of methane, propane, and butane monooxygenases and by some membrane-bound cytochrome P450s. Recently, a family of cytoplasmic P450 enzymes was identified in prokaryotes that allow their host to grow on aliphatic alkanes. One member of this family, CYP153A6 from Mycobacterium sp. HXN-1500, hydroxylates medium-chain-length alkanes (C6 to C11) to 1-alkanols with a maximal turnover number of 70 min−1 and has a regiospecificity of ≥95% for the terminal carbon atom position. Spectroscopic binding studies showed that C6-to-C11 aliphatic alkanes bind in the active site with Kd values varying from ∼20 nM to 3.7 μM. Longer alkanes bind more strongly than shorter alkanes, while the introduction of sterically hindering groups reduces the affinity. This suggests that the substrate-binding pocket is shaped such that linear alkanes are preferred. Electron paramagnetic resonance spectroscopy in the presence of the substrate showed the formation of an enzyme-substrate complex, which confirmed the binding of substrates observed in optical titrations. To rationalize the experimental observations on a molecular scale, homology modeling of CYP153A6 and docking of substrates were used to provide the first insight into structural features required for terminal alkane hydroxylation. PMID:16816194

  15. CYP153A6, a soluble P450 oxygenase catalyzing terminal-alkane hydroxylation.

    PubMed

    Funhoff, Enrico G; Bauer, Ulrich; García-Rubio, Inés; Witholt, Bernard; van Beilen, Jan B

    2006-07-01

    The first and key step in alkane metabolism is the terminal hydroxylation of alkanes to 1-alkanols, a reaction catalyzed by a family of integral-membrane diiron enzymes related to Pseudomonas putida GPo1 AlkB, by a diverse group of methane, propane, and butane monooxygenases and by some membrane-bound cytochrome P450s. Recently, a family of cytoplasmic P450 enzymes was identified in prokaryotes that allow their host to grow on aliphatic alkanes. One member of this family, CYP153A6 from Mycobacterium sp. HXN-1500, hydroxylates medium-chain-length alkanes (C6 to C11) to 1-alkanols with a maximal turnover number of 70 min(-1) and has a regiospecificity of > or =95% for the terminal carbon atom position. Spectroscopic binding studies showed that C6-to-C11 aliphatic alkanes bind in the active site with Kd values varying from approximately 20 nM to 3.7 microM. Longer alkanes bind more strongly than shorter alkanes, while the introduction of sterically hindering groups reduces the affinity. This suggests that the substrate-binding pocket is shaped such that linear alkanes are preferred. Electron paramagnetic resonance spectroscopy in the presence of the substrate showed the formation of an enzyme-substrate complex, which confirmed the binding of substrates observed in optical titrations. To rationalize the experimental observations on a molecular scale, homology modeling of CYP153A6 and docking of substrates were used to provide the first insight into structural features required for terminal alkane hydroxylation.

  16. Stable Isotope Labeled n-Alkanes to Assess Digesta Passage Kinetics through the Digestive Tract of Ruminants

    PubMed Central

    Warner, Daniel; Ferreira, Luis M. M.; Breuer, Michel J. H.; Dijkstra, Jan; Pellikaan, Wilbert F.

    2013-01-01

    We describe the use of carbon stable isotope (13C) labeled n-alkanes as a potential internal tracer to assess passage kinetics of ingested nutrients in ruminants. Plant cuticular n-alkanes originating from intrinsically 13C labeled ryegrass plants were pulse dosed intraruminally in four rumen-cannulated lactating dairy cows receiving four contrasting ryegrass silage treatments that differed in nitrogen fertilization level (45 or 90 kg nitrogen ha−1) and maturity (early or late). Passage kinetics through the gastrointestinal tract were derived from the δ13C (i.e. the ratio 13C:12C) in apparently undigested fecal material. Isotopic enrichment was observed in a wide range of long-chain n-alkanes (C27–C36) and passage kinetics were determined for the most abundant C29, C31 and C33 n-alkanes, for which a sufficiently high response signal was detected by combustion isotope ratio mass spectrometry. Basal diet treatment and carbon chain length of n-alkanes did not affect fractional passage rates from the rumen (K1) among individual n-alkanes (3.71–3.95%/h). Peak concentration time and transit time showed a quantitatively small, significant (p≤0.002) increase with carbon chain length. K1 estimates were comparable to those of the 13C labeled digestible dry matter fraction (3.38%/h; r = 0.61 to 0.71; p≤0.012). A literature review has shown that n-alkanes are not fermented by microorganisms in the rumen and affirms no preferential depletion of 13C versus 12C. Our results suggest that 13C labeled n-alkanes can be used as nutrient passage tracers and support the reliability of the δ13C signature of digestible feed nutrients as a tool to measure nutrient-specific passage kinetics. PMID:24124493

  17. Communication: Site-dependent reactivity between chlorine atoms and mixed-chain-length alkanethiolate monolayers

    NASA Astrophysics Data System (ADS)

    Lee, David Y.; Kandel, S. Alex

    2013-10-01

    The chemical reaction of atomic chlorine with mixed monolayers of alkanethiolates having different chain lengths was investigated. In situ scanning tunneling microscopy was used to acquire time-lapsed series of images, allowing the measurement of the effect of monolayer structure and composition on reactivity. The rate of chemical reaction is strongly site-dependent. In particular, the boundary between two different-length alkanethiolates greatly promotes the reactivity of nearby molecules, much more so than any other native defect typical of single-component alkanethiolate monolayers.

  18. Butyric acid esterification kinetics over Amberlyst solid acid catalysts: the effect of alcohol carbon chain length.

    PubMed

    Pappu, Venkata K S; Kanyi, Victor; Santhanakrishnan, Arati; Lira, Carl T; Miller, Dennis J

    2013-02-01

    The liquid phase esterification of butyric acid with a series of linear and branched alcohols is examined. Four strong cation exchange resins, Amberlyst™ 15, Amberlyst™ 36, Amberlyst™ BD 20, and Amberlyst™ 70, were used along with para-toluenesulfonic acid as a homogeneous catalyst. The effect of increasing alcohol carbon chain length and branching on esterification rate at 60°C is presented. For all catalysts, the decrease in turnover frequency (TOF) with increasing carbon chain length of the alcohol is described in terms of steric hindrance, alcohol polarity, and hydroxyl group concentration. The kinetics of butyric acid esterification with 2-ethylhexanol using Amberlyst™ 70 catalyst is described with an activity-based, pseudo-homogeneous kinetic model that includes autocatalysis by butyric acid.

  19. Effect of Composition and Chain Length on χ Parameter of Polyolefin Blends: A Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Khare, Rajesh; Ravichandran, Ashwin; Chen, Chau-Chyun

    Polymer blends exhibit complex phase behavior which is governed by several factors including temperature, composition and molecular weight of components. The thermodynamics of polymer blends is commonly described using the χ parameter. While variety of experimental studies exist on identifying the factors affecting the χ parameter, a detailed molecular scale understanding of these is a topic of current research. We have studied the effect of blend composition and chain length on χ parameter values for two model polyolefin blends. The blends studied are: polyisobutylene (PIB)/polybutadiene (PBD) and polyethylene (PE)/atactic polypropylene (aPP). Molecular dynamics simulations in combination with the integral equation theory formalism proposed by Schweizer and Curro [Journal of Chemical Physics, 91, 5059 (1989)] are used to determine the χ parameter for these systems and thereby study the effect of blend composition and chain length. The resulting χ parameter values are explained in terms of the molecular structure of these polymeric systems.

  20. Effects of Nanoparticle Morphology and Acyl Chain Length on Spontaneous Lipid Transfer Rates

    SciTech Connect

    Xia, Yan; Li, Ming; Charubin, Kamil; Liu, Ying; Heberle, Frederick A.; Katsaras, John; Jing, Benxin; Zhu, Yingxi; Nieh, Mu-Ping

    2015-11-05

    In this paper, we report on studies of lipid transfer rates between different morphology nanoparticles and lipids with different length acyl chains. The lipid transfer rate of dimyristoylphosphatidylcholine (di-C14, DMPC) in discoidal “bicelles” (0.156 h–1) is 2 orders of magnitude greater than that of DMPC vesicles (ULVs) (1.1 × 10–3 h–1). For both bicellar and ULV morphologies, increasing the acyl chain length by two carbons [going from di-C14 DMPC to di-C16, dipalmitoylphosphatidylcholine (DPPC)] causes lipid transfer rates to decrease by more than 2 orders of magnitude. Results from small angle neutron scattering (SANS), differential scanning calorimetry (DSC), and fluorescence correlation spectroscopy (FCS) are in good agreement. Finally, the present studies highlight the importance of lipid dynamic processes taking place in different morphology biomimetic membranes.

  1. Effects of Nanoparticle Morphology and Acyl Chain Length on Spontaneous Lipid Transfer Rates

    DOE PAGES

    Xia, Yan; Li, Ming; Charubin, Kamil; ...

    2015-11-05

    In this paper, we report on studies of lipid transfer rates between different morphology nanoparticles and lipids with different length acyl chains. The lipid transfer rate of dimyristoylphosphatidylcholine (di-C14, DMPC) in discoidal “bicelles” (0.156 h–1) is 2 orders of magnitude greater than that of DMPC vesicles (ULVs) (1.1 × 10–3 h–1). For both bicellar and ULV morphologies, increasing the acyl chain length by two carbons [going from di-C14 DMPC to di-C16, dipalmitoylphosphatidylcholine (DPPC)] causes lipid transfer rates to decrease by more than 2 orders of magnitude. Results from small angle neutron scattering (SANS), differential scanning calorimetry (DSC), and fluorescence correlationmore » spectroscopy (FCS) are in good agreement. Finally, the present studies highlight the importance of lipid dynamic processes taking place in different morphology biomimetic membranes.« less

  2. Effect of chain length on binding of fatty acids to Pluronics in microemulsions.

    PubMed

    James-Smith, Monica A; Shekhawat, Dushyant; Cheung, Sally; Moudgil, Brij M; Shah, Dinesh O

    2008-03-15

    We investigated the effect of fatty acid chain length on the binding capacity of drug and fatty acid to Pluronic F127-based microemulsions. This was accomplished by using turbidity experiments. Pluronic-based oil-in-water microemulsions of various compositions were synthesized and titrated to turbidity with concentrated Amitriptyline, an antidepressant drug. Sodium salts of C(8), C(10), or C(12) fatty acid were used in preparation of the microemulsion and the corresponding binding capacities were observed. It has been previously determined that, for microemulsions prepared with sodium caprylate (C(8) fatty acid soap), a maximum of 11 fatty acid molecules bind to the microemulsion per 1 molecule of Pluronic F127 and a maximum of 12 molecules of Amitriptyline bind per molecule of F127. We have found that with increasing the chain length of the fatty acid salt component of the microemulsion, the binding capacity of both the fatty acid and the Amitriptyline to the microemulsion decreases. For sodium salts of C(8), C(10) and C(12) fatty acids, respectively, a maximum of approximately 11, 8.4 and 8.3 molecules of fatty acid molecules bind to 1 Pluronic F127 molecule. We propose that this is due to the decreasing number of free monomers with increasing chain length. As chain length increases, the critical micelle concentration (cmc) decreases, thus leading to fewer monomers. Pluronics are symmetric tri-block copolymers consisting of propylene oxide (PO) and ethylene oxide (EO). The polypropylene oxide block, PPO is sandwiched between two polyethylene oxide (PEO) blocks. The PEO blocks are hydrophilic while PPO is hydrophobic portion in the Pluronic molecule. Due to this structure, we propose that the fatty acid molecules that are in monomeric form most effectively diffuse between the PEO "tails" and bind to the hydrophobic PPO groups.

  3. Communication disruption of guava moth (Coscinoptycha improbana) using a pheromone analog based on chain length.

    PubMed

    Suckling, D M; Dymock, J J; Park, K C; Wakelin, R H; Jamieson, L E

    2013-09-01

    The guava moth, Coscinoptycha improbana, an Australian species that infests fruit crops in commercial and home orchards, was first detected in New Zealand in 1997. A four-component pheromone blend was identified but is not yet commercially available. Using single sensillum recordings from male antennae, we established that the same olfactory receptor neurons responded to two guava moth sex pheromone components, (Z)-11-octadecen-8-one and (Z)-12-nonadecen-9-one, and to a chain length analog, (Z)-13-eicosen-10-one, the sex pheromone of the related peach fruit moth, Carposina sasakii. We then field tested whether this non-specificity of the olfactory neurons might enable disruption of sexual communication by the commercially available analog, using male catch to synthetic lures in traps in single-tree, nine-tree and 2-ha plots. A disruptive pheromone analog, based on chain length, is reported for the first time. Trap catches for guava moth were disrupted by three polyethylene tubing dispensers releasing the analog in single-tree plots (86% disruption of control catches) and in a plots of nine trees (99% disruption). Where peach fruit moth pheromone dispensers were deployed at a density of 1000/ha in two 2-ha areas, pheromone traps for guava moth were completely disrupted for an extended period (up to 470 days in peri-urban gardens in Mangonui and 422 days in macadamia nut orchards in Kerikeri). In contrast, traps in untreated areas over 100 m away caught 302.8 ± 128.1 moths/trap in Mangonui and 327.5 ± 78.5 moths/ trap in Kerikeri. The longer chain length in the pheromone analog has greater longevity than the natural pheromone due to its lower volatility. Chain length analogs may warrant further investigation for mating disruption in Lepidoptera, and screening using single-sensillum recording is recommended.

  4. Enthalpic Effects of Chain Length and Unsaturation on Water Permeability across Droplet Bilayers of Homologous Monoglycerides.

    PubMed

    Lopez, Maria; Evangelista, Sue Ellen; Morales, Melissa; Lee, Sunghee

    2017-01-31

    A deeper understanding of unassisted passive transport processes can better delineate basic lipid dynamics in biological membranes. A droplet interface bilayer (DIB) is made by contacting two aqueous droplets covered with a lipid monolayer, and has increasingly been employed as a model artificial biological membrane. In this study, we have investigated the effect of acyl chain structure of amphiphilic monoglycerides on the osmotic permeability of water across DIB membranes composed of these monoglycerides, where the acyl chain length (C14-C24), number of double bonds (1-4), and the position of double bond are varied systematically along the acyl chains. Both permeability values and activation energies have been extracted for water transport across a lipid bilayer formed of a homologous series of lipids, allowing us to make ready comparisons between the different lipids and potentially better elucidate the contributions that molecular motifs make to the permeation process.

  5. Co-Assembly of Oppositely Charged Particles into Linear Clusters and Chains of Controllable Length

    NASA Astrophysics Data System (ADS)

    Bharti, Bhuvnesh; Findenegg, Gerhard H.; Velev, Orlin D.

    2012-12-01

    Colloidal particles with strongly attractive interactions snap on contact and form permanent, but disordered aggregates. In contrast, AC electric fields allow directional assembly of chains or crystals from repulsive particles by dielectrophoresis (DEP), but these structures fall apart once the field is switched off. We demonstrate how well-organized, permanent clusters and chains of micron-sized particles can be assembled by applying DEP to mixtures of oppositely charged microspheres. We found that the length of the formed chains depends on size ratio as well as the number ratio of the two species, and formulated a statistical model for this assembly mechanism, which is in excellent agreement with the experimental results. The assembly rules resulting from this study form a basis for tailoring new classes of permanent supracolloidal clusters and gels.

  6. Productivity, Disturbance and Ecosystem Size Have No Influence on Food Chain Length in Seasonally Connected Rivers

    PubMed Central

    Warfe, Danielle M.; Jardine, Timothy D.; Pettit, Neil E.; Hamilton, Stephen K.; Pusey, Bradley J.; Bunn, Stuart E.; Davies, Peter M.; Douglas, Michael M.

    2013-01-01

    The food web is one of the oldest and most central organising concepts in ecology and for decades, food chain length has been hypothesised to be controlled by productivity, disturbance, and/or ecosystem size; each of which may be mediated by the functional trophic role of the top predator. We characterised aquatic food webs using carbon and nitrogen stable isotopes from 66 river and floodplain sites across the wet-dry tropics of northern Australia to determine the relative importance of productivity (indicated by nutrient concentrations), disturbance (indicated by hydrological isolation) and ecosystem size, and how they may be affected by food web architecture. We show that variation in food chain length was unrelated to these classic environmental determinants, and unrelated to the trophic role of the top predator. This finding is a striking exception to the literature and is the first published example of food chain length being unaffected by any of these determinants. We suggest the distinctive seasonal hydrology of northern Australia allows the movement of fish predators, linking isolated food webs and potentially creating a regional food web that overrides local effects of productivity, disturbance and ecosystem size. This finding supports ecological theory suggesting that mobile consumers promote more stable food webs. It also illustrates how food webs, and energy transfer, may function in the absence of the human modifications to landscape hydrological connectivity that are ubiquitous in more populated regions. PMID:23776641

  7. Productivity, disturbance and ecosystem size have no influence on food chain length in seasonally connected rivers.

    PubMed

    Warfe, Danielle M; Jardine, Timothy D; Pettit, Neil E; Hamilton, Stephen K; Pusey, Bradley J; Bunn, Stuart E; Davies, Peter M; Douglas, Michael M

    2013-01-01

    The food web is one of the oldest and most central organising concepts in ecology and for decades, food chain length has been hypothesised to be controlled by productivity, disturbance, and/or ecosystem size; each of which may be mediated by the functional trophic role of the top predator. We characterised aquatic food webs using carbon and nitrogen stable isotopes from 66 river and floodplain sites across the wet-dry tropics of northern Australia to determine the relative importance of productivity (indicated by nutrient concentrations), disturbance (indicated by hydrological isolation) and ecosystem size, and how they may be affected by food web architecture. We show that variation in food chain length was unrelated to these classic environmental determinants, and unrelated to the trophic role of the top predator. This finding is a striking exception to the literature and is the first published example of food chain length being unaffected by any of these determinants. We suggest the distinctive seasonal hydrology of northern Australia allows the movement of fish predators, linking isolated food webs and potentially creating a regional food web that overrides local effects of productivity, disturbance and ecosystem size. This finding supports ecological theory suggesting that mobile consumers promote more stable food webs. It also illustrates how food webs, and energy transfer, may function in the absence of the human modifications to landscape hydrological connectivity that are ubiquitous in more populated regions.

  8. Gel Permeation Chromatography Characterization of the Chain Length Distributions in Thiol-Acrylate Photopolymer Networks

    PubMed Central

    Rydholm, Amber E.; Held, Nicole L.; Bowman, Christopher N.; Anseth, Kristi S.

    2008-01-01

    Crosslinked, degradable networks formed from the photopolymerization of thiol and acrylate monomers are explored as potential biomaterials. The degradation behavior and material properties of these networks are influenced by the molecular weight of the nondegradable thiol-polyacrylate backbone chains that form during photopolymerization. Here, gel permeation chromatography was used to characterize the thiol-polyacrylate backbone chain lengths in degraded thiol-acrylate networks. Increasing thiol functionality from 1 to 4 increased the backbone molecular weight (M̄w = 2.3 ± 0.07 × 104 Da for monothiol and 3.6 ± 0.1 × 104 Da for tetrathiol networks). Decreasing thiol functional group concentration from 30 to 10 mol% also increased the backbone lengths (M̄w = 7.3 ± 1.1 × 104 Da for the networks containing 10 mol% thiol groups as compared to 3.6 ± 0.1 × 104 Da for 30 mol% thiol). Finally, the backbone chain lengths were probed at various stages of degradation and an increase in backbone molecular weight was observed as mass loss progressed from 10 to 70%. PMID:19079733

  9. Effects of nutrient recycling and food-chain length on resilience

    SciTech Connect

    DeAngelis, D.L.; Bartell, S.M. ); Brenkert, A.L. )

    1989-11-01

    The attempt to explain the observed structure of ecological food webs has been one of the recent key issues of theoretical ecology. Unquestionably, many factors are involved in determining food-web structure. The dissipation of available energy from one trophic level to the next has been emphasized by Yodzis as the major factor limiting the length of food chains. However, Pimm and Lawton and Pimm have argued that a decrease in relative stability with increasing food-chain length may also be a factor. By relative stability (more commonly, resilience), we mean the rate at which a stable ecological system returns to a steady state following a perturbation. Resilience can be defined more precisely as the inverse of the return time T{sub R}, the time it takes a systems to return a specified fraction of the way toward a steady state following a perturbation. Besides its possible significance to food-web structure, ecosystem resilience is a factor of practical importance, since it is a measure of the rate at which the ecosystem can recover from disturbances. Our purpose is to investigate resilience in food-chain and food-web models as nutrient input and the trophic structure are varied and to offer explanations of the observed model behaviors. In this paper we present the basic results by first using a simple abstract food-chain model at steady state and then showing that these results hold for a more complex food-web simulation model without a constant steady state solution.

  10. Hydrocracking and hydroisomerization of long-chain alkanes and polyolefins over metal-promoted anion-modified transition metal oxides

    SciTech Connect

    Venkatesh, Koppampatti R.; Hu, Jianli; Tierney, John W.; Wender, Irving

    1996-12-01

    A method is described for cracking a feedstock by contacting the feedstock with a metal-promoted anion-modified metal oxide catalyst in the presence of hydrogen gas. The metal oxide of the catalyst is one or more of ZrO{sub 2}, HfO{sub 2}, TiO{sub 2} and SnO{sub 2}, and the feedstock is principally chains of at least 20 carbon atoms. The metal-promoted anion-modified metal oxide catalyst contains one or more of Pt, Ni, Pd, Rh, Ir, Ru, (Mn and Fe) or mixtures of them present between about 0.2% to about 15% by weight of the catalyst. The metal-promoted anion-modified metal oxide catalyst contains one or more of SO{sub 4}, WO{sub 3}, or mixtures of them present between about 0.5% to about 20% by weight of the catalyst.

  11. Hydrocracking and hydroisomerization of long-chain alkanes and polyolefins over metal-promoted anion-modified transition metal oxides

    DOEpatents

    Venkatesh, Koppampatti R.; Hu, Jianli; Tierney, John W.; Wender, Irving

    2001-01-01

    A method of cracking a feedstock by contacting the feedstock with a metal-promoted anion-modified metal oxide catalyst in the presence of hydrogen gas. The metal oxide of the catalyst is one or more of ZrO.sub.2, HfO.sub.2, TiO.sub.2 and SnO.sub.2, and the feedstock is principally chains of at least 20 carbon atoms. The metal-promoted anion-modified metal oxide catalyst contains one or more of Pt, Ni, Pd, Rh, Ir, Ru, (Mn & Fe) or mixtures of them present between about 0.2% to about 15% by weight of the catalyst. The metal-promoted anion-modified metal oxide catalyst contains one or more of SO.sub.4, WO.sub.3, or mixtures of them present between about 0.5% to about 20% by weight of the catalyst.

  12. Chebyshev-polynomial expansion of the localization length of Hermitian and non-Hermitian random chains

    NASA Astrophysics Data System (ADS)

    Hatano, Naomichi; Feinberg, Joshua

    2016-12-01

    We study Chebyshev-polynomial expansion of the inverse localization length of Hermitian and non-Hermitian random chains as a function of energy. For Hermitian models, the expansion produces this energy-dependent function numerically in one run of the algorithm. This is in strong contrast to the standard transfer-matrix method, which produces the inverse localization length for a fixed energy in each run. For non-Hermitian models, as in the transfer-matrix method, our algorithm computes the inverse localization length for a fixed (complex) energy. We also find a formula of the Chebyshev-polynomial expansion of the density of states of non-Hermitian models. As explained in detail, our algorithm for non-Hermitian models may be the only available efficient algorithm for finding the density of states of models with interactions.

  13. Effect of chain length and unsaturation on elasticity of lipid bilayers.

    PubMed Central

    Rawicz, W; Olbrich, K C; McIntosh, T; Needham, D; Evans, E

    2000-01-01

    Micropipette pressurization of giant bilayer vesicles was used to measure both elastic bending k(c) and area stretch K(A) moduli of fluid-phase phosphatidylcholine (PC) membranes. Twelve diacyl PCs were chosen: eight with two 18 carbon chains and degrees of unsaturation from one double bond (C18:1/0, C18:0/1) to six double bonds per lipid (diC18:3), two with short saturated carbon chains (diC13:0, diC14:0), and two with long unsaturated carbon chains (diC20:4, diC22:1). Bending moduli were derived from measurements of apparent expansion in vesicle surface area under very low tensions (0.001-0.5 mN/m), which is dominated by smoothing of thermal bending undulations. Area stretch moduli were obtained from measurements of vesicle surface expansion under high tensions (>0.5 mN/m), which involve an increase in area per molecule and a small-but important-contribution from smoothing of residual thermal undulations. The direct stretch moduli varied little (< +/-10%) with either chain unsaturation or length about a mean of 243 mN/m. On the other hand, the bending moduli of saturated/monounsaturated chain PCs increased progressively with chain length from 0.56 x 10(-19) J for diC13:0 to 1.2 x 10(-19) J for diC22:1. However, quite unexpectedly for longer chains, the bending moduli dropped precipitously to approximately 0.4 x 10(-19) J when two or more cis double bonds were present in a chain (C18:0/2, diC18:2, diC18:3, diC20:4). Given nearly constant area stretch moduli, the variations in bending rigidity with chain length and polyunsaturation implied significant variations in thickness. To test this hypothesis, peak-to-peak headgroup thicknesses h(pp) of bilayers were obtained from x-ray diffraction of multibilayer arrays at controlled relative humidities. For saturated/monounsaturated chain bilayers, the distances h(pp) increased smoothly from diC13:0 to diC22:1 as expected. Moreover, the distances and elastic properties correlated well with a polymer brush model of the

  14. A computational study of vicinal fluorination in 2,3-difluorobutane: implications for conformational control in alkane chains.

    PubMed

    Fox, Stephen J; Gourdain, Stephanie; Coulthurst, Anton; Fox, Clare; Kuprov, Ilya; Essex, Jonathan W; Skylaris, Chris-Kriton; Linclau, Bruno

    2015-01-19

    A comprehensive conformational analysis of both 2,3-difluorobutane diastereomers is presented based on density functional theory calculations in vacuum and in solution, as well as NMR experiments in solution. While for 1,2-difluoroethane the fluorine gauche effect is clearly the dominant effect determining its conformation, it was found that for 2,3-difluorobutane there is a complex interplay of several effects, which are of similar magnitude but often of opposite sign. As a result, unexpected deviations in dihedral angles, relative conformational energies and populations are observed which cannot be rationalised only by chemical intuition. Furthermore, it was found that it is important to consider the free energies of the various conformers, as these lead to qualitatively different results both in vacuum and in solvent, when compared to calculations based only on the electronic energies. In contrast to expectations, it was found that vicinal syn-difluoride introduction in the butane and by extension, longer hydrocarbon chains, is not expected to lead to an effective stabilisation of the linear conformation. Our findings have implications for the use of the vicinal difluoride motif for conformational control.

  15. Chain-length-dependent autocatalytic hydrolysis of fatty acid anhydrides in polyethylene glycol.

    PubMed

    Cao, Cao; Wang, Qing-Biao; Tang, Lin-Jun; Ge, Bing-Qiang; Chen, Zhong-Xiu; Deng, Shao-Ping

    2014-03-27

    Autocatalytic hydrolysis of fatty acid anhydrides induced by the spontaneously formed vesicles has been studied for years. However, whether the reaction autocatalyzed by vesicles formed in diluted solutions applies also to macromolecular crowded conditions remains unknown. The aim of this study is to characterize hydrolysis behavior of fatty acid anhydrides and formation of vesicles in crowded media. Inert macromolecular crowding agents such as polyethylene glycol (PEG) and Dextran were used to probe the impact of external crowding on the autocatalytic hydrolysis of fatty acid anhydrides with varied hydrophobic chain length. Under stringent conditions of crowding, hydrolysis rates of octanoic anhydride, nonanoic anhydride, and decanoic anhydride were found to decrease, but the rates of lauric anhydride and oleic anhydride increased. These results suggest that the effect of the crowding agent on the hydrolysis of fatty acid anhydrides was chain-length-dependent. Characterization of the size and polydispersity of vesicles formed from hydrolyzed fatty acid anhydrides in crowding revealed that long-chain fatty acids formed monodisperse vesicles easier at lower concentrations of PEG. Measurement of the critical aggregation concentration of ionized fatty acid in the presence of PEG showed that crowding media promoted vesicle formation from long-chain fatty acids but inhibited those from fatty acids with fewer carbon atoms. Further investigation of the diffusion property of ionized fatty acids in crowding agents suggested that PEG might create more hydrophobic areas for long-chain fatty acids anhydrides, which subsequently promoted the unreacted anhydride in the aqueous phase to be solubilized in the formed vesicles. This research provides information for understanding the autocatalytic reaction accompanied by self-producing aggregates and the behavior of fatty acids in crowding media.

  16. Polymer chain length effects on fibroblast attachment on nylon-3-modified surfaces.

    PubMed

    Liu, Runhui; Masters, Kristyn S; Gellman, Samuel H

    2012-04-09

    Nylon-3 polymers have a polyamide backbone reminiscent of that found in proteins (β- vs α-amino acid residues, respectively), which makes these materials interesting for biological applications. Because of the versatility of the ring-opening polymerization process and the variety of β-lactam starting materials available, the structure of nylon-3 copolymers is highly amenable to alteration. A previous study showed that relatively subtle changes in the structure or ratio of hydrophobic and cationic subunits that comprise these polymers can result in significant changes in the ability of nylon-3-bearing surfaces to support cell adhesion and spreading. In the present study, we have exploited the highly tailorable nature of these polymers to synthesize new versions possessing a wide range of chain lengths, with the intent of optimizing these materials for use as cell-supportive substrates. We find that longer nylon-3 chains lead to better fibroblast attachment on modified surfaces and that at the optimal chain lengths less hydrophobic subunits are superior. The best polymers we identified are comparable to an RGD-containing peptide in supporting fibroblast attachment. The results described here will help to focus future efforts aimed at refining nylon-3 copolymer substrates for specific tissue engineering applications.

  17. Alkane distribution and carbon isotope composition in fossil leaves: An interpretation of plant physiology in the geologic past

    NASA Astrophysics Data System (ADS)

    Graham, H. V.; Freeman, K. H.

    2014-12-01

    The relative chain-length distribution and carbon-isotope composition of n-alkanes extracted from sedimentary rocks are important geochemical tools for investigating past terrestrial ecosystems. Alkanes preserved in ancient sediments are assumed to be contemporaneous, derived from the same ecosystem, and integrated from the biomass present on the landscape at the time of deposition. Further, there is an underlying assumption that ancient plants exhibited the same metabolic and physiological responses to climate conditions that are observed for modern plants. Interpretations of alkane abundances and isotopic signatures are complicated by the strong influence of phylogenetic affiliation and ecological factors, such as canopy structure. A better understanding of how ecosystem and taxa influence alkane properties, including homologue abundance patterns and leaf-lipid carbon isotope fractionation would help strengthen paleoecological interpretations based on these widely employed plant biomarkers. In this study, we analyze the alkane chain-length distribution and carbon-isotope composition of phytoleim and alkanes (d13Cleaf and d13Clipid) extracted from a selection of Cretaceous and Paleocene fossil leaves from the Guaduas and Cerrejon Formations of Colombia. These data were compared with data for the same families in a modern analogue biome. Photosynthetic and biosynthetic fractionation (∆leaf and elipid) values determined from the fossil material indicate carbon metabolism patterns were similar to modern plants. Fossil data were incorporated in a biomass-weighted mixing model to represent the expected lipid complement of sediment arising from this ecosystem and compared with alkane measurements from the rock matrix. Modeled and observed isotopic and abundance patterns match well for alkane homologs most abundant in plants (i.e., n-C27 to n-C33). The model illustrates the importance of understanding biases in litter flux and taphonomic pressures inherent in the

  18. Composition of leaf n-alkanes in three Satureja montana L. subspecies from the Balkan peninsula: ecological and taxonomic aspects.

    PubMed

    Dodoš, Tanja; Rajčević, Nemanja; Tešević, Vele; Matevski, Vlado; Janaćković, Pedja; Marin, Petar D

    2015-01-01

    The composition of the epicuticular leaf n-alkanes of eight populations of three Satureja montana subspecies (S. montana L. subsp. pisidica (Wettst.) Šilić, S. montana L. subsp. montana, and S. montana L. subsp. variegata (Host) P. W. Ball), from central and western areas of the Balkan Peninsula was characterized by GC-FID and GC/MS analyses. In the leaf waxes, 15 n-alkane homologs with chain-lengths ranging from C21 to C35 were identified. The main n-alkane in almost all samples was n-nonacosane (C29 ), but differences in the contents of three other dominant n-alkanes allowed separating the coastal from the continental populations. The diversity and variability of the epicuticular-leaf-n-alkane patterns and their relation to different geographic and bioclimatic parameters were analyzed by several statistical methods (principal component, discriminant, and cluster analyses as well as the Mantel test). All tests showed a high correlation between the leaf n-alkane pattern and the geographical distribution of the investigated populations, confirming the differentiation between S. montana subsp. pisidica and the other two subspecies. The S. montana subsp. variegata and S. montana subsp. montana populations are geographically closer and their differentiation according to the leaf-n-alkane patterns was not clear, even though there was some indication of discrimination between them. Moreover, most of the bioclimatic parameters related to temperature were highly correlated with the differentiation of the coastal and the continental populations.

  19. Ceramide acyl chain length markedly influences miscibility with palmitoyl sphingomyelin in bilayer membranes.

    PubMed

    Westerlund, Bodil; Grandell, Pia-Maria; Isaksson, Y Jenny E; Slotte, J Peter

    2010-07-01

    Ceramides are precursors of major sphingolipids and can be important cellular effectors. The biological effects of ceramides have been suggested to stem from their biophysical effects on membrane structure affecting the lateral and transbilayer organization of other membrane components. In this study we investigated the effect of acyl chain composition in ceramides (C4-C24:1) on their miscibility with N-palmitoyl-sphingomyelin (PSM) using differential scanning calorimetry. We found that short-chain (C4 and C8) ceramides induced phase separation and lowered the T (m) and enthalpy of the PSM endotherm. We conclude that short-chain ceramides were more miscible in the fluid-phase than in the gel-phase PSM bilayers. Long-chain ceramides induced apparent heterogeneity in the bilayers. The main PSM endotherm decreased in cooperativity and enthalpy with increasing ceramide concentration. New ceramide-enriched components could be seen in the thermograms at all ceramide concentrations above X (Cer) = 0.05. These broad components had higher T (m) values than pure PSM. C24:1 ceramide exhibited complex behavior in the PSM bilayers. The miscibility of C24:1 ceramide with PSM at low (X (Cer) = 0.05-0.10) concentrations was exceptionally good according to the cooperativity of the transition. At higher concentrations, multiple components were detected, which might have arisen from interdigitated gel-phases formed by this very asymmetric ceramide. The results of this study indicate that short-chain and long-chain ceramides have very different effects on the sphingomyelin bilayers. There also seems to be a correlation between their miscibility in binary systems and the effect of ceramides of different hydrophobic length on sphingomyelin-rich domains in multicomponent membranes.

  20. Protein–Ligand Interactions: Thermodynamic Effects Associated with Increasing the Length of an Alkyl Chain

    PubMed Central

    2013-01-01

    Thermodynamic parameters were determined for complex formation between the Grb2 SH2 domain and tripeptides of the general form Ac-pTyr-Xaa-Asn in which the Xaa residue bears a linear alkyl chain varying in length from 1–5 carbon atoms. Binding affinity increases upon adding a methylene group to the Ala derivative, but further chain extension gives no extra enhancement in potency. The thermodynamic signatures of the ethyl and n-propyl derivatives are virtually identical as are those for the n-butyl and n-pentyl analogues. Crystallographic analysis of the complexes reveals a high degree of similarity in the structure of the domain and the bound ligands with the notable exception that there is a gauche interaction in the side chains in the bound conformations of ligands having n-propyl, n-butyl, and n-pentyl groups. However, eliminating this unfavorable interaction by introducing a Z-double bond into the side chain of the n-propyl analogue does not result in an increase in affinity. Increases in the amount of nonpolar surface that is buried upon ligand binding correlate with favorable changes in ΔH°, but these are usually offset by corresponding unfavorable changes in −TΔS°; there is little correlation of ΔCp with changes in the amount of buried nonpolar surface. PMID:24349642

  1. Radiation crosslinking of a bacterial medium-chain-length poly(hydroxyalkanoate) elastomer from tallow.

    PubMed

    Ashby, R D; Cromwick, A M; Foglia, T A

    1998-07-01

    Pseudomonas resinovorans produces a medium-chain-length poly(hydroxyalkanoate) (MCL-PHA) copolymer when grown on tallow (PHA-tal). This polymer had a repeat unit composition ranging from C4 to C14 with some mono-unsaturation in the C12 and C14 alkyl side chains. Thermal analysis indicated that the polymer was semi-crystalline with a melting temperature (T(m)) of 43.5 +/- 0.2 degrees C and a glass transition temperature (Tg) of -43.4 +/- 2.0 degrees C. The presence of unsaturated side chains allowed crosslinking by gamma-irradiation. Irradiated polymer films had decreased solubility in organic solvents that indicated an increase in the crosslinking density within the film matrix. The addition of linseed oil to the gamma-irradiated film matrix enhanced polymer recovery while minimizing chain scission. Linseed oil also caused a decrease in the enthalpy of fusion (delta Hm) of the films (by an average of 60%) as well as enhanced mineralization. The effects of crosslinking on the mechanical properties and biodegradability of the polymer were determined. Radiation had no effect on the storage modulus (E') of the polymer. However, radiation doses of 25 and 50 kGy did increase the Young modulus of the polymer by 129 and 114%, and the tensile strength of the polymer by 76 and 35%, respectively. Finally, the formation of a higher crosslink density within the polymer matrix decreased the biodegradability of the PHA films.

  2. The role of discharge variation in scaling of drainage area and food chain length in rivers

    USGS Publications Warehouse

    Sabo, John L.; Finlay, Jacques C.; Kennedy, Theodore A.; Post, David M.

    2010-01-01

    Food chain length (FCL) is a fundamental component of food web structure. Studies in a variety of ecosystems suggest that FCL is determined by energy supply, environmental stability, and/or ecosystem size, but the nature of the relationship between environmental stability and FCL, and the mechanism linking ecosystem size to FCL, remain unclear. Here we show that FCL increases with drainage area and decreases with hydrologic variability and intermittency across 36 North American rivers. Our analysis further suggests that hydrologic variability is the mechanism underlying the correlation between ecosystem size and FCL in rivers. Ecosystem size lengthens river food chains by integrating and attenuating discharge variation through stream networks, thereby enhancing environmental stability in larger river systems.

  3. The role of discharge variation in scaling of drainage area and food chain length in rivers.

    PubMed

    Sabo, John L; Finlay, Jacques C; Kennedy, Theodore; Post, David M

    2010-11-12

    Food chain length (FCL) is a fundamental component of food web structure. Studies in a variety of ecosystems suggest that FCL is determined by energy supply, environmental stability, and/or ecosystem size, but the nature of the relationship between environmental stability and FCL, and the mechanism linking ecosystem size to FCL, remain unclear. Here we show that FCL increases with drainage area and decreases with hydrologic variability and intermittency across 36 North American rivers. Our analysis further suggests that hydrologic variability is the mechanism underlying the correlation between ecosystem size and FCL in rivers. Ecosystem size lengthens river food chains by integrating and attenuating discharge variation through stream networks, thereby enhancing environmental stability in larger river systems.

  4. Effect of surfactant alkyl chain length on soil cadmium desorption using surfactant/ligand systems.

    PubMed

    Shin, Mari; Barrington, Suzelle F; Marshall, William D; Kim, Jin-Woo

    2005-02-01

    The effect of surfactant alkyl chain length on soil Cd desorption was studied using nonionic surfactants of polyethylene oxide (PEO) of PEO chain lengths of 7.5 (Triton X-114), 9.5 (Triton X-100), 30 (Triton X-305), or 40 units (Triton X-405) in combination with the I- ligand. Triplicate 1 g soil samples were equilibrated with 15 ml of surfactant-ligand mixture, at concentrations of 0.025, 0.50 or 0.10, and 0.0, 0.168 or 0.336 mol/l, respectively. After shaking the samples for 24 h, the supernatant fraction was analyzed for Cd content to determine the percent of Cd desorbed from the soil. After five successive washings, 53%, 40% and 25% of Cd had been desorbed by 0.025, 0.050 or 0.10 mol/l of Triton X-114, respectively, in the presence of 0.336 mol/l of I-, whereas with the same conditions, Triton X-100 desorbed 61%, 57% and 56% Cd and either Triton X-305 or Triton X-405 desorbed 51, 40 and 14 to 16% Cd. The most efficient Cd desorption was obtained using 0.025 mol/l Triton X-100 in admixture with 0.336 mol/l I-. Increased surfactant concentration was detrimental to Cd desorption consistent with a process that blocked ligand access to the soil particle surface. After 5 washings,the cumulative cadmium desorption decreased with increasing surfactant alkyl chain length, indicating that the metal-ligand complexes are preferably stabilized by the micelles' hydrophobic octyl phenyl (OP) group rather than by the hydrophilic PEO group. In the absence of ligand, the surfactants alone desorbed less than 1% Cd from the contaminated soil, suggesting that the ligand, rather than the surfactant, extracts the metal, to be subsequently stabilized within the surfactant micelles.

  5. Acyl chain length and charge effect on Tamoxifen-lipid model membrane interactions

    NASA Astrophysics Data System (ADS)

    Bilge, Duygu; Kazanci, Nadide; Severcan, Feride

    2013-05-01

    Tamoxifen (TAM), which is an antiestrogenic agent, is widely used during chemotherapy of breast, pancreas, brain and liver cancers. In this study, TAM and model membrane interactions in the form of multilamellar vesicles (MLVs) were studied for lipids containing different acyl chain length and different charge status as a function of different TAM (1, 6, 9 and 15 mol%) concentrations. Zwitterionic lipids namely dipalmitoyl phosphatidylcholine (DPPC), and dimyristoylphosphatidylcholine (DMPC) lipids were used to see the acyl chain length effect and anionic dipalmitoyl phosphtidylglycerol (DPPG) lipid was used to see the charge effect. For this purpose Fourier transform-infrared (FTIR) spectroscopic and differential scanning calorimetric (DSC) techniques have been conducted. For zwitterionic lipid, concentration dependent different action of TAM was observed both in the gel and liquid crystalline phases by significantly increasing the lipid order and decreasing the dynamics for 1 mol% TAM, while decreasing the lipid order and increasing the dynamics of the lipids for higher concentrations (6, 9 and 15 mol%). However, different than neutral lipids, the dynamics and disorder of DPPG liposome increased for all TAM concentrations. The interactions between TAM and head group of multilamellar liposomes was monitored by analyzing the Cdbnd O stretching and PO2- antisymmetric double bond stretching bands. Increasing Tamoxifen concentrations led to a dehydration around these functional groups in the polar part of the lipids. DSC studies showed that for all types of lipids, TAM eliminates the pre-transition, shifts the main phase transition to lower temperatures and broadened the phase transition curve. The results indicate that not the acyl chain length but the charge status of the polar head group induces different effects on lipid membranes order and dynamics.

  6. Dependence of micelle size and shape on detergent alkyl chain length and head group.

    PubMed

    Oliver, Ryan C; Lipfert, Jan; Fox, Daniel A; Lo, Ryan H; Doniach, Sebastian; Columbus, Linda

    2013-01-01

    Micelle-forming detergents provide an amphipathic environment that can mimic lipid bilayers and are important tools for solubilizing membrane proteins for functional and structural investigations in vitro. However, the formation of a soluble protein-detergent complex (PDC) currently relies on empirical screening of detergents, and a stable and functional PDC is often not obtained. To provide a foundation for systematic comparisons between the properties of the detergent micelle and the resulting PDC, a comprehensive set of detergents commonly used for membrane protein studies are systematically investigated. Using small-angle X-ray scattering (SAXS), micelle shapes and sizes are determined for phosphocholines with 10, 12, and 14 alkyl carbons, glucosides with 8, 9, and 10 alkyl carbons, maltosides with 8, 10, and 12 alkyl carbons, and lysophosphatidyl glycerols with 14 and 16 alkyl carbons. The SAXS profiles are well described by two-component ellipsoid models, with an electron rich outer shell corresponding to the detergent head groups and a less electron dense hydrophobic core composed of the alkyl chains. The minor axis of the elliptical micelle core from these models is constrained by the length of the alkyl chain, and increases by 1.2-1.5 Å per carbon addition to the alkyl chain. The major elliptical axis also increases with chain length; however, the ellipticity remains approximately constant for each detergent series. In addition, the aggregation number of these detergents increases by ∼16 monomers per micelle for each alkyl carbon added. The data provide a comprehensive view of the determinants of micelle shape and size and provide a baseline for correlating micelle properties with protein-detergent interactions.

  7. The effect of elastomer chain length on properties of silicone-modified polyimide adhesives

    NASA Technical Reports Server (NTRS)

    St.clair, A. K.; St.clair, T. L.; Ezzell, S.

    1981-01-01

    A series of polyimides containing silicone elastomers was synthesized in order to study the effects of the elastomer chain length on polymer properties. The elastomer with repeat units varying from n=10 to 105 was chemically reacted into the backbone of an addition polyimide oligomer via reactive aromatic amine groups. Glass transition temperatures of the elastomer and polyimide phases were observed by torsional braid analysis. The elastomer-modified polyimides were tested as adhesives for bonding titanium in order to determine their potential for aerospace applications. Adhesive lap shear tests were performed before and after aging bonded specimens at elevated temperatures.

  8. Shape control of the magnetic iron oxide nanoparticles under different chain length of reducing agents

    SciTech Connect

    Ngoi, Kuan Hoon; Chia, Chin-Hua Zakaria, Sarani; Chiu, Wee Siong

    2015-09-25

    We report on the effect of using reducing agents with different chain-length on the synthesis of iron oxide nanoparticles by thermal decomposition of iron (III) acetylacetonate in 1-octadecene. This modification allows us to control the shape of nanoparticles into spherical and cubic iron oxide nanoparticles. The highly monodisperse 14 nm spherical nanoparticles are obtained under 1,2-dodecanediol and average 14 nm edge-length cubic iron oxide nanoparticles are obtained under 1,2-tetradecanediol. The structural characterization such as transmission electron microscope (TEM) and X-ray diffraction (XRD) shows similar properties between two particles with different shapes. The vibrating sample magnetometer (VSM) shows no significant difference between spherical and cubic nanoparticles, which are 36 emu/g and 37 emu/g respectively and superparamagnetic in nature.

  9. Succession of Alkane Conformational Motifs Bound within Hydrophobic Supramolecular Capsular Assemblies.

    PubMed

    Barnett, J Wesley; Gibb, Bruce C; Ashbaugh, Henry S

    2016-10-06

    n-Alkane encapsulation experiments within dimeric octa-acid cavitand capsules in water reveal a succession of packing motifs from extended, to helical, to hairpin, to spinning top structures with increasing chain length. Here, we report a molecular simulation study of alkane conformational preferences within these host-guest assemblies to uncover the factors stabilizing distinct conformers. The simulated alkane conformers follow the trends inferred from (1)H NMR experiments, while guest proton chemical shifts evaluated from Gauge Invariant Atomic Orbital calculations provide further evidence our simulations capture guest packing within these assemblies. Analysis of chain length and dihedral distributions indicates that packing under confinement to minimize nonpolar guest and host interior contact with water largely drives the transitions. Mean intramolecular distance maps and transfer free energy differences suggest the extended and helical motifs are members of a larger family of linear guest structures, for which the guest gauche population increases with increasing chain length to accommodate the chains within the complex. Breaks observed between the helical/hairpin and hairpin/spinning top motifs, on the other hand, indicate the hairpin and spinning top conformations are distinct from the linear family. Our results represent the first bridging of empirical and simulation data for flexible guests encapsulated within confined nanospaces, and constitute an effective strategy by which guest packing motifs within artificial or natural compartments can be rationalized and/or predicted a priori.

  10. Self-Aggregation of Amphiphilic Dendrimer in Aqueous Solution: The Effect of Headgroup and Hydrocarbon Chain Length.

    PubMed

    Zhang, Pei; Xu, Xiaohui; Zhang, Minghui; Wang, Jinben; Bai, Guangyue; Yan, Haike

    2015-07-28

    The self-aggregation of amphiphilic dendrimers G1QPAMCm based on poly(amidoamine) PAMAM possessing the same hydrophilic group but differing in alkyl chain length in aqueous solution was investigated. Differences in the chemical structures lead to significant specificities in the aggregate building process. A variety of physicochemical parameters presented monotonous regularity with the increase in alkyl chain length in multibranched structure, as traditional amphiphilic molecules. A significant difference, however, existed in the morphology and the microenvironment of the microdomain of the aggregates, with G1QPAMCm with an alkyl chain length of 16 intending to form vesicles. To obtain supporting information about the aggregation mechanism, the thermodynamic parameters of micellization, the free Gibbs energy ΔGmic, and the entropy ΔSmic were derived subsequently, of which the relationship between the hydrophobic chain length and the thermodynamic properties indicated that the self-assembly process was jointly driven by enthalpy and entropy. Other than traditional surfactants, the contribution of enthalpy has not increased identically to the increase in hydrophobic interactions, which depends on the ratio of the alkyl chain length to the radius in the headgroup. Continuous increases in the hydrophobic chain length from 12 to 16 lead to the intracohesion of the alkyl chain involved in the process of self-assembly, weakening the hydrophobic interactions, and the increase in -ΔHmic, which offers an explanation of the formation of vesicular structures.

  11. Production of medium chain length fatty alcohols from glucose in Escherichia coli

    PubMed Central

    Youngquist, J. Tyler; Schumacher, Martin H.; Rose, Joshua P.; Raines, Thomas C.; Politz, Mark C.; Copeland, Matthew F.; Pfleger, Brian F.

    2013-01-01

    Metabolic engineering offers the opportunity to produce a wide range of commodity chemicals that are currently derived from petroleum or other non-renewable resources. Microbial synthesis of fatty alcohols is an attractive process because it can control the distribution of chain lengths and utilize low cost fermentation substrates. Specifically, primary alcohols with chain lengths of 12 to 14 carbons have many uses in the production of detergents, surfactants, and personal care products. The current challenge is to produce these compounds at titers and yields that would make them economically competitive. Here, we demonstrate a metabolic engineering strategy for producing fatty alcohols from glucose. To produce a high level of 1-dodecanol and 1-tetradecanol, an acyl-ACP thioesterase (BTE), an acyl-CoA ligase (FadD), and an acyl-CoA/aldehyde reductase (MAACR) were overexpressed in an engineered strain of Escherichia coli. Yields were improved by balancing expression levels of each gene, using a fed-batch cultivation strategy, and adding a solvent to the culture for extracting the product from cells. Using these strategies, a titer of over 1.6 g/L fatty alcohol with a yield of over 0.13 g fatty alcohol / g carbon source was achieved. These are the highest reported yield of fatty alcohols produced from glucose in E. coli. PMID:24141053

  12. The effect of chain length on protein solubilization in polymer-based vesicles (polymersomes).

    PubMed

    Pata, Veena; Dan, Nily

    2003-10-01

    Using a mean-field analysis we derive a consistent model for the perturbation of a symmetric polymeric bilayer due to the incorporation of transmembrane proteins, as a function of the polymer molecular weight and the protein dimensions. We find that the mechanism for the inhibition of protein incorporation in polymeric bilayers differs from that of their inclusion in polymer-carrying lipid vesicles; in polymersomes, the equilibrium concentration of transmembrane proteins decreases as a function of the thickness mismatch between the protein and the bilayer core, whereas in liposomes the presence of polymer chains affects the protein adsorption kinetics. Despite the increased stiffness of polymer bilayers (when compared to lipid ones), their perturbation decay length and range of protein-protein interaction is found to be relatively long. The energetic penalty due to protein adsorption increases relatively slowly as a function of the polymer chain length due to the self-assembled nature of the polymer bilayer. As a result, we predict that transmembrane proteins may be incorporated in significant numbers even in bilayers where the thickness mismatch is large.

  13. Production of medium chain length fatty alcohols from glucose in Escherichia coli.

    PubMed

    Youngquist, J Tyler; Schumacher, Martin H; Rose, Joshua P; Raines, Thomas C; Politz, Mark C; Copeland, Matthew F; Pfleger, Brian F

    2013-11-01

    Metabolic engineering offers the opportunity to produce a wide range of commodity chemicals that are currently derived from petroleum or other non-renewable resources. Microbial synthesis of fatty alcohols is an attractive process because it can control the distribution of chain lengths and utilize low cost fermentation substrates. Specifically, primary alcohols with chain lengths of 12 to 14 carbons have many uses in the production of detergents, surfactants, and personal care products. The current challenge is to produce these compounds at titers and yields that would make them economically competitive. Here, we demonstrate a metabolic engineering strategy for producing fatty alcohols from glucose. To produce a high level of 1-dodecanol and 1-tetradecanol, an acyl-ACP thioesterase (BTE), an acyl-CoA ligase (FadD), and an acyl-CoA/aldehyde reductase (MAACR) were overexpressed in an engineered strain of Escherichia coli. Yields were improved by balancing expression levels of each gene, using a fed-batch cultivation strategy, and adding a solvent to the culture for extracting the product from cells. Using these strategies, a titer of over 1.6 g/L fatty alcohol with a yield of over 0.13 g fatty alcohol/g carbon source was achieved. These are the highest reported yield of fatty alcohols produced from glucose in E. coli.

  14. Effect of polymer chain length on membrane perturbation activity of cationic phenylene ethynylene oligomers and polymers.

    PubMed

    Wang, Ying; Jones, Emmalee M; Tang, Yanli; Ji, Eunkyung; Lopez, Gabriel P; Chi, Eva Y; Schanze, Kirk S; Whitten, David G

    2011-09-06

    The interactions of poly(phenylene ethynylene)- (PPE-) based cationic conjugated polyelectrolytes (CPEs) and oligo(phenylene ethynylene)s (OPEs) with different model lipid membrane systems were investigated to gain insight into the relationship between molecular structure and membrane perturbation ability. The CPE and OPE compounds exhibit broad-spectrum antimicrobial activity, and cell walls and membranes are believed to be their main targets. To better understand how the size, in terms of the number of repeat units, of the CPEs and OPEs affects their membrane disruption activities, a series of PPE-based CPEs and OPEs were synthesized and studied. A number of photophysical techniques were used to investigate the interactions of CPEs and OPEs with model membranes, including unilamellar vesicles and lipid monolayers at the air/water interface. CPE- or OPE-induced dye leakage from vesicles reveals that the CPEs and OPEs selectively perturb model bacterial membranes and that their membrane perturbation abilities are highly dependent on molecular size. Consistent with dye-leakage assay results, the CPEs and OPEs also exhibit chain-length-dependent ability to insert into 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG) monolayers. Our results suggest that, for PPE-based CPE and OPE antimicrobials, chain length can be tuned to optimize their membrane perturbation ability.

  15. Influence of Solute Charge and Pyrrolidinium Ionic Liquid Alkyl Chain Length on Probe Rotational Reorientation Dynamics

    SciTech Connect

    Guo, Jianchang; Mahurin, Shannon Mark; Baker, Gary A; Hillesheim, Patrick C; Dai, Sheng; Shaw, Robert W

    2014-01-01

    In recent years, the effect of molecular charge on the rotational dynamics of probe solutes in room temperature ionic liquids (RTILs) has been a subject of growing interest. For the purpose of extending our understanding of charged solute behavior within RTILs, we have studied the rotational dynamics of three illustrative xanthene fluorescent probes within a series of N-alkylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([Cnmpyr][Tf2N]) RTILs with different n-alkyl chain lengths (n = 3, 4, 6, 8, or 10) using time-resolved fluorescence anisotropy decay. The rotational dynamics of the neutral probe rhodamine B dye lies between the stick and slip boundary conditions due to the influence of specific hydrogen bonding interactions. The rotation of the negatively-charged sulforhodamine 640 is slower than that of its positively-charged counterpart rhodamine 6G. An analysis based upon Stokes-Einstein-Debye hydrodynamics indicates that SR640 adheres to stick boundary conditions due to specific interactions, whereas the faster rotation of R6G is attributed to weaker electrostatic interactions. No dependence of the rotational dynamics on the solvent alkyl chain length was observed for any of the three dyes, suggesting that the specific interactions between dyes and RTILs are independent of this solvent parameter.

  16. The effect of oxygen heteroatoms on the single molecule conductance of saturated chains.

    PubMed

    Wierzbinski, Emil; Yin, Xing; Werling, Keith; Waldeck, David H

    2013-04-25

    Single molecule conductance measurements on alkanedithiols and alkoxydithiols (dithiolated oligoethers) were performed using the STM-controlled break junction method in order to ascertain how the oxygen heteroatoms in saturated linear chains impact the molecular conductance. The experimental results show that the difference in conductance increases with chain length, over the range studied. Comparisons with electronic structure calculations and previous work on alkanes indicate that the conductance of the oligoethers is lower than that of alkane chains with the same length. Electronic structure calculations allow the difference in the conductance of these two families of molecules to be traced to differences in the spatial distribution of the molecular orbitals that contribute most to the conductance. A pathway analysis of the electronic coupling through the chain is used to explain how the difference in conductance between the alkane and oligoether molecules depends on the chain length.

  17. Synthesis Gas (Syngas)-Derived Medium-Chain-Length Polyhydroxyalkanoate Synthesis in Engineered Rhodospirillum rubrum

    PubMed Central

    Heinrich, Daniel; Raberg, Matthias; Fricke, Philipp; Kenny, Shane T.; Morales-Gamez, Laura; Babu, Ramesh P.; O'Connor, Kevin E.

    2016-01-01

    ABSTRACT The purple nonsulfur alphaproteobacterium Rhodospirillum rubrum S1 was genetically engineered to synthesize a heteropolymer of mainly 3-hydroxydecanoic acid and 3-hydroxyoctanoic acid [P(3HD-co-3HO)] from CO- and CO2-containing artificial synthesis gas (syngas). For this, genes from Pseudomonas putida KT2440 coding for a 3-hydroxyacyl acyl carrier protein (ACP) thioesterase (phaG), a medium-chain-length (MCL) fatty acid coenzyme A (CoA) ligase (PP_0763), and an MCL polyhydroxyalkanoate (PHA) synthase (phaC1) were cloned and expressed under the control of the CO-inducible promoter PcooF from R. rubrum S1 in a PHA-negative mutant of R. rubrum. P(3HD-co-3HO) was accumulated to up to 7.1% (wt/wt) of the cell dry weight by a recombinant mutant strain utilizing exclusively the provided gaseous feedstock syngas. In addition to an increased synthesis of these medium-chain-length PHAs (PHAMCL), enhanced gene expression through the PcooF promoter also led to an increased molar fraction of 3HO in the synthesized copolymer compared with the Plac promoter, which regulated expression on the original vector. The recombinant strains were able to partially degrade the polymer, and the deletion of phaZ2, which codes for a PHA depolymerase most likely involved in intracellular PHA degradation, did not reduce mobilization of the accumulated polymer significantly. However, an amino acid exchange in the active site of PhaZ2 led to a slight increase in PHAMCL accumulation. The accumulated polymer was isolated; it exhibited a molecular mass of 124.3 kDa and a melting point of 49.6°C. With the metabolically engineered strains presented in this proof-of-principle study, we demonstrated the synthesis of elastomeric second-generation biopolymers from renewable feedstocks not competing with human nutrition. IMPORTANCE Polyhydroxyalkanoates (PHAs) are natural biodegradable polymers (biopolymers) showing properties similar to those of commonly produced petroleum-based nondegradable

  18. Pruned-enriched Rosenbluth method: Simulations of {theta} polymers of chain length up to 1000000

    SciTech Connect

    Grassberger, P. |

    1997-09-01

    We present an algorithm for simulating flexible chain polymers. It combines the Rosenbluth-Rosenbluth method with recursive enrichment. Although it can be applied also in more general situations, it is most efficient for three-dimensional {theta} polymers on the simple-cubic lattice. There it allows high statistics simulations of chains of length up to N=10{sup 6}. For storage reasons, this is feasable only for polymers in a finite volume. For free {theta} polymers in infinite volume, we present very high statistics runs with N=10000. These simulations fully agree with previous simulations made by Hegger and Grassberger [J. Chem. Phys. {bold 102}, 6681 (1995)] with a similar but less efficient algorithm, showing that logarithmic corrections to mean field behavior are much stronger than predicted by field theory. But the finite volume simulations show that the density inside a collapsed globule scales with the distance from the {theta} point as predicted by mean field theory, in contrast to claims in the work mentioned above. In addition to the simple-cubic lattice, we also studied two versions of the bond fluctuation model, but with much shorter chains. Finally, we show that our method can be applied also to off-lattice models, and illustrate this with simulations of a model studied in detail by Freire {ital et al.} [Macromolecules {bold 19}, 452 (1986) and later work]. {copyright} {ital 1997} {ital The American Physical Society}

  19. Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains

    PubMed Central

    Liao, Weinan; Ren, Jie; Wang, Kun; Wang, Shun; Zeng, Feng; Wang, Ying; Sun, Fengzhu

    2016-01-01

    The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC). Under a fixed high order of MC, the parameters might not be accurately estimated owing to the limitation of sequencing depth. In our study, we investigate an alternative to FOMC to model background sequences with the data-driven Variable Length Markov Chain (VLMC) in metatranscriptomic data. The VLMC originally designed for long sequences was extended to apply to high-throughput sequencing reads and the strategies to estimate the corresponding parameters were developed. The flexible number of parameters in VLMC avoids estimating the vast number of parameters of high-order MC under limited sequencing depth. Different from the manual selection in FOMC, VLMC determines the MC order adaptively. Several beta diversity measures based on VLMC were applied to compare the bacterial RNA-Seq and metatranscriptomic datasets. Experiments show that VLMC outperforms FOMC to model the background sequences in transcriptomic and metatranscriptomic samples. A software pipeline is available at https://d2vlmc.codeplex.com. PMID:27876823

  20. Bridging Adhesion of Mussel-Inspired Peptides: Role of Charge, Chain Length, and Surface Type

    PubMed Central

    2015-01-01

    The 3,4-dihydroxyphenylalanine (Dopa)-containing proteins of marine mussels provide attractive design paradigms for engineering synthetic polymers that can serve as high performance wet adhesives and coatings. Although the role of Dopa in promoting adhesion between mussels and various substrates has been carefully studied, the context by which Dopa mediates a bridging or nonbridging macromolecular adhesion to surfaces is not understood. The distinction is an important one both for a mechanistic appreciation of bioadhesion and for an intelligent translation of bioadhesive concepts to engineered systems. On the basis of mussel foot protein-5 (Mfp-5; length 75 res), we designed three short, simplified peptides (15–17 res) and one relatively long peptide (30 res) into which Dopa was enzymatically incorporated. Peptide adhesion was tested using a surface forces apparatus. Our results show that the short peptides are capable of weak bridging adhesion between two mica surfaces, but this adhesion contrasts with that of full length Mfp-5, in that (1) while still dependent on Dopa, electrostatic contributions are much more prominent, and (2) whereas Dopa surface density remains similar in both, peptide adhesion is an order of magnitude weaker (adhesion energy Ead ∼ −0.5 mJ/m2) than full length Mfp-5 adhesion. Between two mica surfaces, the magnitude of bridging adhesion was approximately doubled (Ead ∼ −1 mJ/m2) upon doubling the peptide length. Notably, the short peptides mediate much stronger adhesion (Ead ∼ −3.0 mJ/m2) between mica and gold surfaces, indicating that a long chain length is less important when different interactions are involved on each of the two surfaces. PMID:25540823

  1. Bridging adhesion of mussel-inspired peptides: role of charge, chain length, and surface type.

    PubMed

    Wei, Wei; Yu, Jing; Gebbie, Matthew A; Tan, Yerpeng; Martinez Rodriguez, Nadine R; Israelachvili, Jacob N; Waite, J Herbert

    2015-01-27

    The 3,4-dihydroxyphenylalanine (Dopa)-containing proteins of marine mussels provide attractive design paradigms for engineering synthetic polymers that can serve as high performance wet adhesives and coatings. Although the role of Dopa in promoting adhesion between mussels and various substrates has been carefully studied, the context by which Dopa mediates a bridging or nonbridging macromolecular adhesion to surfaces is not understood. The distinction is an important one both for a mechanistic appreciation of bioadhesion and for an intelligent translation of bioadhesive concepts to engineered systems. On the basis of mussel foot protein-5 (Mfp-5; length 75 res), we designed three short, simplified peptides (15-17 res) and one relatively long peptide (30 res) into which Dopa was enzymatically incorporated. Peptide adhesion was tested using a surface forces apparatus. Our results show that the short peptides are capable of weak bridging adhesion between two mica surfaces, but this adhesion contrasts with that of full length Mfp-5, in that (1) while still dependent on Dopa, electrostatic contributions are much more prominent, and (2) whereas Dopa surface density remains similar in both, peptide adhesion is an order of magnitude weaker (adhesion energy E(ad) ∼ -0.5 mJ/m(2)) than full length Mfp-5 adhesion. Between two mica surfaces, the magnitude of bridging adhesion was approximately doubled (E(ad) ∼ -1 mJ/m(2)) upon doubling the peptide length. Notably, the short peptides mediate much stronger adhesion (E(ad) ∼ -3.0 mJ/m(2)) between mica and gold surfaces, indicating that a long chain length is less important when different interactions are involved on each of the two surfaces.

  2. Characterization of a Novel Subgroup of Extracellular Medium-Chain-Length Polyhydroxyalkanoate Depolymerases from Actinobacteria

    PubMed Central

    Gangoiti, Joana; Santos, Marta; Prieto, María Auxiliadora; de la Mata, Isabel; Llama, María J.

    2012-01-01

    Nineteen medium-chain-length (mcl) poly(3-hydroxyalkanoate) (PHA)-degrading microorganisms were isolated from natural sources. From them, seven Gram-positive and three Gram-negative bacteria were identified. The ability of these microorganisms to hydrolyze other biodegradable plastics, such as short-chain-length (scl) PHA, poly(ε-caprolactone) (PCL), poly(ethylene succinate) (PES), and poly(l-lactide) (PLA), has been studied. On the basis of the great ability to degrade different polyesters, Streptomyces roseolus SL3 was selected, and its extracellular depolymerase was biochemically characterized. The enzyme consisted of one polypeptide chain of 28 kDa with a pI value of 5.2. Its maximum activity was observed at pH 9.5 with chromogenic substrates. The purified enzyme hydrolyzed mcl PHA and PCL but not scl PHA, PES, and PLA. Moreover, the mcl PHA depolymerase can hydrolyze various substrates for esterases, such as tributyrin and p-nitrophenyl (pNP)-alkanoates, with its maximum activity being measured with pNP-octanoate. Interestingly, when poly(3-hydroxyoctanoate-co-3-hydroxyhexanoate [11%]) was used as the substrate, the main hydrolysis product was the monomer (R)-3-hydroxyoctanoate. In addition, the genes of several Actinobacteria strains, including S. roseolus SL3, were identified on the basis of the peptide de novo sequencing of the Streptomyces venezuelae SO1 mcl PHA depolymerase by tandem mass spectrometry. These enzymes did not show significant similarity to mcl PHA depolymerases characterized previously. Our results suggest that these distinct enzymes might represent a new subgroup of mcl PHA depolymerases. PMID:22865072

  3. ELISA assays and alcohol: increasing carbon chain length can interfere with detection of cytokines.

    PubMed

    von Maltzan, Kristine; Pruett, Stephen B

    2011-02-01

    Enzyme-linked immunosorbent assays (ELISAs) are frequently used in studies on cytokine production in response to treatment of cell cultures or laboratory animals. When an ELISA assay is performed on cell culture supernatants, samples often contain the treatment agents. The purpose of the present study was to determine if some of the agents evaluated might inhibit cytokine detection by interfering with the ELISA, leaving the question of whether cytokine production was inhibited unanswered. Mouse and human cytokine ELISA kits from BD Biosciences were used according to the manufacturer's instructions. Cytokine proteins were subjected to one to five carbon alcohols at 86.8mM (methanol, ethanol, 1-propanol, 2-propanol, n-butanol, and n-pentanol). After treating cell cultures with alcohols of different carbon chain lengths, we found that some of the alcohols interfered with measurement of some cytokines by ELISA, thus making their effects on cytokine production by cells in culture unclear. Increasing carbon chain length of straight chain alcohols positively correlated with their ability to inhibit detection of tumor necrosis factor alpha (TNF-α) and interleukin 10 (IL-10), but not with the detection of interleukin 6 (IL-6), interleukin 8, (IL-8), and interleukin 12 (IL-12). To avoid misinterpretation of treatment effects, ELISA assays should be tested with the reference protein and the treatment agent first, before testing biological samples. These results along with other recent results we obtained using circular dichroism indicate that alcohols with two or more carbons can directly alter protein conformation enough to disrupt binding in an ELISA (shown in the present study) or to inhibit ligand-induced conformational changes (results not shown). Such direct effects have not been given enough consideration as a mechanism of ethanol action in the immune system.

  4. Spatial and temporal variability in air concentrations of short-chain (C10-C13) and medium-chain (C14-C17) chlorinated n-alkanes measured in the U.K. atmosphere.

    PubMed

    Barber, Jonathan L; Sweetman, Andy J; Thomas, Gareth O; Braekevelt, Eric; Stern, Gary A; Jones, Kevin C

    2005-06-15

    Two studies were carried out on short-chain (C10-C13) and medium-chain (C14-C17) polychlorinated n-alkanes (sPCAs and mPCAs) in U.K. air samples. The first study entailed taking 20 24-h air samples with a pair of Hi-Vol air samplers at the Hazelrigg field station, near Lancaster University. These samples were carefully selected to coincide with times when air masses were predicted to have a fairly constant back trajectory for 24 h and to give a broad spectrum of different origins. The second study was a spatial survey of PCAs in the air at 20 outdoor sites in northern England and four indoor locations in Lancaster, using polyurethane foam (PUF) disk passive air samplers. Levels of the sPCAs in the Hi-Vol samples ranged from <185 to 3430 pg m(-3) (average 1130 pg m(-3)) and were higher than those previously measured at this site in 1997. Levels of the mPCAs ranged from <811 to 14500 pg m(-3) (average 3040 pg m(-3)); that is, they were higher than sPCAs. Both sPCA and mPCA air concentrations are of the same order of magnitude as PAH at this site. Back trajectory analysis showed that the history of the air mass in the 48 h prior to sampling had an important effect on the concentrations observed, with overland samples having higher levels than oceanic, implying that the U.K. is probably responsible for most of the PCAs measured in the U.K. atmosphere. Amounts of both sPCAs and mPCAs in the passive air samples followed a rural-urban gradient. PCAs appear to be released from multiple sources around the country, as a result of the diffusive, open industrial and construction use of the technical mixtures.

  5. Effect of Heparin Oligomer Chain Length on the Activation of Valvular Interstitial Cells

    PubMed Central

    Pedron, Sara; Kasko, Andrea M.; Peinado, Carmen; Anseth, Kristi S.

    2010-01-01

    A key event in connective tissue remodeling involves the transformation of fibroblasts to myofibroblasts, also revealed by expression of α-smooth muscle actin (α-SMA). However, misregulation of this transition can lead to fibrosis, an overgrowth and hardening of tissue due to excess extracellular matrix deposition, a process that is linked to heart valve disease and many others. Both disease treatment and regenerative strategies would benefit from strategies for the controlled delivery and presentation of bioactive factors that can promote or suppress this transformation. In this regard, the ability of heparin to complex a plethora of growth factors offers a broad range of possibilities for this purpose. Here, the effects of heparin chain length and structure on valvular interstitial cell (VIC) phenotypic expression were explored. Heparin from porcine intestinal mucosa was depolymerized with heparinase and fractionated to obtain oligosaccharides of different sizes. VICs cultured with octasaccharides and decasaccharides exhibited higher expression of a-SMA when compared to other saccharides and full-length heparin. No activation of VICs was observed in response to full-length heparin presence in media. PMID:20446725

  6. Exploring extraction/dissolution procedures for analysis of starch chain-length distributions.

    PubMed

    Wu, Alex Chi; Li, EnPeng; Gilbert, Robert G

    2014-12-19

    The analysis of starch chain-length distributions (CLDs) is important for understanding starch biosythesis-structure-property relations. It is obtained by analyzing the number distribution of the linear glucan chains released by enzymatic debranching of starch α-(1→6) glycosidic bonds for subsequent characterization by techniques such as fluorophore-assisted carbohydrate electrophoresis (FACE) or size-exclusion chromatography (SEC). Current literature pretreatments for debranching prior to CLD determination involve varying protocols, which might yield artifactual results. This paper examines the two widely used starch dissolution treatments with dimethyl sulfoxide (DMSO) containing 0.5% (w/w) lithium bromide (DMSO-LiBr) at 80°C and with aqueous alkaline (i.e. NaOH) solvents at 100 ˚C. Analyses by FACE with a very high range of degree of polymerization, and by SEC, of the CLD of barley starches with different structures show the following. (1) The NaOH treatment, even at a dilute concentration, causes significant degradation at higher degrees of polymerization, leading to quantitatively incorrect CLD results in longer amylopectin and in amylose chains. (2) Certain features in both amylopectin and amylose fractions of the CLD reduced to bumps or are missing with NaOH treatment. (3) Overestimation of amylose chains in starch CLD due to incomplete amylopectin dissolution with dilute NaOH concentration. These results indicate starch dissolution with DMSO-LiBr is the method of choice for minimizing artifacts. An improved pretreatment protocol is presented for starch CLD analysis by FACE and SEC.

  7. Clusterin: full-length protein and one of its chains show opposing effects on cellular lipid accumulation

    PubMed Central

    Matukumalli, Suvarsha Rao; Tangirala, Ramakrishna; Rao, C. M.

    2017-01-01

    Proteins, made up of either single or multiple chains, are designed to carry out specific biological functions. We found an interesting example of a two-chain protein where administration of one of its chains leads to a diametrically opposite outcome than that reported for the full-length protein. Clusterin is a highly glycosylated protein consisting of two chains, α- and β-clusterin. We have investigated the conformational features, cellular localization, lipid accumulation, in vivo effects and histological changes upon administration of recombinant individual chains of clusterin. We demonstrate that recombinant α- and β-chains exhibit structural and functional differences and differ in their sub-cellular localization. Full-length clusterin is known to lower lipid levels. In contrast, we find that β-chain-treated cells accumulate 2-fold more lipid than controls. Interestingly, α-chain-treated cells do not show such increase. Rabbits injected with β-chain, but not α-chain, show ~40% increase in weight, with adipocyte hypertrophy, liver and kidney steatosis. Many, sometimes contrasting, roles are ascribed to clusterin in obesity, metabolic syndrome and related conditions. Our findings of differential localization and activities of individual chains of clusterin should help in understanding better the roles of clusterin in metabolism. PMID:28120874

  8. Effect of varying the 1-4 intramolecular scaling factor in atomistic simulations of long-chain N-alkanes with the OPLS-AA model.

    PubMed

    Ye, Xianggui; Cui, Shengting; de Almeida, Valmor F; Khomami, Bamin

    2013-03-01

    A comprehensive molecular dynamics simulation study of n-alkanes using the optimized potential for liquid simulation with all-atoms (OPLS-AA) force field at ambient condition has been performed. Our results indicate that while simulations with the OPLS-AA force field accurately predict the liquid state mass density for n-alkanes with carbon number equal or less than 10, for n-alkanes with carbon number equal or exceeding 12, the OPLS-AA force field with the standard scaling factor for the 1-4 intramolecular Van der Waals and electrostatic interaction gives rise to a quasi-crystalline structure. We found that accurate predictions of the liquid state properties are obtained by successively reducing the aforementioned scaling factor for each increase of the carbon number beyond n-dodecane. To better understand the effects of reducing the scaling factor, its influence on the torsion potential profile, and the corresponding gauche-trans conformer distribution, heat of vaporization, melting point, and self-diffusion coefficient for n-dodecane were investigated. This relatively simple procedure enables more accurate predictions of the thermo-physical properties of longer n-alkanes.

  9. Effect of Varying the 1-4 Intramolecular Scaling Factor in Atomistic Simulations of Long-Chain N-alkanes with the OPLS-AA Model

    SciTech Connect

    de Almeida, Valmor F; Ye, Xianggui; Cui, Shengting; Khomami, Bamin

    2013-01-01

    A comprehensive molecular dynamics simulation study of n-alkanes using the Optimized Potential for Liquid Simulation-All Atoms (OPLS-AA) force field at ambient condition has been performed. Our results indicate that while simulations with the OPLS-AA force field accurately predict the liquid state mass density for n-alkanes with carbon number equal or less than 10, for n-alkanes with carbon number equal or exceeding 12, the OPLS-AA force field with the standard scaling factor for the 1-4 intramolecular Van der Waals and electrostatic interaction gives rise to a quasi-crystalline structure. We found that accurate predictions of the liquid state properties are obtained by successively reducing the aforementioned scaling factor for each increase of the carbon number beyond n-dodecane. To better un-derstand the effects of reducing the scaling factor, we analyzed the variation of the torsion potential pro-file with the scaling factor, and the corresponding impact on the gauche-trans conformer distribution, heat of vaporization, melting point, and self-diffusion coefficient for n-dodecane. This relatively simple procedure thus allows for more accurate predictions of the thermo-physical properties of longer n-alkanes.

  10. Influence of chain lengths of liquid crystals on cholic acid detection

    NASA Astrophysics Data System (ADS)

    He, Sihui; Liang, Wenlang; Fang, Jiyu; Wu, Shin-Tson

    2013-09-01

    The concentration level of bile acids is a useful indicator for the diagnosis of liver diseases since individual suffering from liver diseases often has a sharp increase in bile acid concentration. Here we present a sensor platform based on the anchoring transition of nematic liquid crystal (LC), 4', 4-alkylcyanobiphenyls (nCB, n=5-8), at the surfactant-laden LC/aqueous interfaces for the detection of cholic acid (CA) in aqueous solution. In the sensor platform, the competitive adsorption of CA at the surfactant-laden LC/aqueous interface triggers a homeotropic-to-planar anchoring transition of the LC at the interface. We find the detection limit, which is the minimum concentration of CA required to trigger the LC transition, increases with the increase of the chain length of nCB.

  11. Synthesis of medium-chain length capsinoids from coconut oil catalyzed by Candida rugosa lipases.

    PubMed

    Trbojević Ivić, Jovana; Milosavić, Nenad; Dimitrijević, Aleksandra; Gavrović Jankulović, Marija; Bezbradica, Dejan; Kolarski, Dušan; Veličković, Dušan

    2017-03-01

    A commercial preparation of Candida rugosa lipases (CRL) was tested for the production of capsinoids by esterification of vanillyl alcohol (VA) with free fatty acids (FA) and coconut oil (CO) as acyl donors. Screening of FA chain length indicated that C8-C12 FA (the most common FA found in CO triglycerides) are the best acyl-donors, yielding 80-85% of their specific capsinoids. Hence, when CO, which is rich in these FA, was used as the substrate, a mixture of capsinoids (vanillyl caprylate, vanillyl decanoate and vanillyl laurate) was obtained. The findings presented here suggest that our experimental method can be applied for the enrichment of CO with capsinoids, thus giving it additional health promoting properties.

  12. Effect of surfactant chain length on drug release kinetics from microemulsion-laden contact lenses.

    PubMed

    Maulvi, Furqan A; Desai, Ankita R; Choksi, Harsh H; Patil, Rahul J; Ranch, Ketan M; Vyas, Bhavin A; Shah, Dinesh O

    2017-03-31

    The effect of surfactant chain lengths [sodium caprylate (C8), Tween 20 (C12), Tween 80 (C18)] and the molecular weight of block copolymers [Pluronic F68 and Pluronic F 127] were studied to determine the stability of the microemulsion and its effect on release kinetics from cyclosporine-loaded microemulsion-laden hydrogel contact lenses in this work. Globule size and dilution tests (transmittance) suggested that the stability of the microemulsion increases with increase in the carbon chain lengths of surfactants and the molecular weight of pluronics. The optical transmittance of direct drug-laden contact lenses [DL-100] was low due to the precipitation of hydrophobic drugs in the lenses, while in microemulsion-laden lenses, the transmittance was improved when stability of the microemulsion was achieved. The results of in vitro release kinetics revealed that drug release was sustained to a greater extent as the stability of microemulsion was improved as well. This was evident in batch PF127-T80, which showed sustained release for 15days in comparison to batch DL-100, which showed release up to 7days. An in vivo drug release study in rabbit tear fluid showed significant increase in mean residence time (MRT) and area under curve (AUC) with PF-127-T80 lenses (stable microemulsion) in comparison to PF-68-SC lenses (unstable microemulsion) and DL-100 lenses. This study revealed the correlation between the stability of microemulsion and the release kinetics of drugs from contact lenses. Thus, it was inferred that the stable microemulsion batches sustained the release of hydrophobic drugs, such as cyclosporine from contact lenses for an extended period of time without altering critical lens properties.

  13. Degradation of medium-chain-length polyhydroxyalkanoates in tropical forest and mangrove soils.

    PubMed

    Lim, Siew-Ping; Gan, Seng-Neon; Tan, Irene K P

    2005-07-01

    Bacterial polyhydroxyalkanoates (PHAs) are perceived to be a suitable alternative to petrochemical plastics because they have similar material properties, are environmentally degradable, and are produced from renewable resources. In this study, the in situ degradation of medium-chain-length PHA (PHAMCL) films in tropical forest and mangrove soils was assessed. The PHAMCL was produced by Pseudomonas putida PGA1 using saponified palm kernel oil (SPKO) as the carbon source. After 112 d of burial, there was 16.7% reduction in gross weight of the films buried in acidic forest soil (FS), 3.0% in the ones buried in alkaline forest soil by the side of a stream (FSst) and 4.5% in those buried in mangrove soil (MS). There was a slight decrease in molecular weight for the films buried in FS but not for the films buried in FSst and in MS. However, no changes were observed for the melting temperature, glass transition temperature, monomer compositions, structure, and functional group analyses of the films from any of the burial sites during the test period. This means that the integral properties of the films were maintained during that period and degradation was by surface erosion. Scanning electron microscopy of the films from the three sites revealed holes on the film surfaces which could be attributed to attack by microorganisms and bigger organisms such as detritivores. For comparison purposes, films of polyhydroxybutyrate (PHB), a short-chain-length PHA, and polyethylene (PE) were buried together with the PHAMCL films in all three sites. The PHB films disintegrated completely in MS and lost 73.5% of their initial weight in FSst, but only 4.6% in FS suggesting that water movement played a major role in breaking up the brittle PHB films. The PE films did not register any weight loss in any of the test sites.

  14. Chain length distributions in linear polyaddition proceeding in nano-scale small volumes without mass transfer

    NASA Astrophysics Data System (ADS)

    Szymanski, R.; Sosnowski, S.

    2017-01-01

    Computer simulations (Monte Carlo and numerical integration of differential equations) and theoretical analysis show that the statistical nature of polyaddition, both irreversible and reversible one, affects the way the macromolecules of different lengths are distributed among the small volume nano-reactors (droplets in this study) at any reaction time. The corresponding droplet distributions in respect to the number of reacting chains as well as the chain length distributions depend, for the given reaction time, on rate constants of polyaddition kp and depolymerization kd (reversible process), and the initial conditions: monomer concentration and the number of its molecules in a droplet. As a model reaction, a simple polyaddition process (M)1+(M)1 ⟶ ⟵ (M)2 , (M)i+(M)j ⟶ ⟵ (M)i+j was chosen, enabling to observe both kinetic and thermodynamic (apparent equilibrium constant) effects of a small number of reactant molecules in a droplet. The average rate constant of polymerization is lower than in a macroscopic system, depending on the average number of reactant molecules in a droplet. The apparent equilibrium constants of polymerization Ki j=[(M)i +j] ¯ /([(M)i] ¯ [(M)j] ¯ ) appear to depend on oligomer/polymer sizes as well as on the initial number of monomer molecules in a droplet. The corresponding equations, enabling prediction of the equilibrium conditions, were derived. All the analyzed effects are observed not only for ideally dispersed systems, i.e. with all droplets containing initially the same number of monomer (M)1 molecules, but also when initially the numbers of monomer molecules conform the Poisson distribution, expected for dispersions of reaction mixtures.

  15. Shorter Food Chain Length in Ancient Lakes: Evidence from a Global Synthesis

    PubMed Central

    Doi, Hideyuki; Vander Zanden, M. Jake; Hillebrand, Helmut

    2012-01-01

    Food webs may be affected by evolutionary processes, and effective evolutionary time ultimately affects the probability of species evolving to fill the niche space. Thus, ecosystem history may set important evolutionary constraints on community composition and food web structure. Food chain length (FCL) has long been recognized as a fundamental ecosystem attribute. We examined historical effects on FCL in large lakes spanning >6 orders of magnitude in age. We found that food chains in the world’s ancient lakes (n = 8) were significantly shorter than in recently formed lakes (n = 10) and reservoirs (n = 3), despite the fact that ancient lakes harbored much higher species richness, including many endemic species. One potential factor leading to shorter FCL in ancient lakes is an increasing diversity of trophic omnivores and herbivores. Speciation could simply broaden the number of species within a trophic group, particularly at lower trophic levels and could also lead to a greater degree of trophic omnivory. Our results highlight a counter-intuitive and poorly-understood role of evolutionary history in shaping key food web properties such as FCL. PMID:22701583

  16. The Role of Chain Length in Nonergodicity Factor and Fragility of Polymers

    SciTech Connect

    Sokolov, Alexei P

    2010-01-01

    The mechanism that leads to different fragility values upon approaching the glass transition remains a topic of active discussion. Many researchers are trying to find an answer in the properties of the frozen glassy state. Following this approach, we focus here on a previously proposed relationship between the fragility of glass-formers and their nonergodicity factor, determined by inelastic X-ray scattering (IXS) in the glass. We extend this molecular liquid study to two model polymers; polystyrene (PS) and polyisobutylene (PIB);for which we change the molecular weight. Polymers offer the opportunity to change the fragility without altering the chemical structure, just by changing the chain length. Thus, we specifically chose PS and PIB because they exhibit opposite dependences of fragility with molecular weight. Our analysis for these two polymers reveals no unique correlation between the fragility and the nonergodicity parameter. Even after a recently suggested correction for a possible contribution of the relaxation, the correlation is not restored. We discuss possible causes for the failure of the fragility-nonergodicity factor correlation, emphasizing the features that are specific to polymers. We speculate that polymers might have specific contributions to fragility related to the chain connectivity that are absent in nonpolymeric systems.

  17. Biodegradation of a medium-chain-length polyhydroxyalkanoate in tropical river water.

    PubMed

    Ho, Yen-Him; Gan, Seng-Neon; Tan, Irene K P

    2002-01-01

    The medium-chain-length polyhydroxyalkanoate (PHA(MCL)) produced by Pseudomonas putida PGA1 using saponified palm kernel oil as the carbon source could degrade readily in water taken from Kayu Ara River in Selangor, Malaysia. A weight loss of 71.3% of the PHA film occurred in 86 d. The pH of the river water medium fell from 7.5 (at d 0) to 4.7 (at d 86), and there was a net release of CO2. In sterilized river water, the PHA film also lost weight and the pH of the water fell, but to lesser extents. The C8 monomer of the PHA was completely removed after 6 d of immersion in the river water, while the proportions of the other monomers (C10, C12, and C14) were reversed from that of the undegraded PHA. By contrast, the monomer composition of the PHA immersed in sterilized river water did not change significantly from that of the undegraded PHA. Scanning electron microscopy showed physical signs of degradation on the PHA film immersed in the river water, but the film immersed in sterilized river water was relatively unblemished. The results thus indicate that the PHA(MCL) was degraded in tropical river water by biologic as well as nonbiologic means. A significant finding is that shorter-chain monomers were selectively removed throughout the entire PHA molecule, and this suggests enzymatic action.

  18. Increased mean aliphatic lipid chain length in left ventricular hypertrophy secondary to arterial hypertension

    PubMed Central

    Evaristi, Maria Francesca; Caubère, Céline; Harmancey, Romain; Desmoulin, Franck; Peacock, William Frank; Berry, Matthieu; Turkieh, Annie; Barutaut, Manon; Galinier, Michel; Dambrin, Camille; Polidori, Carlo; Miceli, Cristina; Chamontin, Bernard; Koukoui, François; Roncalli, Jerôme; Massabuau, Pierre; Smih, Fatima; Rouet, Philippe

    2016-01-01

    Abstract About 77.9 million (1 in 4) American adults have high blood pressure. High blood pressure is the primary cause of left ventricular hypertrophy (LVH), which represents a strong predictor of future heart failure and cardiovascular mortality. Previous studies have shown an altered metabolic profile in hypertensive patients with LVH. The goal of this study was to identify blood metabolomic LVH biomarkers by 1H NMR to provide novel diagnostic tools for rapid LVH detection in populations of hypertensive individuals. This cross-sectional study included 48 hypertensive patients with LVH matched with 48 hypertensive patients with normal LV size, and 24 healthy controls. Two-dimensional targeted M-mode echocardiography was performed to measure left ventricular mass index. Partial least squares discriminant analysis was used for the multivariate analysis of the 1H NMR spectral data. From the 1H NMR-based metabolomic profiling, signals coming from methylene (–CH2–) and methyl (–CH3) moieties of aliphatic chains from plasma lipids were identified as discriminant variables. The –CH2–/–CH3 ratio, an indicator of the mean length of the aliphatic lipid chains, was significantly higher (P < 0.001) in the LVH group than in the hypertensive group without LVH and controls. Receiver operating characteristic curve showed that a cutoff of 2.34 provided a 52.08% sensitivity and 85.42% specificity for discriminating LVH (AUC = 0.703, P-value < 0.001). We propose the –CH2–/–CH3 ratio from plasma aliphatic lipid chains as a biomarker for the diagnosis of left ventricular remodeling in hypertension. PMID:27861330

  19. Biogeographic variation of foliar n-alkanes of Juniperus communis var. saxatilis Pallas from the Balkans.

    PubMed

    Rajčević, Nemanja; Janaćković, Pedja; Dodoš, Tanja; Tešević, Vele; Marin, Petar D

    2014-12-01

    The composition of the epicuticular n-alkanes isolated from the leaves of ten populations of Juniperus communis L. var. saxatilis Pallas from central (continental) and western (coastal) areas of the Balkan Peninsula was characterized by GC-FID and GC/MS analyses. In the leaf waxes, 14 n-alkane homologues with chain-lengths ranging from C22 to C35 were identified. All samples were dominated by n-tritriacontane (C33 ), but differences in two other dominant n-alkanes allowed separating the coastal from the continental populations. Several statistical methods (ANOVA, principal component, discriminant, and cluster analyses as well as the Mantel test) were deployed to analyze the diversity and variability of the epicuticular-leaf-n-alkane patterns of the ten natural populations of J. communis var. saxatilis and their relation to different geographic and bioclimatic parameters. Cluster analysis showed a high correlation of the leaf-n-alkane patterns with the geographical distribution of the investigated samples, differentiating the coastal from the continental populations of this taxon. Several bioclimatic parameters related to aridity were highly correlated with this differentiation.

  20. Methyl ketones in high altitude Ecuadorian Andosols confirm excellent conservation of plant-specific n-alkane patterns

    NASA Astrophysics Data System (ADS)

    Jansen, B.; Nierop, K. G. J.

    2009-04-01

    Montane forest composition and specifically the position of the upper forest line (UFL) is very sensitive to climate change and human interference. As a consequence, reconstructions of past altitudinal UFL dynamics and forest species composition are crucial instruments to infer relationships between climate change and vegetation dynamics, and assess the impact of (pre)historic human settlement. One of the most detailed methods available to date to reconstruct past vegetation dynamics is the analysis of fossil pollen. Unfortunately, fossil pollen analysis does not distinguish beyond family or generic level in most cases, while its spatial resolution is limited amongst others by windblown dispersal of pollen, affecting the accuracy of pollen based reconstructions of UFL positions. To overcome these limitations, we developed a new method based on the analysis of plant-specific groups of biomarkers preserved in suitable archives, such as peat deposits, that are unravelled into the plant species of origin by the newly developed VERHIB model. In a study of UFL positions in the Northern Ecuadorian Andes we found longer chain-length n-alkanes, (C19-C35) to occur in plant-specific patterns in the dominant vegetation in the area as well as preliminary soil and peat samples. A crucial factor in determining the applicability of these n-alkanes as biomarkers for past vegetation is their preservation in soils and peat deposits. Therefore, we investigated the preservation of C19-C35 n-alkanes in a peat core and in five excavations along an altitudinal transect (3500-3860 m.a.s.l) in the study area. We were able to establish that n-methyl ketones are the main degradation product of the n-alkanes in question, while the degradation of the n-alkanes was the main source of the n-methyl ketones. This allowed us to use the relationship between the concentrations and carbon chain length patterns of n-alkanes and n-methyl ketones to assess possible (selective) degradation of the n-alkanes

  1. Production of long chain alcohols and alkanes upon coexpression of an acyl-ACP reductase and aldehyde-deformylating oxgenase with a bacterial type-I fatty acid synthase in E. coli

    DOE PAGES

    Coursolle, Dan; Shanklin, John; Lian, Jiazhang; ...

    2015-06-23

    Microbial long chain alcohols and alkanes are renewable biofuels that could one day replace petroleum-derived fuels. Here we report a novel pathway for high efficiency production of these products in Escherichia coli strain BL21(DE3). We first identified the acyl-ACP reductase/aldehyde deformylase combinations with the highest activity in this strain. Next, we used catalase coexpression to remove toxic byproducts and increase the overall titer. Finally, by introducing the type-I fatty acid synthase from Corynebacterium ammoniagenes, we were able to bypass host regulatory mechanisms of fatty acid synthesis that have thus far hampered efforts to optimize the yield of acyl-ACP-derived products inmore » BL21(DE3). When all these engineering strategies were combined with subsequent optimization of fermentation conditions, we were able to achieve a final titer around 100 mg/L long chain alcohol/alkane products including a 57 mg/L titer of pentadecane, the highest titer reported in E. coli BL21(DE3) to date. The expression of prokaryotic type-I fatty acid synthases offer a unique strategy to produce fatty acid-derived products in E. coli that does not rely exclusively on the endogenous type-II fatty acid synthase system.« less

  2. Production of long chain alcohols and alkanes upon coexpression of an acyl-ACP reductase and aldehyde-deformylating oxygenase with a bacterial type-I fatty acid synthase in E. coli.

    PubMed

    Coursolle, Dan; Lian, Jiazhang; Shanklin, John; Zhao, Huimin

    2015-09-01

    Microbial long chain alcohols and alkanes are renewable biofuels that could one day replace petroleum-derived fuels. Here we report a novel pathway for high efficiency production of these products in Escherichia coli strain BL21(DE3). We first identified the acyl-ACP reductase/aldehyde deformylase combinations with the highest activity in this strain. Next, we used catalase coexpression to remove toxic byproducts and increase the overall titer. Finally, by introducing the type-I fatty acid synthase from Corynebacterium ammoniagenes, we were able to bypass host regulatory mechanisms of fatty acid synthesis that have thus far hampered efforts to optimize the yield of acyl-ACP-derived products in BL21(DE3). When all these engineering strategies were combined with subsequent optimization of fermentation conditions, we were able to achieve a final titer around 100 mg L(-1) long chain alcohol/alkane products including a 57 mg L(-1) titer of pentadecane, the highest titer reported in E. coli BL21(DE3) to date. The expression of prokaryotic type-I fatty acid synthases offer a unique strategy to produce fatty acid-derived products in E. coli that does not rely exclusively on the endogenous type-II fatty acid synthase system.

  3. Production of long chain alcohols and alkanes upon coexpression of an acyl-ACP reductase and aldehyde-deformylating oxgenase with a bacterial type-I fatty acid synthase in E. coli

    SciTech Connect

    Coursolle, Dan; Shanklin, John; Lian, Jiazhang; Zhao, Huimin

    2015-06-23

    Microbial long chain alcohols and alkanes are renewable biofuels that could one day replace petroleum-derived fuels. Here we report a novel pathway for high efficiency production of these products in Escherichia coli strain BL21(DE3). We first identified the acyl-ACP reductase/aldehyde deformylase combinations with the highest activity in this strain. Next, we used catalase coexpression to remove toxic byproducts and increase the overall titer. Finally, by introducing the type-I fatty acid synthase from Corynebacterium ammoniagenes, we were able to bypass host regulatory mechanisms of fatty acid synthesis that have thus far hampered efforts to optimize the yield of acyl-ACP-derived products in BL21(DE3). When all these engineering strategies were combined with subsequent optimization of fermentation conditions, we were able to achieve a final titer around 100 mg/L long chain alcohol/alkane products including a 57 mg/L titer of pentadecane, the highest titer reported in E. coli BL21(DE3) to date. The expression of prokaryotic type-I fatty acid synthases offer a unique strategy to produce fatty acid-derived products in E. coli that does not rely exclusively on the endogenous type-II fatty acid synthase system.

  4. Myosin Heavy Chain Expression Can Vary over the Length of Jaw and Leg Muscles

    PubMed Central

    Korfage, J.A.M.; Kwee, K.E.; Everts, V.; Langenbach, G.E.J.

    2016-01-01

    Muscle fiber type classification can be determined by its myosin heavy chain (MyHC) composition based on a few consecutive sections. It is generally assumed that the MyHC expression of a muscle fiber is the same over its length since neural stimulation and systemic influences are supposed to be the same over its length. We analyzed this in detail in three muscle types: the temporalis (closer) and digastricus (opener; both first brachial arch), and the medial gastrocnemius (somite). Sections of the muscles were incubated with monoclonal antibodies against various MyHC isoforms, and the distribution of these isoforms within individual fibers was followed over a distance of approximately 1 mm. The staining intensity of a fiber was measured and compared with the other fibers in the section. In the temporalis, digastricus, and gastrocnemius, 46, 11, and 15%, respectively, of their MyHC-I fibers showed a variation in the staining intensity over the length of their fibers, as well as 47, 87, and 22%, respectively, of their MyHC-IIA fibers. Most variable fibers were found amongst those with an overall relative intermediate staining intensity, which are presumably hybrid fibers. We conclude that different parts of a muscle fiber can have different fiber type compositions and, thus, contractile properties. Some muscle parts might reach their maximum contraction peak sooner or later than a muscle part a few microns further away. Next to stimulation by the nerve and systemic influences, local influences might also have an impact on the MyHC expression of the fiber. PMID:26950765

  5. Leaf n-alkanes as characters differentiating coastal and continental Juniperus deltoides populations from the Balkan Peninsula.

    PubMed

    Rajčević, Nemanja; Janaćković, Pedja; Dodoš, Tanja; Tešević, Vele; Bojović, Srdjan; Marin, Petar D

    2014-07-01

    The composition of the cuticular n-alkanes isolated from the leaves of nine populations of Juniperus deltoides R.P.Adams from continental and coastal areas of the Balkan Peninsula was characterized by GC-FID and GC/MS analyses. In the leaf waxes, 14 n-alkane homologues with chain-lengths ranging from C22 to C35 were identified. n-Tritriacontane (C33 ) was dominant in the waxes of all populations, but variations between the populations in the contents of all n-alkanes were observed. Several statistical methods (ANOVA, principal component, discriminant, and cluster analyses) were used to investigate the diversity and variability of the cuticular-leaf-n-alkane patterns of the nine J. deltoides populations. This is the first report on the n-alkane composition for this species. The multivariate statistical analyses evidenced a high correlation of the leaf-n-alkane pattern with the geographical distribution of the investigated samples, differentiating the coastal from the continental populations of this taxon.

  6. Regioselective ω-hydroxylation of medium-chain n-alkanes and primary alcohols by CYP153 enzymes from Mycobacterium marinum and Polaromonas sp. strain JS666.

    PubMed

    Scheps, Daniel; Malca, Sumire Honda; Hoffmann, Helen; Nestl, Bettina M; Hauer, Bernhard

    2011-10-07

    The oxofunctionalization of saturated hydrocarbons is an important goal in basic and applied chemistry. Biocatalysts like cytochrome P450 enzymes can introduce oxygen into a wide variety of molecules in a very selective manner, which can be used for the synthesis of fine and bulk chemicals. Cytochrome P450 enzymes from the CYP153A subfamily have been described as alkane hydroxylases with high terminal regioselectivity. Here we report the product yields resulting from C(5)-C(12) alkane and alcohol oxidation catalyzed by CYP153A enzymes from Mycobacterium marinum (CYP153A16) and Polaromonas sp. (CYP153A P. sp.). For all reactions, byproduct formation is described in detail. Following cloning and expression in Escherichia coli, the activity of the purified monooxygenases was reconstituted with putidaredoxin (CamA) and putidaredoxin reductase (CamB). Although both enzyme systems yielded primary alcohols and α,ω-alkanediols, each one displayed a different oxidation pattern towards alkanes. For CYP153A P. sp. a predominant ω-hydroxylation activity was observed, while CYP153A16 possessed the ability to catalyze both ω-hydroxylation and α,ω-dihydroxylation reactions.

  7. Investigating C4 Grass Contributions to N-alkane Based Paleoclimate Reconstructions

    NASA Astrophysics Data System (ADS)

    Doman, C. E.; Enders, S. K.; Chadwick, O.; Freeman, K. H.

    2014-12-01

    Plant wax n-alkanes are long-chain, saturated hydrocarbons contained within the protective waxy cuticle on leaves. These lipids are pervasive and persistent in soils and sediments and thus are ideal biomarkers of ancient terrestrial organic matter. In ecosystems dominated by C3 plants, the relationship between the carbon isotopic value of whole leaves and lipids is fairly well documented, but this relationship has not been fully investigated for plants that use C4 photosynthesis. In both cases, it is unclear if the isotopic relationships are sensitive to environmental conditions, or reflect inherited characteristics. This study used a natural climate gradient on the Kohala peninsula of Hawaii to investigate relationships between climate and the δ13C and δ2H values of n-alkanes in C3 and C4 plants. δ13C of C3 leaves and lipids decreased 5 ‰ from the driest to the wettest sites, consistent with published data. Carbon isotope values of C4 plants showed no relationship to moisture up to 1000 mm mean annual precipitation (MAP). Above this threshold, δ 13C values were around 10‰ more depleted, likely due to a combination of canopy effects and C4 grasses growing in an uncharacteristically wet and cold environment. In C3 plants, the fractionation between leaf and lipid carbon isotopes did not vary with MAP, which allows estimations of δ13C leaf to be made from alkanes preserved in ancient sediments. Along this transect, C3 plants produce around twice the quantity of n-alkanes as C4 grasses. C4 grasses produce longer carbon chains. As a result, n-alkanes in the geologic record will be biased towards C3 plants, but the presence of alkanes C33 and C35 indicate the contributions of C4 grasses. In both C3 and C4 plants, average chain length increased with mean annual precipitation, but the taxonomic differences in chain length were greater than environmental differences. Hydrogen isotopes of n-alkanes show no trends with MAP, but do show clear differences between plant

  8. Effect of the chain length on the structure of ionic liquids: from spatial heterogeneity to ionic liquid crystals.

    PubMed

    Ji, Yumeng; Shi, Rui; Wang, Yanting; Saielli, Giacomo

    2013-01-31

    Ionic liquids with intermediate nonpolar cationic side-chain lengths are known to have nanoscale spatial heterogeneities with nonpolar tail domains separated by a continuous polar network. In this work, we use coarse-grained molecular dynamics simulations to show that, when the nonpolar cationic side chain is sufficiently long, due to the stronger van der Waals interactions between the side chains, the structure of ionic liquids goes through a transition from spatially heterogeneous to liquid crystalline-like. For XMIm(+)/NO(3)(-) ionic liquids, change occurs when the number of carbon groups on the cationic side chain varies from 14 to 16. In the liquid crystal-like phase, the cationic side chains tend to be parallel to each other, while the cationic head groups and anions, although being mostly layered perpendicularly to the direction along the side chains, still form a continuous polar network.

  9. Fidelity of fossil n-alkanes from leaf to paleosol and applications to the Paleocene-Eocene Thermal Maximum

    NASA Astrophysics Data System (ADS)

    Bush, R. T.; McInerney, F. A.; Baczynski, A. A.; Wing, S. L.

    2011-12-01

    Long chain n-alkanes (C21-C35) are well-known as biomarkers of terrestrial plants. They can be preserved across a wide range of terrestrial and marine environments, survive in the sedimentary record for millions of years, and can serve as proxies for ancient environments. Most n-alkane records are derived from sediments rather than directly from fossil leaves. However, little is known about the fidelity of the n-alkane record: how and where leaf preservation relates to n-alkane preservation and how patterns of n-alkane carbon isotope ratios (δ13C) compare to living relatives. To examine these questions, we analyzed n-alkanes from fluvial sediments and individual leaf fossils collected in the Bighorn Basin, Wyoming, across the Paleocene-Eocene Thermal Maximum (PETM) carbon isotope excursion. We assessed the fidelity of the n-alkane signature from individual fossil leaves via three separate means. 1) Spatial variations were assessed by comparing n-alkane concentrations on a fossil leaf and in sediments both directly adjacent to the leaf and farther away. Absolute concentrations were greater within the compression fossil than in the directly adjacent sediment, which were in turn greater than in more distant sediment. 2) n-Alkane abundances and distributions were examined in fossil leaves having a range of preservational quality, from fossils with intact cuticle to carbonized fossils lacking cuticle and higher-order venation. The best preserved fossils preserved a higher concentration of n-alkanes and showed the most similar n-alkane distribution to living relatives. However, a strong odd over even predominance suggests a relatively unmodified plant source occurred in all samples regardless of preservation state. 3) n-Alkane δ13C values were measured for both fossil leaves and their living relatives. Both the saw-tooth pattern of δ13C values between odd and even chain lengths and the general decrease in δ13C values with increasing chain length are consistent with

  10. Effect of chain length on thermal conversion of alkoxy-substituted copper phthalocyanine precursors.

    PubMed

    Fukuda, Takamitsu; Kikukawa, Yuu; Tsuruya, Ryota; Fuyuhiro, Akira; Ishikawa, Naoto; Kobayashi, Nagao

    2011-11-21

    A series of dialkoxy-substituted copper phthalocyanine (CuPc) precursors (4a-4d) have been prepared by treating phthalonitrile with the corresponding lithium alkoxide under mild conditions. The precursors exhibited high solubilities in common organic solvents, including acetone, toluene, tetrahydrofuran (THF), CH(2)Cl(2), and CHCl(3). Elongation of the alkoxy chains improved the solubilities of the precursors effectively, and accordingly, the butoxy-substituted derivative (4d) showed the highest solubility among 4a-4d. X-ray crystallography clarified that the conjugated skeletons of 4a-4d are all isostructural, and have two alkoxy groups in a syn-conformation fashion, leading to highly bent structures. Thermal conversions of the precursors examined by thermogravimetry (TG) and differential thermal analysis (DTA) demonstrate that 4a was converted into CuPc via two distinct exothermic processes in the 200-250 °C temperature range, while 4d exhibits only one exothermic signal in the DTA. In the field emission scanning electron microscopy (FESEM) images of 4a, the presence of two types of distinct crystal morphology (prismatic and plate-like crystals) can be recognized, implying that the two observed exothermic processes in the DTA can be attributed to the different crystal morphologies of the samples rather than the step-by-step elimination of the alkoxy groups. The thermal formation of CuPc from the precursors has been unambiguously confirmed by X-ray powder diffraction, UV-vis spectroscopy, and elemental analysis. The precursors were converted into CuPc at lower temperature with increasing chain length, presumably because of the increased void volume in the crystals. Thermal conversion performed in the solution phase results in a bright blue-colored solution with prominent absorption bands in the 650-700 nm region, strongly supporting the formation of CuPc.

  11. Environmental swap energy and role of configurational entropy in transfer of small molecules from water into alkanes

    NASA Astrophysics Data System (ADS)

    Smejtek, Pavel; Word, Robert C.

    2004-01-01

    We studied the effect of segmented solvent molecules on the free energy of transfer of small molecules from water into alkanes (hexane, heptane, octane, decane, dodecane, tetradecane, and hexadecane). For these alkanes we measured partition coefficients of benzene, 3-methylindole (3MI), 2,3,4,6-tetrachlorophenol (TeCP), and 2,4,6-tribromophenol (TriBP) at 3, 11, 20, 3, and 47 °C. For 3MI, TeCP, and TriBP the dependence of free energy of transfer on length of alkane chains was found to be very different from that for benzene. In contrast to benzene, the energy of transfer for 3MI, TeCP, and TriBP was independent of the number of carbons in alkanes. To interpret data, we used the classic Flory-Huggins (FH) theory of concentrated polymer solutions for the alkane phase. For benzene, the measured dependence of energy of transfer on the number of carbons in alkanes agreed well with predictions based on FH model in which the size of alkane segments was obtained from the ratio of molar volumes of alkanes and the solute. We show that for benzene, the energy of transfer can be divided into two components, one called environmental swap energy (ESE), and one representing the contribution of configurational entropy of alkane chains. For 3MI, TeCP, and TriBP the contribution of configurational entropy was not measurable even though the magnitude of the effect predicted from the FH model for short chain alkanes was as much as 20 times greater than experimental uncertainties. From the temperature dependence of ESE we obtained enthalpy and entropy of transfer for benzene, 3MI, TeCP, and TriBP. Experimental results are discussed in terms of a thermodynamic cycle considering creation of cavity, insertion of solute, and activation of solute-medium attractive interactions. Our results suggest that correcting experimental free energy of transfer by Flory-Huggins configurational entropy term is not generally appropriate and cannot be applied indiscriminately.

  12. Assessing carbon and hydrogen isotopic fractionation of diesel fuel n-alkanes during progressive evaporation.

    PubMed

    Muhammad, Syahidah A; Hayman, Alan R; Van Hale, Robert; Frew, Russell D

    2015-01-01

    Compound-specific isotope analysis offers potential for fingerprinting of diesel fuels, however, possible confounding effects of isotopic fractionation due to evaporation need to be assessed. This study measured the fractionation of the stable carbon and hydrogen isotopes in n-alkane compounds in neat diesel fuel during evaporation. Isotope ratios were measured using a continuous flow gas chromatograph/isotope ratio mass spectrometer. Diesel samples were progressively evaporated at 24 ± 2°C for 21 days. Increasing depletion of deuterium in nC12-nC17 alkanes in the remaining liquid with increasing carbon chain length was observed. Negligible carbon isotope fractionation was observed. Preferential vaporization was measured for the shorter chain n-alkanes and the trend decreased with increasing chain length. The decrease in δ(2) H values indicates the preferential vaporization of the isotopically heavier species consistent with available quantitative data for hydrocarbons. These results are most important in the application of stable isotope technology to forensic analysis of diesel.

  13. Polymerase chain reaction-restriction fragment length polymorphism authentication of raw meats from game birds.

    PubMed

    Rojas, María; González, Isabel; Fajardo, Violeta; Martín, Irene; Hernández, Pablo E; García, Teresa; Martín, Rosario

    2008-01-01

    Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis has been applied to the identification of meats from quail (Coturnix coturnix), pheasant (Phasianus colchicus), red-legged partridge (Alectoris rufa), guinea fowl (Numida meleagris), capercaillie (Tetrao urogallus), Eurasian woodcock (Scolopax rusticola), woodpigeon (Columba palumbus), and song thrush (Turdus philomelos). PCR amplification was performed using a set of primers flanking a conserved region of approximately 720 base pairs (bp) from the mitochondrial 12S rRNA gene. Restriction site analysis based on sequence data from this DNA fragment permitted the selection of AluI and BfaI endonucleases for species identification. The restriction profiles obtained when amplicons were digested with the chosen enzymes allowed the unequivocal identification of all game bird species analyzed. However, the use of the PCR-RFLP technique described is limited to raw meat authentication. It is not suitable for cooked products because thermal treatment strongly accelerates DNA degradation leading to difficulties in amplifying the 720 bp fragment.

  14. Bilayer registry in a multicomponent asymmetric membrane: Dependence on lipid composition and chain length

    SciTech Connect

    Polley, Anirban; Mayor, Satyajit; Rao, Madan E-mail: madan@ncbs.res.in

    2014-08-14

    A question of considerable interest to cell membrane biology is whether phase segregated domains across an asymmetric bilayer are strongly correlated with each other and whether phase segregation in one leaflet can induce segregation in the other. We answer both these questions in the affirmative, using an atomistic molecular dynamics simulation to study the equilibrium statistical properties of a 3-component asymmetric lipid bilayer comprising an unsaturated palmitoyl-oleoyl-phosphatidyl-choline, a saturated sphingomyelin, and cholesterol with different composition ratios. Our simulations are done by fixing the composition of the upper leaflet to be at the coexistence of the liquid ordered (l{sub o})-liquid disordered (l{sub d}) phases, while the composition of the lower leaflet is varied from the phase coexistence regime to the mixed l{sub d} phase, across a first-order phase boundary. In the regime of phase coexistence in each leaflet, we find strong transbilayer correlations of the l{sub o} domains across the two leaflets, resulting in bilayer registry. This transbilayer correlation depends sensitively upon the chain length of the participating lipids and possibly other features of lipid chemistry, such as degree of saturation. We find that the l{sub o} domains in the upper leaflet can induce phase segregation in the lower leaflet, when the latter is nominally in the mixed (l{sub d}) phase.

  15. Is average chain length of plant lipids a potential proxy for vegetation, environment and climate changes?

    NASA Astrophysics Data System (ADS)

    Wang, M.; Zhang, W.; Hou, J.

    2015-04-01

    Average chain length (ACL) of leaf wax components preserved in lacustrine sediments and soil profiles has been widely adopted as a proxy indicator for past changes in vegetation, environment and climate during the late Quaternary. The fundamental assumption is that woody plants produce leaf waxes with shorter ACL values than non-woody plants. However, there is a lack of systematic survey of modern plants to justify the assumption. Here, we investigated various types of plants at two lakes, Blood Pond in the northeastern USA and Lake Ranwu on the southeastern Tibetan Plateau, and found that the ACL values were not significantly different between woody and non-woody plants. We also compiled the ACL values of modern plants in the literatures and performed a meta-analysis to determine whether a significant difference exists between woody and non-woody plants at single sites. The results showed that the ACL values of plants at 19 out of 26 sites did not show a significant difference between the two major types of plants. This suggests that extreme caution should be taken in using ACL as proxy for past changes in vegetation, environment and climate.

  16. MODEL AND CELL MEMBRANE PARTITIONING OF PERFLUOROOCTANESULFONATE IS INDEPENDENT OF THE LIPID CHAIN LENGTH

    PubMed Central

    Xie, Wei; Ludewig, Gabriele; Wang, Kai; Lehmler, Hans-Joachim

    2009-01-01

    Perfluorooctanesulfonic acid (PFOS) is a persistent environmental pollutant that may cause adverse health effects in humans and animals by interacting with and disturbing of the normal properties of biological lipid assemblies. To gain further insights into these interactions, we investigated the effect of PFOS potassium salt on dimyristoyl- (DMPC), dipalmitoyl- (DPPC) and distearoylphosphatidylcholine (DSPC) model membranes using fluorescence anisotropy measurements and differential scanning calorimetry (DSC) and on the cell membrane of HL-60 human leukemia cells and freshly isolated rat alveolar macrophages using fluorescence anisotropy measurements. PFOS caused a concentration-dependent decrease of the main phase transition temperature (Tm) and an increased peak width (ΔTw) in both the fluorescence anisotropy and the DSC experiments, with a rank order DMPC > DPPC > DSPC. PFOS caused a fluidization of the gel phase of all phosphatidylcholines investigated, but had the opposite effect on the liquid crystalline phase. The apparent partition coefficients of PFOS between the phosphatidylcholine bilayer and the bulk aqueous phase were largely independent of the phosphatidylcholine chain length and ranged from 4.4 × 104 to 8.8 × 104. PFOS also significantly increased the fluidity of membranes of cells. These findings suggest that PFOS readily partitions into lipid assemblies, independent of their composition, and may cause adverse biological effects by altering their fluidity in a manner that depends on the membrane cooperativity and state (e.g., gel versus liquid crystalline phase) of the lipid assembly. PMID:19932010

  17. Chain-length and mode-delocalization dependent amide-I anharmonicity in peptide oligomers.

    PubMed

    Zhao, Juan; Wang, Jianping

    2012-06-07

    The diagonal anharmonicities of the amide-I mode in the alanine oligomers are examined in the normal-mode basis by ab initio calculations. The selected oligomers range from dimer to heptamer, in either the α-helical or β-sheet conformations. It is found that the anharmonicity varies from mode to mode within the same oligomer. For a given amide-I mode, the anharmonicity is closely related to the delocalization extent of the mode: the less it delocalizes, the larger the anharmonicity it has. Thus, the single-mode potential energy distribution (PED(max)) can be used as an indicator of the magnitude of the anharmonicity. It is found that as the peptide chain length increases, the averaged diagonal anharmonicity generally decreases; however, the sum of the averaged diagonal and off-diagonal anharmonicities within a peptide roughly remains a constant for all the oligomers examined, indicating the excitonic characteristics of the amide-I modes. Excitonic coupling tends to decrease the diagonal anharmonicities in a coupled system with multiple chromophores, which explains the observed behavior of the anharmonicities. The excitonic nature of the amide-I band in peptide oligomers is thus verified by the anharmonic computations. Isotopic substitution effect on the anharmonicities and mode localizations of the amide-I modes in peptides is also discussed.

  18. The interacting effects of temperature and food chain length on trophic abundance and ecosystem function.

    PubMed

    Beveridge, Oliver S; Humphries, Stuart; Petchey, Owen L

    2010-05-01

    1. While much is known about the independent effects of trophic structure and temperature on density and ecosystem processes, less is known about the interaction(s) between the two. 2. We manipulated the temperature of laboratory-based bacteria-protist communities that contained communities with one, two, or three trophic levels, and recorded species' densities and bacterial decomposition. 3. Temperature, food chain length and their interaction produced significant responses in microbial density and bacterial decomposition. Prey and resource density expressed different patterns of temperature dependency during different phases of population dynamics. The addition of a predator altered the temperature-density relationship of prey, from a unimodal trend to a negative one. Bacterial decomposition was greatest in the presence of consumers at higher temperatures. 4. These results are qualitatively consistent with a recent model of direct and indirect temperature effects on resource-consumer population dynamics. Results highlight and reinforce the importance of indirect effects of temperature mediated through trophic interactions. Understanding and predicting the consequences of environmental change will require that indirect effects, trophic structure, and individual species' tolerances be incorporated into theory and models.

  19. Low-temperature spectrum of correlation lengths of the XXZ chain in the antiferromagnetic massive regime

    NASA Astrophysics Data System (ADS)

    Dugave, Maxime; Göhmann, Frank; Kozlowski, Karol K.; Suzuki, Junji

    2015-08-01

    We consider the spectrum of correlation lengths of the spin-\\displaystyle \\frac{1}{2} XXZ chain in the antiferromagnetic massive regime. These are given as ratios of eigenvalues of the quantum transfer matrix of the model. The eigenvalues are determined by integrals over certain auxiliary functions and by their zeros. The auxiliary functions satisfy nonlinear integral equations. We analyse these nonlinear integral equations in the low-temperature limit. In this limit we can determine the auxiliary functions and the expressions for the eigenvalues as functions of a finite number of parameters which satisfy finite sets of algebraic equations, the so-called higher-level Bethe ansatz equations. The behaviour of these equations, if we send the temperature T to zero, is different for zero and non-zero magnetic field h. If h is zero the situation is much like in the case of the usual transfer matrix. Non-trivial higher-level Bethe ansatz equations remain which determine certain complex excitation parameters as functions of hole parameters which are free on a line segment in the complex plane. If h is non-zero, on the other hand, a remarkable restructuring occurs, and all parameters which enter the description of the quantum transfer matrix eigenvalues can be interpreted entirely in terms of particles and holes which are freely located on two curves when T goes to zero. Dedicated to Professor Baxter on the occasion of his 75th birthday.

  20. Exploring medium-chain-length polyhydroxyalkanoates production in the engineered yeast Yarrowia lipolytica.

    PubMed

    Gao, Cuijuan; Qi, Qingsheng; Madzak, Catherine; Lin, Carol Sze Ki

    2015-09-01

    Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) are a large class of biopolymers that have attracted extensive attention as renewable and biodegradable bio-plastics. They are naturally synthesized via fatty acid de novo biosynthesis pathway or β-oxidation pathway from Pseudomonads. The unconventional yeast Yarrowia lipolytica has excellent lipid/fatty acid catabolism and anabolism capacity depending of the mode of culture. Nevertheless, it cannot naturally synthesize PHA, as it does not express an intrinsic PHA synthase. Here, we constructed a genetically modified strain of Y. lipolytica by heterologously expressing PhaC1 gene from P. aeruginosa PAO1 with a PTS1 peroxisomal signal. When in single copy, the codon optimized PhaC1 allowed the synthesis of 0.205 % DCW of PHA after 72 h cultivation in YNBD medium containing 0.1 % oleic acid. By using a multi-copy integration strategy, PHA content increased to 2.84 % DCW when the concentration of oleic acid in YNBD was 1.0 %. Furthermore, when the recombinant yeast was grown in the medium containing triolein, PHA accumulated up to 5.0 % DCW with as high as 21.9 g/L DCW, which represented 1.11 g/L in the culture. Our results demonstrated the potential use of Y. lipolytica as a promising microbial cell factory for PHA production using food waste, which contains lipids and other essential nutrients.

  1. Nanostructure of mixtures of protic ionic liquids and lithium salts: effect of alkyl chain length.

    PubMed

    Méndez-Morales, Trinidad; Carrete, Jesús; Rodríguez, Julio R; Cabeza, Óscar; Gallego, Luis J; Russina, Olga; Varela, Luis M

    2015-02-21

    The bulk structure of mixtures of two protic ionic liquids, propylammonium nitrate and butylammonium nitrate, with a salt with a common anion, is analyzed at room temperature by means of small angle X-ray scattering and classical molecular dynamics simulations. The study of several structural properties, such as density, radial distribution functions, spatial distribution functions, hydrogen bonds, coordination numbers and velocity autocorrelation functions, demonstrates that increasing the alkyl chain length of the alkylammonium cation results in more segregated, better defined polar and apolar domains, the latter having a larger size. This increase, ascribed to the erosion of the H-bond network in the ionic liquid polar regions as salt is added, is confirmed by means of small angle X-ray scattering measurements, which show a clear linear increase of the characteristic spatial sizes of the studied protic ionic liquids with salt concentration, similar to that previously reported for ethylammonium nitrate (J. Phys. Chem. B, 2014, 118, 761-770). In addition, larger ionic liquid cations lead to a lower degree of hydrogen bonding and to more sparsely packed three-dimensional structures, which are more easily perturbed by the addition of lithium salts.

  2. Mutagenicity Assessment of Organophosphates using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Assay

    PubMed Central

    Bhinder, Preety; Chaudhry, Asha

    2013-01-01

    Objectives: In this study we have evaluated the mutagenicity of organophosphate pesticides acephate, chlorpyrifos, and profenofos using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay with the mosquito Culex quinquefasciatus taken as an experimental model. Materials and Methods: Second instar larvae were treated with LC20 of each pesticide for 24 h and mutations induced in the sequence of mitochondrial COII gene (690bp) were studied from restriction patterns generated with AluI, PacI, and PsiI restriction endonucleases. Results: Variations in the number and size of digested fragments were recorded from treated individuals compared with controls showing that the restriction enzymes created a cut at different locations. In addition, sequences of COII gene from control and treated individuals were also used to confirm the RFLP patterns. From the sequence alignment data, it was found that mutations caused the destruction and generation of restriction sites in the gene sequence of treated individuals. Conclusion: This study indicates that all the three pesticides had potential to induce mutations in the normal sequence of COII gene and also advocates the use of PCR-RFLP assay as an efficient, rapid, and sensitive technique to detect mutagenicity of pesticides. PMID:24403735

  3. Influence of alkyl chain length on the surface activity of antibacterial polymers derived from ROMP.

    PubMed

    Altay, Esra; Yapaöz, Melda Altıkatoğlu; Keskin, Bahadır; Yucesan, Gundoğ; Eren, Tarik

    2015-03-01

    The purpose of this study is to understand the antibacterial properties of cationic polymers on solid surfaces by investigating the structure-activity relationships. The polymer synthesis was carried via ring opening metathesis polymerization (ROMP) of oxanorbornene derivatives. Modulation of molecular weights and alkyl chain lengths of the polymers were studied to investigate the antibacterial properties on the glass surface. Fluorescein (Na salt) staining contact angle measurements were used to characterize the positive charge density and hydrophobicity on the polymer coated surfaces. Positive charge density for the surface coated polymers with molecular weights of 3000 and 10,000 g mol(-1) is observed to be in the range of 2.3-28.5 nmol cm(-2). The ROMP based cationic pyridinium polymer with hexyl unit exhibited the highest bactericidal efficiency against Escherichia coli on solid surface killing 99% of the bacteria in 5 min. However, phenyl and octyl functionalized quaternary pyridinium groups exhibited lower biocidal properties on the solid surfaces compared to their solution phase biocidal properties. Studying the effect of threshold polymer concentrations on the antibacterial properties indicated that changing the concentrations of polymer coatings on the solid surface dramatically influences antibacterial efficiency.

  4. Imidiazolium based ionic liquids: effects of different anions and alkyl chains lengths on the barley seedlings.

    PubMed

    Cvjetko Bubalo, Marina; Hanousek, Karla; Radošević, Kristina; Gaurina Srček, Višnja; Jakovljević, Tamara; Radojčić Redovniković, Ivana

    2014-03-01

    We studied the effects of five imidiazolium based ionic liquids with different anions and length of alkyl chains linked to imidazolium ring on the early development of barley (Hordeum vulgare). The inhibitory effect depends on the ionic liquids concentration and chemical structure, whereby the most toxic one was [C10mim][Br], followed by [C7mim][Br], [C4mim][Br], [C4mim][CH3CO2] and [C4mim][BF4]. Both anion and cation structures affected the toxicity of ionic liquid indicating that selection of more biocompatible anions such as [CH3CO2] does not necessarily indicate lower toxicity. Alternation in the extent of oxidative stress and antioxidant enzymes activities were found in barley plants due to ionic liquid treatments. When seedlings were exposed to higher concentrations of ionic liquids, antioxidant system could not effectively remove reactive oxidative species, leading to lipid peroxidation and damage of the photosynthetic system. However, overall data indicated that the performance of barley seedling was improved when all measured enzymes involved in scavenging of reactive oxygen species (ROS) were increased with special emphasis on GPX activities. Since there are no studies about ionic liquid (IL) toxicity in plants, that simultaneously evaluates the antioxidative enzyme system in response to different ILs, this work is valuable for gaining knowledge about the protection mechanism of plants from oxidative stress caused by IL exposure.

  5. Quantum chemical analysis of thermodynamics of 2D cluster formation of alkanes at the water/vapor interface in the presence of aliphatic alcohols.

    PubMed

    Vysotsky, Yu B; Kartashynska, E S; Belyaeva, E A; Fainerman, V B; Vollhardt, D; Miller, R

    2015-11-21

    Using the quantum chemical semi-empirical PM3 method it is shown that aliphatic alcohols favor the spontaneous clusterization of vaporous alkanes at the water surface due to the change of adsorption from the barrier to non-barrier mechanism. A theoretical model of the non-barrier mechanism for monolayer formation is developed. In the framework of this model alcohols (or any other surfactants) act as 'floats', which interact with alkane molecules of the vapor phase using their hydrophobic part, whereas the hydrophilic part is immersed into the water phase. This results in a significant increase of contact effectiveness of alkanes with the interface during the adsorption and film formation. The obtained results are in good agreement with the existing experimental data. To test the model the thermodynamic and structural parameters of formation and clusterization are calculated for vaporous alkanes C(n)H(2n+2) (n(CH3) = 6-16) at the water surface in the presence of aliphatic alcohols C(n)H(2n+1)OH (n(OH) = 8-16) at 298 K. It is shown that the values of clusterization enthalpy, entropy and Gibbs' energy per one monomer of the cluster depend on the chain lengths of corresponding alcohols and alkanes, the alcohol molar fraction in the monolayers formed, and the shift of the alkane molecules with respect to the alcohol molecules Δn. Two possible competitive structures of mixed 2D film alkane-alcohol are considered: 2D films 1 with single alcohol molecules enclosed by alkane molecules (the alcohols do not form domains) and 2D films 2 that contain alcohol domains enclosed by alkane molecules. The formation of the alkane films of the first type is nearly independent of the surfactant type present at the interface, but depends on their molar fraction in the monolayer formed and the chain length of the compounds participating in the clusterization, whereas for the formation of the films of the second type the interaction between the hydrophilic parts of the surfactant is

  6. Late Quaternary environmental changes inferred from n-alkane evidence in coastal area of southern Hainan Island, China

    NASA Astrophysics Data System (ADS)

    Wang, Mengyuan; Zheng, Zhuo

    2016-04-01

    The studied core was a coastal core in Hainan Island, China. It is in length of 49.01m and divided into four Units (MIS 1~MIS 6) according to lithology description. The Optically Stimulated Luminescence (OSL) attributes the sediments from Unit 3 to the Oxygen Isotope Stage of MIS 5e (Unit 3b and 3c) and 5d (Unit 3a). To interpret the origination of organic carbons and to reconstruct paleovegetation changes, n-alkane, δ13C and TOC have been used in the present research. The result of n-alkanes distribution indicates a series of changes of sedimentary environment and terrestrial input. The shallow water facies at Unit 2, 3a and 4 is mainly characterized by short carbon chain n-alkanes and relatively low concentration. Contrasting with that of deep-water marine facies of MIS 5e (Unit 3b), the n-alkane pattern is typical bimodal and the main peaks are both in short and long carbon chains. During Unit 3b-1 (MIS 5e), more terrestrial original n-alkanes contribute to the concentration of TOC than oceanic. Organic matter source is mainly terrestrial origination. Total organic matter input mechanism of TLG-01 correlates with sediment grain size (average grain size). Total organic carbon input is enhanced with the increasing of fine grain size component. The variation of CPI (25-33) value in this study correlates with hydrological energy. The highest CPI (25-33) value is shown in the high sea level period of MIS 5e, comparing with that in MIS 5d and MIS 1. High CPI value corresponds to high TOC and average grain size (Φ) value. In the weak hydrological energy sedimentary environment, more terrestrial organic matter, together with TOC, deposit in the study area. ACL (25-33) index display higher values in the interglacial period (MIS 5 and MIS 1) than MIS 3 (sediments weathered during MIS 2) and MIS 6. Paq proxy, together with δ13C, estimates the mangrove growing depth in MIS 5e. The correlation between δ13C and each carbon chain alkane state stabilize and turbulence of

  7. Density functional steric analysis of linear and branched alkanes.

    PubMed

    Ess, Daniel H; Liu, Shubin; De Proft, Frank

    2010-12-16

    Branched alkane hydrocarbons are thermodynamically more stable than straight-chain linear alkanes. This thermodynamic stability is also manifest in alkane bond separation energies. To understand the physical differences between branched and linear alkanes, we have utilized a novel density functional theory (DFT) definition of steric energy based on the Weizäcker kinetic energy. Using the M06-2X functional, the total DFT energy was partitioned into a steric energy term (E(s)[ρ]), an electrostatic energy term (E(e)[ρ]), and a fermionic quantum energy term (E(q)[ρ]). This analysis revealed that branched alkanes have less (destabilizing) DFT steric energy than linear alkanes. The lower steric energy of branched alkanes is mitigated by an equal and opposite quantum energy term that contains the Pauli component of the kinetic energy and exchange-correlation energy. Because the steric and quantum energy terms cancel, this leaves the electrostatic energy term that favors alkane branching. Electrostatic effects, combined with correlation energy, explains why branched alkanes are more stable than linear alkanes.

  8. Density Functional Steric Analysis of Linear and Branched Alkanes

    SciTech Connect

    Ess, Daniel H.; Liu, Shubin; De Proft, Frank

    2010-11-18

    Branched alkane hydrocarbons are thermodynamically more stable than straight-chain linear alkanes. This thermodynamic stability is also manifest in alkane bond separation energies. To understand the physical differences between branched and linear alkanes, we have utilized a novel density functional theory (DFT) definition of steric energy based on the Weizäcker kinetic energy. Using the M06-2X functional, the total DFT energy was partitioned into a steric energy term (Ee[[ρ]), an electrostatic energy term (Ee[ρ]), and a fermionic quantum energy term (Eq[[ρ]). This analysis revealed that branched alkanes have less (destabilizing) DFT steric energy than linear alkanes. The lower steric energy of branched alkanes is mitigated by an equal and opposite quantum energy term that contains the Pauli component of the kinetic energy and exchange-correlation energy. Because the steric and quantum energy terms cancel, this leaves the electrostatic energy term that favors alkane branching. Electrostatic effects, combined with correlation energy, explains why branched alkanes are more stable than linear alkanes.

  9. Re-assessing the role of plant community change and climate in the PETM n-alkane record

    NASA Astrophysics Data System (ADS)

    Bush, R. T.; Baczynski, A. A.; McInerney, F. A.; Chen, D.

    2012-12-01

    The terrestrial leaf wax n-alkane record of the Paleocene-Eocene Thermal Maximum (PETM) in the Bighorn Basin, Wyoming, shows large excursions in both carbon isotope (δ13C) values and n-alkane average chain length (ACL). At the onset of the PETM, ACL values increase from ~28.5 to ~30.1 while the negative carbon isotope excursion (CIE) is 4-6‰ in magnitude and larger than δ13C records from other materials. It has been hypothesized previously that both the ACL excursion and the large magnitude of the CIE were caused by a concurrent turnover in the local flora from a mixed conifer/angiosperm community before the PETM to a different suite of angiosperm species during the PETM. Here, we present the results of a meta-analysis of data (>2000 data from 89 sources, both published and unpublished) on n-alkane amounts and chain length distributions in modern plants from around the world. We applied the data in two sets of comparisons: 1) within and among plant groups such as herbs and graminoids, and 2) between plants and climate, using reported collection locations for outdoor plants and climate values generated via GIS extraction of WorldClim modeled data. We show that angiosperms, as group, produce more n-alkanes than do gymnosperms by 1-2 orders of magnitude, and this means that the gymnosperm contribution to a mixed soil n-alkane pool would be negligible, even in an ecosystem where gymnosperms dominated (i.e. the pre/post-PETM ecosystems). The modern plant data also demonstrate that turnover of the plant community during the PETM, even among only the angiosperm species, is likely not the source of the observed ACL excursion. First, we constructed "representative" groups of PETM and pre/post-PETM communities using living relative species at the Chicago Botanic Garden and find no significant difference in chain length distributions between the two groups. Second and moreover, the modern plant data reveal that n-alkane chain length distributions are tremendously variable

  10. Attenuating HIV Tat/TAR-mediated protein expression by exploring the side chain length of positively charged residues.

    PubMed

    Wu, Cheng-Hsun; Chen, Yi-Ping; Liu, Shing-Lung; Chien, Fan-Ching; Mou, Chung-Yuan; Cheng, Richard P

    2015-12-07

    RNA is a drug target involved in diverse cellular functions and viral processes. Molecules that inhibit the HIV TAR RNA-Tat protein interaction may attenuate Tat/TAR-dependent protein expression and potentially serve as anti-HIV therapeutics. By incorporating positively charged residues with mixed side chain lengths, we designed peptides that bind TAR RNA with enhanced intracellular activity. Tat-derived peptides that were individually substituted with positively charged residues with varying side chain lengths were evaluated for TAR RNA binding. Positively charged residues with different side chain lengths were incorporated at each Arg and Lys position in the Tat-derived peptide to enhance TAR RNA binding. The resulting peptides showed enhanced TAR RNA binding affinity, cellular uptake, nuclear localization, proteolytic resistance, and inhibition of intracellular Tat/TAR-dependent protein expression compared to the parent Tat-derived peptide with no cytotoxicity. Apparently, the enhanced inhibition of protein expression by these peptides was not determined by RNA binding affinity, but by proteolytic resistance. Despite the high TAR binding affinity, a higher binding specificity would be necessary for practical purposes. Importantly, altering the positively charged residue side chain length should be a viable strategy to generate potentially useful RNA-targeting bioactive molecules.

  11. Systematic investigation of zinc aminoalkylphosphonates: influence of the alkyl chain lengths on the structure formation.

    PubMed

    Schmidt, Corinna; Stock, Norbert

    2012-03-05

    With the high-throughput (HT) methodology, the bifunctional aminoalkylphosphonic acids (AAPA) linker molecules 2-aminoethyl- (AEPA), 3-aminopropyl- (APPA), and 4-aminobutylphosphonic acid (ABPA) [HO(3)P-C(n)H(2n)-NH(2) (n = 2-4)] and zinc nitrate were used to synthesize new metal phosphonates in order to investigate the influence of the alkyl chain length on the structure formation. The systematic investigations led to one known (ZnO(3)PC(2)H(4)NH(2)) and six new compounds: one using AEPA, three using APPA, and two using ABPA. The crystal structures of five compounds were determined by single crystal X-ray diffraction, using X-ray powder diffraction (XRPD) data as well as structure modeling employing force field methods. For compound 1, Zn(O(3)P-C(2)H(4)-NH(3))(NO(3))(H(2)O) (monoclinic, Cc, a = 4.799(1) Å, b = 29.342(6) Å, c = 5.631(1) Å, β = 91.59(3)°, V = 792.7(3) Å(3), Z = 4), and compound 2, Zn(2)(OH)(O(3)P-C(3)H(6)-NH(3))(NO(3)) (monoclinic, P2/c, a = 12.158(2) Å, b = 5.0315(10) Å, c = 13.952(3) Å, β = 113.23(3)°, V = 784.3(3) Å(3), Z = 2), the structures were determined using single crystal X-ray diffraction data. The crystal structures of [Zn(O(3)P-C(3)H(6)-NH(2))]·H(2)O (3) (monoclinic, P2(1)/c, a = 9.094(2) Å, b = 5.0118(7) Å, c = 16.067(4) Å, β = 90.38(2)°, V = 732.3(2) Å(3), Z = 4) and Zn(O(3)P-C(4)H(8)-NH(2)) (5) (monoclinic, P2(1)/c, a = 8.570(7) Å, b = 8.378(4) Å, c = 9.902(6) Å, β = 90.94(5)°, V = 710.9(8) Å(3), Z = 4) were determined using XRPD data. The structural model for compound 6, Zn(O(3)P-C(4)H(8)-NH(3))(NO(3))(H(2)O), was established using lattice parameters from XRPD data and following crystal structure modeling employing force field methods. The structures depend strongly on the alkyl chain length n. For n = 2 and 4 isoreticular compounds are observed, while n = 3 leads to new structures. Larger amounts of all compounds were obtained employing scale-up syntheses in a conventional oven as well as in a microwave

  12. Dual influences of ecosystem size and disturbance on food chain length in streams.

    PubMed

    McHugh, Peter A; McIntosh, Angus R; Jellyman, Phillip G

    2010-07-01

    The number of trophic transfers occurring between basal resources and top predators, food chain length (FCL), varies widely in the world's ecosystems for reasons that are poorly understood, particularly for stream ecosystems. Available evidence indicates that FCL is set by energetic constraints, environmental stochasticity, or ecosystem size effects, although no single explanation has yet accounted for FCL patterns in a broad sense. Further, whether environmental disturbance can influence FCL has been debated on both theoretical and empirical grounds for quite some time. Using data from sixteen South Island, New Zealand streams, we determined whether the so-called ecosystem size, disturbance, or resource availability hypotheses could account for FCL variation in high country fluvial environments. Stable isotope-based estimates of maximum trophic position ranged from 2.6 to 4.2 and averaged 3.5, a value on par with the global FCL average for streams. Model-selection results indicated that stream size and disturbance regime best explained across-site patterns in FCL, although resource availability was negatively correlated with our measure of disturbance; FCL approached its maximum in large, stable springs and was <3.5 trophic levels in small, fishless and/or disturbed streams. Community data indicate that size influenced FCL, primarily through its influence on local fish species richness (i.e., via trophic level additions and/or insertions), whereas disturbance did so via an effect on the relative availability of intermediate predators (i.e., predatory invertebrates) as prey for fishes. Overall, our results demonstrate that disturbance can have an important food web-structuring role in stream ecosystems, and further imply that pluralistic explanations are needed to fully understand the range of structural variation observed for real food webs.

  13. Production and characterization of medium-chain-length polyhydroxyalkanoates by Pseudomonas mosselii TO7.

    PubMed

    Chen, Yi-Jr; Huang, Yan-Chia; Lee, Chia-Yin

    2014-08-01

    The polyhydroxyalkanoate (PHA) production and growth of Pseudomonas mosselii TO7, a newly isolated Pseudomonas species from the wastewater of a vegetable oil manufacturing facility, was analyzed. Phenotypic analysis and phylogenetic analysis of the 16S rRNA gene revealed that it is closely related to Pseudomonas mosselii. In the presence of palm kernel and soybean oils, P. mosselii TO7 produced up to 50% cell dry weight (CDW) medium-chain-length (MCL) PHAs comprising high poly(3-hydroxyoctanoate) (P(3HO)) content; P(3HO) content increased to 45% CDW when grown in octanoate using a single-step culture process. The PHA monomer was identified by (13)C nuclear magnetic resonance spectroscopy. The average molecular weight and polydispersity index of PHA were 218.30 ± 31.73 and 2.21 ± 0.18, respectively. The PHA produced by P. mosselii TO7 in the presence of palm kernel oil had two melting temperature (Tm) values of 37.2°C and 55.7°C with melting enthalpy (ΔHm) values of 51.09 J g(-1) and 26.57 J g(-1), respectively. Inhibition analyses using acrylic and 2-bromooctanoic acids revealed β-oxidation as the primary pathway for MCL-PHA biosynthesis using octanoic acid. Moreover, Pseudomonas putida GPp104 PHA(-), harboring the PHA synthase genes of P. mosselii (phaC1pm and phaC2pm) was used for heterologous expression, which demonstrated that phaC1pm is the main PHA synthesis enzyme, and 3-hydroxyoctanoyl-CoA is its major substrate. This was the first report of a P. mosselii TO7 isolate producing high-yield P(3HO) through utilization of plant oils.

  14. Graphic model for calculating the entropy of C11H24 alkanes with allowance for multiple non-valence interactions through three atoms along the chain of a molecule

    NASA Astrophysics Data System (ADS)

    Nilov, D. Yu.; Smolyakov, V. M.

    2016-08-01

    A fourteen-constant graphic scheme is proposed for evaluating the thermodynamic properties of branched paraffin hydrocarbons. Absolute entropy S f, 298 gas of 159 alkanes, of which 157 alkanes have yet to be studied experimentally, are calculated using 105 experimental data S f, 298 K, gas for alkanes CH4-C32H66.

  15. Solid-fluid and solid-solid equilibrium in hard sphere united atom models of n-alkanes: rotator phase stability.

    PubMed

    Cao, M; Monson, P A

    2009-10-22

    We present a study of the phase behavior for models of n-alkanes with chain lengths up to C(21) based on hard sphere united atom models of methyl and methylene groups, with fixed bond lengths and C-C-C bond angles. We extend earlier work on such models of shorter alkanes by allowing for gauche conformations in the chains. We focus particularly on the orientational order about the chain axes in the solid phase near the melting point, and our model shows how the loss of this orientational order leads to the formation of rotator phases. We have made extensive calculations of the thermodynamic properties of the models as well as order parameters for tracking the degree of orientational order around the chain axis. Depending on the chain length and whether the carbon number is even or odd, the model exhibits both a rotator phase and a more orientationally ordered solid phase in addition to the fluid phase. Our results indicate that the transition between the two solid phases is first-order with a small density change. The results are qualitatively similar to those seen experimentally and show that rotator phases can appear in models of alkanes without explicit treatment of attractive forces or explicit treatment of the hydrogen atoms in the chains.

  16. [Composition of n-alkanes in soils of the Yellow River Estuary Wetlands and their potential as organic matter source indicators].

    PubMed

    Yao, Peng; Yin, Hong-Zhen; Yao, Qing-Zhen; Chen, Hong-Tao; Liu, Yue-Liang

    2012-10-01

    Abstract: Surface soil samples from the Yellow River Estuary Wetlands were analyzed for total organic carbon (TOC) and n-alkanes. Molecular indicators of n-alkanes were calculated and their potential as organic matter source indicators was discussed and compared among different sampling areas and times. C25-C33 n-alkanes with odd-to-even predominance were observed in most surface soils of the wetlands, suggesting the dominant contribution of terrestrial higher plants for the soil organic matter (SOM), and the ubiquitous presence of unresolved complex mixture indicated the presence of petroleum contamination. Total n-alkane concentrations in soils varied from 0.57 microg x g(-1) to 3.90 microg x g(-1), and distinct spatial and temporal differences were observed. In April 2009 (dry season), total n-alkane concentration was higher than that in June 2009 (during water-sediment regulation) with the maximum concentration observed at the core area of the wetlands, followed by the north side of the Yellow River after the last pontoon bridge, and the abandoned channel area of the Yellow River. The opposite trend of total n-alkane concentration was observed in June. The variation of total n-alkane concentration at two sampling time points were positively correlated with TOC and negatively correlated with sediment grain size, suggesting the influence of hydro-environment on the accumulation of soil organic matter. Molecular indicators of n-alkanes, such as average chain length (ACL), odd-even predominance (OEP), alkane index (AI), carbon preference index (CPI) and Terrigenous/ Aquatic Ratio (TAR) indicated that the maturity of organic matter in soils of the wetlands was low, and the dominant source of the SOM was terrestrial higher plants and mainly herbaceous plants. Compared with other indicators, TAR is better in reflecting the variation of hydro-environment.

  17. Microbial biosynthesis of alkanes.

    PubMed

    Schirmer, Andreas; Rude, Mathew A; Li, Xuezhi; Popova, Emanuela; del Cardayre, Stephen B

    2010-07-30

    Alkanes, the major constituents of gasoline, diesel, and jet fuel, are naturally produced by diverse species; however, the genetics and biochemistry behind this biology have remained elusive. Here we describe the discovery of an alkane biosynthesis pathway from cyanobacteria. The pathway consists of an acyl-acyl carrier protein reductase and an aldehyde decarbonylase, which together convert intermediates of fatty acid metabolism to alkanes and alkenes. The aldehyde decarbonylase is related to the broadly functional nonheme diiron enzymes. Heterologous expression of the alkane operon in Escherichia coli leads to the production and secretion of C13 to C17 mixtures of alkanes and alkenes. These genes and enzymes can now be leveraged for the simple and direct conversion of renewable raw materials to fungible hydrocarbon fuels.

  18. Hydrocarbon Metabolism by Brevibacterium erythrogenes: Normal and Branched Alkanes1

    PubMed Central

    Pirnik, M. P.; Atlas, R. M.; Bartha, R.

    1974-01-01

    Branched- and straight-chain alkanes are metabolized by Brevibacterium erythrogenes by means of two distinct pathways. Normal alkanes (e.g., n-pentadecane) are degraded, after terminal oxidation, by the beta-oxidation system operational in fatty acid catabolism. Branched alkanes like pristane (2,6,10,14-tetramethylpentadecane) and 2-methylundecane are degraded as dicarboxylic acids, which also undergo beta-oxidation. Pristane-derived intermediates are observed to accumulate, with time, as a series of dicarboxylic acids. This dicarboxylic acid pathway is not observed in the presence of normal alkanes. Release of 14CO2 from [1-14C]pristane is delayed, or entirely inhibited, in the presence of n-hexadecane, whereas CO2 release from n-hexadecane remains unaffected. These results suggest an inducible dicarboxylic acid pathway for degradation of branched-chain alkanes. PMID:4852318

  19. Long-chain alkanes and fatty acids from Ludwigia octovalvis weed leaf surface waxes as short-range attractant and ovipositional stimulant to Altica cyanea (Weber) (Coleoptera: Chrysomelidae).

    PubMed

    Mitra, S; Sarkar, N; Barik, A

    2017-01-30

    The importance of leaf surface wax compounds from the rice-field weed Ludwigia octovalvis (Jacq.) Raven (Onagraceae) was determined in the flea beetle Altica cyanea (Weber) (Coleoptera: Chrysomelidae). Extraction, thin layer chromatography and GC-MS and GC-FID analyses of surface waxes of young, mature and senescent leaves revealed 20, 19 and 19 n-alkanes between n-C15 and n-C35, respectively; whereas 14, 14 and 12 free fatty acids between C12:0 and C22:0 fatty acids were identified in young, mature and senescent leaves, respectively. Tricosane was predominant n-alkane in young and mature leaves, whilst eicosane predominated in senescent leaves. Heneicosanoic acid, palmitic acid and docosanoic acid were the most abundant free fatty acids in young, mature and senescent leaves, respectively. A. cyanea females showed attraction to 0.25 mature leaf equivalent surface waxes compared with young or senescent leaves in a short glass Y-tube olfactometer bioassay. The insects were attracted to a synthetic blend of 0.90, 1.86, 1.83, 1.95, 0.50 and 0.18 µg ml-1 petroleum ether of hexadecane, octadecane, eicosane, tricosane, palmitic acid and alpha-linolenic acid, respectively, comparable with the proportions as present in 0.25 mature leaf equivalent surface waxes. A. cyanea also laid eggs on a filter paper moistened with 0.25 mature leaf equivalent surface waxes or a synthetic blend of 0.90, 1.86, 1.83, 1.95, 0.50 and 0.18 µg ml-1 petroleum ether of hexadecane, octadecane, eicosane, tricosane, palmitic acid and alpha-linolenic acid, respectively. This finding could provide a basis for monitoring of the potential biocontrol agent in the field.

  20. Synthesis of medium chain length fatty acid ethyl esters in engineered Escherichia coli using endogenously produced medium chain fatty acids.

    PubMed

    Fan, Liping; Liu, Junfeng; Nie, Kaili; Liu, Luo; Wang, Fang; Tan, Tianwei; Deng, Li

    2013-07-10

    Microbial biosynthesis of fatty acid-derived biofuels from renewable carbon sources has attracted significant attention in recent years. Free fatty acids (FFAs) can be used as precursors for the production of micro-diesel. The expression of codon optimized two plants (Umbellularia californica and Cinnamomum camphora) medium-chain acyl-acyl carrier protein (ACP) thioesterase genes (ucFatB and ccFatB) in Escherichia coli resulted in a very high level of extractable medium-chain-specific hydrolytic activity and caused large accumulation of medium-chain free fatty acids. By heterologous co-expression of acyl-coenzyme A:diacylglycerol acyltransferase from Acinetobacter baylyi ADP1, specific plant thioesterases in E. coli, with supplementation of exogenous ethanol, resulted in drastic changes in fatty acid ethyl esters (FAEEs) composition ranging from 12:0 to 18:1. Through an optimized microbial shake-flask fermentation of two modified E. coli strains, yielded FFAs and FAEEs in the concentration of approximately 500 mg L(-1)/250 mg L(-1) and 2.01 mg g(-1)/1.99 mg g(-1), respectively. The optimal ethanol level for FAEEs yield in the two recombinant strains was reached at the 3% ethanol concentration, which was about 5.4-fold and 1.93-fold higher than that of 1% ethanol concentration.

  1. Synthesis, characterization, and surface wettability properties of amine functionalized graphene oxide films with varying amine chain lengths.

    PubMed

    Shanmugharaj, A M; Yoon, J H; Yang, W J; Ryu, Sung Hun

    2013-07-01

    Surface functionalization of graphene oxide (GO) an important graphene precursor using alkylamines of varying chain lengths followed by thermal treatment resulted in the formation of superhydrophobic surfaces. Alkylamines consisting of hydrophobic long chain alkyl groups and hydrophilic amine groups were chemically reacted to the GO surface via two types of reactions viz. (i) amidation reaction between amine groups and carboxylic acid sites of GO and (ii) nucleophilic substitution reactions between amine and epoxy groups on GO surface. Successful grafting of alkylamines was confirmed using Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance ((1)H NMR), and thermogravimetric analysis (TGA). Alkylamine-modified GO surfaces showed enhanced roughness, and this effect was more pronounced with increasing amine chain length. Water contact angle measurements revealed that the hydrophobic nature of graphene depended on the chain length of the grafted alkylamines, and this fact may be corroborated to the decrease in the surface energy values. Our results indicate that superhydrophobic graphene films can be produced by thermal treatment of hexadecylamine- and octadecylamine-grafted GO films. These results will provide valuable guidance for the design and manufacture of graphene-based biomaterials, medical instruments, structural composites, electronics, and renewable energy devices.

  2. Potentiation decay of synapses and length distributions of synfire chains self-organized in recurrent neural networks.

    PubMed

    Miller, Aaron; Jin, Dezhe Z

    2013-12-01

    Synfire chains are thought to underlie precisely timed sequences of spikes observed in various brain regions and across species. How they are formed is not understood. Here we analyze self-organization of synfire chains through the spike-timing dependent plasticity (STDP) of the synapses, axon remodeling, and potentiation decay of synaptic weights in networks of neurons driven by noisy external inputs and subject to dominant feedback inhibition. Potentiation decay is the gradual, activity-independent reduction of synaptic weights over time. We show that potentiation decay enables a dynamic and statistically stable network connectivity when neurons spike spontaneously. Periodic stimulation of a subset of neurons leads to formation of synfire chains through a random recruitment process, which terminates when the chain connects to itself and forms a loop. We demonstrate that chain length distributions depend on the potentiation decay. Fast potentiation decay leads to long chains with wide distributions, while slow potentiation decay leads to short chains with narrow distributions. We suggest that the potentiation decay, which corresponds to the decay of early long-term potentiation of synapses, is an important synaptic plasticity rule in regulating formation of neural circuity through STDP.

  3. Influence of alkyl chain length on charge transport in symmetrically substituted poly(2,5-dialkoxy- p -phenylenevinylene) polymers

    NASA Astrophysics Data System (ADS)

    Tuladhar, Sachetan M.; Sims, Marc; Kirkpatrick, James; Maher, Robert C.; Chatten, Amanda J.; Bradley, Donal D. C.; Nelson, Jenny; Etchegoin, Pablo G.; Nielsen, Christian B.; Massiot, Philippe; George, Wayne N.; Steinke, Joachim H. G.

    2009-01-01

    We report on the hole transport characteristics, as measured by time of flight, of a family of symmetrically substituted dialkoxy poly( p -phenylenevinylene) polymers with different side-chain length. As side-chain length is decreased, the magnitude of the hole mobility μh increases while the field dependence of μh becomes more positive and the temperature dependence of μh becomes stronger. For the shortest side-chain derivative studied, μh exceeds 10-4cm2V-1s-1 at electric fields greater than 105Vcm-1 . The trend in magnitude of μh with side-chain length is consistent with the expected increase in electronic wave-function overlap as interchain separation decreases, while the trends in electric-field and temperature dependences of μh are consistent with increasing site energy disorder. We show that the electrostatic contribution to the site energy difference for pairs of oligomers follows the observed trend as a function of interchain separation, although the pairwise contribution is too small to explain the data quantitatively. Nonresonant Raman spectroscopy is used to characterize the microstructure of our films. We construct spatial maps of the Raman ratio I1280/I1581 and confirm an expected decrease in average film density with side-chain extension. The structural heterogeneity in the maps is analyzed but no clear correlation is observed with transport properties, suggesting that the structural variations relevant for charge transport occur on a length scale finer than the resolution of ˜1μm .

  4. Mg2+-Dependent Control of the Spatial Arrangement of Rhodococcus erythropolis PR4 Cells in Aqueous-Alkane Two Phase Culture Containing n-Dodecane

    PubMed Central

    Takihara, Hayato; Akase, Yumiko; Sunairi, Michio; Iwabuchi, Noriyuki

    2016-01-01

    We recently reported that a close relationship exists between alkane carbon-chain length, cell growth, and translocation frequency in Rhodococcus. In the present study, we examined the regulation of the spatial arrangement of cells in aqueous-alkane two phase cultures. An analysis of the effects of minerals on cell localization revealed that changes in the concentration of MgSO4 in two phase cultures containing n-dodecane (C12) altered cell localization from translocation to adhesion and vice versa. Our results indicate that the spatial arrangement of cells in two phase culture systems is controlled through the regulation of MgSO4 concentrations. PMID:27180641

  5. Fatty acid-induced injury in developing piglet intestine: effect of degree of saturation and carbon chain length.

    PubMed

    Velasquez, O R; Tso, P; Crissinger, K D

    1993-06-01

    Luminal perfusion with the long-chain fatty acid (LCFA) oleate in concentrations similar to that found in premature infant formula produces a dose- and age-dependent mucosal injury in developing intestine. To investigate whether this lipid-induced phenomenon is a function of the degree of saturation and/or chain length of the fatty acid, 51Cr-EDTA plasma-to-lumen clearance was measured in jejunum and ileum of 1-d-, 3-d-, 2-wk-, and 1-mo-old piglets after perfusion with 5-mM solutions of different medium-chain saturated fatty acids and saturated and unsaturated LCFA. Mono- and polyunsaturated LCFA produced significant increases in jejunal permeability. In general, this effect was greater in piglets < or = 2 wk old compared with 1-mo-old animals, but no differences were observed among the unsaturated LCFA within an age group. In contrast, the alterations in mucosal permeability induced by medium-chain fatty acids were overall more attenuated than those induced by LCFA. Our results suggest that developing intestine is vulnerable to the injurious effect of dietary fatty acids and that the lipid-induced changes in mucosal permeability appear to be a function of the fatty acid chain length. The degree of saturation of the fatty acid does not alter its cytotoxic effects.

  6. Solvation Energy of Ions in Polymers: Effects of Chain Length and Connectivity on Saturated Dipoles near Ions.

    PubMed

    Liu, Lijun; Nakamura, Issei

    2017-04-03

    We illustrate the effects of chain connectivity on the solvation energy of ions immersed in polymer liquids by developing a new coarse-grained molecular dynamics simulation. Our theory accounts for the dielectric response of the polymers through the connection of dipolar, monomeric units with nonlinear springs. In stark contrast to the standard Born solvation energy of ions, our results depend substantially on the chain length of the polymers. We also demonstrate the marked difference in the solvation energies of the ions immersed in non-polymeric particle mixtures, single-component polymers, polymer blends, and block copolymers. Thus, we suggest that the chain architecture of polymers is a key factor in ion solvation, whereas this feature is often inadequately considered in main theory and simulation literature. Our results are consistent with those predicted by previous coarse-grained mean-field theories when the dipole moment of the polymer compositions is relatively small. However, we also demonstrate that the strong ion-dipole and dipole-dipole interactions cause the chain-like association of the monomeric units, resulting in a qualitative discrepancy between the mean-field theory and simulation. Such a strong electrostatic correlation may reverse the dependence of the chain length on the solvation energy of the ions in the polymers.

  7. Development of environmentally friendly coatings and paints using medium-chain-length poly(3-hydroxyalkanoates) as the polymer binder.

    PubMed

    van der Walle, G A; Buisman, G J; Weusthuis, R A; Eggink, G

    1999-01-01

    Unsaturated medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHAs) produced by Pseudomonas putida from linseed oil fatty acids (LOFA) and tall oil fatty acids (TOFA), were used as the polymer binder in the formulation of high solid alkyd-like paints. The relatively high concentration of unsaturated alkyl side chains incorporated into the PHA resins resulted in oxidative drying PHA paints having excellent coating properties. The homogeneously pigmented PHA coatings yielded high-gloss, smooth and strong films upon curing and showed an excellent flexibility, a good adhesion to different substrates, cohesive film properties and resistance to chipping.

  8. Transition-state enthalpy and entropy effects on reactivity and selectivity in hydrogenolysis of n-alkanes.

    PubMed

    Flaherty, David W; Iglesia, Enrique

    2013-12-11

    Statistical mechanics and transition state (TS) theory describe rates and selectivities of C-C bond cleavage in C2-C10 n-alkanes on metal catalysts and provide a general description for the hydrogenolysis of hydrocarbons. Mechanistic interpretation shows the dominant role of entropy, over enthalpy, in determining the location and rate of C-C bond cleavage. Ir, Rh, and Pt clusters cleave C-C bonds at rates proportional to coverages of intermediates derived by removing 3-4 H-atoms from n-alkanes. Rate constants for C-C cleavage reflect large activation enthalpies (ΔH(‡), 217-257 kJ mol(-1)) that are independent of chain length and C-C bond location in C4+ n-alkanes. C-C bonds cleave because of large, positive activation entropies (ΔS(‡), 164-259 J mol(-1) K(-1)) provided by H2 that forms with TS. Kinetic and independent spectroscopic evidence for the composition and structure of these TS give accurate estimates of ΔS(‡) for cleavage at each C-C bond. Large differences between rate constants for ethane and n-decane (~10(8)) reflect an increase in the entropy of gaseous alkanes retained at the TS. The location of C-C bond cleavage depends solely on the rotational entropies of alkyl chains attached to the cleaved C-C bond, which depend on their chain length. Such entropy considerations account for the ubiquitous, but previously unexplained, preference for cleaving nonterminal C-C bonds in n-alkanes. This mechanistic analysis and thermodynamic treatment illustrates the continued utility of such approaches even for hydrogenolysis reactions, with complexity seemingly beyond the reach of classical treatments, and applies to catalytic clusters beyond those reported here (0.6-2.7 nm; Ir, Rh, Pt).

  9. Modeling the influence of alkane molecular structure on secondary organic aerosol formation.

    PubMed

    Aumont, Bernard; Camredon, Marie; Mouchel-Vallon, Camille; La, Stéphanie; Ouzebidour, Farida; Valorso, Richard; Lee-Taylor, Julia; Madronich, Sasha

    2013-01-01

    Secondary Organic Aerosols (SOA) production and ageing is a multigenerational oxidation process involving the formation of successive organic compounds with higher oxidation degree and lower vapor pressure. Intermediate Volatility Organic Compounds (IVOC) emitted to the atmosphere are expected to be a substantial source of SOA. These emitted IVOC constitute a complex mixture including linear, branched and cyclic alkanes. The explicit gas-phase oxidation mechanisms are here generated for various linear and branched C10-C22 alkanes using the GECKO-A (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere) and SOA formation is investigated for various homologous series. Simulation results show that both the size and the branching of the carbon skeleton are dominant factors driving the SOA yield. However, branching appears to be of secondary importance for the particle oxidation state and composition. The effect of alkane molecular structure on SOA yields appears to be consistent with recent laboratory observations. The simulated SOA composition shows, however, an unexpected major contribution from multifunctional organic nitrates. Most SOA contributors simulated for the oxidation of the various homologous series are far too reduced to be categorized as highly oxygenated organic aerosols (OOA). On a carbon basis, the OOA yields never exceeded 10% regardless of carbon chain length, molecular structure or ageing time. This version of the model appears clearly unable to explain a large production of OOA from alkane precursors.

  10. Determination of oligomeric chain length distributions at surfaces using ToF-SIMS: segregation effects and polymer properties

    NASA Astrophysics Data System (ADS)

    Gardella, Joseph A.; Mahoney, Christine M.

    2004-06-01

    While many XPS and SIMS studies of polymers have detected and quantified segregation of low surface energy blocks or components in copolymers and polymer blends [D. Briggs, in: D.R. Clarke, S. Suresh, I.M. Ward (Eds.), Surface Analysis of Polymers by XPS and Static SIMS, Cambridge University Press, Cambridge, 1998 (Chapter 5).], this paper reports ToF-SIMS studies of direct measurement of the segment length distribution at the surface of siloxane copolymers. These data allow insight into the segregation of particular portions of the oligomeric distribution; specifically, in this study, longer PDMS oligomers segregated at the expense of shorter PDMS chains. We have reported XPS analysis of competitive segregation effects for short PDMS chains [Macromolecules 35 (13) (2002) 5256]. In this study, a series of poly(ureaurethane)-poly(dimethylsiloxane) (PUU-PDMS) copolymers have been synthesized containing varying ratios of G-3 and G-9 (G- X describes the average segment length of the PDMS added), while maintaining a constant overall siloxane weight percentage (10, 30, and 60%). These copolymers were utilized as model systems to study the preferential segregation of certain siloxane segment lengths to the surface over others. ToF-SIMS analysis of PUU-PDMS copolymers has yielded high-mass range copolymer fragmentation patterns containing intact PDMS segments. For the first time, this information is utilized to determine PDMS segment length distributions at the copolymer surface as compared to the bulk. The results show that longer siloxane segment lengths are preferentially segregating to the surface over shorter chain lengths. These results also show the importance of ToF-SIMS and mass spectrometry in the development of new materials containing low molecular weight amino-propyl-terminated siloxanes.

  11. An experimental and theoretical approach to investigate the effect of chain length on aminothiol adsorption and assembly on gold.

    PubMed

    Bedford, Erin; Humblot, Vincent; Méthivier, Christophe; Pradier, Claire-Marie; Gu, Frank; Tielens, Frederik; Boujday, Souhir

    2015-10-05

    Despite the numerous studies on the self-assembled monolayers (SAMs) of alkylthiols on gold, the mechanisms involved, especially the nature and influence of the thiol-gold interface are still under debate. In this work the adsorption of aminothiols on Au(111) surfaces has been studied by using surface IR and X-ray photoelectron spectroscopy (XPS) as well as by density functional theory (DFT) modeling. Two aminothiols were used, cysteamine (CEA) and mercaptoundecylamine (MUAM), which contain two and eleven carbon atoms, respectively. By combining experimental and theoretical methods, it was possible to draw a molecular picture of the thiol-gold interface. The long-chain aminothiol produced better ordered SAMs, but, interestingly, the XPS data showed different sulfur binding environments depending on the alkyl chain length; an additional peak at low binding energy was observed upon CEA adsorption, which indicates the presence of sulfur in a different environment. DFT modeling showed that the positions of the sulfur atoms in the SAMs on gold with similar unit cells [(2√3×2√3)R30°] depended on the length of the alkyl chain. Short-chain alkylthiol SAMs were adsorbed more strongly than long-chain thiol SAMs and were shown to induce surface reconstruction by extracting atoms from the surface, possibly forming adatom/vacancy combinations that lead to the additional XPS peak. In the case of short alkylthiols, the thiol-gold interface governs the layer, CEA adsorbs strongly, and the mechanism is closer to single-molecule adsorption than self-assembly, whereas for long chains, interactions between alkyl chains drive the system to self-assembly, leading to a higher level of SAM organization and restricting the influence of the sulfur-gold interface.

  12. Seasonal variation of leaf wax n-alkane production and δ(2)H values from the evergreen oak tree, Quercus agrifolia.

    PubMed

    Sachse, Dirk; Dawson, Todd E; Kahmen, Ansgar

    2015-01-01

    In order to understand the timing of leaf wax synthesis in higher plants, we analysed the variability in leaf wax n-alkane concentration, composition (expressed as average chain length (ACL)), and δ(2)Hwax values as well as plant source water δ(2)H values (xylem and leaf water) in the evergreen tree Quercus agrifolia over a period of 9 months, beginning with leaf flush. We identified three distinct periods of leaf development with the first month following leaf flush being characterized by de novo synthesis and possibly removal of n-alkanes. During the following 3 months, n-alkane concentrations increased sevenfold and δ(2)Hwax and ACL values increased, suggesting this period was the major leaf wax n-alkane formation period. During the remaining 4 months of the experiment, stable values suggest cessation of leaf wax n-alkane formation. We find that n-alkane synthesis in Q. agrifolia takes place over 4 months, substantially longer than that observed for deciduous trees.

  13. Novel transparent zirconium-based hybrid material with multilayered nanostructures: studies of surface dewettability toward alkane liquids.

    PubMed

    Masheder, Benjamin; Urata, Chihiro; Cheng, Dalton F; Hozumi, Atsushi

    2013-01-01

    We have successfully prepared unique inorganic-organic hybrid materials that demonstrate excellent transparency and dewettability toward various alkane liquids (n-hexadecane, n-dodecane and n-decane) without relying on conventional surface roughening and perfluorination. Such coatings were made using a novel family of hybrid materials generated by substituting carboxylic acids, with a range of alkyl chain lengths (CH(3)(CH(2))(x-2)COOH where x = total carbon number, i.e., 10, 12, 14, 16, 18, 22, or 24, into zirconium (Zr) tetra-propoxide complexes. This precursor was then mixed with acetic acid and spincast to produce transparent thin Zr-carboxylic acid (ZrCA(x)) hybrid films using a nonhydrolytic sol-gel process. Fourier transform infrared spectroscopy provided proof of Zr-O-Zr network formation in the films upon casting and also followed changes to the physical nature (liquid-like or solid-like) of the alkyl chain assemblies depending upon alkyl chain length. X-ray diffractometry revealed that the hybrid films prepared using the longer chain carboxylic acids (ZrCA(x≥18)) spontaneously self-assembled into lamella structures with d-spacings ranging from 29.5 to 32.7 Angstroms, depending on the length of the alkyl chain. On the other hand the remaining films (ZrCA(x<18)) showed no such ordering. Moreover, the dynamic dewetting behavior of our hybrid films with alkane liquids was also strongly affected by alkyl chain length. ZrCA(x) films with x = 12, 14, and 16 showed the best dynamic oleophobicity among the seven hybrid films. In particular, small volume alkane droplets (5 μL) could be easily set in motion to move across and off ZrCA(14) film surfaces without pinning at low tilt angles (~6°).

  14. Formulation of oil-in-water β-carotene microemulsions: effect of oil type and fatty acid chain length.

    PubMed

    Roohinejad, Shahin; Oey, Indrawati; Wen, Jingyuan; Lee, Sung Je; Everett, David W; Burritt, David J

    2015-05-01

    The impact of oil type and fatty acid chain length on the development of food-grade microemulsions for the entrapment of β-carotene was investigated. The microemulsion region of a ternary phase diagram containing short chain monoglycerides was larger than for di- and triglycerides when Tween 80 was used as surfactant. The cytotoxicity of microemulsions composed of a 30% monoglyceride oil, 20% Tween 80 and 50% aqueous buffer were evaluated using an in vitro cell culture model (human epithelial colorectal adenocarcinoma, Caco-2). The cytotoxicity test showed that the viability of Caco-2 cells against β-carotene microemulsions at concentrations of 0.03125% (v/v) was higher than 90%. This study suggests that short chain monoglycerides could be used with Tween 80 to prepare transparent β-carotene-encapsulated O/W microemulsions in the particle size range of 12-100 nm.

  15. Comparison of united-atom potentials for the simulation of vapor-liquid equilibria and interfacial properties of long-chain n-alkanes up to n-C100.

    PubMed

    Müller, Erich A; Mejía, Andrés

    2011-11-10

    Canonical ensemble molecular dynamics (MD) simulations are reported which compute both the vapor-liquid equilibrium properties (vapor pressure and liquid and vapor densities) and the interfacial properties (density profiles, interfacial tensions, entropy and enthalpy of surface formation) of four long-chained n-alkanes: n-decane (n-C(10)), n-eicosane (n-C(20)), n-hexacontane (n-C(60)), and n-decacontane (n-C(100)). Three of the most commonly employed united-atom (UA) force fields for alkanes (SKS: Smit, B.; Karaborni, S.; Siepmann, J. I. J. Chem. Phys. 1995,102, 2126-2140; J. Chem. Phys. 1998,109, 352; NERD: Nath, S. K.; Escobedo, F. A.; de Pablo, J. J. J. Chem. Phys. 1998, 108, 9905-9911; and TraPPE: Martin M. G.; Siepmann, J. I. J. Phys. Chem. B1998, 102, 2569-2577.) are critically appraised. The computed results have been compared to the available experimental data and those fitted using the square gradient theory (SGT). In the latter approach, the Lennard-Jones chain equation of state (EoS), appropriately parametrized for long hydrocarbons, is used to model the homogeneous bulk phase Helmholtz energy. The MD results for phase equilibria of n-decane and n-eicosane exhibit sensible agreement both to the experimental data and EoS correlation for all potentials tested, with the TraPPE potential showing the lowest deviations. However, as the molecular chain increases to n-hexacontane and n-decacontane, the reliability of the UA potentials decreases, showing notorious subpredictions of both saturated liquid density and vapor pressure. Based on the recommended data and EoS results for the heaviest hydrocarbons, it is possible to attest, that in this extreme, the TraPPE potential shows the lowest liquid density deviations. The low absolute values of the vapor pressure preclude the discrimination among the three UA potentials studied. On the other hand, interfacial properties are very sensitive to the type of UA potential thus allowing a differentiation of the

  16. Lipid transfer between phosphatidylcholine vesicles and human erythrocytes: exponential decrease in rate with increasing acyl chain length.

    PubMed

    Ferrell, J E; Lee, K J; Huestis, W H

    1985-06-04

    The rate of phospholipid transfer from sonicated phospholipid vesicles to human erythrocytes has been studied as a function of membrane concentration and lipid acyl chain composition. Phospholipid transfer exhibits saturable first-order kinetics with respect to both cell and vesicle membrane concentrations. This kinetic behavior is consistent either with transfer during transient contact between cell and vesicle surfaces (but only if the fraction of the cell surface susceptible to such interaction is small) or with transfer of monomers through the aqueous phase. The acyl chain composition of the transferred phospholipid affects the transfer kinetics profoundly; for homologous saturated phosphatidylcholines, the rate of transfer decreases exponentially with increasing acyl chain length. This behavior is consistent with passage of phospholipid monomers through a polar phase, which might be the bulk aqueous phase( as in the monomer transfer model) or the hydrated head-group regions of a cell-vesicle complex (transient collision model). Collisional transfer also predicts that intercell transfer of phospholipids should be slow compared to cell-vesicle transfer, as surface charge and steric effects should prevent close apposition of donor and acceptor membranes. This is not found; dilauroylphosphatidylcholine transfers rapidly between red cells. Thus, the observed relationship between acyl chain length and intermembrane phospholipid transfer rates likely reflects the energetics of monomer transfer through the aqueous phase.

  17. Designing greener plasticizers: Effects of alkyl chain length and branching on the biodegradation of maleate based plasticizers.

    PubMed

    Erythropel, Hanno C; Brown, Tobin; Maric, Milan; Nicell, Jim A; Cooper, David G; Leask, Richard L

    2015-09-01

    The ubiquitous presence of the plasticizer di (2-ethylhexyl) phthalate (DEHP) in the environment is of concern due to negative biological effects associated with it and its metabolites. In particular, the metabolite mono (2-ethylhexyl) phthalate (MEHP) is a potential endocrine disruptor. Earlier work had identified the diester di (2-ethylhexyl) maleate (DEHM) as a potential greener candidate plasticizer to replace DEHP, yet its biodegradation rate was reported to be slow. In this study, we modified the side chains of maleate diesters to be linear (i.e., unbranched) alkyl chains that varied in length from ethyl to n-octyl. The plasticization efficiency of these compounds blended into PVC at 29 wt.% increased with the overall length of the molecule, but all compounds performed as well as or better than comparable samples with DEHP. Tests conducted with the equally long DEHM and dihexyl maleate (DHM) showed that branching has no effect on glass transition temperature (Tg) reduction efficiency. Biodegradation experiments with the common soil bacterium Rhodococcus rhodocrous in the presence of the plasticizer showed acceptable hydrolysis rates of maleates with unbranched side chains, while the branched DEHM showed almost no degradation. The addition of hexadecane as auxiliary carbon source improved hydrolysis rates. Temporary buildup of the respective monoester of the compounds were observed, but only in the case of the longest molecule, dioctyl maleate (DOM), did this buildup lead to growth inhibition of the bacteria. Maleates with linear side chains, if designed and tested properly, show promise as potential candidate plasticizers as replacements for DEHP.

  18. Hydrogen isotopic composition of individual n-alkanes as an intrinsic tracer for bioremediation and source identification of petroleum contamination.

    PubMed

    Pond, Kristy L; Huang, Yongsong; Wang, Yi; Kulpa, Charles F

    2002-02-15

    The isotopic signatures of crude oil hydrocarbons are potentially powerful intrinsic tracers to their origins and the processes by which the oils are modified in the environment. Stable carbon isotopic data are of limited use for studying petroleum contaminants because of the relatively small amount of isotopic fractionation that occurs during natural processes. Hydrogen isotopes, in contrast, are commonly fractionated to a much greater extent and as a result display larger variations in delta values. We studied the effect of in vitro aerobic biodegradation on the hydrogen isotopic composition of individual n-alkanes from crude oil. The isotopic analysis was conducted using gas chromatography-thermal conversion-isotope ratio mass spectrometry. In general, biodegradation rates decreased with increasing hydrocarbon chain length, consistent with previous studies. More importantly the n-alkanes that were degraded at the fastest rates (n-C15 to n-C18) also showed the largest overall isotopic fractionation (approximately 12-25 per thousand deuterium enrichment), suggesting that the lower molecular weight n-alkanes can be used to monitor in-situ bioremediation of crude oil contamination. The hydrogen isotopic compositions of the longer chain alkanes (n-C19 to n-C27) were relatively stable during biodegradation (<5%o overall deuterium enrichment), indicating that these compounds are effective tracers for oil-source identification studies.

  19. Effect of perfluoroalkyl chain length on monolayer behavior of partially fluorinated oleic acid molecules at the air-water interface.

    PubMed

    Baba, Teruhiko; Takai, Katsuki; Takagi, Toshiyuki; Kanamori, Toshiyuki

    2013-01-01

    A series of oleic acid (OA) analogs containing terminal perfluoroalkyl groups (CF3, C2F5, n-C3F7, n-C4F9 or n-C8F17) was synthesized to clarify how the fluorinated chain length affects the stability and molecular packing of liquid-expanded OA monolayers at the air-water interface. Although the substitution of terminal CF3 group for CH3 in OA had no effect on monolayer stability, further fluorination led to a gradual increase in monolayer stability at 25 °C. Surface pressure-area isotherm revealed that partially fluorinated OA analogs form more expanded monolayers than OA at low surface pressures, and that the monolayer behavior of OA analogs with the even-carbon numbered fluorinated chain is almost the same as that of OA upon monolayer compression, whereas the behavior of OA analogs with the odd-carbon numbered fluorinated chain significantly differs from that of OA. These results indicate: (i) the terminal short part (at least C2 residue) in OA predominantly determines the liquid-expanded monolayer stability; (ii) the molecular packing state of OA may be perturbed by the substitution of a short odd-carbon numbered fluorinated chain; (iii) hence, OA analogs with even-carbon numbered chain are considered to be preferable as hydrophobic building blocks for the synthesis of fluorinated phospholipids.

  20. Effect of ceramide acyl chain length on skin permeability and thermotropic phase behavior of model stratum corneum lipid membranes.

    PubMed

    Janůšová, Barbora; Zbytovská, Jarmila; Lorenc, Petr; Vavrysová, Helena; Palát, Karel; Hrabálek, Alexandr; Vávrová, Kateřina

    2011-03-01

    Stratum corneum ceramides play an essential role in the barrier properties of skin. However, their structure-activity relationships are poorly understood. We investigated the effects of acyl chain length in the non-hydroxy acyl sphingosine type (NS) ceramides on the skin permeability and their thermotropic phase behavior. Neither the long- to medium-chain ceramides (8-24 C) nor free sphingosine produced any changes of the skin barrier function. In contrast, the short-chain ceramides decreased skin electrical impedance and increased skin permeability for two marker drugs, theophylline and indomethacin, with maxima in the 4-6C acyl ceramides. The thermotropic phase behavior of pure ceramides and model stratum corneum lipid membranes composed of ceramide/lignoceric acid/cholesterol/cholesterol sulfate was studied by differential scanning calorimetry and infrared spectroscopy. Differences in thermotropic phase behavior of these lipids were found: those ceramides that had the greatest impact on the skin barrier properties displayed the lowest phase transitions and formed the least dense model stratum corneum lipid membranes at 32°C. In conclusion, the long hydrophobic chains in the NS-type ceramides are essential for maintaining the skin barrier function. However, this ability is not shared by their short-chain counterparts despite their having the same polar head structure and hydrogen bonding ability.

  1. Composition-based effective chain length for prediction of protein folding rates

    NASA Astrophysics Data System (ADS)

    Chang, Le; Wang, Jun; Wang, Wei

    2010-11-01

    Folding rate prediction is a useful way to find the key factors affecting folding kinetics of proteins. Structural information is more or less required in the present prediction methods, which limits the application of these methods to various proteins. In this work, an “effective length” is defined solely based on the composition of a protein, namely, the number of specific types of amino acids in a protein. A physical theory based on a minimalist model is employed to describe the relation between the folding rates and the effective length of proteins. Based on the resultant relationship between folding rates and effective length, the optimal sets of amino acids are found through the enumeration over all possible combinations of amino acids. This optimal set achieves a high correlation (with the coefficient of 0.84) between the folding rates and the optimal effective length. The features of these amino acids are consistent with our model and landscape theory. Further comparisons between our effective length and other factors are carried out. The effective length is physically consistent with structure-based prediction methods and has the best predictability for folding rates. These results all suggest that both entropy and energetics contribute importantly to folding kinetics. The ability to accurately and efficiently predict folding rates from composition enables the analysis of the kinetics for various kinds of proteins. The underlying physics in our method may be helpful to stimulate further understanding on the effects of various amino acids in folding dynamics.

  2. Effects of chain length and pH on the uptake and distribution of perfluoroalkyl substances in maize (Zea mays).

    PubMed

    Krippner, Johanna; Brunn, Hubertus; Falk, Sandy; Georgii, Sebastian; Schubert, Sven; Stahl, Thorsten

    2014-01-01

    Maize is the most important grain crop grown for human nutrition, animal fodder and biogas production worldwide. Nonetheless, no systematic studies have been undertaken on these plants to examine the uptake mechanisms for perfluoroalkyl substances (PFASs) dependent upon chain length and pH value. The aim of the present study was therefore to determine the influence of chain length (C4 to C10) and pH value (pH 5, pH 6, pH 7) on the uptake and distribution of seven perfluoroalkyl carboxylic acids (PFCAs) and three perfluoroalkane sulfonic acids (PFSAs) by maize in nutrient solution experiments under controlled conditions in a climate chamber. A pH-dependent uptake was observed for perfluorodecanoic acid (PFDA) with an uptake rate of 2.51 μg g(-1) at pH 5 compared to 1.52 μg g(-1) root dry weight (DW) per day (d) at pH 7. Perfluorobutanoic acid (PFBA) had the highest uptake rate within the group of PFCAs with an average of 2.46 μg g(-1) root DWd(-1) and perfluorooctane sulfonic acid (PFOS) had the highest uptake rate (3.63 μg g(-1) root DWd(-1)) within the group of PFSAs. The shoot:root ratio for shorter-chain PFCAs (≤ C7) and PFBS (C4) was >2.0, which indicates that shorter-chain PFASs are transferred predominantly and at higher concentrations to the shoot. In contrast, long-chain PFCAs such as perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA) and perfluorodecanoic acid (PFDA) as well as the PFASs perfluorohexane sulfonic acid (PFHxS) and perfluorooctane sulfonic acid (PFOS) accumulated at higher concentrations in the roots of maize plants with a shoot:root ratio of <1.0.

  3. Effect of temperature and cationic chain length on the physical properties of ammonium nitrate-based protic ionic liquids.

    PubMed

    Capelo, S Bouzón; Méndez-Morales, T; Carrete, J; López Lago, E; Vila, J; Cabeza, O; Rodríguez, J R; Turmine, M; Varela, L M

    2012-09-13

    We report a systematic study of the effect of the cationic chain length and degree of hydrogen bonding on several equilibrium and transport properties of the first members of the alkylammonium nitrate protic ionic liquids (PILs) family (ethylammonium, propylammonium, and butylammonium nitrate) in the temperature range between 10 and 40 °C. These properties were observed by means of several experimental techniques, including density, surface tension, refractometry, viscosimetry, and conductimetry. The dilatation coefficients and compressibilities, as well as the Rao coefficients, were calculated, and an increase of these magnitudes with alkyl chain length was detected. Moreover, the surface entropies and enthalpies of the studied PILs were analyzed, and the temperature dependence of the surface tension was observed to be describable by means of a harmonic oscillator model with surface energies and critical temperatures that are increasing functions of the cationic chain length. Moreover, the refractive indexes were measured and the thermo-optic coefficient and Abbe numbers were calculated, and the contribution of the electrostrictive part seemed to dominate the temperature dependence of the electric polarization. The electric conductivity and the viscosity were measured and the influence of the degree of hydrogen bonding in the supercooled liquid region analyzed. Hysteresis loops were detected in freezing-melting cycles and the effect of the length of the alkyl chain of the cation on the size of the loop analyzed, showing that longer chains lead to a narrowing of the supercooled region. The temperature dependence of the conductivity was studied in the Vogel-Fulcher-Tamman (VFT) framework and the fragility indices, the effective activation energies, and the Vogel temperatures obtained. A high-temperature Arrhenius analysis was also performed, and the activation energies of conductivity and viscosity were calculated, showing that these transport processes are

  4. Low-temperature spectral dynamics of single TDI molecules in n-alkane matrixes.

    PubMed

    Mackowski, Sebastian; Wörmke, Stephan; Ehrl, Moritz; Bräuchle, Christoph

    2008-01-01

    We report on studies of the influence of the matrix on the spectral dynamics of the zero-phonon-line (ZPL) emission by means of single molecule spectroscopy at low temperature. The host-guest system combinations consist of terrylenediimide (TDI) molecules embedded in four n-alkane matrixes of hexane, heptane, pentadecane, and hexadecane. Excitations into the broad vibronic absorption band and spectrally dispersed detection allows us to monitor fluorescence of single TDI molecules as a function of time. In the case of long-chain n-alkanes (pentadecane and hexadecane), the ZPL line is quite stable, showing spectral jumps of moderate frequency of less than 10 cm(-1) with an average time between the jumps of 10 s. In a clear contrast, the spectral dynamics of TDI molecules embedded within the short-length n-alkane matrixes (heptane and hexane) feature much more frequent spectral jumps that occur on a broader energy scale. The results suggest that matrixes composed of short-chain molecules are more susceptible to translations and/or rotations, which influence the fluorescence of single guest chromophores.

  5. Polypropylene non-woven meshes with conformal glycosylated layer for lectin affinity adsorption: the effect of side chain length.

    PubMed

    Ye, Xiang-Yu; Huang, Xiao-Jun; Xu, Zhi-Kang

    2014-03-01

    The unique characteristics of polypropylene non-woven meshes (PPNWMs), like random network of overlapped fibers, multiple connected pores and overall high porosity, make them high potentials for use as separation or adsorption media. Meanwhile, carbohydrates can specifically recognize certain lectin through multivalent interactions. Therefore glycosylated PPNWMs, combing the merits of both, can be regarded as superior affinity membranes for lectin adsorption and purification. Here, we describe a versatile strategy for the glycosylation of PPNWMs. Two hydrophilic polymers with different side chain length, poly(2-hydroxyethyl methacrylate) (PHEMA) and poly(oligo(ethylene glycol) methacrylate) (POEGMA), were first conformally tethered on the polypropylene fiber surface by a modified plasma pretreatment and benzophenone (BP) entrapment UV irradiation process. Then glucose ligands were bound through the reaction between the hydroxyl group and acetyl glucose. Chemical changes of the PPNWMs surface were monitored by FT-IR/ATR. SEM pictures show that conformal glucose ligands can be achieved through the modified process. After deprotection, the glycosylated PPNWMs became superhydrophilic and had high specific recognition capability toward Concanavalin A (Con A). Static Con A adsorption experiments were further performed and the results indicate that fast adsorption kinetics and high binding capacity can be accomplished at the same time. We also found that increasing the side chain length of polymer brushes had positive effect on protein binding capacity due to improved chain mobility. Model studies suggest a multilayer adsorption behavior of Con A.

  6. Solvent-mediated folding of dicarboxylate dianions: aliphatic chain length dependence and origin of the IR intensity quenching.

    PubMed

    Wanko, Marius; Wende, Torsten; Montes Saralegui, Marta; Jiang, Ling; Rubio, Angel; Asmis, Knut R

    2013-12-21

    We combine infrared photodissociation spectroscopy with quantum chemical calculations to characterize the hydration behavior of microsolvated dicarboxylate dianions, (CH2)m(COO(-))2·(H2O)n, as a function of the aliphatic chain length m. We find evidence for solvent-mediated folding transitions, signaled by the intensity quenching of the symmetric carboxylate stretching modes, for all three species studied (m = 2, 4, 8). The number of water molecules required to induce folding increases monotonically with the chain length and is n = 9-12, n = 13, and n = 18-19 for succinate (m = 2), adipate (m = 4), and sebacate (m = 8), respectively. In the special case of succinate, the structural transition is complicated by the possibility of bridging water molecules that bind to both carboxylates with merely minimal chain deformation. On the basis of vibrational calculations on a set of model systems, we identify the factors responsible for intensity quenching. In particular, we find that the effect of hydrogen bonds on the carboxylate stretching mode intensities is strongly orientation dependent.

  7. Hepatic fatty acid uptake is regulated by the sphingolipid acyl chain length

    PubMed Central

    Park, Woo-Jae; Park, Joo-Won; Merrill, Alfred H.; Storch, Judith; Pewzner-Jung, Yael; Futerman, Anthony H.

    2015-01-01

    Ceramide synthase 2 (CerS2) null mice cannot synthesize very-long acyl chain (C22-C24) ceramides resulting in significant alterations in the acyl chain composition of sphingolipids. We now demonstrate that hepatic triacylglycerol (TG) levels are reduced in liver but not in adipose tissue or skeletal muscle in the CerS2 null mouse, both before and after feeding with a high fat diet (HFD), where no weight gain was observed and large hepatic nodules appeared. Uptake of both BODIPY-palmitate and [3H]-palmitate were also abrogated in hepatocytes and liver. The role of a number of key proteins involved in fatty acid uptake was examined, including FATP5, CD36/FAT, FABPpm and cytoplasmic FABP1. Levels of FATP5 and FABP1 were decreased in CerS2 null mouse liver, whereas CD36/FAT levels were significantly elevated and CD36/FAT was also mislocalized upon insulin treatment. Moreover, treatment of hepatocytes with C22-C24-ceramides down-regulated CD36/FAT levels. Infection of CerS2 null mice with recombinant adeno-associated virus (rAAV)-CerS2 restored normal TG levels and corrected the mislocalization of CD36/FAT, but had no effect on the intracellular localization or levels of FATP5 or FABP1. Together, these results demonstrate that hepatic fatty acid uptake via CD36/FAT can be regulated by altering the acyl chain composition of sphingolipids. PMID:25241943

  8. Evaluation of long-chain alcohols as diet composition markers in goats grazing heathland areas.

    PubMed

    Ferreira, L M M; Celaya, R; Santos, A S; Guedes, C M V; Rodrigues, M A M; Mayes, R W; Osoro, K

    2012-04-01

    An experiment was conducted to assess the potential of long-chain alcohols (LCOH), in alternative or combined with alkanes and long-chain fatty acids (LCFA), as faecal markers to estimate the diet composition of goats grazing heathland vegetation with associated improved pastures. A total of seven diets were offered across the grazing season. The diets were composed of mixtures of herb species (Lolium perenne and Trifolium repens) and woody species (Erica spp., Calluna vulgaris and Ulex gallii) in an attempt to simulate diet selection of goats on these complex vegetation areas. The diet composition was estimated using LCOH markers alone or combined with alkanes, LCFA and alkanes+LCFA, by least square optimization procedures. The data showed large differences between plant species in their LCOH profile. Generally, plant species showed higher LCOH concentrations than those of alkanes and lower than LCFA markers. Faecal recovery of LCOH was incomplete and increased in a linear manner (P < 0.001) with the carbon-chain length, and was influenced by diet composition and its digestibility. The diet composition estimates based on LCOH alone were more accurate (P < 0.05) than those using alkanes or LCFA alone. Results showed that the combination of LCOH with alkanes, LCFA and alkanes+LCFA resulted in more accurate (P < 0.05) estimates of diet composition, indicating that LCOH provided different discriminatory information to that of alkanes and LCFA, helping in the discrimination of the plant species used in this experiment. Results indicate that correction of faecal LCOH concentrations to incomplete faecal recovery is necessary to obtain more accurate estimates of diet composition. Nevertheless, it seemed that the use of a less accurate recovery correction on LCOH markers had a lower impact on the accuracy of estimates than that of alkanes and LCFA.

  9. Room temperature ionic liquids: A simple model. Effect of chain length and size of intermolecular potential on critical temperature

    NASA Astrophysics Data System (ADS)

    Chapela, Gustavo A.; Guzmán, Orlando; Díaz-Herrera, Enrique; del Río, Fernando

    2015-04-01

    A model of a room temperature ionic liquid can be represented as an ion attached to an aliphatic chain mixed with a counter ion. The simple model used in this work is based on a short rigid tangent square well chain with an ion, represented by a hard sphere interacting with a Yukawa potential at the head of the chain, mixed with a counter ion represented as well by a hard sphere interacting with a Yukawa potential of the opposite sign. The length of the chain and the depth of the intermolecular forces are investigated in order to understand which of these factors are responsible for the lowering of the critical temperature. It is the large difference between the ionic and the dispersion potentials which explains this lowering of the critical temperature. Calculation of liquid-vapor equilibrium orthobaric curves is used to estimate the critical points of the model. Vapor pressures are used to obtain an estimate of the triple point of the different models in order to calculate the span of temperatures where they remain a liquid. Surface tensions and interfacial thicknesses are also reported.

  10. Morphology and electrochemical properties of perfluorosulfonic acid ionomers for vanadium flow battery applications: effect of side-chain length.

    PubMed

    Ding, Cong; Zhang, Huamin; Li, Xianfeng; Zhang, Hongzhang; Yao, Chuan; Shi, Dingqin

    2013-07-01

    Perfluorosulfonic acid ionomers (PFSI) with different side-chain lengths have been investigated with respect to their morphology and electrochemical properties in vanadium flow batteries (VFB). The results indicated that the membrane with the shortest side chains (SSC-M2) displayed small ion clusters and a low degree of hydrophobic-hydrophilic separation, which is favourable to reduce the cross-over of vanadium ions in the VFB. SSC-M2 shows a similar proton conductivity to Nafion, which carries longer ionic side chains but with much lower ion permeability. As a result, the VFB assembled with SSC-M2 exhibited a superior coulombic efficiency and a voltage efficiency close to that of Nafion115. In situ mass transfer revealed that SSC-M2 had a remarkably low degree of vanadium and water transfer across the membrane, which resulted in lower capacity fading than in the case of Nafion115. These results indicate that a membrane with short side chains is an ideal option in the fabrication of high-performance VFBs with low capacity loss.

  11. Room temperature ionic liquids: A simple model. Effect of chain length and size of intermolecular potential on critical temperature.

    PubMed

    Chapela, Gustavo A; Guzmán, Orlando; Díaz-Herrera, Enrique; del Río, Fernando

    2015-04-21

    A model of a room temperature ionic liquid can be represented as an ion attached to an aliphatic chain mixed with a counter ion. The simple model used in this work is based on a short rigid tangent square well chain with an ion, represented by a hard sphere interacting with a Yukawa potential at the head of the chain, mixed with a counter ion represented as well by a hard sphere interacting with a Yukawa potential of the opposite sign. The length of the chain and the depth of the intermolecular forces are investigated in order to understand which of these factors are responsible for the lowering of the critical temperature. It is the large difference between the ionic and the dispersion potentials which explains this lowering of the critical temperature. Calculation of liquid-vapor equilibrium orthobaric curves is used to estimate the critical points of the model. Vapor pressures are used to obtain an estimate of the triple point of the different models in order to calculate the span of temperatures where they remain a liquid. Surface tensions and interfacial thicknesses are also reported.

  12. Variable camshaft timing system utilizing changes in length of portions of a chain or belt

    SciTech Connect

    Butterfield, R.P.; Smith, F.R.

    1992-10-06

    This patent describes an internal combustion engine. It comprises: a first rotatable member, the first rotatable member being rotatable about a first axis; a second rotatable member; endless drive means interconnecting the first rotatable member and the second rotatable member for simultaneous rotation of the rotatable members; first hydraulic tensioning means; and means for transferring hydraulic fluid from one of the first tensioning means and the second tensioning means to the other of the first tensioning means and the second tensioning means to increase the length of one of the first portion and the second portion and decrease the length of the other of the first portion and the portion and thereby change the position of the second rotatable member about its axis of rotation relative to the first rotatable member.

  13. The transfection efficiency of calix[4]arene-based lipids: the role of the alkyl chain length.

    PubMed

    Mochizuki, Shinichi; Nishina, Koichi; Fujii, Shota; Sakurai, Kazuo

    2015-02-01

    The size, surface charge, and microstructure of lipoplexes comprising cationic lipids and nucleic acids are important factors for transfection efficiency. As these properties are largely determined by the cationic lipids used, a number of studies on the relationship between cationic lipids and the transfection efficiency have been reported. Among the many cationic lipids, lipids with multivalent cationic head groups are expected to be potent transfection reagents. Here, we prepared calix[4]arene-based lipids with different alkyl chain lengths from C3 to C15 and evaluated the relationship between the alkyl chain length and the transfection efficiency. C6 lipoplexes exhibited the highest transfection efficiency among all lipoplexes. The gene expression with C9 and C12 lipoplexes was slightly lower than that with C6 lipoplexes. C3 lipoplexes hardly induced gene expression, while C15 lipoplexes exhibited no complexation with plasmid DNA. Although all lipoplexes exhibited nearly identical characteristics, they exhibited different behaviours in terms of the interactions between the lipoplexes and anionic micelles comprising phosphatidylserine, a model of endosomal vehicle. After mixing with phosphatidylserine micelles, C6 lipoplexes released the bound plasmid DNA at pH 5 but not at pH 7, indicating that they can interact with the late endosomal membrane after being incorporated into cells. No plasmid DNA was released from C9 or C12 lipoplexes at either pH values. Thus, the alkyl chain length of cationic lipids is related to their interaction with the endosomal compartment and can provide a basis for the design of novel transfection reagents.

  14. Detailed chemical kinetic models for large n-alkanes and iso-alkanes found in conventional and F-T diesel fuels

    SciTech Connect

    Westbrook, C K; Pitz, W J; Curran, H J; Mehl, M

    2008-12-15

    Detailed chemical kinetic models are needed to simulate the combustion of current and future transportation fuels. These models should represent the various chemical classes in these fuels. Conventional diesel fuels are composed of n-alkanes, iso-alkanes, cycloalkanes and aromatics (Farrell et al. 2007). For future fuels, there is a renewed interest in Fischer-Tropsch (F-T) processes which can be used to synthesize diesel and other transportation fuels from biomass, coal and natural gas. F-T diesel fuels are expected to be similar to F-T jet fuels which are commonly comprised of iso-alkanes with some n-alkanes (Smith and Bruno, 2008). Thus, n-alkanes and iso-alkanes are common chemical classes in these conventional and future fuels. This paper reports on the development of chemical kinetic models of large n-alkanes and iso-alkanes to represent these chemical classes in conventional and future fuels. Two large iso-alkanes are 2,2,4,4,6,8,8-heptamethylnonane, which is a primary reference fuel for diesel, and isooctane, a primary reference fuel for gasoline. Other iso-alkanes are branched alkanes with a single methyl side chain, typical of most F-T fuels. The chemical kinetic models are then used to predict the effect of these fuel components on ignition characteristics under conditions found in internal combustion engines.

  15. How to Prepare Long Multi-Block Heteropolymer Chains with AN Ordered Sequence and Controllable Block Lengths

    NASA Astrophysics Data System (ADS)

    Wu, Chi; Xie, Zuowei

    2003-03-01

    It had been a long dream in polymer science to synthesize long multi-block heteropolymers with an ordered chain sequence and controllable block lengths. Using ionic or living free radical polymerization, one can prepare copolymers with few blocks, such as diblock and triblock copolymers. The most plausible result with a reasonable yield in this direction was penta-block copolymer. In another way, one could attach each end of polymer blocks with a reactive functional group and then join them together to form a long multi-block heteropolymer chain. However, the functional ends are normally wrapped and hidden inside the coiled polymer blocks in solution, which dramatically reduces their reactivity, so that longer polymer chains cannot be formed in such a way. Recently, combining polymer physics and synthetic chemistry, we have invented a novel self-assembly assisted polypolymerization (SAAP) method to connect 10-100 polymer blocks together to form long multi-block heteropolymer chains with an ordered sequence and controllable narrowly distributed block lengths. The schematic principle is as follows. To demonstrate the principle of SAAP, we used a typical triblock copolymer, poly(methyl methacry-late)-b-polystyrene-b-poly(methylmethacrylate), PMNA-PS-PMMA, prepared by anionic polymeri-zation. The detail of synthesizing the triblock copolymer is not what we try to address here and can be found elsewhere. The number average molar masses of the PMMA and PS blocks used were 7.00 x 102 g/mol and 1.68 x 104 g/mol, respectively. The polydispersity index (Mw/Mn) is 1.25. The ionic ends of the two PMMA blocks were terminated with an excess amount of oxalyl chloride (ClOC-COCl), which led to functional groups (-OC-COCl) at the two ends. The triblock copolymer was soluble in a solvent mixture of methyl acetate and acetonitrile (10.0:1.0, v/v) when the solution temperature was higher than 45 oC. As the temperature decreases, they could self-assemble into a core-shell micelle

  16. Involvement of an alkane hydroxylase system of Gordonia sp. strain SoCg in degradation of solid n-alkanes.

    PubMed

    Lo Piccolo, Luca; De Pasquale, Claudio; Fodale, Roberta; Puglia, Anna Maria; Quatrini, Paola

    2011-02-01

    Enzymes involved in oxidation of long-chain n-alkanes are still not well known, especially those in gram-positive bacteria. This work describes the alkane degradation system of the n-alkane degrader actinobacterium Gordonia sp. strain SoCg, which is able to grow on n-alkanes from dodecane (C(12)) to hexatriacontane (C(36)) as the sole C source. SoCg harbors in its chromosome a single alk locus carrying six open reading frames (ORFs), which shows 78 to 79% identity with the alkane hydroxylase (AH)-encoding systems of other alkane-degrading actinobacteria. Quantitative reverse transcription-PCR showed that the genes encoding AlkB (alkane 1-monooxygenase), RubA3 (rubredoxin), RubA4 (rubredoxin), and RubB (rubredoxin reductase) were induced by both n-hexadecane and n-triacontane, which were chosen as representative long-chain liquid and solid n-alkane molecules, respectively. Biotransformation of n-hexadecane into the corresponding 1-hexadecanol was detected by solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME/GC-MS) analysis. The Gordonia SoCg alkB was heterologously expressed in Escherichia coli BL21 and in Streptomyces coelicolor M145, and both hosts acquired the ability to transform n-hexadecane into 1-hexadecanol, but the corresponding long-chain alcohol was never detected on n-triacontane. However, the recombinant S. coelicolor M145-AH, expressing the Gordonia alkB gene, was able to grow on n-triacontane as the sole C source. A SoCg alkB disruption mutant that is completely unable to grow on n-triacontane was obtained, demonstrating the role of an AlkB-type AH system in degradation of solid n-alkanes.

  17. Characterization of an extracellular medium-chain-length poly(3-hydroxyalkanoate) depolymerase from Pseudomonas alcaligenes LB19.

    PubMed

    Kim, Do Young; Nam, Jin Sik; Rhee, Young Ha

    2002-01-01

    An extracellular medium-chain-length poly(3-hydroxyalkanoate) (MCL-PHA) depolymerase from an isolate, Pseudomonas alcaligenes LB19, was purified to electrophoretic homogeneity by hydrophobic interaction chromatography using Octyl-Sepharose CL-4B and gel permeation chromatography using Sephadex G-150. The molecular mass of the enzyme, which consisted of a single polypeptide chain, was approximately 27.6 kDa. The pI value of the enzyme was estimated to be 5.7, and its maximum activity was observed at pH 9.0 and 45 degreesC. The enzyme was significantly inactivated by EDTA and phenylmethylsulfonyl fluoride (PMSF) but insensitive to dithiothreitol. It was also markedly inhibited by 0.1% Tween 80 and 0.05% Triton X-100. The purified enzyme could hydrolyze various types of bacterial aliphatic and aromatic MCL-PHAs but not poly(3-hydroxybutyrate), polycaprolactone, and poly(L-lactide). Biodegradation rates of the aromatic MCL-PHAs were significantly lower than those of the aliphatic MCL-PHAs, regardless of the compositions and types of aromatic substituents. It was able to hydrolyze medium-chain-length p-nitrophenylalkanoates more efficiently than the shorter-chain forms. The main hydrolysis products of poly(3-hydroxynonanoate) were identified as monomer units. The results demonstrated in this study suggest that the MCL-PHA depolymerase from P. alcaligenes LB19 is a distinct enzyme, which are different from those of other MCL-PHA degrading bacteria in its quaternary structure, pI value, sensitivity to EDTA and PMSF, and hydrolysis products of MCL-PHA.

  18. Photoinduced intramolecular charge transfer in push-pull polyenes: effects of solvation, electron-donor group, and polyenic chain length.

    PubMed

    Akemann, Walther; Laage, Damien; Plaza, Pascal; Martin, Monique M; Blanchard-Desce, Mireille

    2008-01-17

    Subpicosecond absorption spectroscopy is used to characterize the primary photoinduced processes in a class of push-pull polyenes bearing a julolidine end group as the electron donor and a diethylthiobarbituric acid end group as the electron acceptor. The excited-state decay time and relaxation pathway have been studied for four polyenes of increasing chain length (n = 2-5 double bonds) in aprotic solvents of different solvation time, polarity, and viscosity. Intramolecular charge transfer (ICT) leading to a transient state of cyanine-like structure (fully conjugated with no bond length alternation) is observed in all polar solvents at a solvent dependent rate, but the reaction is not observed in cyclohexane, a nonpolar solvent. In polar solvents, the reaction time increases with the average solvation time but remains slightly larger, except in the viscous solvent triacetin. These facts are interpreted as an indication that both solvent reorganization and internal restructuring are involved in the ICT-state formation. The observed photodynamics resemble those we previously found for another class of polyenes bearing a dibutylaniline group as the donor, including a similar charge-transfer rate in spite of the larger electron donor character of the julolidine group. This observation brings further support to the proposal that an intramolecular coordinate is involved in the charge-transfer reaction, possibly a torsional motion of the donor end group. On the other hand, relaxation of the ICT state leads to cis-trans isomerization or crossing to the triplet state, depending on the length of the polyenic chain. In dioxane, tetrahydrofuran, and triacetin, the ICT state of the shorter chains (n = 2, 3) relaxes to the isomer with a viscosity-dependent rate, while that of the longer ones (n = 4, 5) leads to the triplet state with a viscosity-independent rate, as expected. In acetonitrile, the ICT-state lifetime is generally much shorter. A change from photoisomerization to

  19. Microemulsion breakdown by pervaporation technique: effect of the alkyl chain length of n-alkanol, a cosurfactant of the microemulsion.

    PubMed

    Moulay, Saâd; Hadj-Ziane, Amel Zafour; Canselier, Jean-Paul

    2007-07-15

    Two sets of microemulsions, cyclohexane- and water-rich ones, were prepared with the following n-alkanols as cosurfactants: n-propanol, n-butanol, n-pentanol, and n-hexanol. The results showed the influence of the alkyl chain length of the n-alkanol on the permselectivity properties of the pervaporation technique in the breakdown of the microemulsions. The variations of the total flux rate J and the enrichment factor beta were in parallel with the effect of the cosurfactant on the swelling extent of the PDMS membrane.

  20. Anaerobic Coculture of Microalgae with Thermosipho globiformans and Methanocaldococcus jannaschii at 68°C Enhances Generation of n-Alkane-Rich Biofuels after Pyrolysis

    PubMed Central

    Matsuyama, Shigeru; Igarashi, Kensuke; Utsumi, Motoo; Shiraiwa, Yoshihiro; Kuwabara, Tomohiko

    2013-01-01

    We tested different alga-bacterium-archaeon consortia to investigate the production of oil-like mixtures, expecting that n-alkane-rich biofuels might be synthesized after pyrolysis. Thermosipho globiformans and Methanocaldococcus jannaschii were cocultured at 68°C with microalgae for 9 days under two anaerobic conditions, followed by pyrolysis at 300°C for 4 days. Arthrospira platensis (Cyanobacteria), Dunaliella tertiolecta (Chlorophyta), Emiliania huxleyi (Haptophyta), and Euglena gracilis (Euglenophyta) served as microalgal raw materials. D. tertiolecta, E. huxleyi, and E. gracilis cocultured with the bacterium and archaeon inhibited their growth and CH4 production. E. huxleyi had the strongest inhibitory effect. Biofuel generation was enhanced by reducing impurities containing alkanenitriles during pyrolysis. The composition and amounts of n-alkanes produced by pyrolysis were closely related to the lipid contents and composition of the microalgae. Pyrolysis of A. platensis and D. tertiolecta containing mainly phospholipids and glycolipids generated short-carbon-chain n-alkanes (n-tridecane to n-nonadecane) and considerable amounts of isoprenoids. E. gracilis also produced mainly short n-alkanes. In contrast, E. huxleyi containing long-chain (31 and 33 carbon atoms) alkenes and very long-chain (37 to 39 carbon atoms) alkenones, in addition to phospholipids and glycolipids, generated a high yield of n-alkanes of various lengths (n-tridecane to n-pentatriacontane). The gas chromatography-mass spectrometry (GC-MS) profiles of these n-alkanes were similar to those of native petroleum crude oils despite containing a considerable amount of n-hentriacontane. The ratio of phytane to n-octadecane was also similar to that of native crude oils. PMID:23183975

  1. Anaerobic coculture of microalgae with Thermosipho globiformans and Methanocaldococcus jannaschii at 68°C enhances generation of n-alkane-rich biofuels after pyrolysis.

    PubMed

    Yamane, Kunio; Matsuyama, Shigeru; Igarashi, Kensuke; Utsumi, Motoo; Shiraiwa, Yoshihiro; Kuwabara, Tomohiko

    2013-02-01

    We tested different alga-bacterium-archaeon consortia to investigate the production of oil-like mixtures, expecting that n-alkane-rich biofuels might be synthesized after pyrolysis. Thermosipho globiformans and Methanocaldococcus jannaschii were cocultured at 68°C with microalgae for 9 days under two anaerobic conditions, followed by pyrolysis at 300°C for 4 days. Arthrospira platensis (Cyanobacteria), Dunaliella tertiolecta (Chlorophyta), Emiliania huxleyi (Haptophyta), and Euglena gracilis (Euglenophyta) served as microalgal raw materials. D. tertiolecta, E. huxleyi, and E. gracilis cocultured with the bacterium and archaeon inhibited their growth and CH(4) production. E. huxleyi had the strongest inhibitory effect. Biofuel generation was enhanced by reducing impurities containing alkanenitriles during pyrolysis. The composition and amounts of n-alkanes produced by pyrolysis were closely related to the lipid contents and composition of the microalgae. Pyrolysis of A. platensis and D. tertiolecta containing mainly phospholipids and glycolipids generated short-carbon-chain n-alkanes (n-tridecane to n-nonadecane) and considerable amounts of isoprenoids. E. gracilis also produced mainly short n-alkanes. In contrast, E. huxleyi containing long-chain (31 and 33 carbon atoms) alkenes and very long-chain (37 to 39 carbon atoms) alkenones, in addition to phospholipids and glycolipids, generated a high yield of n-alkanes of various lengths (n-tridecane to n-pentatriacontane). The gas chromatography-mass spectrometry (GC-MS) profiles of these n-alkanes were similar to those of native petroleum crude oils despite containing a considerable amount of n-hentriacontane. The ratio of phytane to n-octadecane was also similar to that of native crude oils.

  2. An analytical approximation for the orientation-dependent excluded volume of tangent hard sphere chains of arbitrary chain length and flexibility

    NASA Astrophysics Data System (ADS)

    van Westen, Thijs; Vlugt, Thijs J. H.; Gross, Joachim

    2012-07-01

    Onsager-like theories are commonly used to describe the phase behavior of nematic (only orientationally ordered) liquid crystals. A key ingredient in such theories is the orientation-dependent excluded volume of two molecules. Although for hard convex molecular models this is generally known in analytical form, for more realistic molecular models that incorporate intramolecular flexibility, one has to rely on approximations or on computationally expensive Monte Carlo techniques. In this work, we provide a general correlation for the excluded volume of tangent hard-sphere chains of arbitrary chain length and flexibility. The flexibility is introduced by means of the rod-coil model. The resulting correlation is of simple analytical form and accurately covers a wide range of pure component excluded volume data obtained from Monte Carlo simulations of two-chain molecules. The extension to mixtures follows naturally by applying simple combining rules for the parameters involved. The results for mixtures are also in good agreement with data from Monte Carlo simulations. We have expressed the excluded volume as a second order power series in sin (γ), where γ is the angle between the molecular axes. Such a representation is appealing since the solution of the Onsager Helmholtz energy functional usually involves an expansion of the excluded volume in Legendre coefficients. Both for pure components and mixtures, the correlation reduces to an exact expression in the limit of completely linear chains. The expression for mixtures, as derived in this work, is thereby an exact extension of the pure component result of Williamson and Jackson [Mol. Phys. 86, 819-836 (1995)], 10.1080/00268979500102391.

  3. Growth factor controls on the distribution and carbon isotope composition of n-alkanes in leaf wax

    NASA Astrophysics Data System (ADS)

    Jia, C.; Xie, S.; Huang, X.

    2012-12-01

    Cuticular wax plays pivotal physiological and ecological roles in the interactions between plants and the environments in which they grow. Plant-derived long-chain alkanes are more resistant to decay than other biochemical polymers. n-Alkane distributions (Carbon Preference Index (CPI) values and Average Chain Length (ACL) values) and carbon isotopic values are used widely in palaeoenvironmental reconstruction. However, there is little information available on how growth stages of the plant might influence the abundance of n-alkanes in the natural environment. In this study, we analyzed n-alkane distributions and carbon isotope data from two tree species (Cinnamomum camphora (L.) Presl. and Liquidambar formosana Hance) collected monthly from 2009 to 2011 in Nanwang Shan, Wuhan, Hubei Province. CPI values for n-alkanes from C. camphora remained stable in autumn and winter but fluctuated dramatically during spring and autumn each year. Positive correlations between CPI values and the relative content of (C27+C29) were observed in both sun and shade leaves of C. camphora from April to July. In L. formosana, CPI values decreased gradually from April to December. A similar trend was observed in all three years suggesting that growth stages rather than temperature or relative humidity affected the CPI values on a seasonal timescale. In the samples of L. formosana ACL values were negatively correlated with CPI values in the growing season (from April to July) and positively correlated with CPI values in the other seasons. The δ13C values of C29 and C31 n-alkanes displayed more negative carbon isotopic values in autumn and winter compared with leaves sampled at the start of the growing season from both trees. The δ13C values of C29 and C31 n-alkanes of L. formosana decreased from April to December. These results demonstrate the importance of elucidating the growing factors that influence the distribution and δ13C values of alkanes in modern leaves prior to using CPI

  4. Formation of undulated lamellar structure from ABC block terpolymer blends with different chain lengths

    NASA Astrophysics Data System (ADS)

    Matsushita, Yushu; Suzuki, Jiro; Izumi, Yuuki; Matsuoka, Kohei; Takahashi, Shuji; Aoyama, Yoshitaka; Mihira, Tomohiro; Takano, Atsushi

    2010-11-01

    The effect of molecular weight distribution of ABC linear terpolymers on the formation of periodic structures was investigated. Three poly(isoprene-b-styrene-b-2-vinylpridine) triblockterpolymers with molecular weights of 26k, 96k, and 150k were blended variously. Three-phase, four-layer lamellar structures were observed when polydispersity index (PDI) was low, but it has been found that simple lamellar structure with flat surface transforms into an undulated lamellar one, where two interfaces, i.e., I/S and S/P, are both undulated, and they are synchronizing each other if PDI exceeds the critical value. This new structure could be formed due to the periodic and "weak" localization of three chains along the domain interfaces, which produces periodic surfaces with nonconstant mean curvatures. With further increase of PDI, the blend macroscopically phase-separated into different microphase-separated structures.

  5. Epigenetic Control of Salmonella enterica O-Antigen Chain Length: A Tradeoff between Virulence and Bacteriophage Resistance

    PubMed Central

    Cota, Ignacio; Sánchez-Romero, María Antonia; Hernández, Sara B.; Pucciarelli, M. Graciela; García-del Portillo, Francisco; Casadesús, Josep

    2015-01-01

    The Salmonella enterica opvAB operon is a horizontally-acquired locus that undergoes phase variation under Dam methylation control. The OpvA and OpvB proteins form intertwining ribbons in the inner membrane. Synthesis of OpvA and OpvB alters lipopolysaccharide O-antigen chain length and confers resistance to bacteriophages 9NA (Siphoviridae), Det7 (Myoviridae), and P22 (Podoviridae). These phages use the O-antigen as receptor. Because opvAB undergoes phase variation, S. enterica cultures contain subpopulations of opvAB OFF and opvAB ON cells. In the presence of a bacteriophage that uses the O-antigen as receptor, the opvAB OFF subpopulation is killed and the opvAB ON subpopulation is selected. Acquisition of phage resistance by phase variation of O-antigen chain length requires a payoff: opvAB expression reduces Salmonella virulence. However, phase variation permits resuscitation of the opvAB OFF subpopulation as soon as phage challenge ceases. Phenotypic heterogeneity generated by opvAB phase variation thus preadapts Salmonella to survive phage challenge with a fitness cost that is transient only. PMID:26583926

  6. Modification of soy protein hydrolysates by Maillard reaction: Effects of carbohydrate chain length on structural and interfacial properties.

    PubMed

    Li, Weiwei; Zhao, Haibo; He, Zhiyong; Zeng, Maomao; Qin, Fang; Chen, Jie

    2016-02-01

    This study investigated the effects of carbohydrate chain length on the structural and interfacial properties of the Maillard reaction conjugates of soy protein hydrolysates (Mw>30 kDa). The covalent attachment of sugars to soy peptides was confirmed by amino acid analysis and examination of the Fourier-transform infrared spectra. The results suggested that the emulsion stability of the conjugates increased as the length of the carbohydrate chains increased. The surface activity measurement revealed that the soy peptide-dextran conjugates were closely packed and that each molecule occupied a small area of the interface. It was further confirmed that the soy peptide-dextran conjugates formed a thick adsorbed layer at the oil-water interface, as observed in the confocal laser scanning micrographs. The interfacial layer of soy peptides was rheologically complex with broad linear viscoelastic region and strong elastic modulus, and the soy peptide-dextran conjugates might form multilayer adsorption at the interface. This study suggested that the improved surface properties of the soy peptide-dextran conjugates were a result of the strong membrane formed by the closely packed molecular and multilayer adsorption at the interface, which provided steric hindrance to flocculation.

  7. Rod shaped oxovanadium(IV) Schiff base complexes: Synthesis, mesomorphism and influence of flexible alkoxy chain lengths

    NASA Astrophysics Data System (ADS)

    Gupta, Bishop Dev; Datta, Chitraniva; Das, Gobinda; Bhattacharjee, Chira R.

    2014-06-01

    A series of oxovanadium(IV) complexes of bidentate [N,O] donor Schiff-base ligands of the type [VO(L)2], [L = N-(4-n-alkoxysalicylaldimine)-4‧-octadecyloxyaniline, n = 8, 10, 12, 14, 16 and 18] have been synthesized. The compounds were characterized by elemental analyses, Fourier transform infrared spectroscopy (FTIR), 1H, 13C nuclear magnetic resonance (NMR), ultraviolet-visible spectroscopy (UV-Vis), and fast atom bombardment (FAB) mass spectrometry. The mesomorphic behavior of the compounds was studied by polarized optical microscopy (POM) and differential scanning calorimetry (DSC). The ligands and complexes are all thermally stable exhibiting smectic mesomorphism. The ligands 8-OR to16-OR show SmC phase at ∼113-118 °C and an unidentified SmX phase reminiscent of soft crystal at ∼77-91 °C whereas the complexes all showed SmA phases. Interestingly the complexes with C10 and C12 alkoxy chain length exhibited additionally SmC phases also. The melting points of the ligands linearly increases whereas mesophase to isotropic transition temperature decreases as a function of increasing carbon chain length of alkoxy arm while no trend was apparently noticeable for the complexes.

  8. Synthesis and Photophysical Properties of Soluble Low-Bandgap Thienothiophene Polymers with Various Alkyl Side-Chain Lengths

    SciTech Connect

    Bae, W. J.; Scilla, C.; Duzhko, V. V.; Jo, Jang; Coughlin, E. B.

    2011-05-27

    We report the facile synthesis and characterization of a class of thienothiophene polymers with various lengths of alkyl side chains. A series of 2-alkylthieno[3,4-b]thiophene monomers (Ttx) have been synthesized in a two-step protocol in an overall yield of 28–37%. Poly(2-alkylthieno[3,4-b]thiophenes) (PTtx, alkyl: pentyl, hexyl, heptyl, octyl, and tridecyl) were synthesized by oxidative polymerization with FeCl₃ or via Grignard metathesis (GRIM) polymerization methods. The polymers are readily soluble in common organic solvents. The polymers synthesized by GRIM polymerization method (PTtx-G) have narrower molecular weight distribution (Ð) with lower molecular weight (Mn) than those synthesized by oxidative polymerization (PTtx-O). The band structures of the polymers with various lengths of alkyl side chains were investigated by UV–vis spectroscopy, cyclic voltammetry, and ultraviolet photoelectron spectroscopy. These low-bandgap polymers are good candidates for organic transistors, organic light-emitting diodes, and organic photovoltaic cells.

  9. Genetically assembled fluorescent biosensor for in situ detection of bio-synthesized alkanes.

    PubMed

    Wu, Wei; Zhang, Lei; Yao, Lun; Tan, Xiaoming; Liu, Xufeng; Lu, Xuefeng

    2015-06-03

    Construction of highly efficient microbial cell factories producing drop-in biofuel alkanes is severely limited due to the lack of a fast detection method against alkanes. Here we first developed a sensitive fluorescent biosensor for rapid and in situ monitoring of intracellular alkane synthesis. Using GFP as reporter, the biosensor could actively respond to the intracellular alkane products, especially for the mid- and long-chain alkanes synthesized in the recombinant Escherichia coli and give a concentration-dependent fluorescence response. Our results also suggested the feasibility of developing high-throughput strategies basing on the alkane biosensor device in E. coli, and thus will greatly facilitate the application of directed evolution strategies to further improve the alkane-producing microbial cell factories.

  10. Reflectance spectroscopy of organic compounds: 1. Alkanes

    USGS Publications Warehouse

    Clark, R.N.; Curchin, J.M.; Hoefen, T.M.; Swayze, G.A.

    2009-01-01

    Reflectance spectra of the organic compounds comprising the alkane series are presented from the ultraviolet to midinfrared, 0.35 to 15.5 /??m. Alkanes are hydrocarbon molecules containing only single carbon-carbon bonds, and are found naturally on the Earth and in the atmospheres of the giant planets and Saturn's moon, Titan. This paper presents the spectral properties of the alkanes as the first in a series of papers to build a spectral database of organic compounds for use in remote sensing studies. Applications range from mapping the environment on the Earth, to the search for organic molecules and life in the solar system and throughout the. universe. We show that the spectral reflectance properties of organic compounds are rich, with major diagnostic spectral features throughout the spectral range studied. Little to no spectral change was observed as a function of temperature and only small shifts and changes in the width of absorption bands were observed between liquids and solids, making remote detection of spectral properties throughout the solar system simpler. Some high molecular weight organic compounds contain single-bonded carbon chains and have spectra similar to alkanes even ' when they fall into other families. Small spectral differences are often present allowing discrimination among some compounds, further illustrating the need to catalog spectral properties for accurate remote sensing identification with spectroscopy.

  11. Second-generation functionalized medium-chain-length polyhydroxyalkanoates: the gateway to high-value bioplastic applications.

    PubMed

    Tortajada, Marta; da Silva, Luiziana Ferreira; Prieto, María Auxiliadora

    2013-03-01

    Polyhydroxyalkanoates (PHAs) are biodegradable biocompatible polyesters, which accumulate as granules in the cytoplasm of many bacteria under unbalanced growth conditions. Medium-chain-length PHAs (mcl-PHAs), characterized by C6-C14 branched monomer chains and typically produced by Pseudomonas species, are promising thermoelastomers, as they can be further modified by introducing functional groups in the side chains. Functionalized PHAs are obtained either by feeding structurally related substrates processed through the beta-oxidation pathway, or using specific strains able to transform sugars or glycerol into unsaturated PHA by de novo fatty-acid biosynthesis. Functionalized mcl-PHAs provide modified mechanical and thermal properties, and consequently have new processing requirements and highly diverse potential applications in emergent fields such as biomedicine. However, process development and sample availability are limited due to the toxicity of some precursors and still low productivity, which hinder investigation. Conversely, improved mutant strains designed through systems biology approaches and cofeeding with low-cost substrates may contribute to the widespread application of these biopolymers. This review focuses on recent developments in the production of functionalized mcl-PHAs, placing particular emphasis on strain and bioprocess design for cost-effective production.

  12. Designing green plasticizers: influence of alkyl chain length on biodegradation and plasticization properties of succinate based plasticizers.

    PubMed

    Erythropel, Hanno C; Dodd, Patrick; Leask, Richard L; Maric, Milan; Cooper, David G

    2013-04-01

    Phthalate diesters such as di (2-ethylhexyl) phthalate (DEHP) are considered ubiquitous contaminants and are poorly biodegraded in the environment. Moreover, both the parent compound and stable metabolites such as mono (2-ethylhexyl) phthalate (MEHP) are linked to several negative impacts on the environment and human health. Earlier work established that saturated diester compounds, such as succinates, showed better biodegradation characteristics and comparable plasticizer properties compared to DEHP. In this work we examine the effect of alkyl chain length of succinate molecules on plasticizer and biodegradation properties. This included both the side chains (n-ethyl to n-octyl) as well as substituents on the middle part of the succinate molecule. We showed that the common soil bacterium Rhodococcus rhodocrous could rapidly break down all unsubstituted succinates, without the appearance of stable metabolites. Furthermore, the organisms used the plasticizer metabolites as carbon source. The introduction of a large cyclohexyl substituent on the succinate resulted in a poorer degradation rate. Glass Transition Temperature (Tg) measurements were performed to evaluate plasticizer properties and showed that longer side chains reduced the Tg more efficiently, while large cyclohexyl substituents on the succinate decreased this effect. However, all compounds performed better or equal to DEHP at reducing the Tg.

  13. Cloning, high level expression, purification, and crystallization of the full length Clostridium botulinum neurotoxin type E light chain.

    PubMed

    Agarwal, Rakhi; Eswaramoorthy, Subramaniam; Kumaran, Desigan; Dunn, John J; Swaminathan, Subramanyam

    2004-03-01

    The catalytic activity of the highly potent botulinum neurotoxins are confined to their N-terminal light chains ( approximately 50kDa). A full-length light chain for the type E neurotoxin with a C-terminal 6x His-tag, BoNT/E-LC, has been cloned in a pET-9c vector and over-expressed in BL21 (DE3) cells. BoNT/E-LC was purified to homogeneity by affinity chromatography on Ni-NTA agarose followed by exclusion chromatography using a Superdex-75 sizing column. The purified protein has very good solubility and can be stored stably at -20 degrees C; however, it seems to undergo auto-proteolysis when stored at temperature #10878;4-10 degrees C. BoNT/E-LC is active on its natural substrate, the synaptosomal associated 25kDa protein, SNAP-25, indicating that it retains a native-like conformation and therefore can be considered as a useful tool in studying the structure/function of the catalytic light chain. Recombinant BoNT/E-LC has been crystallized under five different conditions and at various pHs. Crystals diffract to better than 2.1A.

  14. Pruned-enriched Rosenbluth method: Simulations of θ polymers of chain length up to 1 000 000

    NASA Astrophysics Data System (ADS)

    Grassberger, Peter

    1997-09-01

    We present an algorithm for simulating flexible chain polymers. It combines the Rosenbluth-Rosenbluth method with recursive enrichment. Although it can be applied also in more general situations, it is most efficient for three-dimensional θ polymers on the simple-cubic lattice. There it allows high statistics simulations of chains of length up to N=106. For storage reasons, this is feasable only for polymers in a finite volume. For free θ polymers in infinite volume, we present very high statistics runs with N=10 000. These simulations fully agree with previous simulations made by Hegger and Grassberger [J. Chem. Phys. 102, 6681 (1995)] with a similar but less efficient algorithm, showing that logarithmic corrections to mean field behavior are much stronger than predicted by field theory. But the finite volume simulations show that the density inside a collapsed globule scales with the distance from the θ point as predicted by mean field theory, in contrast to claims in the work mentioned above. In addition to the simple-cubic lattice, we also studied two versions of the bond fluctuation model, but with much shorter chains. Finally, we show that our method can be applied also to off-lattice models, and illustrate this with simulations of a model studied in detail by Freire et al. [Macromolecules 19, 452 (1986) and later work].

  15. Heat evolution of micelle formation, dependence of enthalpy, and heat capacity on the surfactant chain length and head group.

    PubMed

    Opatowski, Ella; Kozlov, Michael M; Pinchuk, Ilya; Lichtenberg, Dov

    2002-02-15

    Micelle formation by many surfactants is endothermic at low temperatures but exothermic at high temperatures. In this respect, dissociation of micelles (demicellization) is similar to dissolving hydrocarbons in water. However, a remarkable difference between the two processes is that dissolving hydrocarbons is isocaloric at about 25 degrees C, almost independently of the hydrocarbon chain length, whereas the temperature (T*) at which demicellization of different surfactants is athermal varies over a relatively large range. We have investigated the temperature dependence of the heat of demicellization of three alkylglucosides with hydrocarbon chains of 7, 8, and 9 carbon atoms. At about 25 degrees C, the heat of demicellization of the three studied alkylglucosides varied within a relatively small range (DeltaH=-7.8+/-0.4 kJ/mol). The temperature dependence of DeltaH(demic) indicates that within the studied temperature range the heat capacity of demicellization (DeltaC(P,demic)) is about constant. The value of DeltaC(P,demic) exhibited an apparently linear dependence on the surfactant's chain length (DeltaC(P,demic)/n(CH(2))=47+/-7 kJ/mol K). Our interpretation of these results is that (i) the transfer of the head groups from micelles to water is exothermic and (ii) the temperature dependence of the heat associated with water-hydrocarbon interactions is only slightly affected by the head group. This implies that the deviation of the value of T* from 25 degrees C results from the contribution of the polar head to the overall heat of demicellization. Calorimetric studies of other series of amphiphiles will have to be conducted to test whether the latter conclusion is general.

  16. Engineered biosynthesis of plant polyketides: chain length control in an octaketide-producing plant type III polyketide synthase.

    PubMed

    Abe, Ikuro; Oguro, Satoshi; Utsumi, Yoriko; Sano, Yukie; Noguchi, Hiroshi

    2005-09-14

    The chalcone synthase (CHS) superfamily of type III polyketide synthases (PKSs) produces a variety of plant secondary metabolites with remarkable structural diversity and biological activities (e.g., chalcones, stilbenes, benzophenones, acrydones, phloroglucinols, resorcinols, pyrones, and chromones). Here we describe an octaketide-producing novel plant-specific type III PKS from aloe (Aloe arborescens) sharing 50-60% amino acid sequence identity with other plant CHS-superfamily enzymes. A recombinant enzyme expressed in Escherichia coli catalyzed seven successive decarboxylative condensations of malonyl-CoA to yield aromatic octaketides SEK4 and SEK4b, the longest polyketides known to be synthesized by the structurally simple type III PKS. Surprisingly, site-directed mutagenesis revealed that a single residue Gly207 (corresponding to the CHS's active site Thr197) determines the polyketide chain length and product specificity. Small-to-large substitutions (G207A, G207T, G207M, G207L, G207F, and G207W) resulted in loss of the octaketide-forming activity and concomitant formation of shorter chain length polyketides (from triketide to heptaketide) including a pentaketide chromone, 2,7-dihydroxy-5-methylchromone, and a hexaketide pyrone, 6-(2,4-dihydroxy-6-methylphenyl)-4-hydroxy-2-pyrone, depending on the size of the side chain. Notably, the functional diversity of the type III PKS was shown to evolve from simple steric modulation of the chemically inert single residue lining the active-site cavity accompanied by conservation of the Cys-His-Asn catalytic triad. This provided novel strategies for the engineered biosynthesis of pharmaceutically important plant polyketides.

  17. Effect of suppression of arabinoxylan synthetic genes in wheat endosperm on chain length of arabinoxylan and extract viscosity.

    PubMed

    Freeman, Jackie; Lovegrove, Alison; Wilkinson, Mark David; Saulnier, Luc; Shewry, Peter Robert; Mitchell, Rowan Andrew Craig

    2016-01-01

    Arabinoxylan (AX) is the dominant component within wheat (Triticum aestivum L.) endosperm cell walls, accounting for 70% of the polysaccharide. The viscosity of aqueous extracts from wheat grain is a key trait influencing the processing for various end uses, and this is largely determined by the properties of endosperm AX. We have previously shown dramatic effects on endosperm AX in transgenic wheat by down-regulating either TaGT43_2 or TaGT47_2 genes (orthologues to IRX9 and IRX10 in Arabidopsis, respectively) implicated in AX chain extension and the TaXAT1 gene responsible for monosubstitution by 3-linked arabinose. Here, we use these transgenic lines to investigate the relationship between amounts of AX in soluble and insoluble fractions, the chain-length distribution of these measured by intrinsic viscosity and the overall effect on extract viscosity. In transgenic lines expressing either the TaGT43_2 or TaGT47_2 RNAi transgenes, the intrinsic viscosities of water-extractable (WE-AX) and of a water-insoluble alkaline-extracted fraction (AE-AX) were decreased by between 10% and 50% compared to control lines. In TaXAT1 RNAi lines, there was a 15% decrease in intrinsic viscosity of WE-AX but no consistent effect on that of AE-AX. All transgenic lines showed decreases in extract viscosity with larger effects in TaGT43_2 and TaGT47_2 RNAi lines (by up to sixfold) than in TaXAT1 RNAi lines (by twofold). These effects were explained by the decreases in amount and chain length of WE-AX, with decreases in amount having the greater influence. Extract viscosity from wheat grain can therefore be greatly decreased by suppression of single gene targets.

  18. How to reduce resistance to movement of alkane liquid drops across tilted surfaces without relying on surface roughening and perfluorination.

    PubMed

    Urata, Chihiro; Masheder, Benjamin; Cheng, Dalton F; Hozumi, Atsushi

    2012-12-21

    Alkylsilane-derived monolayer-covered surfaces generally display a reasonably good level of hydrophobicity but poor oleophobicity. Here, we demonstrate that the physical attributes of alkylsilane-derived surfaces (liquid-like or solid-like) are dependent on the alkyl chain length and density, and these factors subsequently have significant influence upon the dynamic dewetting behavior toward alkanes (C(n)H(2n+2), where n = 7-16). In this study, we prepared and characterized hybrid films through a simple sol-gel process based on the cohydrolysis and co-condensation of a mixture of a range of alkyltriethoxysilanes (C(n)H(2n+1)Si(OEt)(3), where n = 3, 6, 8, 10, 12, 14, 16, and 18) and tetramethoxysilane (TMOS). Surprisingly, when the carbon number (C(n)) of alkyl chain was 10 and below, the produced hybrid films were all smooth, highly transparent, and showed negligible contact angle (CA) hysteresis. On these hybrid surfaces, 5 μL drops of alkanes (n-hexadecane, n-dodecane, and n-decane) could move easily at low tilt angles (<5°) without pinning. On the other hand, when the C(n) exceeded 12, both transparency and mobility of probe liquids significantly worsened. In the former case, TMOS molecules played key roles in both forming continuous films (as a binder) and improving flexibility of alkyl chains (as a molecular spacer), resulting in the smooth liquid-like surfaces. Silylation of the hybrid film and subsequent dynamic CA measurements proved the presence of silanol groups on the outermost surfaces and demonstrated that the dynamic dewettability of hybrid films worsened as packing densities increased. Additionally, solvent effects (high affinity) between the alkyl chains and alkane liquids imparted a more liquid-like character to the surface. Thanks to these simple physical effects, the resistance to the alkane droplet motion across tilted surfaces was markedly reduced. With the longer carbon chains, the chain mobility was strictly inhibited by mutual interactions

  19. Alkyl chain length-dependent surface reaction of dodecahydro-N-alkylcarbazoles on Pt model catalysts

    SciTech Connect

    Gleichweit, Christoph; Amende, Max; Bauer, Udo; Schernich, Stefan; Höfert, Oliver; Lorenz, Michael P. A.; Zhao, Wei; Bachmann, Philipp; Papp, Christian; Müller, Michael; Koch, Marcus; Wasserscheid, Peter; Libuda, Jörg; Steinrück, Hans-Peter

    2014-05-28

    The concept of liquid organic hydrogen carriers (LOHC) holds the potential for large scale chemical storage of hydrogen at ambient conditions. Herein, we compare the dehydrogenation and decomposition of three alkylated carbazole-based LOHCs, dodecahydro-N-ethylcarbazole (H{sub 12}-NEC), dodecahydro-N-propylcarbazole (H{sub 12}-NPC), and dodecahydro-N-butylcarbazole (H{sub 12}-NBC), on Pt(111) and on Al{sub 2}O{sub 3}-supported Pt nanoparticles. We follow the thermal evolution of these systems quantitatively by in situ high-resolution X-ray photoelectron spectroscopy. We show that on Pt(111) the relevant reaction steps are not affected by the different alkyl substituents: for all LOHCs, stepwise dehydrogenation to NEC, NPC, and NBC is followed by cleavage of the C–N bond of the alkyl chain starting at 380–390 K. On Pt/Al{sub 2}O{sub 3}, we discern dealkylation on defect sites already at 350 K, and on ordered, (111)-like facets at 390 K. The dealkylation process at the defects is most pronounced for NEC and least pronounced for NBC.

  20. Quantifying Dimer and Trimer Formation of Tri-n-butyl Phosphates in Different Alkane Diluents: FTIR Study.

    PubMed

    Vo, Quynh N; Unangst, Jaclynn L; Nguyen, Hung D; Nilsson, Mikael

    2016-07-21

    Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous metal-ion-extracting reagents, is an important ligand used in solvent extraction processes for the recovery of uranium and plutonium from spent nuclear fuel, as well as other non-nuclear applications. Ligand-ligand and organic solvent-ligand interactions play an important role in these processes. The self-association behavior of TBP in various alkane diluents of different chain lengths (8, 12, and 16 carbons) and a branched alkane (iso-octane) was investigated by Fourier transform infrared spectroscopic measurements. By careful deconvolution of the spectra into multiple peaks, our results indicate that TBP self-associates to form not only dimers, as previous studies showed, but also trimers in the practical concentration range. Using a mathematical fitting procedure, the dimerization and trimerization constants were determined. As expected, these equilibrium constants are dependent on the solvent used. As the alkane chain for linear hydrocarbon solvents becomes longer, dimerization decreases whereas trimerization increases. For the more branched hydrocarbon, we observe a significantly higher dimerization constant. These effects are most likely due to the intermolecular van der Waals interactions between the butyl tails of each TBP molecule and the diluent hydrocarbon chain as all solvents in this study are relatively nonpolar.

  1. Silencing of StKCS6 in potato periderm leads to reduced chain lengths of suberin and wax compounds and increased peridermal transpiration

    PubMed Central

    Serra, Olga; Soler, Marçal; Hohn, Carolin; Franke, Rochus; Schreiber, Lukas; Prat, Salomé; Molinas, Marisa; Figueras, Mercè

    2009-01-01

    Very long chain aliphatic compounds occur in the suberin polymer and associated wax. Up to now only few genes involved in suberin biosynthesis have been identified. This is a report on the isolation of a potato (Solanum tuberosum) 3-ketoacyl-CoA synthase (KCS) gene and the study of its molecular and physiological relevance by means of a reverse genetic approach. This gene, called StKCS6, was stably silenced by RNA interference (RNAi) in potato. Analysis of the chemical composition of silenced potato tuber periderms indicated that StKCS6 down-regulation has a significant and fairly specific effect on the chain length distribution of very long-chain fatty acids (VLCFAs) and derivatives, occurring in the suberin polymer and peridermal wax. All compounds with chain lengths of C28 and higher were significantly reduced in silenced periderms, whereas compounds with chain lengths of C26 and lower accumulated. Thus, StKCS6 is preferentially involved in the formation of suberin and wax lipidic monomers with chain lengths of C28 and higher. As a result, peridermal transpiration of the silenced lines was about 1.5-times higher than that of the wild type. Our results convincingly show that StKCS6 is involved in both suberin and wax biosynthesis and that a reduction of the monomeric carbon chain lengths leads to increased rates of peridermal transpiration. PMID:19112170

  2. Effect of linker length between variable domains of single chain variable fragment antibody against daidzin on its reactivity.

    PubMed

    Yusakul, Gorawit; Sakamoto, Seiichi; Pongkitwitoon, Benyakan; Tanaka, Hiroyuki; Morimoto, Satoshi

    2016-07-01

    The peptide linker between variable domains of heavy (VH) and light (VL) chains is one of important factors that influence the characteristics of scFv, including binding activity and specificity against target antigen. The scFvs against daidzin (DZ-scFvs) with different linker lengths were constructed in the format of VH-(GGGGS)n-VL (n = 1, 3, 5, and 7). They were expressed in the hemolymph of silkworm larvae using the Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system, and their reactivity against daidzin and related compounds were evaluated using an indirect competitive enzyme-linked immunosorbent assay (icELISA), which is applicable for quantitative analysis of daidzin. The results showed that the reactivity of scFvs against daidzin was increased, whereas specificity slightly decreased when their peptide linker was lengthened. These results suggested that the linker length of DZ-scFvs contributes to its reactivity. In addition, the results emphasize that the linker length could control the reactivity of DZ-scFvs.

  3. Influence of carbon chain length on the synthesis and yield of fatty amine-coated iron-platinum nanoparticles

    NASA Astrophysics Data System (ADS)

    Taylor, Robert M.; Monson, Todd C.; Gullapalli, Rama R.

    2014-06-01

    Iron oxide nanoparticles are among the most widely used and characterized magnetic nanoparticles. However, metal alloys such as superparamagnetic iron-platinum particles (SIPPs), which have better magnetic properties, are receiving increased attention. Scalable techniques to routinely synthesize SIPPs in bulk need further study. Here, we focus on the role played by the fatty amine ligand in the formation of the bimetallic FePt nanocrystal. More specifically, we compare the effect of varying lengths of fatty amine ligands on the shape, structure, uniformity, composition, and magnetic properties of the SIPPs. We synthesized SIPPs by employing a `green' thermal decomposition reaction using fatty amine ligands containing 12 to 18 carbons in length. Greater fatty amine chain length increased the polydispersity, particle concentration, iron concentration, and the stability of the SIPPs. Additionally, longer reflux times increased the diameter of the particles, but decreased the iron concentration, suggesting that shorter reaction times are preferable. Fourier transform infrared spectroscopy of the SIPPs indicates that the ligands are successfully bound to the FePt cores through the amine group. Superconducting quantum interference device magnetometry measurements suggest that all of the SIPPs were superparamagnetic at room temperature and that SIPPs synthesized using tetradecylamine had the highest saturation magnetization. Our findings indicate that the octadecylamine ligand, which is currently used for the routine synthesis of SIPPs, may not be optimal. Overall, we found that using tetradecylamine and a 30-min reflux reaction resulted in optimal particles with the highest degree of monodispersity, iron content, stability, and saturation magnetization.

  4. Discrimination of the prochiral hydrogens at the C-2 position of n-alkanes by the methane/ammonia monooxygenase family proteins.

    PubMed

    Miyaji, Akimitsu; Miyoshi, Teppei; Motokura, Ken; Baba, Toshihide

    2015-08-14

    The selectivity of ammonia monooxygenase from Nitrosomonas europaea (AMO-Ne) for the oxidation of C4-C8n-alkanes to the corresponding alcohol isomers was examined to show the ability of AMO-Ne to recognize the n-alkane orientation within the catalytic site. AMO-Ne in whole cells produces 1- and 2-alcohols from C4-C8n-alkanes, and the regioselectivity is dependent on the length of the carbon chain. 2-Alcohols produced from C4-C7n-alkanes were predominantly either the R- or S-enantiomers, while 2-octanol produced from n-octane was racemic. These results indicate that AMO-Ne can discriminate between the prochiral hydrogens at the C-2 position, with the degree of discrimination varying according to the n-alkane. Compared to the particulate methane monooxygenase (pMMO) of Methylococcus capsulatus (Bath) and that of Methylosinus trichosporium OB3b, AMO-Ne showed a distinct ability to discriminate between the orientation of n-butane and n-pentane in the catalytic site.

  5. Morphology and phase controlled cobalt nanostructures in magnetic polypropylene nanocomposites: the role of alkyl chain-length in maleic anhydride grafted polypropylene.

    PubMed

    He, Qingliang; Yuan, Tingting; Luo, Zhiping; Haldolaarachchige, Neel; Young, David P; Wei, Suying; Guo, Zhanhu

    2013-04-04

    A novel function of maleic anhydride grafted polypropylene (PP) with different backbone chain-lengths was demonstrated, i.e., in controlling the cobalt morphologies (dispersed polyhedral vs. assembled chain nanostructure), crystalline structures (ε- vs. β-phase), and magnetic property (242 vs. 808 Oe) in the synthesized magnetic PP nanocomposites.

  6. Quantitative vapor-phase IR intensities and DFT computations to predict absolute IR spectra based on molecular structure: I. Alkanes

    NASA Astrophysics Data System (ADS)

    Williams, Stephen D.; Johnson, Timothy J.; Sharpe, Steven W.; Yavelak, Veronica; Oates, R. P.; Brauer, Carolyn S.

    2013-11-01

    Recently recorded quantitative IR spectra of a variety of gas-phase alkanes are shown to have integrated intensities in both the C3H stretching and C3H bending regions that depend linearly on the molecular size, i.e. the number of C3H bonds. This result is well predicted from CH4 to C15H32 by density functional theory (DFT) computations of IR spectra using Becke's three parameter functional (B3LYP/6-31+G(d,p)). Using the experimental data, a simple model predicting the absolute IR band intensities of alkanes based only on structural formula is proposed: For the C3H stretching band envelope centered near 2930 cm-1 this is given by (km/mol) CH_str=(34±1)×CH-(41±23) where CH is number of C3H bonds in the alkane. The linearity is explained in terms of coordinated motion of methylene groups rather than the summed intensities of autonomous -CH2-units. The effect of alkyl chain length on the intensity of a C3H bending mode is explored and interpreted in terms of conformer distribution. The relative intensity contribution of a methyl mode compared to the total C3H stretch intensity is shown to be linear in the number of methyl groups in the alkane, and can be used to predict quantitative spectra a priori based on structure alone.

  7. Quantitative Vapor-phase IR Intensities and DFT Computations to Predict Absolute IR Spectra based on Molecular Structure: I. Alkanes

    SciTech Connect

    Williams, Stephen D.; Johnson, Timothy J.; Sharpe, Steven W.; Yavelak, Veronica; Oats, R. P.; Brauer, Carolyn S.

    2013-11-13

    Recently recorded quantitative IR spectra of a variety of gas-phase alkanes are shown to have integrated intensities in both the C-H stretching and C-H bending regions that depend linearly on the molecular size, i.e. the number of C-H bonds. This result is well predicted from CH4 to C15H32 by DFT computations of IR spectra at the B3LYP/6-31+G(d,p) level of DFT theory. A simple model predicting the absolute IR band intensities of alkanes based only on structural formula is proposed: For the C-H stretching band near 2930 cm-1 this is given by (in km/mol): CH¬_str = (34±3)*CH – (41±60) where CH is number of C-H bonds in the alkane. The linearity is explained in terms of coordinated motion of methylene groups rather than the summed intensities of autonomous -CH2- units. The effect of alkyl chain length on the intensity of a C-H bending mode is explored and interpreted in terms of conformer distribution. The relative intensity contribution of a methyl mode compared to the total C-H stretch intensity is shown to be linear in the number of terminal methyl groups in the alkane, and can be used to predict quantitative spectra a priori based on structure alone.

  8. Application of nitrogen and carbon stable isotopes (δ(15)N and δ(13)C) to quantify food chain length and trophic structure.

    PubMed

    Perkins, Matthew J; McDonald, Robbie A; van Veen, F J Frank; Kelly, Simon D; Rees, Gareth; Bearhop, Stuart

    2014-01-01

    Increasingly, stable isotope ratios of nitrogen (δ(15)N) and carbon (δ(13)C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ(15)N, and carbon range (CR) using δ(13)C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ(15)N or δ(13)C from source to consumer) between trophic levels and among food chains. δ(15)N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰), and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ(13)C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ(13)C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority of

  9. Sensitive detection of n-alkanes using a mixed ionization mode proton-transfer-reaction mass spectrometer

    NASA Astrophysics Data System (ADS)

    Amador-Muñoz, Omar; Misztal, Pawel K.; Weber, Robin; Worton, David R.; Zhang, Haofei; Drozd, Greg; Goldstein, Allen H.

    2016-11-01

    to compare sensitivities for n-alkane detection between experiments. Double hydride abstraction was observed from the reaction with O2+. Sensitivity to CT increased with carbon chain length from n-pentane to n-dodecane, sensitivity to HA increased from n-heptane to n-dodecane and sensitivity to PT increased from n-decane to n-tridecane. Sensitivity to CT exponentially decreased with molecular ionization energy, which is inversely related to the carbon chain length. We introduce a calibrated fragmentation algorithm as a method to determine the concentrations of n-alkanes and demonstrate its effectiveness using a custom n-alkane mixture and a much more complex oil example representing perhaps the most difficult mixture available for application of the method. We define optimum conditions for using the mixed ionization mode to measure n-alkanes in conventional PTR-MS instruments regardless of whether they are equipped with switchable reagent ion (SRI) capabilities.

  10. Physiological function of the Pseudomonas putida PpG6 (Pseudomonas oleovorans) alkane hydroxylase: monoterminal oxidation of alkanes and fatty acids.

    PubMed Central

    Nieder, M; Shapiro, J

    1975-01-01

    Pseudomonas putida PpG6 is able to utilize purified n-alkanes of six to ten carbon atoms for growth. It can also grow on the primary terminal oxidation products of these alkanes and on 1-dodecanol but not on the corresponding 2-ketones or 1,6-hexanediol, adipic acid, or pimelic acid. Revertible point mutants can be isolated which have simultaneously lost the ability to grow on all five n-alkane growth substrates but which can still grow on octanol or nonanol. An acetate-negative mutant defective in isocitrate lysase activity is unable to grow on even-numbered alkanes and fatty acids. Analysis of double mutants defective in acetate and propionate or in acetate and glutarate metabolism shows that alkane carbon is assimilated only via acetyl-coenzyme A and propionyl-coenzyme A. These results support the following conclusions: (i) The n-alkane growth specificity of P. putida PpG6 is due to the substrate specificity of whole-cell alkane hydroxylation; (ii) there is a single alkane hydroxylase enzyme complex; (iii) the physiological role of this complex is to initiate the monoterminal oxidation of alkane chains; and (iv) straight-chain fatty acids from butyric through nonanoic are degraded exclusively by beta-oxidation from the carboxyl end of the molecule. PMID:804473

  11. Phase equilibriums, self-assembly and interactions in two-, three- and four medium-chain length component systems.

    PubMed

    Rosenholm, Jarl B

    2014-03-01

    The Scandinavian surface (surfactant) and colloid science owes much of its success to Per Ekwall and Björn Lindman. In this review the main topics shared by their research groups at Åbo Akademi University in Finland and at Lund University in Sweden are described. The nature of surface active substances (cosolvents, co-surfactants and surfactants) and microemulsions are evaluated. It is shown that the properties of medium-chain length surfactants differ dramatically from long-chain surfactants. The phase equilibriums of binary systems are related to the phase equilibriums of ternary and quaternary systems referred to as microemulsions or more recently also as nanoemulsions. A distinction is made between hydrotrope liquids, detergentless microemulsions, surfactant mixture systems and microemulsions. Three component systems are assembled to "true" quaternary microemulsions. An exceptionally comprehensive network of thermodynamic parameters describing molecular site exchange and micelle formation are derived and related mutually. Gibbs free energy, enthalpy, entropy, volume, heat capacity, expansivity and compressibility can be used to illustrate the degree of aggregation cooperativity and to evaluate whether micelle formation is of a first-, second- or intermediate order phase transition. Theoretical simulations and experimental results show that the associate structures of medium-chain length surfactants are quite open and may be deformed due to small aggregation numbers. The self-assembly occurs over a number of distinct steps at a series of experimentally detectable critical concentrations. Despite the low aggregation tendency their phase behavior equals those of long-chain homologs in surfactant mixture and microemulsion systems. A number of models describing the self-assembly are reviewed. Nuclear magnetic resonance (shift, relaxation rate and diffusion), Laser Raman and infrared spectroscopies were chosen as key instruments for molecular interaction

  12. Amyloid-beta aggregation: selective inhibition of aggregation in mixtures of amyloid with different chain lengths.

    PubMed Central

    Snyder, S W; Ladror, U S; Wade, W S; Wang, G T; Barrett, L W; Matayoshi, E D; Huffaker, H J; Krafft, G A; Holzman, T F

    1994-01-01

    rates of production of different-length A beta and its exposure to radical damage may be factors in the accumulation of A beta in plaques in vivo. Images FIGURE 6 PMID:7811936

  13. The Modality of Enterobacterial Common Antigen Polysaccharide Chain Lengths Is Regulated by o349 of the wec Gene Cluster of Escherichia coli K-12

    PubMed Central

    Barr, Kathleen; Klena, John; Rick, Paul D.

    1999-01-01

    The assembly of the phosphoglyceride-linked form of enterobacterial common antigen (ECAPG) occurs by a mechanism that involves modulation of polysaccharide chain length. However, the genetic determinant of this modulation has not been identified. Site-directed mutagenesis of o349 of the Escherichia coli K-12 wec gene cluster revealed that this locus encodes a Wzz protein that specifically modulates the chain length of ECAPG polysaccharides, and we have designated this locus wzzECA. The WzzECA-mediated modulation of ECAPG polysaccharide chains is the first demonstrated example of Wzz regulation involving a polysaccharide that is not linked to the core-lipid A structure of lipopolysaccharide. PMID:10515954

  14. Evaluating Carbon Isotope Signature of Bulk Organic Matter and Plant Wax Derived n-alkanes from Lacustrine Sediments as Climate Proxies along the Western Side of the Andes

    NASA Astrophysics Data System (ADS)

    Contreras, S.; Werne, J. P.; Araneda, A.; Conejero, C. A.

    2015-12-01

    Sedimentary carbon isotope values (δ13C) of bulk organic matter and long chain (C25 to C35) n-alkanes are among the most long-lived and widely utilized proxies of organic matter and vegetation source. The carbon distribution (e.g. average carbon chain length, ACL) and isotope signature from long chain n-alkanes had been intensively used on paleoclimate studies because they are less influenced by diagenesis, differential preservation of compound classes, and changes in the sources of organic matter than bulk δ13C values. Recently, studies of modern plant n-alkanes have challenged the use of carbon distribution and carbon isotope signature from sedimentary n-alkanes as reliable indicators of vegetation and climate change. The climate in central-south western South America (SA) is projected to become significantly warmer and drier over the next several decades to centuries in response to anthropogenically driven warming. Paleolimnological studies along western SA are critical to obtain more realistic and reliable regional reconstructions of past climate and environments, including vegetation and water budget variability. Here we discuss bulk δ13C, distribution and δ13C in long chain n-alkanes from a suite of ~40 lake surface sediment (core-top) samples spanning the transition from a Mediterranean climate with a patchwork of cultivated vegetation, pastureland, conifers in central Chile to a rainy temperate climate dominated by broadleaf deciduous and evergreen forest. Data are compared to the latitudinal and orographic climatic trends of the Andes based on the climatology (e.g. precipitation and temperature) of the locations of all lakes involved in this study, using monthly gridded reanalysis products of the Climate Forecast System Reanalysis (CFSR), based on the NCEP global forecast model and meteorological stations available in the region, from January 1979 to December 2010 with a 0.5° horizontal resolution.

  15. Diffusion of methane and other alkanes in metal-organic frameworks for natural gas storage

    SciTech Connect

    Borah, B; Zhang, HD; Snurr, RQ

    2015-03-03

    Diffusion of methane, ethane, propane and n-butane was studied within the micropores of several metal organic frameworks (MOFs) of varying topologies, including the MOFs PCN-14, NU-125, NU-1100 and DUT-49. Diffusion coefficients of the pure components, as well as methane/ethane, methane/ propane and methane/butane binary mixtures, were calculated using molecular dynamics simulations to understand the effect of the longer alkanes on uptake of natural gas in MOB. The calculated self diffusion coefficients of all four components are on the order of 10(-8) m(2)/s. The diffusion coefficients of the pure components decrease as a function of chain length in all of the MOFs studied and show different behaviour as a function of loading in different MOB. The self-diffusivities follow the trend DPCN-14 < DNU-125 approximate to DNU-1100 < DDUT-49, which is exactly the reverse order of the densities of the MOFs: PCN-14 > NU-125 approximate to NU-1100 > DUT-49. By comparing the diffusion of pure methane and methane mixtures vvith the higher alkancs, it is observed that the diffusivity of methane is unaffected by the presence of the higher alkanes in the MOFs considered, indicating that the diffusion path of methane is not blocked by the higher alkanes present in natural gas. (C) 2014 Elsevier Ltd. All rights reserved.

  16. Asynchronous evolution of the isotopic composition and amount of precipitation in north China during the Holocene revealed by a record of compound-specific carbon and hydrogen isotopes of long-chain n-alkanes from an alpine lake

    NASA Astrophysics Data System (ADS)

    Rao, Zhiguo; Jia, Guodong; Li, Yunxia; Chen, Jianhui; Xu, Qinghai; Chen, Fahu

    2016-07-01

    Both the timing of the maximum East Asian summer monsoon (EASM) intensity in monsoonal China and the environmental significance of the Chinese stalagmite oxygen isotopic record (δ18O) have been debated. Here, we present a ca. 120-year-resolution compound-specific carbon (δ13C) and hydrogen (δD) isotopes of terrestrial long-chain n-alkanes extracted from a well-dated sediment core from an alpine lake in north China. Our δ13C data, together with previously reported pollen data from a parallel core, demonstrate a humid mid-Holocene from ca. 8-5 ka BP. Assuming that the climatic humidity of north China is an indicator of the EASM intensity, then the maximum EASM intensity occurred in the mid-Holocene. Our δD data reveal a similar long-term trend to the δ18O record from nearby Lianhua Cave, indicating that the synchronous δD and δ18O records faithfully record the δD and δ18O of precipitation, respectively. The most negative δD and δ18O values occur in the early-mid Holocene, from ca. 11-5 ka BP. This contrast in the timing of isotopic variations demonstrates a complex relationship between the isotopic composition of precipitation and precipitation amount, or EASM intensity. Further comparisons indicate a possible linkage between the precipitation amount in north China and the west-east thermal gradient in the equatorial Pacific. In addition, the temperature of the moisture source area may play an important role in determining the isotopic composition of precipitation in monsoonal China.

  17. Graphene oxide derivatives with variable alkyl chain length and terminal functional groups as supports for stabilization of cytochrome c.

    PubMed

    Patila, Michaela; Pavlidis, Ioannis V; Kouloumpis, Antonios; Dimos, Konstantinos; Spyrou, Konstantinos; Katapodis, Petros; Gournis, Dimitrios; Stamatis, Haralambos

    2016-03-01

    In this study we report the ability of reduced and non-reduced graphene oxide-based nanomaterials (GONs), modified with variable alkyl chain length and terminal functional groups, to act as effective scaffolds for the immobilization of cytochrome c (cyt c) using different immobilization procedures. The GONs/cyt c conjugates are characterized by a combination of techniques, namely atomic force microscopy, X-ray photoelectron and FT-IR spectroscopies as well as thermo-gravimetric and differential thermal analysis. The effect of the structure of functional groups and the surface chemistry of GONs on the immobilization efficiency, the peroxidase activity and the stability of the cyt c was investigated and correlated with conformational changes on the protein molecule upon immobilization. The enhanced thermal stability (up to 2-fold) and increased tolerance (up to 25-fold) against denaturing agents observed for immobilized cyt c, indicates that these functionalized GONs are suitable as nanoscaffolds for the development of robust nanobiocatalysts.

  18. Production of medium-chain-length polyhydroxyalkanoates by Pseudomonas aeruginosa with fatty acids and alternative carbon sources.

    PubMed

    Chan, Pui-Ling; Yu, Vincent; Wai, Lam; Yu, Hoi-Fu

    2006-01-01

    In this study, medium-chain-length polyhydroxyalkanoates (mcl-PHAs) were produced by Pseudomonas aeruginosa using different carbon sources. Decanoic acid induced the highest (9.71% [+/- 0.7]) mcl-PHAs accumulation in bacterial cells at 47 h. The cells preferred to accumulate and degrade the polyhydroxyoctanoate than polyhydroxydecanoate (PHD) during early stage and final stage of the growth, respectively. The production cost of mcl-PHAs can be reduced by using edible oils as the carbon source. The bacteria accumulated 6% (+/- 0.7) of mcl-PHAs in the presence of olive oil. Besides, reused oil was another potential carbon source for the reduction of the production cost of mcl-PHAs. Overall, PHD was the major constituent in the accumulated mcl-PHAs.

  19. Electron-correlation effects on the static longitudinal polarizability of polymeric chains. II. Bond-length-alternation effects

    NASA Astrophysics Data System (ADS)

    Champagne, Benoît; Mosley, David H.; Vračko, Marjan; André, Jean-Marie

    1995-08-01

    Ab initio calculations of the static longitudinal polarizability of different molecular hydrogen model chains have been carried out at different levels of approximation to investigate the effects of including electron correlation as well as the variation of these effects as a function of the bond-length alternation of the systems. First, the coupled and uncoupled Hartree-Fock schemes have been employed. To assess the electron-correlation effects, the size-consistent Mo/ller-Plesset treatments limited to second (MP2), third (MP3), and fourth (MP4) order in electron-electron interactions, as well as the coupled-cluster techniques including all double substitutions (CCD), all single and double substitutions (CCSD), and all single and double substitutions with a perturbational estimate of the connected triple excitations [CCSD(T)] have been used. Within the MP4 treatment, a decomposition of the electron-correlation corrections according to the different classes of substitutions and different order highlights the relatively greater importance of the double substitutions at second and third orders. The main findings are that (i) the coupled Hartree-Fock (CHF) technique overestimates the asymptotic static longitudinal polarizability per unit cell for the three types of H2 chains under investigation; (ii) larger basis sets have to be employed when including electron correlation effects, otherwise, the correction is overestimated; (iii) these basis-set effects on the electron-correlation correction are enhanced in the case of the less alternating chains; (iv) using a sufficiently large atomic basis set, at the Mo/ller-Plesset or CCSD(T) levels, the more conjugated the chains, the less the relative magnitude of the electron-correlation correction to the CHF value, whereas using the CCD and CCSD techniques, these relative electron-correlation corrections slightly increase in the case of the less alternating molecular hydrogen chains; and (v) the more conjugated the systems

  20. Interaction and dynamics of (alkylamide + electrolyte) deep eutectics: dependence on alkyl chain-length, temperature, and anion identity.

    PubMed

    Guchhait, Biswajit; Das, Suman; Daschakraborty, Snehasis; Biswas, Ranjit

    2014-03-14

    Here we investigate the solute-medium interaction and solute-centered dynamics in (RCONH2 + LiX) deep eutectics (DEs) via carrying out time-resolved fluorescence measurements and all-atom molecular dynamics simulations at various temperatures. Alkylamides (RCONH2) considered are acetamide (CH3CONH2), propionamide (CH3CH2CONH2), and butyramide (CH3CH2CH2CONH2); the electrolytes (LiX) are lithium perchlorate (LiClO4), lithium bromide (LiBr), and lithium nitrate (LiNO3). Differential scanning calorimetric measurements reveal glass transition temperatures (T(g)) of these DEs are ~195 K and show a very weak dependence on alkyl chain-length and electrolyte identity. Time-resolved and steady state fluorescence measurements with these DEs have been carried out at six-to-nine different temperatures that are ~100-150 K above their individual T(g)s. Four different solute probes providing a good spread of fluorescence lifetimes have been employed in steady state measurements, revealing strong excitation wavelength dependence of probe fluorescence emission peak frequencies. Extent of this dependence, which shows sensitivity to anion identity, has been found to increase with increase of amide chain-length and decrease of probe lifetime. Time-resolved measurements reveal strong fractional power dependence of average rates for solute solvation and rotation with fraction power being relatively smaller (stronger viscosity decoupling) for DEs containing longer amide and larger (weaker decoupling) for DEs containing perchlorate anion. Representative all-atom molecular dynamics simulations of (CH3CONH2 + LiX) DEs at different temperatures reveal strongly stretched exponential relaxation of wavevector dependent acetamide self dynamic structure factor with time constants dependent both on ion identity and temperature, providing justification for explaining the fluorescence results in terms of temporal heterogeneity and amide clustering in these multi-component melts.

  1. Starch with a slow digestion property produced by altering its chain length, branch density, and crystalline structure.

    PubMed

    Ao, Zihua; Simsek, Senay; Zhang, Genyi; Venkatachalam, Mahesh; Reuhs, Bradley L; Hamaker, Bruce R

    2007-05-30

    The hypothesis of increasing the branch density of starch to reduce its digestion rate through partial shortening of amylopectin exterior chains and the length of amylose was investigated. Starch products prepared using beta-amylase, beta-amylase and transglucosidase, maltogenic alpha-amylase, and maltogenic alpha-amylase and transglucosidase showed significant reduction of rapidly digested starch by 14.5%, 29.0%, 19.8%, and 31.0% with a concomitant increase of slowly digested starch by 9.0%, 19.7%, 5.7%, and 11.0%, respectively. The resistant starch content increased from 5.1% to 13.5% in treated starches. The total contents of the prebiotics isomaltose, isomaltotriose, and panose (Isomaltooligosaccharides) were 2.3% and 5.5%, respectively, for beta-amylase/transglucosidase- and maltogenic alpha-amylase/transglucosidase-treated starches. The molecular weight distribution of enzyme-treated starches and their debranched chain length distributions, analyzed using high-performance size-exclusion chromatography with multiangle laser light scattering and refractive index detection (HPSEC-MALLS-RI) and HPSEC-RI, showed distinctly different patterns among starches with different enzyme treatments. A larger proportion of low molecular weight fractions appeared in starches treated additionally with transglucosidase. All enzyme-treated starches showed a mixture of B- and V-type X-ray diffraction patterns, and 1H NMR spectra showed a significant increase of alpha-1,6 linkages. Both the increase of the starch branch density and the crystalline structure in the treated starches likely contribute to their slow digestion property.

  2. State-dependent rotational diffusion of tetracene in n-alkanes. Evidence for a dominant energy relaxation pathway.

    PubMed

    Mize, Hannah E; Blanchard, G J

    2013-12-19

    We have investigated the rotational diffusion of tetracene in the n-alkanes octane through hexadecane. Emission from the S1 state was monitored following excitation to the S1 state or the S2 state. Our data show that fast, non-radiative relaxation from S2 to S1 gives rise to local heating in the immediate vicinity of the chromophore. This local heating effect exhibits a solvent aliphatic chain length dependence for solvents C11 and longer, where solvents with an even number of carbons behave differently than those with an odd number of carbons. These data shed light on the possible origin(s) of odd-even effects in n-alkanes and suggest that a dominant intermolecular relaxation pathway for excess vibrational energy involves the S1 chromophore ring breathing mode (ca. 1383 cm(-1)) and the solvent terminal methyl group rocking mode (1375 cm(-1)).

  3. Effect of alkyl chain length and hydroxyl group functionalization on the surface properties of imidazolium ionic liquids.

    PubMed

    Pensado, Alfonso S; Costa Gomes, Margarida F; Canongia Lopes, José N; Malfreyt, Patrice; Pádua, Agílio A H

    2011-08-14

    Properties of the surface of ionic liquids, such as surface tension, ordering, and charge and density profiles, were studied using molecular simulation. Two types of modification in the molecular structure of imidazolium cations were studied: the length of the alkyl side chain and the presence of a polar hydroxyl group at the end of the side chain. Four ionic liquids were considered: 1-ethyl-3-methylimidazolium tetrafluoroborate, [C(2)C(1)im][BF(4)]; 1-(2-hydroxyethyl)-3-methylimidazolium tetrafluoroborate, [C(2)OHC(1)im][BF(4)]; 1-octyl-3-methylimidazolium tetrafluoroborate, [C(8)C(1)im][BF(4)] and 1-(8-hydroxyoctyl)-3-methylimidazolium tetrafluoroborate, [C(8)OHC(1)im][BF(4)]. The surface tension was calculated using both mechanical and thermodynamic definitions, with consistent treatment of the long-range corrections. The simulations reproduce the available experimental values of surface tension with a maximum deviation of ±10%. This energetic characterization of the interface is completed by microscopic structural analysis of orientational ordering at the interface and density profiles along the direction normal to the interface. The presence of the hydroxyl group modifies the local structure at the interface, leading to a less organized liquid phase. The results allow us to relate the surface tension to the structural ordering at the liquid-vacuum interface.

  4. Free energy calculations in electroactive self-assembled monolayers (SAMs): impact of the chain length on the redox reaction.

    PubMed

    Filippini, Gaelle; Israeli, Yael; Goujon, Florent; Limoges, Benoit; Bonal, Christine; Malfreyt, Patrice

    2011-10-13

    The free energy approach is used to study the effect of the relative chain length of the two constituents of electroactive self-assembled monolayers (SAMs) on gold. In this study, the ferrocene groups are exposed to the electrolyte solution. This situation is achieved by using shorter diluent alkanethiol chains. To this end, the mixed monolayers formed by the self-assembly of 11-ferrocenylundecanethiol and butanethiol FcC(11)S/C(4)S and of 6-ferrocenylhexanethiol and butanethiol FcC(6)S/C(4)S onto a gold surface are studied. Calculation of enthalpy and entropy differences are also performed using molecular simulations. Additionally, the electrochemical signatures of these systems are determined to allow a direct comparison with our calculations. The thermodynamic properties are discussed in terms of enthalpy and entropy changes. Two effects account for the thermodynamic behavior. The first one involves the ion pairing between the ferrocenium group and the perchlorate anion. The second one concerns the desolvation of the first hydration shell of the anions. Finally, this work is also completed with a microscopic description associated with an energy characterization of these SAMs as a function of the surface coverage under conditions close to experiments.

  5. Effects of variation in chain length on ternary polymer electrolyte - Ionic liquid mixture - A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Raju, S. G.; Hariharan, Krishnan S.; Park, Da-Hye; Kang, HyoRang; Kolake, Subramanya Mayya

    2015-10-01

    Molecular dynamics (MD) simulations of ternary polymer electrolyte - ionic liquid mixtures are conducted using an all-atom model. N-alkyl-N-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([CnMPy][TFSI], n = 1, 3, 6, 9) and polyethylene oxide (PEO) are used. Microscopic structure, energetics and dynamics of ionic liquid (IL) in these ternary mixtures are studied. Properties of these four pure IL are also calculated and compared to that in ternary mixtures. Interaction between pyrrolidinium cation and TFSI is stronger and there is larger propensity of ion-pair formation in ternary mixtures. Unlike the case in imidazolium IL, near neighbor structural correlation between TFSI reduces with increase in chain length on cation in both pure IL and ternary mixtures. Using spatial density maps, regions where PEO and TFSI interact with pyrrolidinium cation are identified. Oxygens of PEO are above and below the pyrrolidinium ring and away from the bulky alkyl groups whereas TFSI is present close to nitrogen atom of CnMPy. In pure IL, diffusion coefficient (D) of C3MPy is larger than of TFSI but D of C9MPy and C6MPy are larger than that of TFSI. The reasons for alkyl chain dependent phenomena are explored.

  6. Adsorption of the disinfectant benzalkonium chloride on montmorillonite. Synergistic effect in mixture of molecules with different chain lengths.

    PubMed

    Zanini, Graciela P; Ovesen, Rikke Gleerup; Hansen, H C B; Strobel, Bjarne W

    2013-10-15

    The biocide benzalkonium chloride (BAC) is a mix of cationic alkylbenzyldimethylammonium surfactants having different alkyl chain lengths. A comparative study of adsorption on the phyllosilicate clay montmorillonite of two of these surfactants, with alkyl chains having respectively 12 C atoms (BAC-12) and 14 C atoms (BAC-14), and a mixture of both surfactants is presented in this work. Adsorption isotherms were performed for individual surfactants and for a 1:1 mixture BAC-12+BAC-14. The adsorption was investigated in an ample concentration range that covers almost seven orders of magnitude in concentrations (from 1 nM to 10 mM), range that includes environmentally relevant concentrations. Quantification of BAC was performed by HPLC-UV and LC-MS and the results were completed with powder X-Ray diffraction. The adsorption of both surfactants leads to adsorption isotherms with two well differentiated steps. The first step corresponds almost exclusively to a cation exchange process, and the binding constant is very similar for both surfactants. The second step of the isotherms is observed at higher concentrations and adsorption is mainly driven by lateral interactions between surfactant molecules. The binding constant of this step is larger for BAC-14 than for BAC-12. Adsorption from a BAC-12+BAC-14 mixture shows a synergistic behaviour, possibly due to a better packing arrangement in the interlayer. Calculations show that in natural systems silicate clays are major sorbents of BAC at low concentrations whereas binding to humic acid is predominant at high concentrations.

  7. Electrochemical measurement of lateral diffusion coefficients of ubiquinones and plastoquinones of various isoprenoid chain lengths incorporated in model bilayers.

    PubMed Central

    Marchal, D; Boireau, W; Laval, J M; Moiroux, J; Bourdillon, C

    1998-01-01

    The long-range diffusion coefficients of isoprenoid quinones in a model of lipid bilayer were determined by a method avoiding fluorescent probe labeling of the molecules. The quinone electron carriers were incorporated in supported dimyristoylphosphatidylcholine layers at physiological molar fractions (<3 mol%). The elaborate bilayer template contained a built-in gold electrode at which the redox molecules solubilized in the bilayer were reduced or oxidized. The lateral diffusion coefficient of a natural quinone like UQ10 or PQ9 was 2.0 +/- 0.4 x 10(-8) cm2 s(-1) at 30 degrees C, two to three times smaller than the diffusion coefficient of a lipid analog in the same artificial bilayer. The lateral mobilities of the oxidized or reduced forms could be determined separately and were found to be identical in the 4-13 pH range. For a series of isoprenoid quinones, UQ2 or PQ2 to UQ10, the diffusion coefficient exhibited a marked dependence on the length of the isoprenoid chain. The data fit very well the quantitative behavior predicted by a continuum fluid model in which the isoprenoid chains are taken as rigid particles moving in the less viscous part of the bilayer and rubbing against the more viscous layers of lipid heads. The present study supports the concept of a homogeneous pool of quinone located in the less viscous region of the bilayer. PMID:9545054

  8. The adjuvant activity of fatty acid esters. The role of acyl chain length and degree of saturation.

    PubMed Central

    Bomford, R

    1981-01-01

    Water-in-oil emulsions of metabolizable fatty acid esters, with the non-toxic surfactant Pluronic L122 as emulsifying agent, potentiated the humoral response to bovine serum albumin and staphylococcal toxoid in the mouse. Adjuvant activity was increased by changing the chemical nature of the esters as follows: (i) using a series of ethyl esters, adjuvant activity appeared when the acyl chain length of the fatty acid component was 16 or greater; (ii) isobutyl and isopropyl esters of palmitic acid (C16:0) were superior to ethyl; (iii) the ethyl esters of oleic (C18:1) and linoleic (C18:2) acids were better than stearic (C18:0). Since emulsions prepared with longer chain saturated esters are very viscous or solid at room temperature, and unsaturated esters are chemically reactive, emulsions were prepared with differing proportions of ethyl caprate (C10:0) and butyl stearate. At a ratio of 9:1 the emulsions possessed the low viscosity of ethyl caprate, but gained the adjuvant activity of butyl stearate. 125I-labelled BSA was retained in the footpad to a significantly greater extent than with a caprate emulsion, but reasons are given for believing that slow release of antigen is not the only mechanism of adjuvant activity. The ester emulsions caused more acute but less chronic local inflammation (footpad swelling) than Freund's incomplete adjuvant. PMID:7275184

  9. Intake of small-to-medium-chain saturated fatty acids is associated with peripheral leukocyte telomere length in postmenopausal women.

    PubMed

    Song, Yan; You, Nai-Chieh Y; Song, Yiqing; Kang, Mo K; Hou, Lifang; Wallace, Robert; Eaton, Charles B; Tinker, Lesley F; Liu, Simin

    2013-06-01

    Dietary factors, including dietary fat, may affect the biological aging process, as reflected by the shortening of telomere length (TL), by affecting levels of oxidative stress and inflammatory responses. We examined the direct relations of total and types of dietary fats and fat-rich foods to peripheral leukocyte TL. In 4029 apparently healthy postmenopausal women who participated in the Women's Health Initiative, intakes of total fat, individual fatty acids, and fat-rich foods were assessed by a questionnaire. TL was measured by quantitative polymerase chain reaction. Intake of short-to-medium-chain saturated fatty acids (SMSFAs; aliphatic tails of ≤ 12 carbons) was inversely associated with TL. Compared with participants in other quartiles of SMSFA intake, women who were in the highest quartile (median: 1.29% of energy) had shorter TLs [mean: 4.00 kb (95% CI: 3.89, 4.11 kb)], whereas women in the lowest quartile of intake (median: 0.29% of energy) had longer TLs [mean: 4.13 kb (95% CI: 4.03, 4.24 kb); P-trend = 0.046]. Except for lauric acid, all other individual SMSFAs were inversely associated with TL (P < 0.05). In isoenergetic substitution models, the substitution of 1% of energy from SMSFAs with any other energy source was associated with 119 bp longer TLs (95% CI: 21, 216 bp). Intakes of nonskim milk, butter, and whole-milk cheese (major sources of SMSFAs) were all inversely associated with TL. No significant associations were found with long-chain saturated fatty acids, monounsaturated fatty acids, and polyunsaturated fatty acids. In conclusion, we found that higher intakes of SMSFAs and SMSFA-rich foods were associated with shorter peripheral leukocyte TL among postmenopausal women. These findings suggest the potential roles of SMSFAs in the rate of biological aging.

  10. Chain-like molecules confined in nanopores

    NASA Astrophysics Data System (ADS)

    Huber, Patrick; Soprunyuk, Viktor; Hofmann, Tommy; Knorr, Klaus

    2004-03-01

    We present an x-ray diffraction study on chain-like molecules, i.e. a selection of n-alkane molecules, embedded in the pores of nanoporous silica matrices. The lengths of the hydrocarbon chains are comparable to the mean diameter ( 7nm) of the tubular like nanopores which leads to drastic geometric restrictions. Diffraction patterns, recorded on heating and cooling between 200 K and 310 K, elucidate how the structure and phase behavior of the molecules is affected by the random substrate disorder and the confinement. The confined n-alkanes form close-packed structures by aligning parallel to the pore axis. In the case of the medium-length hydrocarbon chains one basic ordering principle known from the bulk crystalline state, i.e. the lamellar ordering of the molecules, is quenched[1], whereas for shorter n-alkanes this ordering principle survives[2]. The confined solids mimic the orientational order-disorder transitions known from the 3D unconfined crystals albeit in a modified fashion. 1. P. Huber, D. Wallacher, J. Albers, K. Knorr, Europhysics Letters, in press; 2. P. Huber, D. Wallacher, J. Albers, K. Knorr, Journal of Physics: Condensed Matter 15, 309 (2003).

  11. Hydrogen-hydrogen bonds in highly branched alkanes and in alkane complexes: A DFT, ab initio, QTAIM, and ELF study.

    PubMed

    Monteiro, Norberto K V; Firme, Caio L

    2014-03-06

    The hydrogen-hydrogen (H-H) bond or hydrogen-hydrogen bonding is formed by the interaction between a pair of identical or similar hydrogen atoms that are close to electrical neutrality and it yields a stabilizing contribution to the overall molecular energy. This work provides new, important information regarding hydrogen-hydrogen bonds. We report that stability of alkane complexes and boiling point of alkanes are directly related to H-H bond, which means that intermolecular interactions between alkane chains are directional H-H bond, not nondirectional induced dipole-induced dipole. Moreover, we show the existence of intramolecular H-H bonds in highly branched alkanes playing a secondary role in their increased stabilities in comparison with linear or less branched isomers. These results were accomplished by different approaches: density functional theory (DFT), ab initio, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF).

  12. Effect of head group polarity and spacer chain length on the aggregation properties of gemini surfactants in an aquatic environment.

    PubMed

    Borse, Mahendra; Sharma, Vikas; Aswal, V K; Goyal, P S; Devi, Surekha

    2005-04-01

    The aggregation behavior of cationic gemini surfactants with respect to variation in head group polarity and spacer length is studied through conductance, surface tension, viscosity, and small-angle neutron-scattering (SANS) measurements. The critical micellar concentration (cmc), average degree of micelle ionization (beta(ave)), minimum area per molecule of surfactant at the air-water interface (A(min)), surface excess concentration (gamma(max)), and Gibb's free energy of micellization (delta G(mic)) of the surfactants were determined from conductance and surface tension data. The aggregation numbers (N), dimensions of micelles (b/a), effective fractional charge per monomer (alpha), and hydration of micelles (h(E)) were determined from SANS and viscosity data, respectively. The increasing head group polarity of gemini surfactant with spacer chain length of 4 methylene units promotes micellar growth, leading to a decrease in cmc, beta(ave), and delta G(mic) and an increase in N and b/a. This is well supported by the observed increase in hydration (h(E)) of micelles with increase in aggregation number (N) and dimension (b/a) of micelle.

  13. Regioselective alkane hydroxylation with a mutant AlkB enzyme

    DOEpatents

    Koch, Daniel J.; Arnold, Frances H.

    2012-11-13

    AlkB from Pseudomonas putida was engineered using in-vivo directed evolution to hydroxylate small chain alkanes. Mutant AlkB-BMO1 hydroxylates propane and butane at the terminal carbon at a rate greater than the wild-type to form 1-propanol and 1-butanol, respectively. Mutant AlkB-BMO2 similarly hydroxylates propane and butane at the terminal carbon at a rate greater than the wild-type to form 1-propanol and 1-butanol, respectively. These biocatalysts are highly active for small chain alkane substrates and their regioselectivity is retained in whole-cell biotransformations.

  14. Influence of carbon chain length on the synthesis and yield of fatty amine-coated iron-platinum nanoparticles

    PubMed Central

    2014-01-01

    Iron oxide nanoparticles are among the most widely used and characterized magnetic nanoparticles. However, metal alloys such as superparamagnetic iron-platinum particles (SIPPs), which have better magnetic properties, are receiving increased attention. Scalable techniques to routinely synthesize SIPPs in bulk need further study. Here, we focus on the role played by the fatty amine ligand in the formation of the bimetallic FePt nanocrystal. More specifically, we compare the effect of varying lengths of fatty amine ligands on the shape, structure, uniformity, composition, and magnetic properties of the SIPPs. We synthesized SIPPs by employing a ‘green’ thermal decomposition reaction using fatty amine ligands containing 12 to 18 carbons in length. Greater fatty amine chain length increased the polydispersity, particle concentration, iron concentration, and the stability of the SIPPs. Additionally, longer reflux times increased the diameter of the particles, but decreased the iron concentration, suggesting that shorter reaction times are preferable. Fourier transform infrared spectroscopy of the SIPPs indicates that the ligands are successfully bound to the FePt cores through the amine group. Superconducting quantum interference device magnetometry measurements suggest that all of the SIPPs were superparamagnetic at room temperature and that SIPPs synthesized using tetradecylamine had the highest saturation magnetization. Our findings indicate that the octadecylamine ligand, which is currently used for the routine synthesis of SIPPs, may not be optimal. Overall, we found that using tetradecylamine and a 30-min reflux reaction resulted in optimal particles with the highest degree of monodispersity, iron content, stability, and saturation magnetization. PACS 81.07.-b; 75.75.Fk; 61.46.Df PMID:25006334

  15. Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C.

    PubMed

    Brown, Nathan J; Wu, Cindy W; Seurynck-Servoss, Shannon L; Barron, Annelise E

    2008-02-12

    The hydrophobic proteins of lung surfactant (LS), SP-B and SP-C, are critical constituents of an effective surfactant replacement therapy for the treatment of respiratory distress syndrome. Because of concerns and difficulties associated with animal-derived surfactants, recent investigations have focused on the creation of synthetic analogues of the LS proteins. However, creating an accurate mimic of SP-C that retains its biophysical surface activity is extraordinarily challenging given the lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One successful approach that overcomes these difficulties is the use of poly-N-substituted glycines, or peptoids, to mimic SP-C. To develop a non-natural, bioactive mimic of SP-C and to investigate the effects of side chain chemistry and length of the helical hydrophobic region, we synthesized, purified, and performed in vitro testing of two classes of peptoid SP-C mimics: those having a rigid alpha-chiral aromatic helix and those having a biomimetic alpha-chiral aliphatic helix. The length of the two classes of mimics was also systematically altered. Circular dichroism spectroscopy gave evidence that all of the peptoid-based mimics studied here emulated SP-C's secondary structure, forming stable helical structures in solution. Langmuir-Wilhelmy surface balance, fluorescence microscopy, and pulsating bubble surfactometry experiments provide evidence that the aromatic-based SP-C peptoid mimics, in conjunction with a synthetic lipid mixture, have superior surface activity and biomimetic film morphology in comparison to the aliphatic-based mimics and that there is an increase in surface activity corresponding to increasing helical length.

  16. Fossil Leaves and Fossil Leaf n-Alkanes: Reconstructing the First Closed Canopied Rainforests

    NASA Astrophysics Data System (ADS)

    Graham, H. V.; Freeman, K. H.

    2013-12-01

    Although the age and location is disputed, the rise of the first closed-canopy forest is likely linked with the expansion of angiosperms in the late Cretacous or early Cenozoic. The carbon isotope 'canopy effect' reflects the extent of canopy closure, and is well documented in δ13C values of the leaves and leaf lipids in modern forests. To test the extent of canopy closure among the oldest documented angiosperm tropical forests, we analyzed isotopic characteristics of leaf fossils and leaf waxes from the Guaduas and Cerrejón Formations. The Guaduas Fm. (Maastrichtian) contains some of the earliest angiosperm fossils in the Neotropics, and both leaf morphology and pollen records at this site suggest an open-canopy structure. The Cerrejón Fm. (Paleocene) contains what are believed to be the first recorded fossil leaves from a closed-canopy forest. We analyzed the bulk carbon isotope content (δ13Cleaf) of 199 fossil leaves, as well as the n-alkane concentration and chain-length distribution, and δ13C of alkanes (δ13Clipid) of 73 fossil leaves and adjacent sediment samples. Fossil leaves are dominated by eudicots and include ten modern plant families (Apocynaceae, Bombaceae, Euphorbaceae, Fabaceae, Lauraceae, Malvaceae, Meliaceae, Menispermaceae, Moraceae, Sapotaceae). We interpreted extent of canopy coverage based on the range of δ13Cleaf values. The narrow range of δ13C values in leaves from the Guaduas Fm (2.7‰) is consistent with an open canopy. A significantly wider range in values (6.3‰) suggests a closed-canopy signature for site 0315 of the Cerrejón Fm,. In contrast, at Site 0318, a lacustrine deposit, leaves had a narrow range (3.3‰) in δ13C values, and this is not consistent with a closed-canopy, but is consistent with leaf assemblages from a forest edge. Leaves that accumulate in lake sediments tend to be biased toward plants living at the lake edge, which do not experience closed-canopy conditions, and do not express the isotopic

  17. Effect of fatty acyl chain length and structure on the lamellar gel to liquid-crystalline and lamellar to reversed hexagonal phase transitions of aqueous phosphatidylethanolamine dispersions

    SciTech Connect

    Lewis, R.N.A.H.; Mannock, D.A.; McElhaney, R.N.; Turner, D.C.; Gruner, S.M. )

    1989-01-24

    The lamellar gel/liquid-crystalline and the lamellar liquid-crystalline/reversed hexagonal phase transitions of aqueous dispersions of a number of synthetic phosphatidylethanolamines containing linear saturated, branched chain, and alicyclic fatty acyl chains of varying length were studied by differential scanning calorimetry, {sup 31}P nuclear magnetic resonance spectroscopy, and X-ray diffraction. For any given homologous series of phosphatidylethanolamines containing a single chemical class of fatty acids, the lamellar gel/liquid-crystalline phase transition temperature increases and the lamellar liquid-crystalline/reversed hexagonal phase transition temperature decreases with increases in hydrocarbon chain length. For a series of phosphatidylethanolamines of the same hydrocarbon chain length but with different chemical structures, both the lamellar gel/liquid-crystalline and the lamellar liquid-crystalline/reversed hexagonal phase transition temperatures vary markedly and in the same direction. These results suggest that for any given hydrocarbon chain length, there may be a critical thickness at which the liquid-crystalline phosphatidylethanolamine bilayer becomes unstable with respect to inverted nonbilayer phases such as the H{sub II} phase and that the temperature at which this critical thickness is reached is dependent upon that bilayers proximity to the hydrocarbon chain-melting phase transition temperature.

  18. Effect of n-alkanes on asphaltene structuring in petroleum oils.

    PubMed

    Stachowiak, Christian; Viguié, Jean-Romain; Grolier, Jean-Pierre E; Rogalski, Marek

    2005-05-24

    The interactions between asphaltenes and short- to medium-chain n-alkanes were studied using titration microcalorimetry and inverse chromatography. The exothermic heat effects observed upon mixing of asphaltenes and n-alkanes were interpreted in terms of assembling of the two types of compounds into mixed structures. We show that the energy of the interactions between n-alkanes and the asphaltene hydrocarbon chains is close to the energy of the interactions between the asphaltene chains. We propose that the latter interactions are responsible for the formation of the asphaltene aggregates and are the driving force of the aggregate assembly into higher structures.

  19. Angiosperm n-alkane distribution patterns and the geologic record of C4 grassland evolution

    NASA Astrophysics Data System (ADS)

    Henderson, A.; Graham, H. V.; Patzkowsky, M.; Fox, D. L.; Freeman, K. H.

    2012-12-01

    n-Alkane average chain-length (ACL) patterns vary regionally with community composition and climate. To clarify the influence of phylogenetic and community patterns, we compiled and analyzed a global database of published n-alkane abundance for n-C27 to C35 homologs in modern plant specimens (n=205). ACL for waxes in C4 non-woody plants are longer than for woody plants, suggesting ACL can serve as an indicator of the three-dimensional structure of local vegetation. Further, these findings suggest compound-specific isotopic data for longer alkane homologs (C31, C33, C35) will proportionately represent non-woody vegetation and isotope measurements of C29 are more representative of woody vegetation. Thus, the combination of ACL and carbon isotope compositions should allow us to disentangle C3 woody, C3 non-woody, and C4 non-woody signals in terrestrial paleorecords. Application of this approach to the geologic record of Miocene C4 grassland expansion in the US Great Plains and the Siwaliks in Pakistan illustrate two very different transition scenarios. Alkane-specific isotopic data indicate C4 grasslands appeared 2.5 Ma in the Great Plains and 6.5 Ma in the Siwaliks, and ACL analysis indicates that this transition involved the replacement of woody vegetation in the US and the replacement of C3 grasses in Pakistan. Our analysis illustrates that, consistent with differences in the timing of C4 grassland, the drivers of change were likely not the same in these regions. Oxygen isotope records suggest that the more recent transition in the Great Plains was associated with climate cooling and possibly changes in disturbance regimes and that the transition in the Siwaliks was likely associated with warming and drying.

  20. A molecular dynamics study of the effect of thermal boundary conductance on thermal transport of ideal crystal of n-alkanes with different number of carbon atoms

    NASA Astrophysics Data System (ADS)

    Rastgarkafshgarkolaei, Rouzbeh; Zeng, Yi; Khodadadi, J. M.

    2016-05-01

    Phase change materials such as n-alkanes that exhibit desirable characteristics such as high latent heat, chemical stability, and negligible supercooling are widely used in thermal energy storage applications. However, n-alkanes have the drawback of low thermal conductivity values. The low thermal conductivity of n-alkanes is linked to formation of randomly oriented nano-domains of molecules in their solid structure that is responsible for excessive phonon scattering at the grain boundaries. Thus, understanding the thermal boundary conductance at the grain boundaries can be crucial for improving the effectiveness of thermal storage systems. The concept of the ideal crystal is proposed in this paper, which describes a simplified model such that all the nano-domains of long-chain n-alkanes are artificially aligned perfectly in one direction. In order to study thermal transport of the ideal crystal of long-chain n-alkanes, four (4) systems (C20H42, C24H50, C26H54, and C30H62) are investigated by the molecular dynamics simulations. Thermal boundary conductance between the layers of ideal crystals is determined using both non-equilibrium molecular dynamics (NEMD) and equilibrium molecular dynamics (EMD) simulations. Both NEMD and EMD simulations exhibit no significant change in thermal conductance with the molecular length. However, the values obtained from the EMD simulations are less than the values from NEMD simulations with the ratio being nearly three (3) in most cases. This difference is due to the nature of EMD simulations where all the phonons are assumed to be in equilibrium at the interface. Thermal conductivity of the n-alkanes in three structures including liquid, solid, and ideal crystal is investigated utilizing NEMD simulations. Our results exhibit a very slight rise in thermal conductivity values as the number of carbon atoms of the chain increases. The key understanding is that thermal transport can be significantly altered by how the molecules and the

  1. Comparison of Chain-Length Preferences and Glucan Specificities of Isoamylase-Type α-Glucan Debranching Enzymes from Rice, Cyanobacteria, and Bacteria

    PubMed Central

    Utsumi, Yoshinori; Fujita, Naoko; Umeda, Kazuhiro; Sawada, Takayuki; Kubo, Akiko; Abe, Jun-ichi; Colleoni, Christophe; Ball, Steven

    2016-01-01

    It has been believed that isoamylase (ISA)-type α-glucan debranching enzymes (DBEs) play crucial roles not only in α-glucan degradation but also in the biosynthesis by affecting the structure of glucans, although molecular basis on distinct roles of the individual DBEs has not fully understood. In an attempt to relate the roles of DBEs to their chain-length specificities, we analyzed the chain-length distribution of DBE enzymatic reaction products by using purified DBEs from various sources including rice, cyanobacteria, and bacteria. When DBEs were incubated with phytoglycogen, their chain-length specificities were divided into three groups. First, rice endosperm ISA3 (OsISA3) and Eschericia coli GlgX (EcoGlgX) almost exclusively debranched chains having degree of polymerization (DP) of 3 and 4. Second, OsISA1, Pseudomonas amyloderamosa ISA (PsaISA), and rice pullulanase (OsPUL) could debranch a wide range of chains of DP≧3. Third, both cyanobacteria ISAs, Cyanothece ATCC 51142 ISA (CytISA) and Synechococcus elongatus PCC7942 ISA (ScoISA), showed the intermediate chain-length preference, because they removed chains of mainly DP3-4 and DP3-6, respectively, while they could also react to chains of DP5-10 and 7–13 to some extent, respectively. In contrast, all these ISAs were reactive to various chains when incubated with amylopectin. In addition to a great variation in chain-length preferences among various ISAs, their activities greatly differed depending on a variety of glucans. Most strikingly, cyannobacteria ISAs could attack branch points of pullulan to a lesser extent although no such activity was found in OsISA1, OsISA3, EcoGlgX, and PsaISA. Thus, the present study shows the high possibility that varied chain-length specificities of ISA-type DBEs among sources and isozymes are responsible for their distinct functions in glucan metabolism. PMID:27309534

  2. Effect of chain lengths of PEO-PPO-PEO on small unilamellar liposome morphology and stability: an AFM investigation.

    PubMed

    Liang, Xuemei; Mao, Guangzhao; Ng, K Y Simon

    2005-05-01

    The morphology and stability of small unilamellar egg yolk phosphatidylcholine (EggPC) liposomes modified with the Pluronic copolymer (poly (oxyethylene)-poly (oxypropylene)-poly (oxyethylene) (PEO-PPO-PEO)) with different compositions on mica surface have been investigated using atomic force microscopy. Morphology studies reveal significant morphological changes of liposomes upon incorporating the Pluronic copolymer. Bilayers are observed for Pluronic with small hydrophilic (PEO) chain lengths such as L81 [(PEO)2(PPO)40(PEO)2] and L121 [(PEO)4(PPO)60(PEO)4]; bilayer and vesicle coexistence is observed for P85 [(PEO)26(PPO)39.5(PEO)26] and F87 [(PEO)61.1(PPO)39.7(PEO)61.1]; and stable vesicles are observed for F88 [(PEO)103.5(PPO)39.2(PEO)103.5], F127 [(PEO)100(PPO)65(PEO)100], and F108 [(PEO)132.6(PPO)50.3(PEO)132.6]. The micromechanical properties of Pluronic-modified EggPC vesicles were studied by analyzing AFM approaching force curve. The bending modulus (k(c)) of the Pluronic-modified EggPC vesicles increased several-fold compared with that of the pure EggPC vesicles. The significant difference is due to the enhanced rigidity of the EggPC vesicles as a result of the incorporation of PPO molecules and PEO chains. Based on the analysis of onset point by AFM and diameters of vesicles by light scattering, it was concluded that the favorable model to describe the polymer-bilayer interaction is the membrane-spanning model.

  3. Interaction and dynamics of (alkylamide + electrolyte) deep eutectics: Dependence on alkyl chain-length, temperature, and anion identity

    SciTech Connect

    Guchhait, Biswajit; Das, Suman; Daschakraborty, Snehasis; Biswas, Ranjit

    2014-03-14

    Here we investigate the solute-medium interaction and solute-centered dynamics in (RCONH{sub 2} + LiX) deep eutectics (DEs) via carrying out time-resolved fluorescence measurements and all-atom molecular dynamics simulations at various temperatures. Alkylamides (RCONH{sub 2}) considered are acetamide (CH{sub 3}CONH{sub 2}), propionamide (CH{sub 3}CH{sub 2}CONH{sub 2}), and butyramide (CH{sub 3}CH{sub 2}CH{sub 2}CONH{sub 2}); the electrolytes (LiX) are lithium perchlorate (LiClO{sub 4}), lithium bromide (LiBr), and lithium nitrate (LiNO{sub 3}). Differential scanning calorimetric measurements reveal glass transition temperatures (T{sub g}) of these DEs are ∼195 K and show a very weak dependence on alkyl chain-length and electrolyte identity. Time-resolved and steady state fluorescence measurements with these DEs have been carried out at six-to-nine different temperatures that are ∼100–150 K above their individual T{sub g}s. Four different solute probes providing a good spread of fluorescence lifetimes have been employed in steady state measurements, revealing strong excitation wavelength dependence of probe fluorescence emission peak frequencies. Extent of this dependence, which shows sensitivity to anion identity, has been found to increase with increase of amide chain-length and decrease of probe lifetime. Time-resolved measurements reveal strong fractional power dependence of average rates for solute solvation and rotation with fraction power being relatively smaller (stronger viscosity decoupling) for DEs containing longer amide and larger (weaker decoupling) for DEs containing perchlorate anion. Representative all-atom molecular dynamics simulations of (CH{sub 3}CONH{sub 2} + LiX) DEs at different temperatures reveal strongly stretched exponential relaxation of wavevector dependent acetamide self dynamic structure factor with time constants dependent both on ion identity and temperature, providing justification for explaining the fluorescence results in

  4. Progressive Degradation of Crude Oil n-Alkanes Coupled to Methane Production under Mesophilic and Thermophilic Conditions

    PubMed Central

    Cheng, Lei; Shi, Shengbao; Li, Qiang; Chen, Jianfa; Zhang, Hui; Lu, Yahai

    2014-01-01

    Although methanogenic degradation of hydrocarbons has become a well-known process, little is known about which crude oil tend to be degraded at different temperatures and how the microbial community is responded. In this study, we assessed the methanogenic crude oil degradation capacity of oily sludge microbes enriched from the Shengli oilfield under mesophilic and thermophilic conditions. The microbial communities were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes combined with cloning and sequencing. Enrichment incubation demonstrated the microbial oxidation of crude oil coupled to methane production at 35 and 55°C, which generated 3.7±0.3 and 2.8±0.3 mmol of methane per gram oil, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that crude oil n-alkanes were obviously degraded, and high molecular weight n-alkanes were preferentially removed over relatively shorter-chain n-alkanes. Phylogenetic analysis revealed the concurrence of acetoclastic Methanosaeta and hydrogenotrophic methanogens but different methanogenic community structures under the two temperature conditions. Candidate divisions of JS1 and WWE 1, Proteobacteria (mainly consisting of Syntrophaceae, Desulfobacteraceae and Syntrophorhabdus) and Firmicutes (mainly consisting of Desulfotomaculum) were supposed to be involved with n-alkane degradation in the mesophilic conditions. By contrast, the different bacterial phylotypes affiliated with Caldisericales, “Shengli Cluster” and Synergistetes dominated the thermophilic consortium, which was most likely to be associated with thermophilic crude oil degradation. This study revealed that the oily sludge in Shengli oilfield harbors diverse uncultured microbes with great potential in methanogenic crude oil degradation over a wide temperature range, which extend our previous understanding of methanogenic degradation of crude oil alkanes. PMID:25409013

  5. Modeling the phase behavior of H2S+n-alkane binary mixtures using the SAFT-VR+D approach.

    PubMed

    dos Ramos, M Carolina; Goff, Kimberly D; Zhao, Honggang; McCabe, Clare

    2008-08-07

    A statistical associating fluid theory for potential of variable range has been recently developed to model dipolar fluids (SAFT-VR+D) [Zhao and McCabe, J. Chem. Phys. 2006, 125, 104504]. The SAFT-VR+D equation explicitly accounts for dipolar interactions and their effect on the thermodynamics and structure of a fluid by using the generalized mean spherical approximation (GMSA) to describe a reference fluid of dipolar square-well segments. In this work, we apply the SAFT-VR+D approach to real mixtures of dipolar fluids. In particular, we examine the high-pressure phase diagram of hydrogen sulfide+n-alkane binary mixtures. Hydrogen sulfide is modeled as an associating spherical molecule with four off-center sites to mimic hydrogen bonding and an embedded dipole moment (micro) to describe the polarity of H2S. The n-alkane molecules are modeled as spherical segments tangentially bonded together to form chains of length m, as in the original SAFT-VR approach. By using simple Lorentz-Berthelot combining rules, the theoretical predictions from the SAFT-VR+D equation are found to be in excellent overall agreement with experimental data. In particular, the theory is able to accurately describe the different types of phase behavior observed for these mixtures as the molecular weight of the alkane is varied: type III phase behavior, according to the scheme of classification by Scott and Konynenburg, for the H2S+methane system, type IIA (with the presence of azeotropy) for the H2S+ethane and+propane mixtures; and type I phase behavior for mixtures of H2S and longer n-alkanes up to n-decane. The theory is also able to predict in a qualitative manner the solubility of hydrogen sulfide in heavy n-alkanes.

  6. Progressive degradation of crude oil n-alkanes coupled to methane production under mesophilic and thermophilic conditions.

    PubMed

    Cheng, Lei; Shi, Shengbao; Li, Qiang; Chen, Jianfa; Zhang, Hui; Lu, Yahai

    2014-01-01

    Although methanogenic degradation of hydrocarbons has become a well-known process, little is known about which crude oil tend to be degraded at different temperatures and how the microbial community is responded. In this study, we assessed the methanogenic crude oil degradation capacity of oily sludge microbes enriched from the Shengli oilfield under mesophilic and thermophilic conditions. The microbial communities were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes combined with cloning and sequencing. Enrichment incubation demonstrated the microbial oxidation of crude oil coupled to methane production at 35 and 55°C, which generated 3.7±0.3 and 2.8±0.3 mmol of methane per gram oil, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that crude oil n-alkanes were obviously degraded, and high molecular weight n-alkanes were preferentially removed over relatively shorter-chain n-alkanes. Phylogenetic analysis revealed the concurrence of acetoclastic Methanosaeta and hydrogenotrophic methanogens but different methanogenic community structures under the two temperature conditions. Candidate divisions of JS1 and WWE 1, Proteobacteria (mainly consisting of Syntrophaceae, Desulfobacteraceae and Syntrophorhabdus) and Firmicutes (mainly consisting of Desulfotomaculum) were supposed to be involved with n-alkane degradation in the mesophilic conditions. By contrast, the different bacterial phylotypes affiliated with Caldisericales, "Shengli Cluster" and Synergistetes dominated the thermophilic consortium, which was most likely to be associated with thermophilic crude oil degradation. This study revealed that the oily sludge in Shengli oilfield harbors diverse uncultured microbes with great potential in methanogenic crude oil degradation over a wide temperature range, which extend our previous understanding of methanogenic degradation of crude oil alkanes.

  7. Elongated phytoglycogen chain length in transgenic rice endosperm expressing active starch synthase IIa affects the altered solubility and crystallinity of the storage α-glucan

    PubMed Central

    Fujita, Naoko; Toyosawa, Yoshiko; Utsumi, Yoshinori

    2012-01-01

    The relationship between the solubility, crystallinity, and length of the unit chains of plant storage α-glucan was investigated by manipulating the chain length of α-glucans accumulated in a rice mutant. Transgenic lines were produced by introducing a cDNA for starch synthase IIa (SSIIa) from an indica cultivar (SSIIa I, coding for active SSIIa) into an isoamylase1 (ISA1)-deficient mutant (isa1) that was derived from a japonica cultivar (bearing inactive SSIIa proteins). The water-soluble fraction accounted for >95% of the total α-glucan in the isa1 mutant, whereas it was only 35–70% in the transgenic SSIIa I /isa1 lines. Thus, the α-glucans from the SSIIa I /isa1 lines were fractionated into soluble and insoluble fractions prior to the following characterizations. X-ray diffraction analysis revealed a weak B-type crystallinity for the α-glucans of the insoluble fraction, while no crystallinity was confirmed for α-glucans in isa1. Concerning the degree of polymerization (DP) ≤30, the chain lengths of these α-glucans differed significantly in the order of SSIIa I /isa1 insoluble > SSIIa I /isa1 soluble > α-glucans in isa1. The amount of long chains with DP ≥33 was higher in the insoluble fraction α-glucans than in the other two α-glucans. No difference was observed in the chain length distributions of the β-amylase limit dextrins among these α-glucans. These results suggest that in the SSIIa I /isa1 transgenic lines, the unit chains of α-glucans were elongated by SSIIaI, whereas the expression of SSIIaI did not affect the branch positions. Thus, the observed insolubility and crystallinity of the insoluble fraction can be attributed to the elongated length of the outer chains due to SSIIaI. PMID:23048127

  8. Microwave dielectric relaxation spectroscopy study of alkan-1-ol/alkylbenzoate binary solvents.

    PubMed

    Navarro, Ana M; García, Begoña; Ibeas, Saturnino; Hoyuelos, Francisco J; Peñacoba, Indalecio A; Leal, José M

    2013-10-03

    The structure and dynamics of alkan-1-ol/alkylbenzoate binary mixtures have been studied by microwave dielectric relaxation spectroscopy in the 200 MHz to 20 GHz frequency range. The binary mixtures of methanol, ethanol, propan-1-ol, butan-1-ol, and pentan-1-ol with methyl, ethyl, propyl, and butyl benzoates were studied at 298.15 K. The relaxational response of the pure alcohols, pure esters, and their binary mixtures over the full composition range is properly described by the Havriliak-Negami model. The alcohol content, alcohol length, and alkyl side-chain effects on the relaxational properties have been studied for these mixtures over the whole composition range. From the experimental readings, the effective and the corrective Kirkwood and Bruggeman correlation factors have been calculated. The data gathered have been interpreted in terms of the alkyl side-chain effect and their reliance on the mixture composition.

  9. Effect of cation type, alkyl chain length, adsorbate size on adsorption kinetics and isotherms of bromide ionic liquids from aqueous solutions onto microporous fabric and granulated activated carbons.

    PubMed

    Hassan, Safia; Duclaux, Laurent; Lévêque, Jean-Marc; Reinert, Laurence; Farooq, Amjad; Yasin, Tariq

    2014-11-01

    The adsorption from aqueous solution of imidazolium, pyrrolidinium and pyridinium based bromide ionic liquids (ILs) having different alkyl chain lengths was investigated on two types of microporous activated carbons: a fabric and a granulated one, well characterized in terms of surface chemistry by "Boehm" titrations and pH of point of zero charge measurements and of porosity by N2 adsorption at 77 K and CO2 adsorption at 273 K. The influence of cation type, alkyl chain length and adsorbate size on the adsorption properties was analyzed by studying kinetics and isotherms of eight different ILs using conductivity measurements. Equilibrium studies were carried out at different temperatures in the range [25-55 °C]. The incorporation of ILs on the AC porosity was studied by N2 adsorption-desorption measurements at 77 K. The experimental adsorption isotherms data showed a good correlation with the Langmuir model. Thermodynamic studies indicated that the adsorption of ILs onto activated carbons was an exothermic process, and that the removal efficiency increased with increase in alkyl chain length, due to the increase in hydrophobicity of long chain ILs cations determined with the evolution of the calculated octanol-water constant (Kow). The negative values of free energies indicated that adsorption of ILs with long chain lengths having hydrophobic cations was more spontaneous at the investigated temperatures.

  10. Quaternary water in oil microemulsions. 1. Effect of alcohol chain length and concentration on droplet size and exchange of material between droplets

    SciTech Connect

    Lang, J.; Lalem, N.; Zana, R. )

    1991-11-14

    Water solubility, electrical conductivity, and time-resolved fluorescence quenching measurements have been performed in water/chlorobenzene/cationic surfactants/1-alcohol water-in-oil (w/o) microemulsions in order to investigate the effect of alcohol chain length and concentration on various properties of these systems: surfactant aggregation number, N, per aggregate; radius, R{sub w}, of the droplet water core; intensity of attractive interdroplet interactions; onset of percolation of electrical conductivity; and rate constant, k{sub e}, for the exchange of material between droplets through collisions with temporary merging. The variations of these properties with the molar concentration ratio {omega} = (water)/(surfactant) for alcohols of increasing chain length are strikingly similar to those found when investigating the effect of surfactant chain length. In particular, N and R{sub w} and the intensity of attractive interactions decrease when the alcohol chain length increases as predicted by current theory of the stability of w/o microemulsions. For a series of microemulsions based on alkyltrimethylammonium bromide surfactants, the water solubility results indicate that the stability of the microemulsions containing short chain alcohols (propanol, butanol) is determined by the attractive interdroplet interactions. The results give support to the mechanism postulated for electrical conductivity above the percolation threshold, namely, motion of counterions through transient water tubes formed in the droplet clusters present in the systems. Finally, it is shown that simple electrical conductivity and water solubility measurements can yield of quantitative information about the investigated microemulsions.

  11. The Wzy O-antigen polymerase of Yersinia pseudotuberculosis O:2a has a dependence on the Wzz chain-length determinant for efficient polymerization.

    PubMed

    Kenyon, Johanna J; Reeves, Peter R

    2013-12-01

    Lipopolysaccharide is a major immunogenic structure for the pathogen Yersinia pseudotuberculosis, which contains the O-specific polysaccharide (OPS) that is presented on the cell surface. The OPS contains many repeats of the oligosaccharide O-unit and exhibits a preferred modal chain length that has been shown to be crucial for cell protection in Yersinia. It is well established that the Wzz protein determines the preferred chain length of the OPS, and in its absence, the polymerization of O units by the Wzy polymerase is uncontrolled. However, for Y. pseudotuberculosis, a wzz mutation has never been described. In this study, we examine the effect of Wzz loss in Y. pseudotuberculosis serotype O:2a and compare the lipopolysaccharide chain-length profile to that of Escherichia coli serotype O111. In the absence of Wzz, the lipopolysaccharides of the two species showed significant differences in Wzy polymerization. Yersinia pseudotuberculosis O:2a exhibited only OPS with very short chain lengths, which is atypical of wzz-mutant phenotypes that have been observed for other species. We hypothesise that the Wzy polymerase of Y. pseudotuberculosis O:2a has a unique default activity in the absence of the Wzz, revealing the requirement of Wzz to drive O-unit polymerization to greater lengths.

  12. Investigation of the structure of anti-human seminal plasma protein single-chain antibody and its association with linker peptide length.

    PubMed

    Jiang, Xin; Zhai, Jun; Song, Dongkui; Qu, Qingshan; Li, Ming; Xing, Li; Miao, Shuzhai

    2015-09-01

    To enhance the activity of seminoprotein single‑chain variable fragment (γ‑Sm‑ScFv) antibodies, modulation of the length of the linker peptide, which connects the variable region of the heavy chain (VH) and the light chain (VL) of single‑chain antibodies, was performed in the present study. Homologous modeling of single VH and VL were performed, respectively. Subsequently, modeling of the whole ScFv sequence, which was previously modified with added linkers of different lengths was also performed, and the (Gly4Ser)n peptide chain structure was used as the linker. The similarities between VH and VL prior to and following the addition of the linker were compared by applying the algorithm of protein similarity, based on spherical coordinates layering. In addition, changes in the fore and aft distance, and diffusion radius were calculated using a MATLAB tool, based on which changes in structural stability were analyzed. Finally, the single‑chain antibody was assessed in a nude mouse model. When n=3 or n=6, the similarity between the original distance and VH and VL were the highest, and the fore and aft distance and diffusion radius were relatively close. In addition, the nude mouse model indicated that, when n=3 or n=6, the inhibitory rate of the single‑chain antibody against tumor cells was significantly higher, compared with the other linker peptides of different lengths. The effect of structural changes of the linker peptides in the single‑chain antibodies on the whole antibody molecule was examined at different levels using a combination of mathematical modeling, bioinformatics methods and biological experiments. The findings of the present study may provide a foundation for further investigation into the preparation of single‑chain antibodies.

  13. Biosynthesis of medium-chain-length poly(3-hydroxyalkanoates) by volatile aromatic hydrocarbons-degrading Pseudomonas fulva TY16.

    PubMed

    Ni, Yu-Yang; Kim, Do Young; Chung, Moon Gyu; Lee, Sun Hee; Park, Ho-Yong; Rhee, Young Ha

    2010-11-01

    Pseudomonas fulva TY16 biosynthesized medium-chain-length poly(3-hydroxyalkanoates) (MCL-PHAs) containing unsaturated 3-hydroxydodecenoate unit (approximately 8-9%) when grown with volatile aromatic compounds including benzene, toluene, and ethylbenzene as sole carbon substrate. In particular, when cultivated using a continuous feeding system designed to supply toluene at a flow rate of 0.42gL(-1)h(-1) into a 7-L jar fermentor, the growth of the organism reached up to approximately 3.87gL(-1) after the 48h fed-batch fermentation, representing an accumulated cellular MCL-PHA of 58.9% by weight. The obtained MCL-PHA was a copolyester primarily consisting of 3-hydroxydecanoate (55.2%) and 3-hydroxyoctanoate (26.8%) with minor constituents being 3-hydroxyhexanoate (3.7%), 3-hydroxydodecenoate (8.2%), and 3-hydroxydodecanoate (6.1%). The present results suggest that P. fulva TY16 is a promising candidate for the biotechnological conversion of toxic petrochemical wastes to valuable biopolymers.

  14. Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli.

    PubMed

    Dekishima, Yasumasa; Lan, Ethan I; Shen, Claire R; Cho, Kwang Myung; Liao, James C

    2011-08-03

    An Escherichia coli strain was engineered to synthesize 1-hexanol from glucose by extending the coenzyme A (CoA)-dependent 1-butanol synthesis reaction sequence catalyzed by exogenous enzymes. The C4-acyl-CoA intermediates were first synthesized via acetyl-CoA acetyltransferase (AtoB), 3-hydroxybutyryl-CoA dehydrogenase (Hbd), crotonase (Crt), and trans-enoyl-CoA reductase (Ter) from various organisms. The butyryl-CoA synthesized was further extended to hexanoyl-CoA via β-ketothiolase (BktB), Hbd, Crt, and Ter. Finally, hexanoyl-CoA was reduced to yield 1-hexanol by aldehyde/alcohol dehydrogenase (AdhE2). Enzyme activities for the C6 intermediates were confirmed by assays using HPLC and GC. 1-Hexanol was secreted to the fermentation medium under anaerobic conditions. Furthermore, co-expressing formate dehydrogenase (Fdh) from Candida boidinii increased the 1-hexanol titer. This demonstration of 1-hexanol production by extending the 1-butanol pathway provides the possibility to produce other medium chain length alcohols using the same strategy.

  15. Effect of ion-chelating chain lengths in thiophene-based monomers on in situ photoelectrochemical polymerization and photovoltaic performances.

    PubMed

    Song, In Young; Kim, Minjun; Park, Taiho

    2015-06-03

    We synthesized thiophene-based monomers (bis-EDOTs) with different ethylene glycol oligomer (EGO) lengths (TBO3, TBO4, and TBO5) and investigated their polymerization characteristics during photoelectrochemical polymerization (PEP) at the surfaces of dye (D205)-sensitized TiO2 nanocrystalline particles. During the PEP reaction, monomers were expected to diffuse toward neighboring dyes through the growing polymer layers to enable continuous chain growth. We found that the less bulky monomer (TBO3) formed a more compact polymer layer with a high molecular weight. Its diffusion to the active sites through the resulting growing polymer layer was, therefore, limited. We deployed layers of the polymers (PTBO3, PTBO4, and PTBO5) in iodine-free solid-state hybrid solar cells to investigate the lithium ion chelating properties of the polymers as a function of the number of oxygen atoms present in the EGOs. PTBO4 and PTBO5 were capable of chelating lithium ions, yielding a photovoltaic performance that was 142% of the performance obtained without the polymer layers (3.0→5.2%).

  16. Distinguishing Heterodera filipjevi and H. avenae using polymerase chain reaction-restriction fragment length polymorphism and cyst morphology.

    PubMed

    Yan, Guiping; Smiley, Richard W

    2010-03-01

    The cereal cyst nematodes Heterodera filipjevi and H. avenae impede wheat production in the Pacific Northwest (PNW). Accurate identification of cyst nematode species and awareness of high population density in affected fields are essential for designing effective control measures. Morphological methods for differentiating these species are laborious. These species were differentiated using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) of internal transcribed spacer (ITS)-ribosomal (r)DNA with up to six restriction endonucleases (TaqI, HinfI, PstI, HaeIII, RsaI, and AluI). The method was validated by inspecting underbridge structures of cyst vulval cones. Grid soil sampling of an Oregon field infested by both species revealed that H. filipjevi was present at most of the infested grid sites but mixtures of H. avenae and H. filipjevi also occurred. These procedures also detected and differentiated H. filipjevi and H. avenae in soil samples from nearby fields in Oregon and H. avenae in samples from Idaho and Washington. Intraspecific polymorphism was not observed within H. filipjevi or PNW H. avenae populations based on the ITS-rDNA. However, intraspecific variation was observed between H. avenae populations occurring in the PNW and France. Methods described here will improve detection and identification efficiencies for cereal cyst nematodes in wheat fields.

  17. Medium-chain-length poly-3-hydroxyalkanoates-carbon nanotubes composite anode enhances the performance of microbial fuel cell.

    PubMed

    Hindatu, Y; Annuar, M S M; Subramaniam, R; Gumel, A M

    2017-03-25

    Insufficient power generation from a microbial fuel cell (MFC) hampers its progress towards utility-scale development. Electrode modification with biopolymeric materials could potentially address this issue. In this study, medium-chain-length poly-3-hydroxyalkanoates (PHA)/carbon nanotubes (C) composite (CPHA) was successfully applied to modify the surface of carbon cloth (CC) anode in MFC. Characterization of the functional groups on the anodic surface and its morphology was carried out. The CC-CPHA composite anode recorded maximum power density of 254 mW/m(2), which was 15-53% higher than the MFC operated with CC-C (214 mW/m(2)) and pristine CC (119 mW/m(2)) as the anode in a double-chambered MFC operated with Escherichia coli as the biocatalyst. Electrochemical impedance spectroscopy and cyclic voltammetry showed that power enhancement was attributed to better electron transfer capability by the bacteria for the MFC setup with CC-CPHA anode.

  18. Detection and differentiation of filarial parasites by universal primers and polymerase chain reaction-restriction fragment length polymorphism analysis.

    PubMed

    Nuchprayoon, Surang; Junpee, Alisa; Poovorawan, Yong; Scott, Alan L

    2005-11-01

    Filarial nematode parasites are a serious cause of morbidity in humans and animals. Identification of filarial infection using traditional morphologic criteria can be difficult and lead to misdiagnosis. We report on a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based method to detect and differentiate a broad range of filarial species in a single PCR. The first internal transcribed spacer 1 (ITS1) along with the flanking 18S and 5.8S ribosomal DNA (rDNA) were isolated and cloned from Wuchereria bancrofti, Brugia malayi, and Brugia pahangi. Sequence analysis identified conserved sites in the 18S and 5.8S rDNA sequence that could be used as universal priming sites to generate ITS1-distinctive PCR products that were useful for distinguishing filariae at the genus level. The addition of a digestion of the ITS1 PCR product with the restriction endonuclease Ase I generated a fragment profile that allowed differentiation down to the species level for W. bancrofti, B. malayi, B. pahangi, Dirofilaria immitis, and D. repens. The PCR-RFLP of ITS1 rDNA will be useful in diagnosing and differentiating filarial parasites in human, animal reservoir hosts, and mosquito vectors in disease-endemic areas.

  19. Molecular Epidemiology of Leptospirosis in Northern Iran by Nested Polymerase Chain Reaction/Restriction Fragment Length Polymorphism and Sequencing Methods

    PubMed Central

    Zakeri, Sedigheh; Sepahian, Neda; Afsharpad, Mandana; Esfandiari, Behzad; Ziapour, Peyman; Djadid, Navid D.

    2010-01-01

    This study was conducted to investigate the prevalence of Leptospira species in Mazandaran Province of Iran by using nested polymerase chain reaction (PCR)/restriction fragment length polymorphism (RFLP) methods and sequencing analysis. Blood samples (n = 119) were collected from humans suspected of having leptospirosis from different parts of the province in 2007. By using an indirect immunofluorescent antibody test (IFAT), we determined that 35 (29.4%) of 119 suspected cases had leptospiral antibody titers ≥ 1:80, which confirmed the diagnosis of leptospirosis. Nested PCR assay also determined that 60 (50.4%) of 119 samples showed Leptospira infection. Furthermore, 44 (73.3%) of 60 confirmed leptospirosis amplified products were subjected to sequencing analysis. Sequence alignment identified L. interrogans, L. kirschneri, and L. wolffii species. All positive cases diagnosed by IFAT or PCR were in patients who reported contact with animals, high-risk occupational activities, and exposure to contaminated water. Therefore, it is important to increase attention about this disease among physicians and to strengthen laboratory capacity for its diagnosis in infected patients in Iran. PMID:20439973

  20. Structural basis of substrate selectivity of Δ(1)-pyrroline-5-carboxylate dehydrogenase (ALDH4A1): semialdehyde chain length.

    PubMed

    Pemberton, Travis A; Tanner, John J

    2013-10-01

    The enzyme Δ(1)-pyrroline-5-carboxylate (P5C) dehydrogenase (aka P5CDH and ALDH4A1) is an aldehyde dehydrogenase that catalyzes the oxidation of γ-glutamate semialdehyde to l-glutamate. The crystal structures of mouse P5CDH complexed with glutarate, succinate, malonate, glyoxylate, and acetate are reported. The structures are used to build a structure-activity relationship that describes the semialdehyde carbon chain length and the position of the aldehyde group in relation to the cysteine nucleophile and oxyanion hole. Efficient 4- and 5-carbon substrates share the common feature of being long enough to span the distance between the anchor loop at the bottom of the active site and the oxyanion hole at the top of the active site. The inactive 2- and 3-carbon semialdehydes bind the anchor loop but are too short to reach the oxyanion hole. Inhibition of P5CDH by glyoxylate, malonate, succinate, glutarate, and l-glutamate is also examined. The Ki values are 0.27 mM for glyoxylate, 58 mM for succinate, 30 mM for glutarate, and 12 mM for l-glutamate. Curiously, malonate is not an inhibitor. The trends in Ki likely reflect a trade-off between the penalty for desolvating the carboxylates of the free inhibitor and the number of compensating hydrogen bonds formed in the enzyme-inhibitor complex.

  1. Antibacterial Low Molecular Weight Cationic Polymers: Dissecting the Contribution of Hydrophobicity, Chain Length and Charge to Activity.

    PubMed

    Grace, James L; Huang, Johnny X; Cheah, Soon-Ee; Truong, Nghia P; Cooper, Matthew A; Li, Jian; Davis, Thomas P; Quinn, John F; Velkov, Tony; Whittaker, Michael R

    2016-01-01

    The balance of cationicity and hydrophobicity can profoundly affect the performance of antimicrobial polymers. To this end a library of 24 cationic polymers with uniquely low degrees of polymerization was synthesized via Cu(0)-mediated polymerization, using three different cationic monomers and two initiators: providing two different hydrocarbon chain tail lengths (C2 and C12). The polymers exhibited structure-dependent antibacterial activity when tested against a selection of bacteria, viz, Staphylococcus aureus ATCC 29213, Klebsiella pneumoniae ATCC 13883, Acinetobacter baumannii ATCC 19606, and Pseudomonas aeruginosa ATCC 27853 as a representative palette of Gram-positive and Gram-negative ESKAPE pathogens. The five best-performing polymers were identified for additional testing against the polymyxin-resistant A. baumannii ATCC 19606R strain. Polymers having the lowest DP and a C12 hydrophobic tail were shown to provide the broadest antimicrobial activity against the bacteria panel studied as evidenced by lower minimum inhibitory concentrations (MICs). An optimal polymer composition was identified, and its mechanism of action investigated via membrane permeability testing against Escherichia coli. Membrane disruption was identified as the most probable mechanism for bacteria cell killing.

  2. Taxonomic and ecological discrimination of Fagaceae species based on internal transcribed spacer polymerase chain reaction-restriction fragment length polymorphism.

    PubMed

    Coutinho, João Paulo; Carvalho, Ana; Lima-Brito, José

    2014-11-26

    The internal transcribed spacer (ITS) of ribosomal DNA has been used to confirm taxonomic classifications and define phylogenies in several plant species following sequencing or polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) techniques. In this study, co-dominant ITS PCR-RFLP molecular markers were produced in 30 Fagaceae individuals belonging to the Castanea, Fagus and Quercus genera in order to assess the potential of this technique for taxonomic discrimination and determination of phylogenies. The complete ITS region (ITS1-5.8S rRNA-ITS2) was amplified in most of the Fagaceae individuals as a single fragment of ∼700 bp. The ITS amplified products were digested with nine restriction enzymes, but only four (HaeIII, HpaII, TaqI and Sau96I) produced polymorphic/discriminative patterns. The total expected heterozygosity (HE) was 20.31 % and the gene diversity (I), 32.97 %. The ITS polymorphism was higher within the Quercus genus (85.3 %). The ITS PCR-RFLP markers clustered the Fagaceae species according to genus or infrageneric group (in the case of Quercus sp. individuals). Five oaks did not cluster in line with the adopted infrageneric classification, but three of these were grouped according to their actual ecological distributions. The ITS PCR-RFLP markers indicated their potential for phylogenetic studies since all Fagaceae individuals were discriminated according to genus, and most of the oaks were clustered according to infrageneric group or ecological area.

  3. Taxonomic and ecological discrimination of Fagaceae species based on internal transcribed spacer polymerase chain reaction–restriction fragment length polymorphism

    PubMed Central

    Coutinho, João Paulo; Carvalho, Ana; Lima-Brito, José

    2015-01-01

    The internal transcribed spacer (ITS) of ribosomal DNA has been used to confirm taxonomic classifications and define phylogenies in several plant species following sequencing or polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) techniques. In this study, co-dominant ITS PCR–RFLP molecular markers were produced in 30 Fagaceae individuals belonging to the Castanea, Fagus and Quercus genera in order to assess the potential of this technique for taxonomic discrimination and determination of phylogenies. The complete ITS region (ITS1-5.8S rRNA-ITS2) was amplified in most of the Fagaceae individuals as a single fragment of ∼700 bp. The ITS amplified products were digested with nine restriction enzymes, but only four (HaeIII, HpaII, TaqI and Sau96I) produced polymorphic/discriminative patterns. The total expected heterozygosity (HE) was 20.31 % and the gene diversity (I), 32.97 %. The ITS polymorphism was higher within the Quercus genus (85.3 %). The ITS PCR–RFLP markers clustered the Fagaceae species according to genus or infrageneric group (in the case of Quercus sp. individuals). Five oaks did not cluster in line with the adopted infrageneric classification, but three of these were grouped according to their actual ecological distributions. The ITS PCR–RFLP markers indicated their potential for phylogenetic studies since all Fagaceae individuals were discriminated according to genus, and most of the oaks were clustered according to infrageneric group or ecological area. PMID:25429047

  4. Limits of a rapid identification of common Mediterranean sandflies using polymerase chain reaction-restriction fragment length polymorphism

    PubMed Central

    Bounamous, Azzedine; Lehrter, Véronique; Hadj-Henni, Leila; Delecolle, Jean-Claude; Depaquit, Jérôme

    2014-01-01

    A total of 131 phlebotomine Algerian sandflies have been processed in the present study. They belong to the species Phlebotomus bergeroti, Phlebotomus alexandri, Phlebotomus sergenti, Phlebotomus chabaudi, Phlebotomus riouxi, Phlebotomus perniciosus, Phlebotomus longicuspis, Phlebotomus perfiliewi, Phlebotomus ariasi, Phlebotomus chadlii, Sergentomyia fallax, Sergentomyia minuta, Sergentomyia antennata, Sergentomyia schwetzi, Sergentomyia clydei, Sergentomyia christophersi and Grassomyia dreyfussi. They have been characterised by sequencing of a part of the cytochrome b (cyt b), t RNA serine and NADH1 on the one hand and of the cytochrome C oxidase I of the mitochondrial DNA (mtDNA) on the other hand. Our study highlights two sympatric populations within P. sergenti in the area of its type-locality and new haplotypes of P. perniciosus and P. longicuspis without recording the specimens called lcx previously found in North Africa. We tried to use a polymerase chain reaction-restriction fragment length polymorphism method based on a combined double digestion of each marker. These method is not interesting to identify sandflies all over the Mediterranean Basin. PMID:24936911

  5. Haplotyping the human T-cell receptor. beta. -chain gene complex by use of restriction fragment length polymorphisms

    SciTech Connect

    Charmley, P.; Chao, A.; Gatti, R.A. ); Concannon, P. ); Hood, L. )

    1990-06-01

    The authors have studied the genetic segregation of human T-cell receptor {beta}-chain (TCR{beta}) genes on chromosome 7q in 40 CEPH (Centre d'Etude du Polymorphisme Humain) families by using restriction fragment length polymorphisms (RFLPs). They constructed haplotypes from eight RFLPs by using variable- and constant-region cDNA probes, which detect polymorphisms that span more than 600 kilobases of the TCR{beta} gene complex. Analysis of allele distributions between TCR{beta} genes revealed significant linkage disequilibrium between only 6 of the 28 different pairs of RFLPs. This linkage disequilibrium strongly influences the most efficient order to proceed for typing of these RFLPs in order to achieve maximum genetic informativeness, which in this study revealed a 97.3% level of heterozygosity within the TCR{beta} gene complex. The results should provide new insight into recent reports of disease associations with the TCR{beta} gene complex and should assist in designing future experiments to detect or confirm the existence of disease-susceptibility loci in this region of the human genome.

  6. Improved Polymerase Chain Reaction-restriction Fragment Length Polymorphism Genotyping of Toxic Pufferfish by Liquid Chromatography/Mass Spectrometry

    PubMed Central

    Miyaguchi, Hajime

    2016-01-01

    An improved version of a polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method for genotyping toxic pufferfish species by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) is described. DNA extraction is carried out using a silica membrane-based DNA extraction kit. After the PCR amplification using a detergent-free PCR buffer, restriction enzymes are added to the solution without purifying the reaction solution. A reverse-phase silica monolith column and a Fourier transform high resolution mass spectrometer having a modified Kingdon trap analyzer are employed for separation and detection, respectively. The mobile phase, consisting of 400 mM 1,1,1,3,3,3-hexafluoro-2-propanol, 15 mM triethylamine (pH 7.9) and methanol, is delivered at a flow rate of 0.4 ml/min. The cycle time for LC/ESI-MS analysis is 8 min including equilibration of the column. Deconvolution software having an isotope distribution model of the oligonucleotide is used to calculate the corresponding monoisotopic mass from the mass spectrum. For analysis of oligonucleotides (range 26-79 nucleotides), mass accuracy was 0.62 ± 0.74 ppm (n = 280) and excellent accuracy and precision were sustained for 180 hr without use of a lock mass standard. PMID:27684516

  7. Polymerase chain reaction-restriction fragment length polymorphism analysis: a simple method for species identification in food.

    PubMed

    Meyer, R; Höfelein, C; Lüthy, J; Candrian, U

    1995-01-01

    The polymerase chain reaction (PCR) technique was applied to meat species identification in marinated and heat-treated or fermented products and to the differentiation of closely related species. DNA was isolated from meat samples by using a DNA-binding resin and was subjected to PCR analysis. Primers used were complementary to conserved areas of the vertebrate mitochondrial cytochrome b (cytb) gene and yielded a 359 base-pair (bp) fragment, including a variable 307 bp region. Restriction endonuclease analysis based on sequence data of those fragments was used for differentiation among species. Restriction fragment length polymorphisms (RFLPs) were detected when pig, cattle, wild boar, buffalo, sheep, goat, horse, chicken, and turkey amplicons were cut with AluI, RsaI, TaqI, and HinfI. Analysis of sausages indicates the applicability of this approach to food products containing meat from 3 different species. The PCR-RFLP analytical method detected pork in heated meat mixtures with beef at levels below 1%, and the method was confirmed with porcine- and bovine-specific PCR assays by amplifying fragments of their growth hormone genes. Inter- and intraspecific differences of more than 22 animal species with nearly unknown cytb DNA sequences, including hoofed mammals (ungulates), and poultry were determined with PCR-RFLP typing by using 20 different endonucleases. This typing method allowed the discrimination of game meats, including stag, roe deer, chamois, moose, reindeer, kangaroo, springbok, and other antelopes in marinated and heat-treated products.

  8. Solar photothermochemical alkane reverse combustion.

    PubMed

    Chanmanee, Wilaiwan; Islam, Mohammad Fakrul; Dennis, Brian H; MacDonnell, Frederick M

    2016-03-08

    A one-step, gas-phase photothermocatalytic process for the synthesis of hydrocarbons, including liquid alkanes, aromatics, and oxygenates, with carbon numbers (Cn) up to C13, from CO2 and water is demonstrated in a flow photoreactor operating at elevated temperatures (180-200 °C) and pressures (1-6 bar) using a 5% cobalt on TiO2 catalyst and under UV irradiation. A parametric study of temperature, pressure, and partial pressure ratio revealed that temperatures in excess of 160 °C are needed to obtain the higher Cn products in quantity and that the product distribution shifts toward higher Cn products with increasing pressure. In the best run so far, over 13% by mass of the products were C5+ hydrocarbons and some of these, i.e., octane, are drop-in replacements for existing liquid hydrocarbons fuels. Dioxygen was detected in yields ranging between 64% and 150%. In principle, this tandem photochemical-thermochemical process, fitted with a photocatalyst better matched to the solar spectrum, could provide a cheap and direct method to produce liquid hydrocarbons from CO2 and water via a solar process which uses concentrated sunlight for both photochemical excitation to generate high-energy intermediates and heat to drive important thermochemical carbon-chain-forming reactions.

  9. Solar photothermochemical alkane reverse combustion

    PubMed Central

    Chanmanee, Wilaiwan; Islam, Mohammad Fakrul; Dennis, Brian H.; MacDonnell, Frederick M.

    2016-01-01

    A one-step, gas-phase photothermocatalytic process for the synthesis of hydrocarbons, including liquid alkanes, aromatics, and oxygenates, with carbon numbers (Cn) up to C13, from CO2 and water is demonstrated in a flow photoreactor operating at elevated temperatures (180–200 °C) and pressures (1–6 bar) using a 5% cobalt on TiO2 catalyst and under UV irradiation. A parametric study of temperature, pressure, and partial pressure ratio revealed that temperatures in excess of 160 °C are needed to obtain the higher Cn products in quantity and that the product distribution shifts toward higher Cn products with increasing pressure. In the best run so far, over 13% by mass of the products were C5+ hydrocarbons and some of these, i.e., octane, are drop-in replacements for existing liquid hydrocarbons fuels. Dioxygen was detected in yields ranging between 64% and 150%. In principle, this tandem photochemical–thermochemical process, fitted with a photocatalyst better matched to the solar spectrum, could provide a cheap and direct method to produce liquid hydrocarbons from CO2 and water via a solar process which uses concentrated sunlight for both photochemical excitation to generate high-energy intermediates and heat to drive important thermochemical carbon-chain-forming reactions. PMID:26903631

  10. Effect of the polymer chain length of poly(N-isopropylacrylamide) on the temperature-responsive phase transition behavior of its conjugates with [60]fullerene.

    PubMed

    Uchida, Katsumi; Tamura, Atsushi; Yajima, Hirofumi

    2010-03-01

    In order to develop biomedical materials with specific functionalities, thermoresponsive conjugates [poly(N-isopropylacrylamide)-C(60) (PIPAAm-C(60)) ]of [60]fullerene (C(60)) and PIPAAm with two different polymer chain lengths (4 and 20 kDa) were synthesized by atom transfer radical polymerization. The effects of the polymer chain length on the temperature-responsive phase transition behavior of the synthetic PIPAAm-C(60) conjugates were probed by means of various physicochemical techniques. The coexistence of unimers and molecular assemblies of PIPAAm-C(60) was observed by gel permeation chromatography and dynamic light scattering studies in two PIPAAm-C(60) aqueous solutions below their lower critical solution temperatures (LCSTs). Additionally, below their LCSTs, differences in PIPAAm chain length gave rise to changes in the composition of the unimers and molecular assemblies. In response to temperature, the absorbance of the PIPAAm-C(60) aqueous solution changed according to a two-step behavior profile. Increasing temperature during the primary stage, where a change in the absorbance of the PIPAAm-C(60) aqueous solution took place, did not change the transition temperature, regardless of the solution concentration of PIPAAm-C(60). This absorbance change was associated with the phase transition of the molecular assemblies of PIPAAm-C(60). However, at the second stage, the transition temperature shifted to a higher value with the decrease in the concentration of PIPAAm-C(60), in the same manner as free PIPAAm chains. The second change was associated with the phase transition of the unimeric PIPAAm-C(60). Differences in PIPAAm chain length gave rise to the change in the phase transition behavior of PIPAAm-C(60) aqueous solution. Therefore, the chain length of PIPAAm was found to be a predominant factor involved in the solution characteristics of PIPAAm-C(60). Consequently, the PIPAAm-C(60) is expected to be an intelligent biomaterial possessing heat

  11. Binding of cationic pentapeptides with modified side chain lengths to negatively charged lipid membranes: Complex interplay of electrostatic and hydrophobic interactions.

    PubMed

    Hoernke, Maria; Schwieger, Christian; Kerth, Andreas; Blume, Alfred

    2012-07-01

    Basic amino acids play a key role in the binding of membrane associated proteins to negatively charged membranes. However, side chains of basic amino acids like lysine do not only provide a positive charge, but also a flexible hydrocarbon spacer that enables hydrophobic interactions. We studied the influence of hydrophobic contributions to the binding by varying the side chain length of pentapeptides with ammonium groups starting with lysine to lysine analogs with shorter side chains, namely omithine (Orn), alpha, gamma-diaminobutyric acid (Dab) and alpha, beta-diaminopropionic acid (Dap). The binding to negatively charged phosphatidylglycerol (PG) membranes was investigated by calorimetry, FT-infrared spectroscopy (FT-IR) and monolayer techniques. The binding was influenced by counteracting and sometimes compensating contributions. The influence of the bound peptides on the lipid phase behavior depends on the length of the peptide side chains. Isothermal titration calorimetry (ITC) experiments showed exothermic and endothermic effects compensating to a different extent as a function of side chain length. The increase in lipid phase transition temperature was more significant for peptides with shorter side chains. FTIR-spectroscopy revealed changes in hydration of the lipid bilayer interface after peptide binding. Using monolayer techniques, the contributions of electrostatic and hydrophobic effects could clearly be observed. Peptides with short side chains induced a pronounced decrease in surface pressure of PG monolayers whereas peptides with additional hydrophobic interactions decreased the surface pressure much less or even lead to an increase, indicating insertion of the hydrophobic part of the side chain into the lipid monolayer.

  12. A process for microbial hydrocarbon synthesis: Overproduction of fatty acids in Escherichia coli and catalytic conversion to alkanes.

    PubMed

    Lennen, Rebecca M; Braden, Drew J; West, Ryan A; Dumesic, James A; Pfleger, Brian F

    2010-06-01

    The development of renewable alternatives to diesel and jet fuels is highly desirable for the heavy transportation sector, and would offer benefits over the production and use of short-chain alcohols for personal transportation. Here, we report the development of a metabolically engineered strain of Escherichia coli that overproduces medium-chain length fatty acids via three basic modifications: elimination of beta-oxidation, overexpression of the four subunits of acetyl-CoA carboxylase, and expression of a plant acyl-acyl carrier protein (ACP) thioesterase from Umbellularia californica (BTE). The expression level of BTE was optimized by comparing fatty acid production from strains harboring BTE on plasmids with four different copy numbers. Expression of BTE from low copy number plasmids resulted in the highest fatty acid production. Up to a seven-fold increase in total fatty acid production was observed in engineered strains over a negative control strain (lacking beta-oxidation), with a composition dominated by C(12) and C(14) saturated and unsaturated fatty acids. Next, a strategy for producing undecane via a combination of biotechnology and heterogeneous catalysis is demonstrated. Fatty acids were extracted from a culture of an overproducing strain into an alkane phase and fed to a Pd/C plug flow reactor, where the extracted fatty acids were decarboxylated into saturated alkanes. The result is an enriched alkane stream that can be recycled for continuous extractions. Complete conversion of C(12) fatty acids extracted from culture to alkanes has been demonstrated yielding a concentration of 0.44 g L(-1) (culture volume) undecane.

  13. A Process for Microbial Hydrocarbon Synthesis: Overproduction of Fatty Acids in Escherichia coli and Catalytic Conversion to Alkanes

    PubMed Central

    Lennen, Rebecca M.; Braden, Drew J.; West, Ryan M.; Dumesic, James A.; Pfleger, Brian F.

    2013-01-01

    The development of renewable alternatives to diesel and jet fuels is highly desirable for the heavy transportation sector, and would offer benefits over the production and use of short-chain alcohols for personal transportation. Here, we report the development of a metabolically engineered strain of Escherichia coli that overproduces medium-chain length fatty acids via three basic modifications: elimination of β-oxidation, overexpression of the four subunits of acetyl-CoA carboxylase, and expression of a plant acyl–acyl carrier protein (ACP) thioesterase from Umbellularia californica (BTE). The expression level of BTE was optimized by comparing fatty acid production from strains harboring BTE on plasmids with four different copy numbers. Expression of BTE from low copy number plasmids resulted in the highest fatty acid production. Up to a seven-fold increase in total fatty acid production was observed in engineered strains over a negative control strain (lacking β-oxidation), with a composition dominated by C12 and C14 saturated and unsaturated fatty acids. Next, a strategy for producing undecane via a combination of biotechnology and heterogeneous catalysis is demonstrated. Fatty acids were extracted from a culture of an overproducing strain into an alkane phase and fed to a Pd/C plug flow reactor, where the extracted fatty acids were decarboxylated into saturated alkanes. The result is an enriched alkane stream that can be recycled for continuous extractions. Complete conversion of C12 fatty acids extracted from culture to alkanes has been demonstrated yielding a concentration of 0.44 g L−1 (culture volume) undecane. PMID:20073090

  14. Influence of polyethylene glycol chain length on compatibility and release characteristics of ternary solid dispersions of itraconazole in polyethylene glycol/hydroxypropylmethylcellulose 2910 E5 blends.

    PubMed

    Janssens, Sandrien; Denivelle, Samgar; Rombaut, Patrick; Van den Mooter, Guy

    2008-10-02

    The present study aims to elucidate the influence of the polyethylene glycol chain length on the miscibility of PEG/HPMC 2910 E5 polymer blends, the influence of polymer compatibility on the degree of molecular dispersion of itraconazole, and in vitro dissolution. PEG 2000, 6000, 10,000 and 20,000 were included in the study. Solid dispersions were prepared by spray drying and characterized with MDSC, XRPD and in vitro dissolution testing. The polymer miscibility increased with decreasing chain length due to a decrease in the Gibbs free energy of mixing. Recrystallization of itraconazole occurred as soon as a critical temperature of ca. 75 degrees C was reached for the glass transition that represents the ternary amorphous phase. Due to the lower miscibility degree between the longer PEG types and HPMC 2910 E5, the ternary amorphous phase was further separated, leading to a more rapid decrease of the ternary amorphous phase glass transition as a function of PEG and itraconazole weight percentage and hence, itraconazole recrystallization. In terms of release, an advantage of the shorter chain length PEG types (2000, 6000) over the longer chain length PEG types (10,000, 20,000) was observed for the polymer blends with 5% of PEG with respect to the binary itraconazole/HPMC 2910 E5 solid dispersion. Among the formulations with a 15/85 (w/w) PEG/HPMC 2910 E5 ratio on the other hand, there was no difference in the release profile.

  15. Regulation of pyruvate dehydrogenase during infusion of fatty acids of varying chain lengths in the perfused rat heart.

    PubMed

    Latipää, P M; Peuhkurinen, K J; Hiltunen, J K; Hassinen, I E

    1985-12-01

    The effects of a homologous series of fatty acids with a chain length of two to eight on the rate of pyruvate oxidation and covalent interconversions of the pyruvate dehydrogenase complex (PDH) were studied in isolated perfused rat hearts. In the Langendorff-perfused heart beating at 5 Hz against an aortic pressure of 59 mmHg (7.85 kPa), a positive linear correlation was found between the fraction of PDH existing in the active non-phosphorylated form of pyruvate dehydrogenase complex (PDHa) and the pyruvate oxidation rate until the PDHa fraction increased to 48%. This value resulted in a saturation of the citric acid cycle and further activation did not increase the metabolic flux. The PDHa content of the tissue was higher during infusion of odd carbon number fatty acids than during infusion of even carbon number fatty acids. Propionate caused an almost maximal (93%) activation of PDH. A negative correlation was found between the mitochondrial NADH/NAD+ ratio and the PDHa content. A negative correlation was also found between the acetyl-CoA/CoA ratio and the tissue PDHa content. The rate of labelled CO2 production, the specific radioactivity of tissue alanine and the metabolic balance sheet demonstrated that the alanine aminotransferase reaction in the total tissue does not reach equilibrium with the mitochondrial pyruvate pool during propionate oxidation, but the equilibrium is reached during the oxidation of even-number carbon fatty acids. This suggests that pyruvate is formed from propionate-derived metabolites also in the cytosol, although the primary metabolism of propionate occurs in the mitochondria. The results indicate that the rate of pyruvate oxidation in the myocardium is mainly regulated by covalent interconversion of PDH. During propionate oxidation the PDHa content in the tissue can increase beyond the point of saturation of the citric acid cycle and this indicates that feedback inhibition of the enzyme is rate-determining under these conditions.

  16. Process analysis of the conversion of styrene to biomass and medium chain length polyhydroxyalkanoate in a two-phase bioreactor.

    PubMed

    Nikodinovic-Runic, Jasmina; Casey, Eoin; Duane, Gearoid F; Mitic, Dragana; Hume, Aisling R; Kenny, Shane T; O'Connor, Kevin E

    2011-10-01

    The improvement and modeling of a process for the supply of the volatile aromatic hydrocarbon, styrene, to a fermentor for increased biomass production of the medium chain length polyhydroxyalkanoate (mcl-PHA) accumulating bacterium Pseudomonas putida CA-3 was investigated. Fed-batch experiments were undertaken using different methods to provide the styrene. Initial experiments where styrene was supplied as a liquid to the bioreactor had detrimental effects on cell growth and inhibited PHA polymer accumulation. By changing the feed of gaseous styrene to liquid styrene through the air sparger a 5.4-fold increase in cell dry-weight was achieved (total of 10.56 g L(-1)) which corresponds to a fourfold improvement in PHA production (3.36 g L(-1)) compared to previous studies performed in our laboratory (0.82 g L(-1)). In addition this final improved feeding strategy reduced the release of styrene from the fermentor 50-fold compared to initial experiments (0.12 mL total styrene released per 48 h run). An unstructured kinetic model was developed to describe cell growth along with substrate and oxygen utilization. The formation of dispersed gas (air) and liquid (styrene) phases in the medium and the transfer of styrene between the aqueous and dispersed liquid droplet phases was also modeled. The model provided a detailed description of these phase transitions and helped explain how the feeding strategy led to improved process performance in terms of final biomass levels. It also highlighted the key factors to be considered during further process improvement.

  17. Effects of quaternary ammonium chain length on the antibacterial and remineralizing effects of a calcium phosphate nanocomposite

    PubMed Central

    Zhang, Ke; Cheng, Lei; Weir, Michael D; Bai, Yu-Xing; Xu, Hockin HK

    2016-01-01

    Composites containing nanoparticles of amorphous calcium phosphate (NACP) remineralize tooth lesions and inhibit caries. A recent study synthesized quaternary ammonium methacrylates (QAMs) with chain lengths (CLs) of 3–18 and determined their effects on a bonding agent. This study aimed to incorporate these QAMs into NACP nanocomposites for the first time to simultaneously endow the material with antibacterial and remineralizing capabilities and to investigate the effects of the CL on the mechanical and biofilm properties. Five QAMs were synthesized: DMAPM (CL3), DMAHM (CL6), DMADDM (CL12), DMAHDM (CL16), and DMAODM (CL18). Each QAM was incorporated into a composite containing 20% NACP and 50% glass fillers. A dental plaque microcosm biofilm model was used to evaluate the antibacterial activity. The flexural strength and elastic modulus of nanocomposites with QAMs matched those of a commercial control composite (n = 6; P > 0.1). Increasing the CL from 3 to 16 greatly enhanced the antibacterial activity of the NACP nanocomposite (P < 0.05); further increasing the CL to 18 decreased the antibacterial potency. The NACP nanocomposite with a CL of 16 exhibited biofilm metabolic activity and acid production that were 10-fold lesser than those of the control composite. The NACP nanocomposite with a CL of 16 produced 2-log decreases in the colony-forming units (CFU) of total microorganisms, total streptococci, and mutans streptococci. In conclusion, QAMs with CLs of 3–18 were synthesized and incorporated into an NACP nanocomposite for the first time to simultaneously endow the material with antibacterial and remineralization capabilities. Increasing the CL reduced the metabolic activity and acid production of biofilms and caused a 2-log decrease in CFU without compromising the mechanical properties. Nanocomposites exhibiting strong anti-biofilm activity, remineralization effects, and mechanical properties are promising materials for tooth restorations that inhibit

  18. Effect of stereochemistry, chain length and sequence pattern on antimicrobial properties of short synthetic β-sheet forming peptide amphiphiles.

    PubMed

    Ong, Zhan Yuin; Cheng, Junchi; Huang, Yuan; Xu, Kaijin; Ji, Zhongkang; Fan, Weimin; Yang, Yi Yan

    2014-01-01

    In the face of mounting global antibiotics resistance, the identification and development of membrane-active antimicrobial peptides (AMPs) as an alternative class of antimicrobial agent have gained significant attention. The physical perturbation and disruption of microbial membranes by the AMPs have been proposed to be an effective means to overcome conventional mechanisms of drug resistance. Recently, we have reported the design of a series of short synthetic β-sheet folding peptide amphiphiles comprised of recurring (X1Y1X2Y2)n-NH2 sequences where X: hydrophobic amino acids, Y: cationic amino acids and n: number of repeat units. In efforts to investigate the effects of key parameters including stereochemistry, chain length and sequence pattern on antimicrobial effects, systematic d-amino acid substitutions of the lead peptides (IRIK)2-NH2 (IK8-all L) and (IRVK)3-NH2 (IK12-all L) were performed. It was found that the corresponding D-enantiomers exhibited stronger antimicrobial activities with minimal or no change in hemolytic activities, hence translating very high selectivity indices of 407.0 and >9.8 for IK8-all D and IK12-all D respectively. IK8-all D was also demonstrated to be stable to degradation by broad spectrum proteases trypsin and proteinase K. The membrane disrupting bactericidal properties of IK8-all D effectively prevented drug resistance development and inhibited the growth of various clinically isolated MRSA, VRE, Acinetobacter baumanni, Pseudomonas aeruginosa, Cryptococcus. neoformans and Mycobacterium tuberculosis. Significant reduction in intracellular bacteria counts was also observed following treatment with IK8-all D in the Staphylococcus. aureus infected mouse macrophage cell line RAW264.7 (P < 0.01). These results suggest that the d-amino acids substituted β-sheet forming peptide IK8-all D with its enhanced antimicrobial activities and improved protease stability, is a promising therapeutic candidate with potential to combat

  19. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for rapid diagnosis of neonatal sepsis

    PubMed Central

    Rohit, Anusha; Maiti, Biswajit; Shenoy, Shalini; Karunasagar, Indrani

    2016-01-01

    Background & objectives: The difficulties in diagnosis of neonatal sepsis are due to varied clinical presentation, low sensitivity of blood culture which is considered the gold standard and empirical antibiotic usage affecting the outcome of results. Though polymerase chain reaction (PCR) based detection of bacterial 16S rRNA gene has been reported earlier, this does not provide identification of the causative agent. In this study, we used restriction fragment length polymorphism (RFLP) of amplified 16S rRNA gene to identify the organisms involved in neonatal sepsis and compared the findings with blood culture. Methods: Blood samples from 97 neonates were evaluated for diagnosis of neonatal sepsis using BacT/Alert (automated blood culture) and PCR-RFLP. Results: Bacterial DNA was detected by 16S rRNA gene PCR in 55 cases, while BacT/Alert culture was positive in 34 cases. Staphylococcus aureus was the most common organism detected with both methods. Klebsiella spp. was isolated from four samples by culture but was detected by PCR-RFLP in five cases while Acinetobacter spp. was isolated from one case but detected in eight cases by PCR-RFLP. The sensitivity of PCR was found to be 82.3 per cent with a negative predictive value of 85.7 per cent. Eighty of the 97 neonates had prior exposure to antibiotics. Interpretation & conclusions: The results of our study demonstrate that PCR-RFLP having a rapid turnaround time may be useful for the early diagnosis of culture negative neonatal sepsis. PMID:26997017

  20. Lateral Chain Length in Polyalkyl Acrylates Determines the Mobility of Fibronectin at the Cell/Material Interface

    PubMed Central

    2015-01-01

    Cells, by interacting with surfaces indirectly through a layer of extracellular matrix proteins, can respond to a variety of physical properties, such as topography or stiffness. Polymer surface mobility is another physical property that is less well understood but has been indicated to hold the potential to modulate cell behavior. Polymer mobility is related to the glass-transition temperature (Tg) of the system, the point at which a polymer transitions from an amorphous solid to a more liquid-like state. This work shows that changes in polymer mobility translate to interfacial mobility of extracellular matrix proteins adsorbed on the material surface. This study has utilized a family of polyalkyl acrylates with similar chemistry but different degrees of mobility, obtained through increasing length of the side chain. These materials are used, in conjunction with fluorescent fibronectin, to determine the mobility of this interfacial layer of protein that constitutes the initial cell–material interface. Furthermore, the extent of fibronectin domain availability (III9, III10, - the integrin binding site), cell-mediated reorganization, and cell differentiation was also determined. A nonmonotonic dependence of fibronectin mobility on polymer surface mobility was observed, with a similar trend noted in cell-mediated reorganization of the protein layer by L929 fibroblasts. The availability of the integrin-binding site was higher on the more mobile surfaces, where a similar organization of the protein into networks at the material interface was observed. Finally, differentiation of C2C12 myoblasts was seen to be highly sensitive to surface mobility upon inhibition of cell contractility. Altogether, these findings show that polymer mobility is a subtle influence that translates to the cell/material interface through the protein layer to alter the biological activity of the surface. PMID:26715432

  1. Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis.

    PubMed

    Samah, S; Valadez-Moctezuma, E; Peláez-Luna, K S; Morales-Manzano, S; Meza-Carrera, P; Cid-Contreras, R C

    2016-06-03

    Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc. We obtained 5850 bp from the seven regions, and 136 fragments were detected with eight enzymes, 37 of which (27.2%) were polymorphic. We found that 40% of the fragments from the chloroplast regions were polymorphic, 9.8% of the bands detected in the nuclear genes were polymorphic, and 20% of the bands in the mitochondrial locus were polymorphic. trnL-trnF and psbA-trnH were the most variable regions. The Nei and Li/Dice distance was very short, and ranged from 0 to 0.12; indeed, 77 of the 103 genotypes had the same genetic profile. All the xoconostle accessions (acidic fruits) were grouped together without being separated from three genotypes of prickly pear (sweet fruits). We assume that the genetic divergence between prickly pears and xoconostles is very low, and question the number of Opuntia species currently considered in Mexico.

  2. The Effect of Side-Chain Length on the Solid-State Structure and Optical Properties of F8BT: A DFT Study

    NASA Astrophysics Data System (ADS)

    Javad Eslamibidgoli, Mohammad; Lagowski, Jolanta B.

    2012-02-01

    Using the long-range corrected hybrid density functional theory (DFT/B97D) approach, we have performed bulk solid state calculations to investigate the influence of side-chain length on the molecular packing and optical properties of poly (9,9-di-n-octylfluorene-alt-benzothiadiazole) or F8BT. Two different packing structures, the lamellar and nearly hexagonal, were obtained corresponding to longer and shorter side-chains respectively. This behavior can be attributed to the micro-phase separations between the flexible side-chains and the rigid backbones and is in agreement with previous investigations for other hairy-rod polymers. In addition, as a result of the efficient inter-chain interactions for the lamellar structure, the dihedral angle between the F8 and BT units is reduced providing a more planar configuration for the backbone which leads to the decreased band gap (by 0.2-0.3 eV) in comparison to the hexagonal phase and the gas phase with no side-chain. Time-dependent DFT (TDDFT/B3LYP) was also used to study the excited states of the monomer of F8BT optimized in solid-state structures with different side-chain lengths. It is found that the absorption spectrum is red shifted for the polymers with lamellar structure relative to the polymers in hexagonal and gas phases.

  3. Oil-in-water microemulsions stabilized by 3-(N,N- dimethylalkylammonio)propanesulfonate surfactants of varying alkyl chain length: solubilisation of testos-terone propionate.

    PubMed

    Hsieh, Chien-Ming; Warisnoicharoen, Warangkana; Patel, Raju K; Kianfar, Farnoosh; Lawrence, M Jayne

    2017-03-28

    Solubilisation of the poorly-water soluble drug, testosterone propionate, in co-surfactant-free, dilutable, oil-in-water microemulsions stabilized by zwitterionic surfactants of varying alkyl chain length, namely 3-(N,N-dimethyloctylammonio)propanesulfonate and 3-(N,N-dimethyldodecylammonio)propanesulfonate and containing one of four ethyl ester oils, has been investigated. Both 3-(N,N-dimethyloctylammonio)propanesulfonate and 3-(N,N-dimethyldodecylammonio)propanesulfonate-stabilized microemulsions containing two short chain length oils, ethyl butyrate and ethyl caprylate, while only 3-(N,N-dimethyldodecylammonio)propanesulfonate formed microemulsions incorporating the longer chain length oils, ethyl palmitate and ethyl oleate, albeit to a very much reduced extent. Significantly the microemulsions containing the short chain length oils, ethyl butyrate and ethyl caprylate solubilised more testosterone propionate than the corresponding micelles. However, an inverse correlation existed between testosterone propionate solubility in the bulk oil and solubilisation in the microemulsions, in that ethyl caprylate containing microemulsions solubilised more testosterone propionate than those containing an equivalent amount of ethyl butyrate, despite the drug being more soluble in ethyl butyrate. These results suggest that drug solubility in bulk oil is a poor indicator of drug solubility in microemulsions containing that oil, and whether or not the addition of oil improves drug solubility is dependent upon on how it is incorporated within the microemulsion. The longer the chain length of the oil, the more likely the oil is to form a core in the microemulsion droplet, resulting in an additional locus of drug solubilisation and the possibility of an enhanced solubilisation capacity.

  4. Degradation of alkanes by bacteria.

    PubMed

    Rojo, Fernando

    2009-10-01

    Pollution of soil and water environments by crude oil has been, and is still today, an important problem. Crude oil is a complex mixture of thousands of compounds. Among them, alkanes constitute the major fraction. Alkanes are saturated hydrocarbons of different sizes and structures. Although they are chemically very inert, most of them can be efficiently degraded by several microorganisms. This review summarizes current knowledge on how microorganisms degrade alkanes, focusing on the biochemical pathways used and on how the expression of pathway genes is regulated and integrated within cell physiology.

  5. Alkyl Chain Length and Temperature Effects on Structural Properties of Pyrrolidinium-Based Ionic Liquids: A Combined Atomistic Simulation and Small-Angle X-ray Scattering Study

    SciTech Connect

    Li, Song; Bañuelos, José Leobardo; Guo, Jianchang; Anovitz, Lawrence; Rother, Gernot; Shaw, Robert W.; Hillesheim, Patrick C.; Dai, Sheng; Baker, Gary A.; Cummings, Peter T.

    2011-12-21

    Molecular dynamics (MD) simulations of 1-alkyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([CnMPy][Tf₂N], n = 3, 4, 6, 8, 10) were conducted using an all-atom model. Radial distribution functions (RDF) were computed and structure functions were generated to compare with new X-ray scattering experimental results, reported herein. The scattering peaks in the structure functions generally shift to lower Q values with increased temperature for all the liquids in this series. However, the first sharp diffraction peak (FSDP) in the longer alkyl chain liquids displays a marked shift to higher Q values with increasing temperature. Alkyl chain-dependent ordering of the polar groups and increased tail aggregation with increasing alkyl chain length were observed in the partial pair correlation functions and the structure functions. The reasons for the observed alkyl chain-dependent phenomena and temperature effects were explored.

  6. Alkyl Chain Length and Temperature Effects on Structural Properties of Pyrrolidinium-Based Ionic Liquids: A Combined Atomistic Simulation and Small-Angle X-ray Scattering Study.

    SciTech Connect

    Li, Song; Banuelos, Jose Leo; Guo, Jianchang; Anovitz, Lawrence {Larry} M; Rother, Gernot; Shaw, Robert W; Hillesheim, Patrick C; Dai, Sheng; Baker, Gary A; Cummings, Peter T

    2011-01-01

    Molecular dynamics (MD) simulations of 1-alkyl-1-methylpyrrolidinium 12 bis(trifluoromethanesulfonyl)imide ([CnMPy][Tf2N], n = 3, 4, 6, 8, 10) were conducted 13 using an all-atom model. Radial distribution functions (RDF) were computed and structure 14 functions were generated to compare with new X-ray scattering experimental results, 15 reported herein. The scattering peaks in the structure functions generally shift to lower Q 16 values with increased temperature for all the liquids in this series. However, the first sharp 17 diffraction peak (FSDP) in the longer alkyl chain liquids displays a marked shift to higher Q 18 values with increasing temperature. Alkyl chain-dependent ordering of the polar groups and 19 increased tail aggregation with increasing alkyl chain length were observed in the partial pair 20 correlation functions and the structure functions. The reasons for the observed alkyl chain- 21 dependent phenomena and temperature effects were explored.

  7. Modeling the Role of Alkanes, Polycyclic Aromatic Hydrocarbons, and Their Oligomers in Secondary Organic Aerosol Formation

    EPA Science Inventory

    A computationally efficient method to treat secondary organic aerosol (SOA) from various length and structure alkanes as well as SOA from polycyclic aromatic hydrocarbons (PAHs) is implemented in the Community Multiscale Air Quality (CMAQ) model to predict aerosol concentrations ...

  8. High Temperature Chemical Kinetic Combustion Modeling of Lightly Methylated Alkanes

    SciTech Connect

    Sarathy, S M; Westbrook, C K; Pitz, W J; Mehl, M

    2011-03-01

    Conventional petroleum jet and diesel fuels, as well as alternative Fischer-Tropsch (FT) fuels and hydrotreated renewable jet (HRJ) fuels, contain high molecular weight lightly branched alkanes (i.e., methylalkanes) and straight chain alkanes (n-alkanes). Improving the combustion of these fuels in practical applications requires a fundamental understanding of large hydrocarbon combustion chemistry. This research project presents a detailed high temperature chemical kinetic mechanism for n-octane and three lightly branched isomers octane (i.e., 2-methylheptane, 3-methylheptane, and 2,5-dimethylhexane). The model is validated against experimental data from a variety of fundamental combustion devices. This new model is used to show how the location and number of methyl branches affects fuel reactivity including laminar flame speed and species formation.

  9. Interatomic Lennard-Jones potentials of linear and branched alkanes calibrated by Gibbs ensemble simulations for vapor-liquid equilibria

    NASA Astrophysics Data System (ADS)

    Chang, Jaeeon; Sandler, Stanley I.

    2004-10-01

    We propose Lennard-Jones potential parameters for interatomic interactions of linear and branched alkanes based on matching the results of Gibbs ensemble simulations of vapor-liquid equilibria to experimental data. The alkane model is similar as in the OPLS-AA [W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 118, 11225 (1996)], but multiple atom types for carbon based on the number of covalently bonded hydrogen atoms are necessary to accurately reproduce liquid densities and enthalpies of vaporization with the errors of 2.1% and 3.3%, respectively, for hydrocarbons of various chain lengths and structures. We find that the attraction energies of the carbon atoms are almost proportional to the number of covalent hydrogen atoms with each increasing the carbon energy parameter by ≈0.033 kcal/mol. Though the present force field outperforms the OPLS-AA force field for alkanes we studied, systematic deviations for vapor pressures are still observed with errors of 15%-30%, and critical temperatures are slightly underestimated. We think that these shortcomings are probably due to the inadequacy of the two-parameter Lennard-Jones potential, and especially its behavior at short distances.

  10. Effects on the self-assembly of n-alkane/gold nanoparticle mixtures spread at the air-water interface.

    PubMed

    Gagnon, Brandon P; Meli, M-Vicki

    2014-01-14

    Nanoparticle films formed at the air-water interface readily form rigid films, where the nanoparticles irreversibly associate into floating "islands", often riddled with voids and defects, upon solvent evaporation. Improving the nanoparticle mobility in these films is key to achieving control over the nanoparticle packing parameters, which is attractive for a variety of applications. In this study, a variety of n-alkanes were mixed with tetradecanethiol-capped 2 nm gold nanoparticles and studied as Langmuir films at 18 and 32 °C. Pressure-area isotherms at 18 °C reveal a mixed liquid-expanded phase of nanoparticles and alkane at the air-water interface, but only for n-alkanes that are equal to or exceed the nanoparticle capping ligand in carbon chain length. Transmission electron microscopy images of the corresponding films suggest that the nanoparticles are mixed with a continuous hydrocarbon phase at 0 mN/m and that the hydrocarbon is squeezed out of the nanoparticle film during compression.

  11. DNA-directed alkylating agents. 3. Structure-activity relationships for acridine-linked aniline mustards: consequences of varying the length of the linker chain.

    PubMed

    Valu, K K; Gourdie, T A; Boritzki, T J; Gravatt, G L; Baguley, B C; Wilson, W R; Wakelin, L P; Woodgate, P D; Denny, W A

    1990-11-01

    Four series of acridine-linked aniline mustards have been prepared and evaluated for in vitro cytotoxicity, in vivo antitumor activity, and DNA cross-linking ability. The anilines were attached to the DNA-intercalating acridine chromophores by link groups (-O-, -CH2-, -S-, and -SO2-) of widely varying electronic properties, providing four series of widely differing mustard reactivity where the alkyl chain linking the acridine and mustard moieties was varied from two to five carbons. Relationships were sought between chain length and biological properties. Within each series, increasing the chain length did not alter the reactivity of the alkylating moiety but did appear to position it differently on the DNA, since cross-linking ability (measured by agarose gel assay) altered with chain length, being maximal with the C4 analogue. The in vivo antitumor activities of the compounds depended to some extent on the reactivity of the mustard, with the least reactive SO2 compounds being inactive. However, DNA-targeting did appear to allow the use of less reactive mustards, since the S-linked acridine mustards showed significant activity whereas the parent S-mustard did not. Within each active series, the most active compound was the C4 homologue, suggesting some relationship between activity and extent of DNA alkylation.

  12. Fabrication and tribological properties of self-assembled monolayer of n-alkyltrimethoxysilane on silicon: Effect of SAM alkyl chain length

    NASA Astrophysics Data System (ADS)

    Huo, Lixia; Du, Pengcheng; Zhou, Hui; Zhang, Kaifeng; Liu, Peng

    2017-02-01

    It is well known that the self-assembled organic molecules on a solid surface exhibit the friction-reducing performance. However, the effect of the molecular size of the self-assembled organic molecules has not been established. In the present work, self-assembled monolayers (SAMs) of n-alkyltrimethoxysilanes with different alkyl chain lengths (C6, C12, or C18) were fabricated on silicon substrate. The water contact angles of the SAMs increased from 26.8° of the hydroxylated silicon substrate to near 60° after self-assembly. The atomic force microscopy (AFM) analysis results showed that the mean roughness (Ra) of the SAMs decreased with increasing the alkyl chain length. The tribological properties of the SAMs sliding against Al2O3 ball were evaluated on an UMT-2 tribometer, and the worn surfaces of the samples were analyzed by means of Nano Scratch Tester and surface profilometry. It was found that lowest friction coefficient and smallest width of wear were achieved with the SAMs of C12 alkyl chain (C12-SAM). The superior friction reduction and wear resistance of the SAMs in comparison with the bare silicon substrate are attributed to good adhesion of the self-assembled films to the substrate, especially the C12-SAM with desirable alkyl chain length.

  13. Lack of activation of UCP1 in isolated brown adipose tissue mitochondria by glucose-O-ω-modified saturated fatty acids of various chain lengths.

    PubMed

    Breen, Eamon P; Pilgrim, Wayne; Clarke, Kieran J; Yssel, Cristy; Farrell, Mark; Zhou, Jian; Murphy, Paul V; Porter, Richard K

    2013-03-27

    We previously demonstrated that uncoupling protein 1 activity, as measured in isolated brown adipose tissue mitochondria (and as a native protein reconstituted into liposome membranes), was not activated by the non-flippable modified saturated fatty acid, glucose-O-ω-palmitate, whereas activity was stimulated by palmitate alone (40 nM free final concentration). In this study, we investigated whether fatty acid chain length had any bearing on the ability of glucose-O-ω-fatty acids to activate uncoupling protein 1. Glucose-O-ω-saturated fatty acids of various chain lengths were synthesized and tested for their potential to activate GDP-inhibited uncoupling protein 1-dependent oxygen consumption in brown adipose tissue mitochondria, and the results were compared with equivalent non-modified fatty acid controls. Here we demonstrate that laurate (12C), palmitate (16C) and stearate (18C) could activate GDP-inhibited uncoupling protein 1-dependent oxygen consumption in brown adipose tissue mitochondria, whereas there was no activation with glucose-O-ω-laurate (12C), glucose-O-ω-palmitate (16C), glucose-O-ω-stearate (18C), glucose-O-ω-arachidate (20C) or arachidate alone. We conclude that non-flippable fatty acids cannot activate uncoupling protein 1 irrespective of chain length. Our data further undermine the cofactor activation model of uncoupling protein 1 function but are compatible with the model that uncoupling protein 1 functions by flipping long-chain fatty acid anions.

  14. Size and chain length effects on structural behaviors of biphenylcyclohexane-based liquid crystal nanoclusters by a coarse-grained model.

    PubMed

    Liao, Ming-Liang; Ju, Shin-Pon; Chang, Chun-Yi; Huang, Wei-Lin

    2012-06-01

    Size and chain length effects on structural behaviors of liquid crystal nanoclusters were examined by a coarse-grained model and the configurational-bias Monte Carlo (CBMC) simulation. The nanoclusters investigated in this study are composed of the biphenylcyclohexane-based BCH5H liquid crystal molecule and its derivatives. Results of the study show that the average energy decreases (i.e., more negative) as the cluster size (i.e., the number of molecules) increases. With the increasing cluster size, the equilibrium conformation of the nanocluster changes gradually from a pipe-like structure (for the smaller systems) to a ball-like cluster (for the larger systems). The order parameter of the system reduces with the transition of the equilibrium conformation. Regarding the chain length effect, the pipe-like equilibrium conformation (for the smaller systems) was observed more close to a pipe as the length of the tail alkyl chain of the derivatives extended. However, due to the flexibility of the tail alkyl chain, the pipe conformation of the system deflects slightly about its cyclohexyl group as the tail extends further.

  15. Heat conduction in chain polymer liquids: molecular dynamics study on the contributions of inter- and intramolecular energy transfer.

    PubMed

    Ohara, Taku; Yuan, Tan Chia; Torii, Daichi; Kikugawa, Gota; Kosugi, Naohiro

    2011-07-21

    In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7T(c)), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water.

  16. Molecular characterization of extracellular medium-chain-length poly(3-hydroxyalkanoate) depolymerase genes from Pseudomonas alcaligenes strains.

    PubMed

    Kim, Do Young; Kim, Hyun Chul; Kim, Sun Young; Rhee, Young Ha

    2005-06-01

    A bacterial strain M4-7 capable of degrading various polyesters, such as poly(epsilon-caprolactone), poly(3-hydroxybutyrate-co-3-hydroxyvalerate), poly(3-hydroxyoctanoate), and poly(3-hydroxy-5-phenylvalerate), was isolated from a marine environment and identified as Pseudomonas alcaligenes. The relative molecular mass of a purified extracellular medium-chain-length poly(3-hydroxyalkanoate) (MCL-PHA) depolymerase (PhaZ(PalM4-7)) from P. alcaligenes M4-7 was 28.0 kDa, as determined by SDS-PAGE. The PhaZ(PalM4-7) was most active in 50 mM glycine-NaOH buffer (pH 9.0) at 35 degrees C. It was insensitive to dithiothreitol, sodium azide, and iodoacetamide, but susceptible to p-hydroxymercuribenzoic acid, N-bromosuccinimide, acetic anhydride, EDTA, diisopropyl fluorophosphate, phenylmethylsulfonyl fluoride, Tween 80, and Triton X-100. In this study, the genes encoding MCL-PHA depolymerase were cloned, sequenced, and characterized from a soil bacterium, P. alcaligenes LB19 (Kim et al., 2002, Biomacromolecules 3, 291-296) as well as P. alcaligenes M4-7. The structural gene (phaZ(PalLB19)) of MCL-PHA depolymerase of P. alcaligenes LB19 consisted of an 837 bp open reading frame (ORF) encoding a protein of 278 amino acids with a deduced M((r)) of 30,188 Da. However, the MCL-PHA depolymerase gene (phaZ(PalM4-7)) of P. alcaligenes M4-7 was composed of an 834 bp ORF encoding a protein of 277 amino acids with a deduced Mr of 30,323 Da. Amino acid sequence analyses showed that, in the two different polypeptides, a substrate-binding domain and a catalytic domain are located in the N-terminus and in the C-terminus, respectively. The PhaZ(PalLB19) and the PhaZ(PalM4-7) commonly share the lipase box, GISSG, in their catalytic domains, and utilize 111Asn and 110Ser residues, respectively, as oxyanions that play an important role in transition-state stabilization of hydrolytic reactions.

  17. Site-specific PEGylation of hemoglobin at Cys-93(beta): correlation between the colligative properties of the PEGylated protein and the length of the conjugated PEG chain.

    PubMed

    Manjula, B N; Tsai, A; Upadhya, R; Perumalsamy, K; Smith, P K; Malavalli, A; Vandegriff, K; Winslow, R M; Intaglietta, M; Prabhakaran, M; Friedman, J M; Acharya, A S

    2003-01-01

    Increasing the molecular size of acellular hemoglobin (Hb) has been proposed as an approach to reduce its undesirable vasoactive properties. The finding that bovine Hb surface decorated with about 10 copies of PEG5K per tetramer is vasoactive provides support for this concept. The PEGylated bovine Hb has a strikingly larger molecular radius than HbA (1). The colligative properties of the PEGylated bovine Hb are distinct from those of HbA and even polymerized Hb, suggesting a role for the colligative properties of PEGylated Hb in neutralizing the vasoactivity of acellular Hb. To correlate the colligative properties of surface-decorated Hb with the mass of the PEG attached and also its vasoactivity, we have developed a new maleimide-based protocol for the site-specific conjugation of PEG to Hb, taking advantage of the unusually high reactivity of Cys-93(beta) of oxy HbA and the high reactivity of the maleimide to protein thiols. PEG chains of 5, 10, and 20 kDa have been functionalized at one of their hydroxyl groups with a maleidophenyl moiety through a carbamate linkage and used to conjugate the PEG chains at the beta-93 Cys of HbA to generate PEGylated Hbs carrying two copies of PEG (of varying chain length) per tetramer. Homogeneous preparations of (SP-PEG5K)(2)-HbA, (SP-PEG10K)(2)-HbA, and (SP-PEG20K)(2)-HbA have been isolated by ion exchange chromatography. The oxygen affinity of Hb is increased slightly on PEGylation, but the length of the PEG-chain had very little additional influence on the O(2) affinity. Both the hydrodynamic volume and the molecular radius of the Hb increased on surface decoration with PEG and exhibited a linear correlation with the mass of the PEG chain attached. On the other hand, both the viscosity and the colloidal osmotic pressure (COP) of the PEGylated Hbs exhibited an exponential increase with the increase in PEG chain length. In contrast to the molecular volume, viscosity, and COP, the vasoactivity of the PEGylated Hbs was not a

  18. The ability of single-chain surfactants to emulsify an aqueous-based liquid crystal oscillates with odd-even parity of alkyl-chain length.

    PubMed

    Varghese, Nisha; Shetye, Gauri S; Yang, Sijie; Wilkens, Stephan; Smith, Robert P; Luk, Yan-Yeung

    2013-12-15

    The physical properties of many organic molecules often oscillate when the number of carbons in their aliphatic chains changes from odd to even. This odd-even effect for single-chain surfactants in solution is rarely observed. Here, we report the ability of single-chain surfactants to emulsify a class of non-amphiphilic organic salts, disodium cromoglycate (5'DSCG) oscillates as a function of the odd or even number of the aliphatic carbons. This system provides a water-in-oil-in-water emulsion, in which aqueous droplets of 5'DSCG in liquid crystal phases are coated with single-chain surfactants in a bulk carrying aqueous solution. For both surfactants of [Formula: see text] and CH3(CH2)nCOO(-)Na(+), the ability to emulsify 5'DSCG molecules in water is stronger for surfactants with an odd number of sp(3)-hybridized carbon atoms in the aliphatic chains than those with an even number. This observed odd-even effect is consistent with the notion that conventional micelles possess a core of randomly arranged surfactant hydrocarbon tails. However, this water-in-oil-in-water resembles a vesicle system in which the surfactants assemble in a highly ordered structure that separates two aqueous systems. These new self-assembled phases have potential application in the formulation and design of new organic soft materials.

  19. Infrared Spectroscopy of Ionic Liquids Consisting of Imidazolium Cations with Different Alkyl Chain Lengths and Various Halogen or Molecular Anions with and Without a Small Amount of Water.

    PubMed

    Yamada, Toshiki; Tominari, Yukihiro; Tanaka, Shukichi; Mizuno, Maya

    2017-03-27

    Infrared spectroscopy was performed on ionic liquids (ILs) that had imidazolium cations with different alkyl chain lengths and various halogen or molecular anions with and without a small amount of water. The molar concentration normalized absorbance due to +C-H vibrational modes in the range of 3000 to 3200 cm-1 was nearly identical for ILs that had imidazolium cations with different alkyl chain lengths and the same anions. A close correlation was found between the red-shifted +C-H vibrational modes, the chemical shift of +C(2)-H proton, and the energy stabilization of hydrogen-bonding interaction. The vibrational modes of the water molecules interacting with anions in the range between 3300 and 3800 cm-1 was examined. The correlation between the vibrational frequencies of water, the frequencies of +C-H vibrational modes, and the center frequency of intermolecular vibrational modes due to ion pairs was discussed.

  20. A best on-line algorithm for single machine scheduling the equal length jobs with the special chain precedence and delivery time

    NASA Astrophysics Data System (ADS)

    Gu, Cunchang; Mu, Yundong

    2013-03-01

    In this paper, we consider a single machine on-line scheduling problem with the special chains precedence and delivery time. All jobs arrive over time. The chains chainsi arrive at time ri , it is known that the processing and delivery time of each job on the chain satisfy one special condition CD a forehand: if the job J(i)j is the predecessor of the job J(i)k on the chain chaini, then they satisfy p(i)j = p(i)k = p >= qj >= qk , i = 1,2, ---,n , where pj and qj denote the processing time and the delivery time of the job Jj respectively. Obviously, if the arrival jobs have no chains precedence, it shows that the length of the corresponding chain is 1. The objective is to minimize the time by which all jobs have been delivered. We provide an on-line algorithm with a competitive ratio of √2 , and the result is the best possible.

  1. Physicochemical and tribophysical properties of trioctylalkylammonium bis(salicylato)borate (N888n-BScB) ionic liquids: effect of alkyl chain length.

    PubMed

    Gusain, Rashi; Bakshi, Paramjeet S; Panda, Somenath; Sharma, Om P; Gardas, Ramesh; Khatri, Om P

    2017-03-01

    The alkyl chain length of trioctylalkylammonium bis(salicylato)borates (N888n-BScB; n = 6, 8, 10 and 12) was varied to prepare a series of room-temperature ionic liquids, and then their viscosity and rheological properties were investigated. Besides the omnipresent Coulombic interactions, other interactive forces such as van der Waals interactions, hydrogen bonding, inductive forces, dipole-dipole interactions, etc., collectively determine the physicochemical properties of N888n-BScB ionic liquids. The van der Waals interactions and structural geometry of the ammonium cation (N888n) primarily organized the packing orientation of N888n-BScB ionic liquids and controlled their viscosity and rheological properties as a function of the alkyl chain length. The symmetric cation (N8888) increased the viscosity owing to closer packing driven by van der Waals interactions. The N888n-BScB ionic liquids exhibited non-Newtonian shear thinning behaviour. Furthermore, the decrease in viscosity at higher shear rates indicated that interactive forces in the N888n-BScB ionic liquids were disrupted. These ionic liquids, as lubricants, exhibited significantly lower friction (40-50%) and wear (45-69%) in comparison to PEG 300 synthetic lubricating oil. The degrees of reduction in friction and wear were largely influenced by the chain length of the alkyl group. The N888n-BScB ionic liquids with longer alkyl chains were strongly adsorbed on sliding surfaces and provided better lubrication properties than those with shorter alkyl chains. As a result, the coefficients of friction and wear were decreased by increasing the chain length in N888n-BScB ionic liquids. The tribologically induced adsorption of the BScB anion on metal surfaces, electrostatic interactions between ions, the compact and rigid structure of the BScB anion and van der Waals interactions provided by longer alkyl chains in the N888n cation collectively formed a tribochemical thin film of low shear strength, which resulted

  2. Dependence of Mesomorphic Behaviour of Methylene‐Linked Dimers and the Stability of the NTB/NX Phase upon Choice of Mesogenic Units and Terminal Chain Length

    PubMed Central

    Goodby, John W.

    2016-01-01

    Abstract Twelve symmetrical dimeric materials consisting of a nonamethylene (C9) spacer and either phenyl 4‐(4′‐alkylphenyl)benzoate, phenyl 4‐(4′‐alkylcyclohexyl)benzoate or phenyl 4‐(4′‐alkylbicyclohexyl)carboxylate mesogenic units were prepared and their mesogenic behaviour characterised by POM, DSC and XRD. All of the materials exhibited nematic phases with clearing points in excess of 200 °C. Four compounds were found to exhibit the twist‐bend nematic phase, with one material exhibiting a transition from the NTB phase into an anticlinic smectic ‘X’ phase. Across all three series of compounds the length of terminal chain is seen to dictate, to some degree, the type of mesophase formed: shorter terminal chains favour nematic and NTB mesophases, whereas longer terminal aliphatic chains were found to promote smectic phases. PMID:27244550

  3. Dependence of Mesomorphic Behaviour of Methylene-Linked Dimers and the Stability of the NTB /NX Phase upon Choice of Mesogenic Units and Terminal Chain Length.

    PubMed

    Mandle, Richard J; Goodby, John W

    2016-06-27

    Twelve symmetrical dimeric materials consisting of a nonamethylene (C9) spacer and either phenyl 4-(4'-alkylphenyl)benzoate, phenyl 4-(4'-alkylcyclohexyl)benzoate or phenyl 4-(4'-alkylbicyclohexyl)carboxylate mesogenic units were prepared and their mesogenic behaviour characterised by POM, DSC and XRD. All of the materials exhibited nematic phases with clearing points in excess of 200 °C. Four compounds were found to exhibit the twist-bend nematic phase, with one material exhibiting a transition from the NTB phase into an anticlinic smectic 'X' phase. Across all three series of compounds the length of terminal chain is seen to dictate, to some degree, the type of mesophase formed: shorter terminal chains favour nematic and NTB mesophases, whereas longer terminal aliphatic chains were found to promote smectic phases.

  4. Push-Pull Type Oligo(N-annulated perylene)quinodimethanes: Chain Length and Solvent-Dependent Ground States and Physical Properties.

    PubMed

    Zeng, Zebing; Lee, Sangsu; Son, Minjung; Fukuda, Kotaro; Burrezo, Paula Mayorga; Zhu, Xiaojian; Qi, Qingbiao; Li, Run-Wei; Navarrete, Juan T López; Ding, Jun; Casado, Juan; Nakano, Masayoshi; Kim, Dongho; Wu, Jishan

    2015-07-08

    Research on stable open-shell singlet diradicaloids recently became a hot topic because of their unique optical, electronic, and magnetic properties and promising applications in materials science. So far, most reported singlet diradicaloid molecules have a symmetric structure, while asymmetric diradicaloids with an additional contribution of a dipolar zwitterionic form to the ground state were rarely studied. In this Article, a series of new push-pull type oligo(N-annulated perylene)quinodimethanes were synthesized. Their chain length and solvent-dependent ground states and physical properties were systematically investigated by various experimental methods such as steady-state and transient absorption, two-photon absorption, X-ray crystallographic analysis, electron spin resonance, superconducting quantum interference device, Raman spectroscopy, and electrochemistry. It was found that with extension of the chain length, the diradical character increases while the contribution of the zwitterionic form to the ground state becomes smaller. Because of the intramolecular charge transfer character, the physical properties of this push-pull system showed solvent dependence. In addition, density functional theory calculations on the diradical character and Hirshfeld charge were conducted to understand the chain length and solvent dependence of both symmetric and asymmetric systems. Our studies provided a comprehensive understanding on the fundamental structure- and environment-property relationships in the new asymmetric diradicaloid systems.

  5. The chain length of lignan macromolecule from flaxseed hulls is determined by the incorporation of coumaric acid glucosides and ferulic acid glucosides.

    PubMed

    Struijs, Karin; Vincken, Jean-Paul; Doeswijk, Timo G; Voragen, Alphons G J; Gruppen, Harry

    2009-01-01

    Lignan macromolecule from flaxseed hulls is composed of secoisolariciresinol diglucoside (SDG) and herbacetin diglucoside (HDG) moieties ester-linked by 3-hydroxy-3-methylglutaric acid (HMGA), and of p-coumaric acid glucoside (CouAG) and ferulic acid glucoside (FeAG) moieties ester-linked directly to SDG. The linker molecule HMGA was found to account for 11% (w/w) of the lignan macromolecule. Based on the extinction coefficients and RP-HPLC data, it was determined that SDG contributes for 62.0% (w/w) to the lignan macromolecule, while CouAG, FeAG, and HDG contribute for 12.2, 9.0, and 5.7% (w/w), respectively. Analysis of fractions of lignan macromolecule showed that the higher the molecular mass, the higher the proportion of SDG was. An inverse relation between the molecular mass and the proportion (%) CouAG+FeAG was found. Together with the structural information of oligomers of lignan macromolecule obtained after partial saponification, it is hypothesized that the amount of CouAG+FeAG present during biosynthesis determines the chain length of lignan macromolecule. Furthermore, the chain length was estimated from a model describing lignan macromolecule based on structural and compositional data. The average chain length of the lignan macromolceule was calculated to be three SDG moieties with CouAG or FeAG at each of the terminal positions, with a variation between one and seven SDG moieties.

  6. Investigation of double bond conversion, mechanical properties, and antibacterial activity of dental resins with different alkyl chain length quaternary ammonium methacrylate monomers (QAM).

    PubMed

    He, Jingwei; Söderling, Eva; Vallittu, Pekka K; Lassila, Lippo V J

    2013-01-01

    In order to endow dental resin with antibacterial activity, a series of antibacterial quaternary ammonium methacrylate monomers (QAM) with different substituted alkyl chain length (from 10 to 18) were incorporated into commonly used 2,2-bis[4-(2'-hydroxy-3'-methacryloyloxy-propoxy)-phenyl]propane (Bis-GMA)/triethyleneglycol dimethacrylate (TEGDMA) (50 wt/50 wt) dental resin as immobilized antibacterial agents. Double bond conversion (DC), flexural strength (FS) and modulus (FM), and young and mature biofilms inhibition effectiveness of prepared dental resins were studied and Bis-GMA/TEGDMA without QAM was used as reference. Results showed that there was no significant difference on DC, FS, and FM between copolymer with and without 5 wt% QAM. Substituted alkyl chain length of QAM had no influence on DC, FS, and FM of copolymer, but had influence on antibacterial activity of copolymer. Antibacterial activity of copolymer increased with increasing of substituted alkyl chain length of QAM, and the sequence followed as 5%C10 < 5%C11 ≈ 5%C12 < 5%C16 ≈ 5%C18. Copolymers containing C18 and C16 had the best inhibition effectiveness on both young biofilm and mature biofilm, copolymers containing C12 and C11 only had inhibition effectiveness on young biofilm and copolymer containing C10 had none inhibition effectiveness on neither young biofilm nor mature biofilm.

  7. Effect of the phospholipid chain length and head group on beta-phase formation of poly(9,9-dioctylfluorene) enclosed in liposomes.

    PubMed

    Tapia, María J; Monteserín, María; Burrows, Hugh D; Seixas de Melo, João S; Estelrich, Joan

    2013-01-01

    We have studied the effect of head group and alkyl chain length on β-phase formation in poly(9,9-dioctylfluorene) (PFO) solubilized in phospholipid liposomes. Systems studied have three different alkyl chain lengths (1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine [DMPC], 1,2-didodecanoyl-sn-glycero-3-phosphatidylcholine [DLPC], 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine [DPPC]) and head groups (1,2-dimyristoyl-sn-glycero-3-phosphate monosodium salt [DMPA], 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine [DMPE] and 1,2-dimyristoyl-sn-glycero-3-phospho-l-serine sodium salt [DMPS]). Changes in liposome size upon addition of PFO are followed by dynamic light scattering. All the phospholipids induce the formation of PFO β-phase, which is followed by the emission intensity and deconvolution of the absorption spectra. Both the head group and alkyl chain length affect the yield of β-phase. The photophysics of PFO incorporated in liposomes is characterized by stationary and time-resolved fluorescence, whereas the polymer-phospholipid interactions have been studied by the effect of the PFO concentration on the phospholipid phase transitions (differential scanning calorimetry [DSC]).

  8. Solubility of gold nanoparticles as a function of ligand shell and alkane solvent.

    PubMed

    Lohman, Brandon C; Powell, Jeffrey A; Cingarapu, Sreeram; Aakeroy, Christer B; Chakrabarti, Amit; Klabunde, Kenneth J; Law, Bruce M; Sorensen, Christopher M

    2012-05-14

    The solubility of ca. 5.0 nm gold nanoparticles was studied systematically as a function of ligand shell and solvent. The ligands were octane-, decane-, dodecane- and hexadecanethiols; the solvents were the n-alkanes from hexane to hexadecane and toluene. Supernatant concentrations in equilibrium with precipitated superclusters of nanoparticles were measured at room temperature (23 °C) with UV-Vis spectrophotometry. The solubility of nanoparticles ligated with decane- and dodecanethiol was greatest in n-decane and n-dodecane, respectively. In contrast, the solubility of nanoparticles ligated with octane- and hexadecanethiol showed decreasing solubility with increasing solvent chain length. In addition the solubility of the octanethiol ligated system showed a nonmonotonic solvent carbon number functionality with even numbered solvents being better solvents than neighboring odd numbered solvents.

  9. Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review.

    PubMed

    Rittman, Martyn; Gilroy, Emma; Koohya, Hashem; Rodger, Alison; Richards, Adair

    2009-01-01

    Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of BDNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.

  10. Ultrafast charge-transfer reactions of indoline dyes with anchoring alkyl chains of varying length in mesoporous ZnO solar cells.

    PubMed

    Rohwer, Egmont; Minda, Iulia; Tauscher, Gabriele; Richter, Christoph; Miura, Hidetoshi; Schlettwein, Derck; Schwoerer, Heinrich

    2015-04-07

    Dye-sensitized solar cells based on a mesoporous ZnO substrate were sensitized with the indoline derivatives DN91, DN216 and DN285. The chromophore is the same for each of these dyes. They differ from each other in the length of an alkyl chain, which provides a second anchor to the ZnO surface and prolongs cell lifetime. Ultrafast transient absorption measurements reveal a correlation between the length of the alkyl chain and the fastest electron-injection process. The depopulation of the excited state and the associated emergence of the oxidized molecules are dominant spectral features in the transient absorption of the dyes with shorter alkyl chains. A slower picosecond-scale decay proceeds at constant rate for all three derivatives and is assigned to electron transfer into the trap states of ZnO. All assignments are in good agreement with a higher quantum efficiency of charge injection leading to higher short-circuit currents J(sc) for dyes with shorter alkyl chains.

  11. Theoretical investigation on the kinetics and mechanisms of hydroxyl radical-induced transformation of parabens and its consequences for toxicity: Influence of alkyl-chain length.

    PubMed

    Gao, Yanpeng; Ji, Yuemeng; Li, Guiying; An, Taicheng

    2016-03-15

    As emerging organic contaminants (EOCs), the ubiquitous presence of preservative parabens in water causes a serious environmental concern. Hydroxyl radical ((•)OH) is a strong oxidant that can degrade EOCs through photochemistry in surface water environments as well as in advanced oxidation processes (AOPs). To better understand the degradation mechanisms, kinetics, and products toxicity of the preservative parabens in aquatic environments and AOPs, the (•)OH-initiated degradation reactions of the four parabens were investigated systematically using a computational approach. The four studied parabens with increase of alkyl-chain length were methylparaben (MPB), ethylparaben (EPB), propylparaben (PPB), and dibutylparaben (BPB). Results showed that the four parabens can be initially attacked by (•)OH through (•)OH-addition and H-abstraction routes. The (•)OH-addition route was more important for the degradation of shorter alkyl-chain parabens like MPB and EPB, while the H-abstraction route was predominant for the degradation of parabens with longer alkyl-chain for example PPB and BPB. In assessing the aquatic toxicity of parabens and their degradation products using the model calculations, the products of the (•)OH-addition route were found to be more toxic to green algae than original parabens. Although all degradation products were less toxic to daphnia and fish than corresponding parental parabens, they could be still harmful to these aquatic organisms. Furthermore, as alkyl-chain length increased, the ecotoxicity of parabens and their degradation products was found to be also increased.

  12. Effect of n-alkyl chain length on the complexation of phenanthrene and 9-alkyl-phenanthrene with $beta;-cyclodextrin

    NASA Astrophysics Data System (ADS)

    Rima, J.; Aoun, E.; Hanna, K.

    2004-06-01

    The characteristics of host-guest complexation between β-cyclodextrin (β-CD) and phenanthrene derivatives (phenanthrene, n-propyl, n-butyl and n-hexyl-phenanthrene) were investigated by fluorescence spectrometry. Linear and non-linear regression methods were used to estimate the formation constants ( K1). A 1:1 stoichiometric ratio and an effect of n-alkyl chain length on the formation constant were observed for the binary inclusion complex between guest and β-CD. The formation constant dramatically increases with the length of n-alkyl, it starts from the value of 140 l mol -1 for the phenanthrene to reach the value of 580 l mol -1 for hexyl-phenanthrene. The effect of the temperature on the fluorescence intensity of each complex (guest-host) was also studied; and then the thermodynamic parameters were calculated. The main inclusion site seems to be aromatic moiety for short chain molecules, and it moves toward the alkyl chain part, as the chain becomes longer.

  13. Molecular dynamics study of the effect of alkyl chain length on melting points of [CnMIM][PF6] ionic liquids

    SciTech Connect

    Zhang, Y; Maginn, EJ

    2014-01-01

    Based on molecular dynamics simulations, the melting points T-m of a series of 1-alkyl-3-methylimidazolium hexafluorophosphate ionic liquids [CnMIM][PF6] with n = 2, 4, 10, 12, and 14 were studied using the free energy-based pseudosupercritical path (PSCP) method. The experimental trend that the Tm decreases with increasing alkyl chain length for ILs with short alkyl chains and increases for the ones with long alkyl chains was correctly captured. Further analysis revealed that the different trends are the results of the balance between fusion enthalpy and fusion entropy. For the ILs with short alkyl chains (ethyl and butyl groups), fusion entropy plays the dominant role so that [C4MIM][PF6], which has a larger fusion entropy due to its higher liquid phase entropy has the lower melting temperature. As for the ILs with long alkyl chains, due to the enhanced van der Waals interactions brought about by the long non-polar alkyl chains, enthalpy becomes the deciding factor and the melting points increase when the alkyl chain goes from C10 to C14. While the melting points for [C2MIM][PF6] and [C4MIM][PF6] were quantitatively predicted and the trends for the long chain ILs were captured correctly, the absolute melting points for [C10MIM][PF6], [C12MIM][PF6] and [C14MIM][PF6] were systematically overestimated in the simulations. Three possible reasons for the overestimation were studied but all ruled out. Further simulation or experimental studies are needed to explain the difference.

  14. Bond length and electric current oscillation of long linear carbon chains: density functional theory, MpB model, and quantum spin transport studies.

    PubMed

    Oeiras, R Y; da Silva, E Z

    2014-04-07

    Carbon linear atomic chains attached to graphene have experimentally been produced. Motivated by these results, we study the nature of the carbon bonds in these nanowires and how it affects their electrical properties. In the present study we investigate chains with different numbers of atoms and we observe that nanowires with odd number of atoms present a distinct behavior than the ones with even numbers. Using graphene nanoribbons as leads, we identify differences in the quantum transport of the chains with the consequence that even and odd numbered chains have low and high electrical conduction, respectively. We also noted a dependence of current with the wire size. We study this unexpected behavior using a combination of first principles calculations and simple models based on chemical bond theory. From our studies, the electrons of carbon nanowires present a quasi-free electron behavior and this explains qualitatively the high electrical conduction and the bond lengths with unexpected values for the case of odd nanowires. Our study also allows the understanding of the electric conduction dependence with the number of atoms and their parity in the chain. In the case of odd number chains a proposed π-bond (MpB) model describes unsaturated carbons that introduce a mobile π-bond that changes dramatically the structure and transport properties of these wires. Our results indicate that the nature of bonds plays the main role in the oscillation of quantum electrical conduction for chains with even and odd number of atoms and also that nanowires bonded to graphene nanoribbons behave as a quasi-free electron system, suggesting that this behavior is general and it could also remain if the chains are bonded to other materials.

  15. Bond length and electric current oscillation of long linear carbon chains: Density functional theory, MpB model, and quantum spin transport studies

    SciTech Connect

    Oeiras, R. Y.; Silva, E. Z. da

    2014-04-07

    Carbon linear atomic chains attached to graphene have experimentally been produced. Motivated by these results, we study the nature of the carbon bonds in these nanowires and how it affects their electrical properties. In the present study we investigate chains with different numbers of atoms and we observe that nanowires with odd number of atoms present a distinct behavior than the ones with even numbers. Using graphene nanoribbons as leads, we identify differences in the quantum transport of the chains with the consequence that even and odd numbered chains have low and high electrical conduction, respectively. We also noted a dependence of current with the wire size. We study this unexpected behavior using a combination of first principles calculations and simple models based on chemical bond theory. From our studies, the electrons of carbon nanowires present a quasi-free electron behavior and this explains qualitatively the high electrical conduction and the bond lengths with unexpected values for the case of odd nanowires. Our study also allows the understanding of the electric conduction dependence with the number of atoms and their parity in the chain. In the case of odd number chains a proposed π-bond (MpB) model describes unsaturated carbons that introduce a mobile π-bond that changes dramatically the structure and transport properties of these wires. Our results indicate that the nature of bonds plays the main role in the oscillation of quantum electrical conduction for chains with even and odd number of atoms and also that nanowires bonded to graphene nanoribbons behave as a quasi-free electron system, suggesting that this behavior is general and it could also remain if the chains are bonded to other materials.

  16. Poly(oligo(ethylene glycol)acrylamide) brushes by surface initiated polymerization: effect of macromonomer chain length on brush growth and protein adsorption from blood plasma.

    PubMed

    Kizhakkedathu, Jayachandran N; Janzen, Johan; Le, Yevgeniya; Kainthan, Rajesh K; Brooks, Donald E

    2009-04-09

    Three hydrolytically stable polyethyleneglycol (PEG)-based N-substituted acrylamide macromonomers, methoxypolyethyleneglycol (350) acrylamide (MPEG350Am) methoxypolyethyleneglycol (750) acrylamide(MPEG750Am) and methoxypolyethyleneglycol (2000)acrylamide (MPEG2000Am) with increasing PEG chain length were synthesized. Surface-initiated aqueous atom transfer radical polymerization (ATRP) using CuCl/1,1,4,7,10,10-hexamethyl triethylene tetramine (HMTETA) catalyst was utilized to generate dense polymer brushes from these monomers via an ester linker group on the surface of model polystyrene (PS) particles. The molecular weight, hydrodynamic thickness, and graft densities of the grafted polymer layers were controlled by changing the reaction parameters of monomer concentration, addition of Cu(II)Cl2, and sodium chloride. The graft densities of surface-grafted brushes decreased with increasing PEG macromonomer chain length, 350 > 750 > 2000, under similar experimental conditions. The molecular weight of grafts increased with increase in monomer concentration, and only selected conditions produced narrow distributed polymer chains. The molecular weight of grafted polymer chains differs significantly to those formed in solution. The hydrodynamic thicknesses of the grafted polymer layers were fitted to the Daoud and Cotton model (DCM) for brush height on spherical surfaces. The results show that the size of the pendent groups on the polymer chains has a profound effect on the hydrodynamic thickness of the brush for a given degree of polymerization. The new PEG-based surfaces show good protection against nonspecific protein adsorption from blood plasma compared to the bare surface. Protein adsorption decreased with increasing surface density of grafted polymer chains. Poly(MPEG750Am) brushes were more effective in preventing protein adsorption than poly(MPEG350Am) even at low graft densities, presumably due to the increase in PEG content in the grafted layer.

  17. Identity and mechanisms of alkane-oxidizing metalloenzymes from deep-sea hydrothermal vents.

    PubMed

    Bertrand, Erin M; Keddis, Ramaydalis; Groves, John T; Vetriani, Costantino; Austin, Rachel Narehood

    2013-01-01

    Six aerobic alkanotrophs (organism that can metabolize alkanes as their sole carbon source) isolated from deep-sea hydrothermal vents were characterized using the radical clock substrate norcarane to determine the metalloenzyme and reaction mechanism used to oxidize alkanes. The organisms studied were Alcanivorax sp. strains EPR7 and MAR14, Marinobacter sp. strain EPR21, Nocardioides sp. strains EPR26w, EPR28w, and Parvibaculum hydrocarbonoclasticum strain EPR92. Each organism was able to grow on n-alkanes as the sole carbon source and therefore must express genes encoding an alkane-oxidizing enzyme. Results from the oxidation of the radical-clock diagnostic substrate norcarane demonstrated that five of the six organisms (EPR7, MAR14, EPR21, EPR26w, and EPR28w) used an alkane hydroxylase functionally similar to AlkB to catalyze the oxidation of medium-chain alkanes, while the sixth organism (EPR92) used an alkane-oxidizing cytochrome P450 (CYP)-like protein to catalyze the oxidation. DNA sequencing indicated that EPR7 and EPR21 possess genes encoding AlkB proteins, while sequencing results from EPR92 confirmed the presence of a gene encoding CYP-like alkane hydroxylase, consistent with the results from the norcarane experiments.

  18. Identity and mechanisms of alkane-oxidizing metalloenzymes from deep-sea hydrothermal vents

    PubMed Central

    Bertrand, Erin M.; Keddis, Ramaydalis; Groves, John T.; Vetriani, Costantino; Austin, Rachel Narehood

    2013-01-01

    Six aerobic alkanotrophs (organism that can metabolize alkanes as their sole carbon source) isolated from deep-sea hydrothermal vents were characterized using the radical clock substrate norcarane to determine the metalloenzyme and reaction mechanism used to oxidize alkanes. The organisms studied were Alcanivorax sp. strains EPR7 and MAR14, Marinobacter sp. strain EPR21, Nocardioides sp. strains EPR26w, EPR28w, and Parvibaculum hydrocarbonoclasticum strain EPR92. Each organism was able to grow on n-alkanes as the sole carbon source and therefore must express genes encoding an alkane-oxidizing enzyme. Results from the oxidation of the radical-clock diagnostic substrate norcarane demonstrated that five of the six organisms (EPR7, MAR14, EPR21, EPR26w, and EPR28w) used an alkane hydroxylase functionally similar to AlkB to catalyze the oxidation of medium-chain alkanes, while the sixth organism (EPR92) used an alkane-oxidizing cytochrome P450 (CYP)-like protein to catalyze the oxidation. DNA sequencing indicated that EPR7 and EPR21 possess genes encoding AlkB proteins, while sequencing results from EPR92 confirmed the presence of a gene encoding CYP-like alkane hydroxylase, consistent with the results from the norcarane experiments. PMID:23825470

  19. Phase separation in the organic solid state : the influence of quenching protocol in unstable п-alkane blends

    SciTech Connect

    Gilbert, E. P.; Nelson, A.; Sutton, D.; Terrill, N.; Martin, C.; Lal, J.; Lang, E.; Intense Pulsed Neutron Source; Bragg Inst.; Rutherford App. Lab.; Daresbury Lab.

    2005-01-01

    Blends of normal alkanes form lamellar structures, when quenched from the melt, in which the separation of the individual chains may be controlled by the chain-length mismatch, molar composition, isotopic substitution and confinement. 2:1 C{sub 28}H{sub 58}:C{sub 36}D{sub 74} mixtures have been investigated after subjection to a cooling rate varying over three orders of magnitude and intermediate annealing prior to reaching ambient. Quenching at 100 C/min yields similar behavior to intermediate annealing between the pure components' melting points. Slow cooling at 0.1 C/min generates significantly greater ordering and behavior comparable to that obtained from annealing mid-way between the mixing transition and the C{sub 28}H{sub 58} melting point.

  20. Dynamical light scattering for DNA-CTMA:DR1 chains: wormlike semi-flexible model, coil size and persistence length

    NASA Astrophysics Data System (ADS)

    Mitus, A. C.; Radosz, W.; Pawlik, G.; Lazar, C. A.; Kajzar, F.; Rau, I.

    2016-09-01

    Recent experimental Dynamic Light Scattering (DLS) studies of the coil sizes of DNA-CTMA:Rh solutions have lead to numerical discrepancies with theoretical predictions amounting to one-two orders of magnitude.1 In this paper, which has partially character of a tutorial, we present the basic theoretical concepts underlying an analysis of the polymer coil sizes from DLS experiments. In particular, we discuss the limitations of those methods. We present a wormlike model of a polymer chain which is a promising candidate for inferring information about the spatial structure of the DNA chain from experimental data.

  1. [Respiratory activity of bacteria Acinetobacter calcoaceticus TM-31 during assimilation of alkane hydrocarbons].

    PubMed

    Ignatov, O V; Grechkina, E V; Muratova, A Iu; Turkovskaia, O V; Ignatov, V V

    2000-01-01

    The respiratory activity of Acinetobacter calcoaceticus TM-31 with resect to alkane hydrocarbons was studied. The dynamics of oxygen consumption by the cells while assimilating n-hexadecane was assayed by a modified technique using an oxygen electrode. The dependence of cell respiratory activity on the amount of n-hexadecane within the concentration range of 0.03-0.66% was determined. It was demonstrated that the cells also displayed respiratory activity towards other medium-chain n-alkanes: hexane, octane, decane, tridecane, and heptadecane. Thus, we demonstrated the possibility of determining alkanes by measuring the respiratory activities of microorganisms.

  2. Impact of Alkyl Chain Length on the Transition of Hexagonal Liquid Crystal-Wormlike Micelle-Gel in Ionic Liquid-Type Surfactant Aqueous Solutions without Any Additive.

    PubMed

    Hu, Yimin; Han, Jie; Ge, Lingling; Guo, Rong

    2015-11-24

    The search for functional supramolecular aggregations with different structure has attracted interest of chemists because they have the potential in industrial and technological application. Hydrophobic interaction has great influence on the formation of these aggregations, such as hexagonal liquid crystals, wormlike micelles, hydrogels, etc. So a systematical investigation was done to investigate the influence of alkyl chain length of surfactants on the aggregation behavior in water. The aggregation behavior of 1-hexadecyl-3-alkyl imidazolium bromide and water has been systematically investigated. These ionic liquid surfactants are denoted as C16-Cn (n = 2, 3, 4, 6, 8, 9, 10, 12, 14, 16). The rheological behavior and microstructure were characterized via a combination of rheology, cryo-etch scanning electron microscopy, polarization optical microscopy, and X-ray crystallography. The alkyl chain has great influence on the formation of surfactant aggregates in water at the molecular level. With increasing alkyl chain length, different aggregates, such as hexagonal liquid crystals, wormlike micelles, and hydrogels can be fabricated: C16-C2 aqueous solution only forms hexagonal liquid crystal; C16-C3 aqueous solution forms wormlike micelle and hexagonal liquid crystal; C16-C4, C16-C6 and C16-C8 aqueous solutions only form wormlike micelle; C16-C9 aqueous solution experiences a transition between wormlike micelle and hydrogel; C16-C10, C16-C12, C16-C14 and C16-C16 only form hydrogel. The mechanism of the transition of different aggregation with increasing alkyl chain length was also proposed.

  3. Length of the active-site crossover loop defines the substrate specificity of ubiquitin C-terminal hydrolases for ubiquitin chains.

    PubMed

    Zhou, Zi-Ren; Zhang, Yu-Hang; Liu, Shuai; Song, Ai-Xin; Hu, Hong-Yu

    2012-01-01

    UCHs [Ub (ubiquitin) C-terminal hydrolases] are a family of deubiquitinating enzymes that are often thought to only remove small C-terminal peptide tails from Ub adducts. Among the four UCHs identified to date, neither UCH-L3 nor UCH-L1 can catalyse the hydrolysis of isopeptide Ub chains, but UCH-L5 can when it is present in the PA700 complex of the proteasome. In the present paper, we report that the UCH domain of UCH-L5, different from UCH-L1 and UCH-L3, by itself can process the K48-diUb (Lys48-linked di-ubiquitin) substrate by cleaving the isopeptide bond between two Ub units. The catalytic specificity of the four UCHs is dependent on the length of the active-site crossover loop. The UCH domain with a long crossover loop (usually >14 residues), such as that of UCH-L5 or BAP1 [BRCA1 (breast cancer early-onset 1)-associated protein 1], is able to cleave both small and large Ub derivatives, whereas the one with a short loop can only process small Ub derivatives. We also found that elongation of the crossover loop enables UCH-L1 to have isopeptidase activity for K48-diUb in a length-dependent manner. Thus the loop length of UCHs defines their substrate specificity for diUb chains, suggesting that the chain flexibility of the crossover loop plays an important role in determining its catalytic activity and substrate specificity for cleaving isopeptide Ub chains.

  4. Rotational dynamics of coumarin-153 and 4-aminophthalimide in 1-ethyl-3-methylimidazolium alkylsulfate ionic liquids: effect of alkyl chain length on the rotational dynamics.

    PubMed

    Das, Sudhir Kumar; Sarkar, Moloy

    2012-01-12

    Rotational dynamics of two neutral organic solutes, coumarin-153 (C-153) and 4-aminophthalimide (AP), with only the latter having hydrogen-bond-donating ability, has been investigated in a series of 1-ethyl-3-methylimidazolium alkyl sulfate ionic liquids as a function of temperature. The ionic liquids differ only in the length of the linear alkyl side chain (alkyl = ethyl, butyl, hexyl, and octyl) on the anionic moiety. The present study has been undertaken to examine the role of alkyl side chains on the rotational dynamics of the two solutes in these ionic liquids. Analysis of the results using Stokes-Einstein-Debye hydrodynamic theory indicates that the rotational dynamics of C-153 lies between the stick and slip boundary condition in the ethyl analogue and finally reaches subslip condition as in case of the octyl substituent. The observed rotational behavior of C-153 has been explained on the basis of an increase in the size of the solvent, which offers lower friction for solute rotation. On the other hand, AP shows superstick behavior in the ethyl system and exceeds the stick limit in the octyl derivative. Superstick behavior of AP has been attributed to the specific hydrogen-bonding interaction between AP and the sulfate moiety. Proton NMR investigation confirms the hydrogen-bonding interaction between the N-H hydrogen of AP and the ionic liquid. The decrease in rotational coupling constant values for AP with increasing length of alkyl side chains has been attributed to the decrease in the solute-solvent-specific interaction with an increase in the alkyl side chain length on the sulfate moiety.

  5. Importance of the residue Asp 290 on chain length selectivity and catalytic efficiency of recombinant Staphylococcus simulans lipase expressed in E. coli.

    PubMed

    Sayari, Adel; Mosbah, Habib; Gargouri, Youssef

    2007-05-01

    In addition to their physiological importance, microbial lipases, like staphylococcal ones, are of considerable commercial interest for biotechnological applications such as detergents, food production, and pharmaceuticals and industrial synthesis of fine chemicals. The gene encoding the extracellular lipase of Staphylococcus simulans (SSL) was subcloned in the pET-14b expression vector and expressed in Esherichia coli BL21 (DE3). The wild-type SSL was expressed as amino terminal His6-tagged recombinant protein. One-step purification of the recombinant lipase was achieved with nickel metal affinity column. The purified His-tagged SSL (His6-SSL) is able to hydrolyse triacylglycerols without chain length selectivity. The major differences among lipases are reflected in their chemical specificity in the hydrolysis of peculiar ester bonds, and their respective capacity to hydrolyse substrates having different physico-chemical properties. It has been proposed, using homology alignment, that the region around the residue 290 of Staphylococcus hyicus lipase could be involved in the selection of the substrate. To evaluate the importance of this environment, the residue Asp290 of Staphylococcus simulans lipase was mutated to Ala using site-directed mutagenesis. The mutant expression plasmid was also overexpressed in Esherichia coli and purified with a nickel metal affinity column. The substitution of Asp290 by Ala was accompanied by a significant shift of the acyl-chain length specificity of the mutant towards short chain fatty acid esters. Kinetic studies of wild-type SSL and its mutant D290A were carried out, and show essentially that the catalytic efficiency (k cat /K M ) of the mutant was affected. Our results confirmed that Asp290 is important for the chain length selectivity and catalytic efficiency of Staphylococcus simulans lipase.

  6. Liquid-liquid interfaces of semifluorinated alkane diblock copolymers with water, alkanes, and perfluorinated alkanes.

    SciTech Connect

    Perahia, Dvora, Dr.; Pierce, Flint; Tsige, Mesfin; Grest, Gary Stephen, Dr.

    2008-08-01

    The liquid-liquid interface between semifluorinated alkane diblock copolymers of the form F3C(CF2)n-1-(CH2)m-1CH3 and water, protonated alkanes, and perfluorinated alkanes are studied by fully atomistic molecular dynamics simulations. A modified version of the OPLS-AA (Optimized Parameter for Liquid Simulation All-Atom) force field of Jorgensen et al. has been used to study the interfacial behavior of semifluorinated diblocks. Aqueous interfaces are found to be sharp, with correspondingly large values of the interfacial tension. Due to the reduced hydrophobicity of the protonated block compared to the fluorinated block, hydrogen enhancement is observed at the interface. Water dipoles in the interfacial region are found to be oriented nearly parallel to the liquid-liquid interface. A number of protonated alkanes and perfluorinated alkanes are found to be mutually miscible with the semifluorinated diblocks. For these liquids, interdiffusion follows the expected Fickian behavior, and concentration-dependent diffusivities are determined.

  7. Liquid-liquid interfaces of semifluorinated alkane diblock copolymers with water, alkanes, and perfluorinated alkanes.

    PubMed

    Pierce, Flint; Tsige, Mesfin; Perahia, Dvora; Grest, Gary S

    2008-12-18

    The liquid-liquid interface between semifluorinated alkane diblock copolymers of the form F3C(CF2)n-1-(CH2)m-1CH3 and water, protonated alkanes, and perfluorinated alkanes are studied by fully atomistic molecular dynamics simulations. A modified version of the OPLS-AA (Optimized Parameter for Liquid Simulation All-Atom) force field of Jorgensen et al. has been used to study the interfacial behavior of semifluorinated diblocks. Aqueous interfaces are found to be sharp, with correspondingly large values of the interfacial tension. Due to the reduced hydrophobicity of the protonated block compared to the fluorinated block, hydrogen enhancement is observed at the interface. Water dipoles in the interfacial region are found to be oriented nearly parallel to the liquid-liquid interface. A number of protonated alkanes and perfluorinated alkanes are found to be mutually miscible with the semifluorinated diblocks. For these liquids, interdiffusion follows the expected Fickian behavior, and concentration-dependent diffusivities are determined.

  8. Aggregation of Full-length Immunoglobulin Light Chains from Systemic Light Chain Amyloidosis (AL) Patients Is Remodeled by Epigallocatechin-3-gallate.

    PubMed

    Andrich, Kathrin; Hegenbart, Ute; Kimmich, Christoph; Kedia, Niraja; Bergen, H Robert; Schönland, Stefan; Wanker, Erich; Bieschke, Jan

    2017-02-10

    Intervention into amyloid deposition with anti-amyloid agents like the polyphenol epigallocatechin-3-gallate (EGCG) is emerging as an experimental secondary treatment strategy in systemic light chain amyloidosis (AL). In both AL and multiple myeloma (MM), soluble immunoglobulin light chains (LC) are produced by clonal plasma cells, but only in AL do they form amyloid deposits in vivo We investigated the amyloid formation of patient-derived LC and their susceptibility to EGCG in vitro to probe commonalities and systematic differences in their assembly mechanisms. We isolated nine LC from the urine of AL and MM patients. We quantified their thermodynamic stabilities and monitored their aggregation under physiological conditions by thioflavin T fluorescence, light scattering, SDS stability, and atomic force microscopy. LC from all patients formed amyloid-like aggregates, albeit with individually different kinetics. LC existed as dimers, ∼50% of which were linked by disulfide bridges. Our results suggest that cleavage into LC monomers is required for efficient amyloid formation. The kinetics of AL LC displayed a transition point in concentration dependence, which MM LC lacked. The lack of concentration dependence of MM LC aggregation kinetics suggests that conformational change of the light chain is rate-limiting for these proteins. Aggregation kinetics displayed two distinct phases, which corresponded to the formation of oligomers and amyloid fibrils, respectively. EGCG specifically inhibited the second aggregation phase and induced the formation of SDS-stable, non-amyloid LC aggregates. Our data suggest that EGCG intervention does not depend on the individual LC sequence and is similar to the mechanism observed for amyloid-β and α-synuclein.

  9. Impact of chain length on antibacterial activity and hemocompatibility of quaternary N-alkyl and n,n-dialkyl chitosan derivatives.

    PubMed

    Sahariah, Priyanka; Benediktssdóttir, Berglind E; Hjálmarsdóttir, Martha Á; Sigurjonsson, Olafur E; Sørensen, Kasper K; Thygesen, Mikkel B; Jensen, Knud J; Másson, Már

    2015-05-11

    A highly efficient method for chemical modification of chitosan biopolymers by reductive amination to yield N,N-dialkyl chitosan derivatives was developed. The use of 3,6-O-di-tert-butyldimethylsilylchitosan as a precursor enabled the first 100% disubstitution of the amino groups with long alkyl chains. The corresponding mono N-alkyl derivatives were also synthesized, and all the alkyl compounds were then quaternized using an optimized procedure. These well-defined derivatives were studied for antibacterial activity against Gram positive S. aureus, E. faecalis, and Gram negative E. coli, P. aeruginosa, which could be correlated to the length of the alkyl chain, but the order was dependent on the bacterial strain. Toxicity against human red blood cells and human epithelial Caco-2 cells was found to be proportional to the length of the alkyl chain. The most active chitosan derivatives were found to be more selective for killing bacteria than the quaternary ammonium disinfectants cetylpyridinium chloride and benzalkonium chloride, as well as the antimicrobial peptides melittin and LL-37.

  10. Synthesis and spectral characterization of new 1,3,5-triaryl-2-pyrazolines highlighting effect of alkyloxy chain length on fluorescence

    NASA Astrophysics Data System (ADS)

    Abbas, Asghar; Hussain, Safdar; Hafeez, Noureen; Hasan, Aurangzeb; Naseer, Muhammad Moazzam

    2014-06-01

    A series of new 1,3,5-triaryl-2-pyrazolines (1b-12b) having one to twelve carbon alkyloxy side chains were synthesized and characterized on the basis of their spectral (IR, 1H &13C NMR and GC-MS) and microanalytical data. The UV-Vis and emission spectroscopy was used to study the effect of alkyloxy chain length on absorption and fluorescence properties of 1b-12b. All the compounds showed fluorescence in the blue region of the visible spectrum. Interestingly, the alkyloxy chain length strongly affects the emission intensity of 1,3,5-triaryl-2-pyrazoline framework without causing any major blue- or red-shift in the emission wavelength (λmaxem). The absorption and emission maxima (λmaxabs &λmaxem) for compounds (1b-12b) were observed in the range of 337-364 nm and 454-464 nm, respectively. Furthermore, the effect of fluorine substituent on aryl ring present at 3-position of pyrazoline moiety on fluorescence properties is also discussed.

  11. Varying the chain length in N4,N9-diacyl spermines: non-viral lipopolyamine vectors for efficient plasmid DNA formulation.

    PubMed

    Ghonaim, Hassan M; Ahmed, Osama A A; Pourzand, Charareh; Blagbrough, Ian S

    2008-01-01

    The aims of this work are to study the effect of varying the chain length in synthesized N4,N9-diacyl spermines on DNA condensation and then to compare their transfection efficiencies in cell lines. The five novel N4,N9-diacyl lipopolyamines: N4,N9-[didecanoyl, dilauroyl, dimyristoyl, dimyristoleoyl, and dipalmitoyl]-1,12-diamino-4,9-diazadodecane were synthesized from the naturally occurring polyamine spermine. The abilities of these novel compounds to condense DNA and to form nanoparticles were studied using ethidium bromide fluorescence quenching and nanoparticle characterization techniques. Transfection efficiency was studied in FEK4 primary skin cells and in an immortalized cancer cell line (HtTA), and compared with a saturated (distearoyl) analogue and also with the non-liposomal transfection formulation Lipogen, N4,N9-dioleoyl-1,12-diamino-4,9-diazadodecane. By incorporating two aliphatic chains and changing their length in a stepwise manner, we show efficient circular plasmid DNA (pEGFP) formulation and transfection of primary skin and cancer cell lines. Two C14 chains (both saturated or both cis-monounsaturated) were efficient transfecting agents, even in the presence of serum, but they were too toxic. N4,N9-Dioleoyl spermine efficiently condenses pDNA and achieves the highest transfection levels with the highest cell viability among the studied lipopolyamines in cultured cells even in the presence of serum.

  12. The length of the bridging chain in ansa-metallocenes influences their antiproliferative activity against triple negative breast cancer cells (TNBC).

    PubMed

    Beauperin, Matthieu; Top, Siden; Richard, Marie-Aude; Plażuk, Damian; Pigeon, Pascal; Toma, Stefan; Poláčková, Viera; Jaouen, Gérard

    2016-08-16

    In order to examine whether the length of the bridging chain in ansa-ferrocenes affects their antiproliferative activity against MDA-MB-231 triple negative breast cancer cell lines (TNBC), we synthesized derivatives of the type 1-[bis-(4-hydroxyphenyl)]methylidene-[n]ferrocenophane and 1-[(4-hydroxyphenyl)-phenyl]methylidene-[n]ferrocenophane with n = 3, 4, 5. We found that the derivatives of [3]ferrocenophane, the compounds with the shortest bridging chains, are the most active. IC50 values were 0.09 ± 0.01, 2.41 ± 0.10, and 1.85 ± 0.25 μM for the dihydroxyphenyl derivatives, with n = 3, 4, 5, respectively. These differences can be explained in terms of modification of the key metabolites (radical versus quinone methides) within the ansa series depending on the length of the bridging chain. The derivative of [5]ferrocenophane, possessing two -[bis-(4-hydroxyphenyl)]methylidene groups, was also prepared. Surprisingly, this relatively large molecule is also active (IC50 = 2.7 ± 0.3 μM). Two ruthenocenophane analogs were also synthesized. These ruthenium compounds are practically inactive against MDA-MB-231 cells. The unusual chemistry of these different compounds is discussed in terms of elucidating the mechanism underlying their diverse antiproliferative activity, and their specific advantages are evaluated.

  13. Genes involved in alkane degradation in the Alcanivorax hongdengensis strain A-11-3.

    PubMed

    Wang, Wanpeng; Shao, Zongze

    2012-04-01

    Alcanivorax hongdengensis A-11-3 is a newly identified type strain isolated from the surface water of the Malacca and Singapore Straits that can degrade a wide range of alkanes. To understand the degradation mechanism of this strain, the genes encoding alkane hydroxylases were obtained by PCR screening and shotgun sequencing of a genomic fosmid library. Six genes involved in alkane degradation were found, including alkB1, alkB2, p450-1, p450-2, p450-3 and almA. Heterogeneous expression analysis confirmed their functions as alkane oxidases in Pseudomonas putida GPo12 (pGEc47ΔB) or Pseudomonas fluorescens KOB2Δ1. Q-PCR revealed that the transcription of alkB1 and alkB2 was enhanced in the presence of n-alkanes C(12) to C(24); three p450 genes were up-regulated by C(8)-C(16) n-alkanes at different levels, whereas enhanced expression of almA was observed when strain A-11-3 grew with long-chain alkanes (C(24) to C(36)). In the case of branched alkanes, pristane significantly enhanced the expression of alkB1, p450-3 and almA. The six genes enable strain A-11-3 to degrade short (C(8)) to long (C(36)) alkanes that are straight or branched. The ability of A. hongdengensis A-11-3 to thrive in oil-polluted marine environments may be due to this strain's multiple systems for alkane degradation and its range of substrates.

  14. Distribution and primary source analysis of per- and poly-fluoroalkyl substances with different chain lengths in surface and groundwater in two cities, North China.

    PubMed

    Yao, Yiming; Zhu, Hongkai; Li, Bing; Hu, Hongwei; Zhang, Tao; Yamazaki, Eriko; Taniyasu, Sachi; Yamashita, Nobuyoshi; Sun, Hongwen

    2014-10-01

    Per- and poly-fluoroalkyl substances (PFASs) have been widely detected in the hydrosphere. The knowledge on the distribution and composition patterns of PFAS analogues with different chain length significantly contribute to their source analysis. In the present study, a regional scale investigation of PFASs in surface river waters and adjacent ground waters was carried out in two cities of China with potential contamination, Tianjin and Weifang. A total of 31 water samples were collected, and 20 PFASs therein were measured by a high-performance liquid chromatograph-tandem mass spectrometer (HPLC-MS/MS). The possible sources of PFASs in the aquatic environment were assessed primarily by concentration patterns as well as hierarchical cluster analysis. In all 4 rivers investigated in the two cities, perfluoroalkyl carboxylic acids (PFCAs) were the dominant compounds contributing over 70% of the PFASs detected. Perfluorooctanoic acid (PFOA) was the dominant PFCA with a concentration range of 8.58-20.3ng/L in Tianjin and 6.37-25.9ng/L in Weifang, respectively. On the average, the highest concentration was observed in samples from Dagu Drainage Canal (Dagu) in Tianjin and those short-chain PFASs (C4-C6) was detected with a comparable level of the longer-chain PFASs (>C6). Specifically, perfluorobutanoic acid (PFBA) was dominant in the short-chain analogues. This indicates that a remarkably increasing input of short-chain PFASs might be related to wastewater treatment plant effluent or industrial discharges, which could be possibly due to the switch of manufacturing to short-chain products. In Weifang, precipitation and subsequent surface runoff as non-point sources could be significant inputs of PFASs into surface water while groundwater was possibly subjected to severe point sources with ∑PFASs concentration up to ~100ng/L. The inconsistent distribution patterns in groundwater suggest complicated pathways of contamination.

  15. Length of hydrocarbon chain influences location of curcumin in liposomes: Curcumin as a molecular probe to study ethanol induced interdigitation of liposomes.

    PubMed

    El Khoury, Elsy; Patra, Digambara

    2016-05-01

    Using fluorescence quenching of curcumin in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes by brominated derivatives of fatty acids, the location of curcumin has been studied, which indicates length of hydrocarbon chain has an effect on the location of curcumin in liposomes. Change of fluorescence intensity of curcumin with temperature in the presence of liposomes helps to estimate the phase transition temperature of these liposomes, thus, influence of cholesterol on liposome properties has been studied using curcumin as a molecule probe. The cooperativity due to the interactions between the hydrocarbon chains during melting accelerates the phase transition of DPPC liposomes in the presence of high percentage of cholesterol whereas high percentage of cholesterol generates a rather rigid DMPC liposome over a wide range of temperatures. We used ethanol to induce interdigitation between the hydrophobic chains of the lipids and studied this effect using curcumin as fluorescence probe. As a result of interdigitation, curcumin fluorescence is quenched in liposomes. The compact arrangement of the acyl chains prevents curcumin from penetrating deep near the midplane. In the liquid crystalline phase ethanol introduces a kind of order to the more fluid liposome, and does not leave space for curcumin to be inserted away from water.

  16. Polymerase chain reaction-restriction fragment length polymorphism analysis of a 16S rRNA gene fragment for authentication of four clam species.

    PubMed

    Fernandez, Alicia; García, Teresa; Gonzalez, Isabel; Asensio, Luis; Rodriguez, Miguel Angel; Hernández, Pablo E; Martin, Rosario

    2002-04-01

    Specific identification of four clam species, Ruditapes decussatus (grooved carpet shell), Venerupis pullastra (pullet carpet shell), Ruditapes philippinarum (Japanese carpet shell), and Venerupis rhomboides (yellow carpet shell), was achieved by polymerase chain reaction-restriction fragment length polymorphism analysis of a fragment of the mitochondrial 16S rRNA gene. Amplification of DNA isolated from the foot muscle produced fragments of 511 bp for V. pullastra, 523 bp for R. decussatus, 545 bp for R. philippinarum, and 502 bp for V. rhomboides. The restriction profiles obtained by agarose gel electrophoresis when amplicons were digested with endonucleases BsmAI and BsrI allowed unequivocal identification of the four clam species. This approach would be less costly, simpler, and quicker than conventional sequencing of polymerase chain reaction products followed by detailed comparison of individual sequences, especially when large numbers of samples need to be analyzed.

  17. Acyl chain length and saturation modulate interleaflet coupling in asymmetric bilayers: effects on dynamics and structural order.

    PubMed

    Chiantia, Salvatore; London, Erwin

    2012-12-05

    A long-standing question about membrane structure and function is the degree to which the physical properties of the inner and outer leaflets of a bilayer are coupled to one another. Using our recently developed methods to prepare asymmetric vesicles, coupling was investigated for vesicles containing phosphatidylcholine (PC) in the inner leaflet and sphingomyelin (SM) in the outer leaflet. The coupling of both lateral diffusion and membrane order was monitored as a function of PC and SM acyl chain structure. The presence in the outer leaflet of brain SM, which decreased outer-leaflet lateral diffusion, had little effect upon lateral diffusion in inner leaflets composed of dioleoyl PC (i.e., diffusion was only weakly coupled in the two leaflets) but did greatly reduce lateral diffusion in inner leaflets composed of PC with one saturated and one oleoyl acyl chain (i.e., diffusion was strongly coupled in these cases). In addition, reduced outer-leaflet diffusion upon introduction of outer-leaflet milk SM or a synthetic C24:0 SM, both of which have long interdigitating acyl chains, also greatly reduce diffusion of inner leaflets composed of dioleoyl PC, indicative of strong coupling. Strikingly, several assays showed that the ordering of the outer leaflet induced by the presence of SM was not reflected in increased lipid order in the inner leaflet, i.e., there was no detectable coupling between inner and outer leaflet membrane order. We propose a model for how lateral diffusion can be coupled in opposite leaflets and discuss how this might impact membrane function.

  18. CYP63A2, a catalytically versatile fungal P450 monooxygenase capable of oxidizing higher-molecular-weight polycyclic aromatic hydrocarbons, alkylphenols, and alkanes.

    PubMed

    Syed, Khajamohiddin; Porollo, Aleksey; Lam, Ying Wai; Grimmett, Paul E; Yadav, Jagjit S

    2013-04-01

    Cytochrome P450 monooxygenases (P450s) are known to oxidize hydrocarbons, albeit with limited substrate specificity across classes of these compounds. Here we report a P450 monooxygenase (CYP63A2) from the model ligninolytic white rot fungus Phanerochaete chrysosporium that was found to possess a broad oxidizing capability toward structurally diverse hydrocarbons belonging to mutagenic/carcinogenic fused-ring higher-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs), endocrine-disrupting long-chain alkylphenols (APs), and crude oil aliphatic hydrocarbon n-alkanes. A homology-based three-dimensional (3D) model revealed the presence of an extraordinarily large active-site cavity in CYP63A2 compared to the mammalian PAH-oxidizing (CYP3A4, CYP1A2, and CYP1B1) and bacterial aliphatic-hydrocarbon-oxidizing (CYP101D and CYP102A1) P450s. This structural feature in conjunction with ligand docking simulations suggested potential versatility of the enzyme. Experimental characterization using recombinantly expressed CYP63A2 revealed its ability to oxidize HMW-PAHs of various ring sizes, including 4 rings (pyrene and fluoranthene), 5 rings [benzo(a)pyrene], and 6 rings [benzo(ghi)perylene], with the highest enzymatic activity being toward the 5-ring PAH followed by the 4-ring and 6-ring PAHs, in that order. Recombinant CYP63A2 activity yielded monohydroxylated PAH metabolites. The enzyme was found to also act as an alkane ω-hydroxylase that oxidized n-alkanes with various chain lengths (C9 to C12 and C15 to C19), as well as alkyl side chains (C3 to C9) in alkylphenols (APs). CYP63A2 showed preferential oxidation of long-chain APs and alkanes. To our knowledge, this is the first P450 identified from any of the biological kingdoms that possesses such broad substrate specificity toward structurally diverse xenobiotics (PAHs, APs, and alkanes), making it a potent enzyme biocatalyst candidate to handle mixed pollution (e.g., crude oil spills).

  19. Revolutions in rapid amplification of cDNA ends: new strategies for polymerase chain reaction cloning of full-length cDNA ends.

    PubMed

    Schaefer, B C

    1995-05-20

    Rapid amplification of cDNA ends (RACE) is a polymerase chain reaction (PCR)-based technique which was developed to facilitate the cloning of full-length cDNA 5'- and 3'-ends after a partial cDNA sequence has been obtained by other methods. While RACE can yield complete sequences of cDNA ends in only a few days, the RACE procedure frequently results in the exclusive amplification of truncated cDNA ends, undermining efforts to generate full-length clones. Many investigators have suggested modifications to the RACE protocol to improve the effectiveness of the technique. Based on first-hand experience with RACE, a critical review of numerous published variations of the key steps in the RACE method is presented. Also included is a detailed, effective protocol based on RNA ligase-mediated RACE/reverse ligation-mediated PCR, as well as a demonstration of its utility.

  20. Adiabatic Coupling Constant of Nitrobenzene- n-Alkane Critical Mixtures. Evidence from Ultrasonic Spectra and Thermodynamic Data

    NASA Astrophysics Data System (ADS)

    Mirzaev, Sirojiddin Z.; Kaatze, Udo

    2016-09-01

    Ultrasonic spectra of mixtures of nitrobenzene with n-alkanes, from n-hexane to n-nonane, are analyzed. They feature up to two Debye-type relaxation terms with discrete relaxation times and, near the critical point, an additional relaxation term due to the fluctuations in the local concentration. The latter can be well represented by the dynamic scaling theory. Its amplitude parameter reveals the adiabatic coupling constant of the mixtures of critical composition. The dependence of this thermodynamic parameter upon the length of the n-alkanes corresponds to that of the slope in the pressure dependence of the critical temperature and is thus taken another confirmation of the dynamic scaling model. The change in the variation of the coupling constant and of several other mixture parameters with alkane length probably reflects a structural change in the nitrobenzene- n-alkane mixtures when the number of carbon atoms per alkane exceeds eight.

  1. Solute transport in a single fracture involving an arbitrary length decay chain with rock matrix comprising different geological layers.

    PubMed

    Mahmoudzadeh, Batoul; Liu, Longcheng; Moreno, Luis; Neretnieks, Ivars

    2014-08-01

    A model is developed to describe solute transport and retention in fractured rocks. It accounts for advection along the fracture, molecular diffusion from the fracture to the rock matrix composed of several geological layers, adsorption on the fracture surface, adsorption in the rock matrix layers and radioactive decay-chains. The analytical solution, obtained for the Laplace-transformed concentration at the outlet of the flowing channel, can conveniently be transformed back to the time domain by the use of the de Hoog algorithm. This allows one to readily include it into a fracture network model or a channel network model to predict nuclide transport through channels in heterogeneous fractured media consisting of an arbitrary number of rock units with piecewise constant properties. More importantly, the simulations made in this study recommend that it is necessary to account for decay-chains and also rock matrix comprising at least two different geological layers, if justified, in safety and performance assessment of the repositories for spent nuclear fuel.

  2. Conjugated Polyelectrolyte-Sensitized TiO2 Solar Cells: Effects of Chain Length and Aggregation on Efficiency.

    PubMed

    Pan, Zhenxing; Leem, Gyu; Cekli, Seda; Schanze, Kirk S

    2015-08-05

    Two sets of conjugated polyelectrolytes with different molecular weights (Mn) in each set were synthesized. All polymers feature the same conjugated backbone with alternating (1,4-phenylene) and (2,5-thienylene ethynylene) repeating units, but different linkages between the backbone and side chains, namely, oxy-methylene (-O-CH2-) (P1-O-n, where n = 7, 9, and 14) and methylene (-CH2-) (P2-C-n, n = 7, 12, and 18). They all bear carboxylic acid moieties as side chains, which bind strongly to titanium dioxide (TiO2) nanoparticles. The two sets of polymers were used as light-harvesting materials in dye-sensitized solar cells. Despite the difference in molecular weight, polymers within each set have very similar light absorption properties. Interestingly, under the same working conditions, the overall cell efficiency of the P1-O-n series increases with a decreasing molecular weight while the efficiency of the P2-C-n series remains constant regardless of the molecular weight. Steady state photophysical measurements and dynamic light scattering investigation prove that P1-O-n polymers aggregate in solution while P2-C-n series are in the monomeric state. In P1-O-n series, a higher-molecular weight polymer results in a larger aggregate, which reduces the amount of polymers that are adsorbed onto TiO2 films and overall cell efficiency.

  3. Investigating the role of chain and linker length on the catalytic activity of an H 2 production catalyst containing a β-hairpin peptide

    SciTech Connect

    Reback, Matthew L.; Ginovska, Bojana; Buchko, Garry W.; Dutta, Arnab; Priyadarshani, Nilusha; Kier, Brandon L.; Helm, Monte L.; Raugei, Simone; Shaw, Wendy J.

    2016-06-02

    Building on our recent report of an active H2 production catalyst [Ni(PPh2NProp-peptide)2]2+ (Prop=para-phenylpropionic acid, peptide (R10)=WIpPRWTGPR-NH2, p=D-proline, and P2N=1-aza-3,6-diphosphacycloheptane) that contains structured -hairpin peptides, here we investigate how H2 production is effected by: (1) the length of the hairpin (eight or ten residues) and (2) limiting the flexibility between the peptide and the core complex by altering the length of the linker: para-phenylpropionic acid (three carbons) or para-benzoic acid (one carbon). Reduction of the peptide chain length from ten to eight residues increases or maintains the catalytic current for H2 production for all complexes, suggesting a non-productive steric interaction at longer peptide lengths. While the structure of the hairpin appears largely intact for the complexes, NMR data are consistent with differences in dynamic behavior which may contribute to the observed differences in catalytic activity. Molecular dynamics simulations demonstrate that complexes with a one-carbon linker have the desired effect of restricting the motion of the hairpin relative to the complex; however, the catalytic currents are significantly reduced compared to complexes containing a three-carbon linker as a result of the electron withdrawing nature of the -COOH group. These results demonstrate the comple