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Sample records for spacer chain lengths

  1. Length polymorphisms in tRNA intergenic spacers detected by using the polymerase chain reaction can distinguish streptococcal strains and species.

    PubMed Central

    McClelland, M; Petersen, C; Welsh, J

    1992-01-01

    Intergenic tRNA spacers from strains of streptococcal groups A, B, and G were amplified by using the polymerase chain reaction (PCR) at low stringency with consensus tRNA gene primers. Cloning and sequencing showed that many of the homologous intergenic spacers differed in length between species. The sequences of the tRNA genes that flank these polymorphic spacers were determined and used to synthesize fully complementary primers. With these primers at high stringency, PCR products which varied in lengths from 53 to 71 bp, depending on the species or strain, were obtained from streptococcal DNAs, even in the presence of a 1,000-fold mass excess of human DNA. PCR products, the lengths of which could also be used for classification, were obtained at high stringency from a few genera closely related to Streptococcus. No products were obtained from genomic DNAs from more distantly related genera. Production of species- or strain-specific tRNA intergenic length polymorphisms with primers that generate characteristic products from a variety of species within the same genus should be applicable to many organisms, including those that would otherwise be difficult to culture or identify. Images PMID:1378058

  2. Molecular variation analysis of Aspergillus flavus using polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer rDNA region

    PubMed Central

    Zarrin, Majid; Erfaninejad, Maryam

    2016-01-01

    Aspergillus flavus is the second most common disease-causing species of Aspergillus in humans. The fungus is frequently associated with life-threatening infections in immunocompromised hosts. The primary aim of the present study was to analyze the genetic variability among different isolates of A. flavus using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP). A total of 62 A. flavus isolates were tested in the study. Molecular variability was searched for by analysis of the PCR amplification of the internal transcribed spacer (ITS) regions of ribosomal DNA using restriction enzymes. PCR using primers for ITS1 and ITS4 resulted in a product of ~600 bp. Amplicons were subjected to digestion with restriction endonucleases EcoRI, HaeIII and TaqI. Digestion of the PCR products using these restriction enzymes produced different patterns of fragments among the isolates, with different sizes and numbers of fragments, revealing genetic variability. In conclusion, ITS-RFLP is a useful molecular tool in screening for nucleotide polymorphisms among A. flavus isolates. PMID:27588085

  3. Analysis of the rDNA internal transcribed spacer region of the Fusarium species by polymerase chain reaction-restriction fragment length polymorphism

    PubMed Central

    ZARRIN, MAJID; GANJ, FARZANEH; FARAMARZI, SAMA

    2016-01-01

    The Fusarium species are a widely spread phytopathogen identified in an extensive variety of hosts. The Fusarium genus is one of the most heterogeneous fungi and is difficult to classify. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis is a useful method in detection of DNA polymorphism in objective sequences. The aim of the present study was to identify the phylogenetic associations and usefulness of the internal transcribed spacer (ITS) region as a genetic marker within the most clinically important strain of the Fusarium species. A total of 50 strains of Fusarium spp. were used in the study, including environmental, clinical and reference isolates. The primers ITS1 and ITS4 were used in the study. Two restriction enzymes, HaeIII and SmaI, were assessed for the digestion of PCR products. A PCR product of ~550-base pairs was generated for each Fusarium species. The digested products with HaeIII and SmaI demonstrated that the bands generated for the medically significant Fusarium species, including F. solani, F. oxysporum, F. verticillidea, F. proliferatum and F. fujikuri, have different restriction enzyme patterns. In conclusion, it appears that the PCR-RFLP method used in the present study produces a sufficient restriction profile for differentiation of the most medically significant Fusarium species. PMID:27073635

  4. Influence of spacer moiety and length of end chain for the phase stability in complementary, double hydrogen bonded liquid crystals, MA:nOBAs

    NASA Astrophysics Data System (ADS)

    Ashok Kumar, A. V. N.; Chalapathi, P. V.; Srinivasulu, M.; Muniprasad, M.; Potukuchi, D. M.

    2015-01-01

    Supra molecular liquid crystals formed by the Hydrogen Bonding interaction between a non-mesogenic aliphatic dicarboxylic acid viz., COOHsbnd CH2sbnd COOH (Malonic Acid, MA); and mesogenic aromatic, N-(p-n-alkoxy benzoic)Acids, (i.e., nOBAs) for n = 3, 4, 5, 7, 8, 9, 10, 11 and 12, labeled as nOBA:COOHsbnd [CH2]msbnd COOH:nOBAs, abbreviated as MA:nOBAs are reported. 1H NMR and 13C NMR studies confirm the formation of HBLC complexes. Infrared (IR) studies confirm the complementary, double, alternative type of HB. Polarized Optical Microscopy (POM) and Differential Scanning Calorimetry (DSC) studies infer N, SmC, SmX, SmCRE, SmF, SmG LC phase variance. SmX phase exhibiting finger print texture grows in MA:nOBAs for n = 10, 11 and 12 by the interruption of SmC phase with decreasing temperature. Re-Entrant SmC (SmCRE) grows by the cooling of SmX. I-N, N-C, X-CRE, C-G, CRE-F, F-G and G-Solid transitions exhibit first order nature. C-X is found to be second order nature in n = 10 and 11. C-X in n = 12 and X-CRE and CRE-F transitions are found to be weak first order nature. Influence of lengths of end chain (n) and spacer (m) for the overall LC phase [ΔT]LC; tilted phase [ΔT]Tilt; SmC phase [ΔT]C and SmX phase [ΔT]X stabilities is discussed in the wake of data on other HBLCs with similar molecular structure. Prevalence of SmX phase in MA:nOBAs with m = 1 infers repulsive interaction between the π-electronic cloud of aromatic boards of nOBAs. Model molecule predicts a twisted configuration of π-cloud around the molecular long axis. Finger print texture of SmX validates the model.

  5. Solvation dynamics and rotational relaxation of coumarin 153 in mixed micelles of Triton X-100 and cationic gemini surfactants: effect of composition and spacer chain length of gemini surfactants.

    PubMed

    Sonu; Kumari, Sunita; Saha, Subit K

    2016-01-21

    Solvation dynamics and rotational relaxation of coumarin 153 (C-153) in mixed micelles of non-ionic surfactant, Triton X-100 and a series of cationic gemini surfactants, 12-s-12, 2Br with varying polymethylene spacer chain length (s = 3, 6, 8, 12) at different bulk mole fractions of a surfactant were studied. Studies were carried out by means of UV-Vis absorption, steady-state fluorescence and fluorescence anisotropy, time-resolved fluorescence and fluorescence anisotropy, and dynamic light scattering measurements. While micropolarity of the environment around C-153 in mixed micelles increased, the microviscosity decreased with increasing amount of a gemini surfactant. This is because the thickness of the Stern layer of micelles increases as a result of greater extent of penetration of water molecules. Solvation dynamics and rotational relaxation of C-153 become faster with increasing mole fraction of a gemini surfactant in the mixed micelles. Increasing the thickness of the Stern layer leads to an increase in the number of water molecules hydrogen bonded among themselves, resulting in an increase in polarity and microfluidity of the environment. At a given bulk mole fraction of a surfactant, the microviscosity of micelles decreases with increasing the spacer chain length of the gemini surfactant resulting in an increase in the rate of the rotational relaxation process. However, at a given bulk mole fraction of a surfactant, solvation dynamics becomes slower with increasing spacer chain length from s = 3 to 8 because of the increasing degree of counter ion dissociation. The slow rotational relaxation process is mainly due to the lateral diffusion of C-153 along the surface of the micelles. Rotationalmotion of the micelle as a whole is much slower than the lateral diffusion of C-153. PMID:26750436

  6. Effects of spacer length and terminal group on the crystallization and morphology of biscarbamates: a longer spacer does not reduce the melting temperature.

    PubMed

    Khan, Mostofa Kamal; Sundararajan, Pudupadi R

    2013-05-01

    The effects of alkyl side chain and spacer lengths and the type of terminal group on the morphology and crystallization of a homologous series of biscarbamates (model compounds for polyurethanes) were investigated. Biscarbamates were synthesized with alkyl side chains of various lengths ranging from C4 to C18 and an alkyl spacer group with 12 CH2 units (C12 spacer) between the two hydrogen bonding motifs. The crystallization and morphological features are compared with the previously studied biscarbamates with a C6 spacer. As a token example, we also studied a biscarbamate molecule in which the terminal methyl group was replaced by a phenyl group. We stress four important conclusions of the study: (1) A number of studies in the literature found that the longer alkyl spacers reduced the thermal transition temperatures of the molecules, and such behavior was attributed to an increase in the flexibility of the alkyl spacer. However, the results of the present study are to the contrary. With the biscarbamates studied here, the hydrogen-bonding groups on both sides of the C12 spacer act as "anchors", and the longer spacer does not reduce the melting temperatures compared with those with the C6 spacer. (2) The melt viscosity measurements show shear-thinning behavior, which has been mostly observed with polysaccharides and hydrogen-bonded polymers. (3) Avrami analysis shows a two-stage crystallization, which is not commonly observed in organic small molecule systems. (4) The phenyl end group does not add another self-assembly code in terms of π-stacking but acts as a defect. While formation of crystals was observed for biscarbamates with short alkyl side chains with a C6 spacer, an increase in spacer length to C12 induces spherulitic morphology. Although the overall sizes of the spherulites are the same for both spacers, the rate of spherulite growth was higher and the crystallization rate was lower with the C12 spacer compared with the C6 spacer. In contrast with the

  7. The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA

    PubMed Central

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2016-01-01

    Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, andCandida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS)1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories. PMID:27074256

  8. Influence of spacer length on heparin coupling efficiency and fibrinogen adsorption of modified titanium surfaces

    PubMed Central

    Tebbe, David; Thull, Roger; Gbureck, Uwe

    2007-01-01

    Background Chemical bonding of the drug onto surfaces by means of spacer molecules is accompanied with a reduction of the biological activity of the drug due to a constricted mobility since normally only short spacer molecule like aminopropyltrimethoxysilane (APMS) are used for drug coupling. This work aimed to study covalent attachment of heparin to titanium(oxide) surfaces by varying the length of the silane coupling agent, which should affect the biological potency of the drug due to a higher mobility with longer spacer chains. Methods Covalent attachment of heparin to titanium metal and TiO2 powder was carried out using the coupling agents 3-(Trimethoxysilyl)-propylamine (APMS), N- [3-(Trimethoxysilyl)propyl]ethylenediamine (Diamino-APMS) and N1- [3-(Trimethoxy-silyl)-propyl]diethylenetriamine (Triamino-APMS). The amount of bound coupling agent and heparin was quantified photometrically by the ninhydrin reaction and the tolidine-blue test. The biological potency of heparin was determined photometrically by the chromogenic substrate Chromozym TH and fibrinogen adsorption to the modified surfaces was researched using the QCM-D (Quartz Crystal Microbalance with Dissipation Monitoring) technique. Results Zeta-potential measurements confirmed the successful coupling reaction; the potential of the unmodified anatase surface (approx. -26 mV) shifted into the positive range (> + 40 mV) after silanisation. Binding of heparin results in a strongly negatively charged surface with zeta-potentials of approx. -39 mV. The retaining biological activity of heparin was highest for the spacer molecule Triamino-APMS. QCM-D measurements showed a lower viscosity for adsorbed fibrinogen films on heparinised surfaces by means of Triamino-APMS. Conclusion The remaining activity of heparin was found to be highest for the covalent attachment with Triamino-APMS as coupling agent due to the long chain of this spacer molecule and therefore the highest mobility of the drug. Furthermore, the

  9. Impact of Alkyl Spacer Length on Aggregation Pathways in Kinetically Controlled Supramolecular Polymerization.

    PubMed

    Ogi, Soichiro; Stepanenko, Vladimir; Thein, Johannes; Würthner, Frank

    2016-01-20

    We have investigated the kinetic and thermodynamic supramolecular polymerizations of a series of amide-functionalized perylene bisimide (PBI) organogelator molecules bearing alkyl spacers of varied lengths (ethylene to pentylene chains, PBI-1-C2 to PBI-1-C5) between the amide and PBI imide groups. These amide-functionalized PBIs form one-dimensional fibrous nanostructures as the thermodynamically favored states in solvents of low polarity. Our in-depth studies revealed, however, that the kinetic behavior of their supramolecular polymerization is dependent on the spacer length. Propylene- and pentylene-tethered PBIs follow a similar polymerization process as previously observed for the ethylene-tethered PBI. Thus, the monomers of these PBIs are kinetically trapped in conformationally restricted states through intramolecular hydrogen bonding between the amide and imide groups. In contrast, the intramolecularly hydrogen-bonded monomers of butylene-tethered PBI spontaneously self-assemble into nanoparticles, which constitute an off-pathway aggregate state with regard to the thermodynamically stable fibrous supramolecular polymers obtained. Thus, for this class of π-conjugated system, an unprecedented off-pathway aggregate with high kinetic stability could be realized for the first time by introducing an alkyl linker of optimum length (C4 chain) between the amide and imide groups. Our current system with an energy landscape of two competing nucleated aggregation pathways is applicable to the kinetic control over the supramolecular polymerization by the seeding approach. PMID:26699283

  10. 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. PMID:24943491

  11. Rheological response of methylcellulose toward alkanediyl-α,ω-bis(dimethylcetylammonium bromide) surfactants with varying spacer length.

    PubMed

    Shah, Rais Ahmad; Chat, Oyais Ahmad; Maswal, Masrat; Rather, Ghulam Mohammad; Dar, Aijaz Ahmad

    2016-06-25

    The modulation of properties of methylcellulose (MC) by cationic gemini surfactants with varying spacer lengths was studied employing tensiometry, rheometry and turbidimetry. Surface tension measurements anticipate that the gemini surfactant with longer spacer chain length saturates MC at lower concentrations owing to its greater hydrophobicity compared to shorter spacer analogues. Rheometric and turbidimetric measurements suggest that at very low concentrations of gemini surfactants, ion-dipole type of interactions between MC and gemini surfactants promote the extension of polymer chains which is manifested by an initial increase in the low shear viscosity and gelation temperature of MC-gemini surfactant systems, and lowering of turbidity. Such interactions were found to be stronger in case of 16-4-16 than 16-5-16, and almost absent in case of 16-6-16 surfactant system. However at concentrations above CAC, hydrophobic forces operative between MC and gemini surfactants were found to be more for 16-6-16 than that of 16-5-16 and 16-4-16. The final levelling of MC viscosity in presence of all the three gemini surfactants and the variation of gelation temperature suggests the solubilization of network junctions in the surfactant micelles. Moreover, the presence of gemini surfactant strongly affects the interaction of MC with a model hydrophobic drug rifampicin.The results highlight the importance of gemini surfactants and their spacer length in controlling the structural dynamics of MC and its effective use in pharmaceutical and food industry. PMID:27083805

  12. Role of spacer lengths of gemini surfactants in the synthesis of silver nanorods in micellar media

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Santanu; Biswas, Joydeep

    2011-07-01

    In this work, we have prepared Ag-nanorods using biscationic gemini surfactant micelles as the media by a seed-mediated wet synthesis method. Towards this end, we first synthesized Ag-nanoseeds of diameter ~7 nm stabilized by trisodium citrate (as the capping agent). Then these Ag-nanoseeds were used to synthesize Ag-nanorods of different aspect ratios. With decreasing Ag-nanoseed concentration, the aspect ratios of the Ag-nanorods stabilized by these gemini surfactants increased gradually. Various Ag-nanoseeds and Ag-nanospecies were characterized using UV-Vis spectroscopy (to know the surface plasmon bands), transmission electron microscopy (to find out their particle sizes and distribution), energy-dispersive X-ray spectroscopy and X-ray diffraction. When we used micelles derived from gemini surfactants of shorter spacer -(CH2)n- (n = 2 or 4) to stabilize the Ag-nanorods, the λmax of the longitudinal band shifted more towards the blue region compared to that of the gemini surfactant micelles with a longer spacer -(CH2)n- (n = 5, 12) at a given amount of the Ag-nanoseed solution. So, the growth of Ag-nanorods in the gemini micellar solutions depends on the spacer-chain length of gemini surfactants employed.In this work, we have prepared Ag-nanorods using biscationic gemini surfactant micelles as the media by a seed-mediated wet synthesis method. Towards this end, we first synthesized Ag-nanoseeds of diameter ~7 nm stabilized by trisodium citrate (as the capping agent). Then these Ag-nanoseeds were used to synthesize Ag-nanorods of different aspect ratios. With decreasing Ag-nanoseed concentration, the aspect ratios of the Ag-nanorods stabilized by these gemini surfactants increased gradually. Various Ag-nanoseeds and Ag-nanospecies were characterized using UV-Vis spectroscopy (to know the surface plasmon bands), transmission electron microscopy (to find out their particle sizes and distribution), energy-dispersive X-ray spectroscopy and X-ray diffraction. When

  13. Effect of spacer length and type on the biological activity of peptide-polysaccharide matrices.

    PubMed

    Kumai, Jun; Hozumi, Kentaro; Yamada, Yuji; Katagiri, Fumihiko; Kikkawa, Yamato; Nomizu, Motoyoshi

    2016-11-01

    Peptide-polysaccharide matrices can mimic extracellular matrix structure and function and are useful for tissue and cell engineering. The spacer between the peptide and the polysaccharide is important for both peptide conformation and the interaction between the peptide and receptors. Here, the effect of a spacer on the biological activity of peptide-polysaccharide matrices using various lengths of spacers consisting of glycine, β-alanine, and ε-aminocaproic acid has been examined. Active laminin-derived peptides, including a syndecan-binding peptide (AG73: RKRLQVQLSIRT), an integrin αvβ3-binding peptide (A99a: ALRGDN), and an integrin α6β1-binding peptide (A2G10: SYWYRIEASRTG), were used as the peptide ligands and chitosan was used as a polysaccharide matrix. The spacers did not influence the biological activity of the AG73-chitosan matrix. In contrast, the integrin-binding peptide-chitosan matrices showed spacer-dependent activity. Hydrophobic spacers enhanced the cell attachment activity of the A99a-chitosan matrix. A four-glycine spacer showed the strongest effect for the biological activity of the A2G10-chitosan matrix. These results suggested that spacer-optimization for each peptide is important for designing effective peptide-polysaccharide matrices. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 512-520, 2016. PMID:26588050

  14. The chain-length dependence test.

    PubMed

    Stone, Matthew T; Heemstra, Jennifer M; Moore, Jeffrey S

    2006-01-01

    Trends obtained from systematic studies based on chain-length variation have provided valuable insight and understanding into the behavior of m-phenylene ethynylene foldamers. The generalization of this experimental approach, the chain-length dependence test, is useful for studying solution conformation, packing in the solid state, specific intrachain interactions, and the contributions of end groups to a particular property. PMID:16411735

  15. Effect of siloxane spacer length on organosilicon bi-quaternary ammonium amphiphiles.

    PubMed

    Hao, Chuanming; Cui, Yuezhi; Yang, Pengfei; Zhang, Huayong; Mao, Dejiang; Cui, Xiao; Li, Junying

    2015-04-01

    A series of organosilicon Bola-form bi-quaternary ammonium amphiphiles, [OH5C3(C2H5)2N+-(CH2)3-Si(CH2)3-O-(Si(CH3)2O)n-Si(CH2)3⋯(CH2)3-N+(C2H5)2C3H5O]Cl2- (SinN2Cl2, n=0, 4, 6, 8), with the same headgroups and different length of hydrophobic linkage has been synthesized. The critical micelle concentration (CMC) of each amphiphiles was determined by equilibrium surface tension. With the increased length of hydrophobic siloxane spacer, the CMC values follow the order of Si8N2Cl2spacer and its internal oxygen atom, which make the molecular stretch free. The antimicrobial property of Si4N2Cl2 is more effective than others below the concentration of CMC, while the antimicrobial property of Si8N2Cl2 is more effective above the concentration of CMC, which indicated that both the adsorbability in formation of micellar and the hydrophobicity arising from the different length of siloxane spacer are important to inhibit microbe. Moreover, their wetting ability has been characterized by contact angles on various material surfaces. It shows that the higher weight of lipophilic siloxane spacer leads to lower contact angels. PMID:25794442

  16. Synthesis of photoresponsive cholesterol-based azobenzene organogels: dependence on different spacer lengths.

    PubMed

    Ren, Yuchun; Wang, Bin; Zhang, Xiuqing

    2015-01-01

    A series of azobenzene-cholesterol organogel compounds (M 0 -M 12 ) with different spacers were designed and synthesized. The molecular structures were confirmed by (1)H NMR and (13)C NMR spectroscopy. The rapid and reversible photoresponsive properties of the compounds were investigated by UV-vis spectroscopy. Their thermal phase behaviors were studied by DSC. The length of the spacer plays a crucial role in the gelation. Compound M 6 is the only one that can gelate in ethanol, isopropanol and 1-butanol and the reversible gel-sol transitions are also investigated. To obtain visual insight into the microstructure of the gels, the typical structures of the xerogels were studied by SEM. Morphologies of the aggregates change from flower-like, network and rod with different sizes. By using IR and XRD characterization, it is found that intermolecular H-bonding, the solvents and van der Waals interaction are the main contributions to the specific superstructure. PMID:26199664

  17. Extensive length variation in the ribosomal DNA intergenic spacer of yellow perch (Perca flavescens).

    PubMed

    Kakou, Bidénam; Angers, Bernard; Glémet, Hélène

    2016-03-01

    The intergenic spacer (IGS) is located between ribosomal RNA (rRNA) gene copies. Within the IGS, regulatory elements for rRNA gene transcription are found, as well as a varying number of other repetitive elements that are at the root of IGS length heterogeneity. This heterogeneity has been shown to have a functional significance through its effect on growth rate. Here, we present the structural organization of yellow perch (Perca flavescens) IGS based on its entire sequence, as well as the IGS length variation within a natural population. Yellow perch IGS structure has four discrete regions containing tandem repeat elements. For three of these regions, no specific length class was detected as allele size was seemingly normally distributed. However, for one repeat region, PCR amplification uncovered the presence of two distinctive IGS variants representing a length difference of 1116 bp. This repeat region was also devoid of any CpG sites despite a high GC content. Balanced selection may be holding the alleles in the population and would account for the high diversity of length variants observed for adjacent regions. Our study is an important precursor for further work aiming to assess the role of IGS length variation in influencing growth rate in fish. PMID:26841134

  18. Synthesis of photoresponsive cholesterol-based azobenzene organogels: dependence on different spacer lengths

    PubMed Central

    Ren, Yuchun; Zhang, Xiuqing

    2015-01-01

    Summary A series of azobenzene–cholesterol organogel compounds (M 0 –M 12) with different spacers were designed and synthesized. The molecular structures were confirmed by 1H NMR and 13C NMR spectroscopy. The rapid and reversible photoresponsive properties of the compounds were investigated by UV–vis spectroscopy. Their thermal phase behaviors were studied by DSC. The length of the spacer plays a crucial role in the gelation. Compound M 6 is the only one that can gelate in ethanol, isopropanol and 1-butanol and the reversible gel–sol transitions are also investigated. To obtain visual insight into the microstructure of the gels, the typical structures of the xerogels were studied by SEM. Morphologies of the aggregates change from flower-like, network and rod with different sizes. By using IR and XRD characterization, it is found that intermolecular H-bonding, the solvents and van der Waals interaction are the main contributions to the specific superstructure. PMID:26199664

  19. Influence of different length spacers containing enzyme conjugate on functional parameters of progesterone ELISA.

    PubMed

    Shrivastav, Tulsidas G; Chaube, Shail K; Kariya, Kiran P; Prasad, Pramod K V; Kumar, Dinesh

    2013-01-01

    In steroid enzyme immunoassay (EIA), there is an increase or decrease of labeled steroid recognition by antibody due to homologous and heterologous combinations of enzyme conjugate with immunogen that affects sensitivity of the assay. We have introduced three to 18 atomic length linkers between enzyme and steroid moieties and studied their effects on functional parameters such as sensitivity, ED(50), and specificity of progesterone enzyme immunoassays. Progesterone-3-carboxymethyloxime-bovine serum albumin (P-3-CMO-BSA) was used as an immunogen to raise the antiserum in New Zealand white rabbits. Five enzyme conjugates were prepared using 17-α-hydroxy-progesterone-3-carboxymethyloxime (17-α-OH-P-3-CMO) as carboxylic derivative of 17-α-hydroxy-progesterone and horseradish peroxidase (HRP) as label. These were 17-α-OH-P-3-CMO-HRP, 17-α-OH-P-3-CMO-urea-HRP (17-α-OH-P-3-CMO-U-HRP), 17-α-OH-P-3-CMO-ehylenediamine-HRP (17-α-OH-P-3-CMO-EDA-HRP), 17-α-OH-P-3-CMO-carbohydrazide-HRP (17-α-OH-P-3-CMO-CH-HRP), and 17-α-OH-P-3-CMO-adipic acid dihydrazide-6-aminocaproic acid-HRP (17-α-OH-P-3-CMO-ADH-6ACA-HRP). The influence of different atomic length linkers on sensitivity, ED(50), and specificity were studied with reference to label without linker. The results of the present investigation revealed that the incorporation of ADH-6ACA spacer in 17-α-hydroxy-progesterone-enzyme conjugate improved the sensitivity in antigen plus bridge heterologous EIA system. The presence of spacer in enzyme conjugate improved the sensitivity and specificity (cross-reactivity) in some antigen plus bridge heterologous assay of progesterone. PMID:23323985

  20. Binding of 12-s-12 dimeric surfactants to calf thymus DNA: Evaluation of the spacer length influence.

    PubMed

    Sarrión, Beatriz; Bernal, Eva; Martín, Victoria Isabel; López-López, Manuel; López-Cornejo, Pilar; García-Calderón, Margarita; Moyá, María Luisa

    2016-08-01

    Several cationic dimeric surfactants have shown high affinity towards DNA. Bis-quaternary ammonium salts (m-s-m) have been the most common type of dimeric surfactants investigated and it is generally admitted that those that posses a short spacer (s≤3) show better efficiency to bind or compact DNA. However, experimental results in this work show that 12-s-12 surfactants with long spacers make the surfactant/ctDNA complexation more favorable than those with short spacers. A larger contribution of the hydrophobic interactions, which control the binding Gibbs energy, as well as a higher average charge of the surfactant molecules bound to the nucleic acid, which favors the electrostatic attractions, could explain the experimental observations. Dimeric surfactants with intermediate spacer length seem to be the less efficient for DNA binding. PMID:27108208

  1. Autoxidation of medium chain length polyhydroxyalkanoate.

    PubMed

    Schmid, Manfred; Ritter, Axel; Grubelnik, Andreas; Zinn, Manfred

    2007-02-01

    Polyhydroxyalkanoates (PHAs) are a class of biopolymers that are currently the subject of intensive research for various applications (packaging, consumer products, medical applications, etc.). It is known from synthetic polymers that all plastic materials show more or less pronounced autoxidation (aging induced by UV radiation, temperature, heavy metal ions, etc.). There is less knowledge as yet regarding the autoxidation behavior of biopolymers. The autoxidative behavior of medium chain length poly[(R)-3-hydroxyalkanoate] (mcl-PHA) was therefore investigated. mcl-PHA (co)polymers with amounts of 0, 10, 50, and 75 mol % of olefinic side chains with terminal double bonds were tempered at 60 degrees C in air for 3 months. After 1, 2, 4, 8, and 12 weeks, samples were removed and analyzed for changes in chemical and physical properties by sol-gel analysis (Soxhlet extraction), size exclusion chromatography (SEC), infrared analysis (IR), and gas chromatography/flame ionization detection (GC/FID). It became apparent that the content of double bonds greatly influences the autoxidation of mcl-PHA. A low amount of unsaturated moiety (0 and 10 mol %) resulted in chain scission, whereas samples with 50 and 75 mol % olefinic side chains showed cross-linking and became insoluble after a few weeks. Kinetic data of oxidation behavior were investigated by performing isothermal DSC experiments at elevated temperatures. The kinetic data combined with the experiment enabled the gelation time to be predicted and the shelf-life of mcl-PHA to be estimated. Because of the detected sensitivity of mcl-PHA regarding autoxidation, it is recommended that these biopolymers should be stored cold (at least -5 degrees C) and in an inert gas atmosphere or stabilized by suitable additives (antioxidants). PMID:17291081

  2. The spacer arm length in cell-penetrating peptides influences chitosan/siRNA nanoparticle delivery for pulmonary inflammation treatment

    NASA Astrophysics Data System (ADS)

    Jeong, Eun Ju; Choi, Moonhwan; Lee, Jangwook; Rhim, Taiyoun; Lee, Kuen Yong

    2015-11-01

    Although chitosan and its derivatives have been frequently utilized as delivery vehicles for small interfering RNA (siRNA), it is challenging to improve the gene silencing efficiency of chitosan-based nanoparticles. In this study, we hypothesized that controlling the spacer arm length between a cell-penetrating peptide (CPP) and a nanoparticle could be critical to enhancing the cellular uptake as well as the gene silencing efficiency of conventional chitosan/siRNA nanoparticles. A peptide consisting of nine arginine units (R9) was used as a CPP, and the spacer arm length was controlled by varying the number of glycine units between the peptide (R9Gn) and the nanoparticle (n = 0, 4, and 10). Various physicochemical characteristics of R9Gn-chitosan/siRNA nanoparticles were investigated in vitro. Increasing the spacing arm length did not significantly affect the complex formation between R9Gn-chitosan and siRNA. However, R9G10-chitosan was much more effective in delivering genes both in vitro and in vivo compared with non-modified chitosan (without the peptide) and R9-chitosan (without the spacer arm). Chitosan derivatives modified with oligoarginine containing a spacer arm can be considered as potential delivery vehicles for various genes.Although chitosan and its derivatives have been frequently utilized as delivery vehicles for small interfering RNA (siRNA), it is challenging to improve the gene silencing efficiency of chitosan-based nanoparticles. In this study, we hypothesized that controlling the spacer arm length between a cell-penetrating peptide (CPP) and a nanoparticle could be critical to enhancing the cellular uptake as well as the gene silencing efficiency of conventional chitosan/siRNA nanoparticles. A peptide consisting of nine arginine units (R9) was used as a CPP, and the spacer arm length was controlled by varying the number of glycine units between the peptide (R9Gn) and the nanoparticle (n = 0, 4, and 10). Various physicochemical characteristics of

  3. The effect of the hydrophilic spacer length on the functionality of a mercury-supported tethered bilayer lipid membrane.

    PubMed

    Becucci, Lucia; Faragher, Robert J; Schwan, Adrian

    2015-02-01

    A biomimetic membrane consisting of a thiolipid monolayer tethered to a mercury electrode, with a dioleoylphosphatidylcholine (DOPC) monolayer on top of it, was fabricated. The thiolipid, referred to as DPOL, consisted of an octaethyleneoxy (OEO) chain terminated at one end with a lipoic acid residue and covalently linked at the other end to two phytanyl chains. The functionality of this biomimetic membrane, referred to as a tethered bilayer lipid membrane (tBLM), was tested by incorporating gramicidin and alamethicin and verifying their ion channel activity. Advantages and drawbacks with respect to a tBLM using a thiolipid, referred to as DPTL, with a tetraethyleneoxy (TEO) chain were examined by using electrochemical impedance spectroscopy, potential-step chronocoulometry and cyclic voltammetry. The maximum charge surface density of potassium ions stored in the OEO spacer amounts to 70μCcm(-2), as compared to a charge surface density of 45μCcm(-2) in the TEO spacer. The lipid bilayer moiety of the DPOL/DOPC tBLM is somewhat leakier than that of the DPTL/DOPC tBLM at potentials negative of about -0.65V vs. the saturated calomel electrode. The estimated value of the surface dipole potential of the OEO spacer amounts to -0.180V and is, therefore, smaller than that, -0.230V, of the TEO spacer. PMID:25180906

  4. The spacer arm length in cell-penetrating peptides influences chitosan/siRNA nanoparticle delivery for pulmonary inflammation treatment.

    PubMed

    Jeong, Eun Ju; Choi, Moonhwan; Lee, Jangwook; Rhim, Taiyoun; Lee, Kuen Yong

    2015-12-21

    Although chitosan and its derivatives have been frequently utilized as delivery vehicles for small interfering RNA (siRNA), it is challenging to improve the gene silencing efficiency of chitosan-based nanoparticles. In this study, we hypothesized that controlling the spacer arm length between a cell-penetrating peptide (CPP) and a nanoparticle could be critical to enhancing the cellular uptake as well as the gene silencing efficiency of conventional chitosan/siRNA nanoparticles. A peptide consisting of nine arginine units (R9) was used as a CPP, and the spacer arm length was controlled by varying the number of glycine units between the peptide (R9Gn) and the nanoparticle (n = 0, 4, and 10). Various physicochemical characteristics of R9Gn-chitosan/siRNA nanoparticles were investigated in vitro. Increasing the spacing arm length did not significantly affect the complex formation between R9Gn-chitosan and siRNA. However, R9G10-chitosan was much more effective in delivering genes both in vitro and in vivo compared with non-modified chitosan (without the peptide) and R9-chitosan (without the spacer arm). Chitosan derivatives modified with oligoarginine containing a spacer arm can be considered as potential delivery vehicles for various genes. PMID:26568525

  5. The Effects of Spacer Length and Composition on Aptamer-Mediated Cell-Specific Targeting with Nanoscale PEGylated Liposomal Doxorubicin.

    PubMed

    Xing, Hang; Li, Ji; Xu, Weidong; Hwang, Kevin; Wu, Peiwen; Yin, Qian; Li, Zhensheng; Cheng, Jianjun; Lu, Yi

    2016-06-16

    Aptamer-based targeted drug delivery systems have shown significant promise for clinical applications. Although much progress has been made in this area, it remains unclear how PEG coating would affect the selective binding of DNA aptamers and thus influence the overall targeting efficiency. To answer this question, we herein report a systematic investigation of the interactions between PEG and DNA aptamers on the surface of liposomes by using a series of nanoscale liposomal doxorubicin formulations with different DNA aptamer and PEG modifications. We investigated how the spatial size and composition of the spacer molecules affected the targeting ability of the liposome delivery system. We showed that a spacer of appropriate length was critical to overcome the shielding from surrounding PEG molecules in order to achieve the best targeting effect, regardless of the spacer composition. Our findings provide important guidelines for the design of aptamer-based targeted drug delivery systems. PMID:27123758

  6. Influence of the linking spacer length and type on the enantioseparation ability of β-cyclodextrin functionalized monoliths.

    PubMed

    Guo, Jialiang; Xiao, Yuan; Lin, Yuanjing; Zhang, Qiaoxuan; Chang, Yiqun; Crommen, Jacques; Jiang, Zhengjin

    2016-05-15

    In order to investigate the effect of the linking spacer on the enantioseparation ability of β-cyclodextrin (β-CD) functionalized polymeric monoliths, three β-CD-functionalized organic polymeric monoliths with different spacer lengths were prepared by using three amino-β-CDs, i.e. mono-6-amino-6-deoxy-β-CD, mono-6-ethylenediamine-6-deoxy-β-CD, mono-6-hexamethylenediamine-6-deoxy-β-CD, as starting materials. These amino-β-CDs reacted with glycidyl methacrylate to produce functional monomers which were then copolymerized with ethylene dimethacrylate. The enantioseparation ability of the three monoliths was evaluated using 14 chiral acidic compounds, including mandelic acid derivatives, nonsteroidal anti-inflammatory drugs, N-derivatized amino acids, and chiral herbicides under optimum chromatographic conditions. Notably, the poly(GMA-NH2-β-CD-co-EDMA) column provides higher enantioresolution and enantioselectivity than the poly(GMA-EDA-β-CD-co-EDMA) and poly(GMA-HDA-β-CD-co-EDMA) columns for most tested chiral analytes. Furthermore, the enantioseparation performance of triazole-linker containing monoliths was compared to that of ethylenediamine-linker containing monoliths. The results indicate that the enantioselectivity of β-CD monolithic columns is strongly related to the length and type of spacer tethering β-CD to the polymeric support. PMID:26992519

  7. Theory of microphase separation on side-chain liquid-crystalline polymers with flexible spacers.

    PubMed

    Hernández-Jiménez, M; Westfahl, H

    2007-05-01

    We model a melt of monodisperse side-chain liquid-crystalline polymers as a melt of comb copolymers in which the side groups are rod-coil diblock copolymers. We consider both excluded-volume and Maier-Saupe interactions. The first acts among any pair of segments while the latter acts only between rods. Using a free-energy functional calculated from this microscopic model, we study the spinodal stability of the isotropic phase against density and orientational fluctuations. The phase diagram obtained in this way predicts nematic and smectic instabilities as well as the existence of microphases or phases with modulated wave vector but without nematic ordering. Such microphases are the result of the competition between the incompatibility among the blocks and the connectivity constraints imposed by the spacer and the backbone. Also the effects of the polymerization degree and structural conformation of the monomeric units on the phase behavior of the side-chain liquid-crystalline polymers are studied. PMID:17541501

  8. Selection of Enzymes for Terminal Restriction Fragment Length Polymorphism Analysis of Fungal Internally Transcribed Spacer Sequences▿ †

    PubMed Central

    Alvarado, Pablo; Manjón, Jose L.

    2009-01-01

    Terminal restriction fragment length polymorphism (TRFLP) profiling of the internally transcribed spacer (ITS) ribosomal DNA of unknown fungal communities is currently unsupported by a broad-range enzyme-choosing rationale. An in silico study of terminal fragment size distribution was therefore performed following virtual digestion (by use of a set of commercially available 135 type IIP restriction endonucleases) of all published fungal ITS sequences putatively annealing to primers ITS1 and ITS4. Different diversity measurements were used to rank primer-enzyme pairs according to the richness and evenness that they showed. Top-performing pairs were hierarchically clustered to test for data dependency. The enzyme set composed of MaeII, BfaI, and BstNI returned much better results than randomly chosen enzyme sets in computer simulations and is therefore recommended for in vitro TRFLP profiling of fungal ITSs. PMID:19465521

  9. Tailoring the spacer type and length in push-pull chromophores. Insights from a systematic theoretical study

    NASA Astrophysics Data System (ADS)

    Kerkines, Ioannis S. K.; Lathiotakis, Nektarios N.; Theodorakopoulos, Giannoula; Petsalakis, Ioannis D.

    2016-06-01

    The predicting ability of Mulliken-type formulae in estimating the charge-transfer (CT) excitation energy in "push-pull" donor-bridge-acceptor (D-B-A) systems is evaluated systematically by tailoring the length of an oligoenic spacer bridge separating an N,N-dimethylanilino (DMA) donor and a dicyanovinyl (DCV) acceptor. In order to achieve satisfactory agreement with time-dependent density functional theory (TDDFT) values, the D⋯A distance and charge separation inside the D-B-A system are replaced with rigorously calculated "effective" values, while using "superdonor-superacceptor" energetics. The proposed modified Mulliken formula has the potential to be of significant assistance for cases when direct TDDFT calculation of the CT state is unfeasible.

  10. Structural, biocomplexation and gene delivery properties of hydroxyethylated gemini surfactants with varied spacer length.

    PubMed

    Zakharova, Lucia Ya; Gabdrakhmanov, Dinar R; Ibragimova, Alsu R; Vasilieva, Elmira A; Nizameev, Irek R; Kadirov, Marsil K; Ermakova, Elena A; Gogoleva, Natalia E; Faizullin, Dzhigangir A; Pokrovsky, Andrey G; Korobeynikov, Vladislav A; Cheresiz, Sergey V; Zuev, Yuriy F

    2016-04-01

    Gemini surfactants with hexadecyl tails and hydroxyethylated head groups bridged with tetramethylene (G4), hexamethylene (G6) and dodecamethylene (G12) spacers were shown to self-assemble at the lower critical micelle concentration compared to their conventional m-s-m analogs. The lipoplex formation and the plasmid DNA transfer into different kinds of host cells were studied. In the case of eukaryotic cells, high transfection efficacy has been demonstrated for DNA-gemini complexes, which increased as follows: G6G4>G12 has been obtained in the case of transformation of bacterial cells with plasmid DNA-gemini complexes, mediated by electroporation technique. Solely G6 shows transformation efficacy exceeding the control result (uncomplexed DNA), while the inhibitory effect occurs for G4 and G12. Analysis of physico-chemical features of single surfactants and lipoplexes shows that compaction and condensation effects change as follows: G6

  11. Inclusion of a furin-sensitive spacer enhances the cytotoxicity of ribotoxin restrictocin containing recombinant single-chain immunotoxins.

    PubMed

    Goyal, A; Batra, J K

    2000-01-15

    Chimaeric toxins have considerable therapeutic potential to treat various malignancies. We have previously used the fungal ribonucleolytic toxin restrictocin to make chimaeric toxins in which the ligand was fused at either the N-terminus or the C-terminus of the toxin. Chimaeric toxins containing ligand at the C-terminus of restrictocin were shown to be more active than those having ligand at the N-terminus of the toxin. Here we describe the further engineering of restrictocin-based chimaeric toxins, anti-TFR(scFv)-restrictocin and restrictocin-anti-TFR(scFv), containing restrictocin and a single chain fragment variable (scFv) of a monoclonal antibody directed at the human transferrin receptor (TFR), to enhance their cell-killing activity. To promote the independent folding of the two proteins in the chimaeric toxin, a linear flexible peptide, Gly-Gly-Gly-Gly-Ser, was inserted between the toxin and the ligand to generate restrictocin-linker-anti-TFR(scFv) and anti-TFR(scFv)-linker-restrictocin. A 12-residue spacer, Thr-Arg-His-Arg-Gln-Pro-Arg-Gly-Trp-Glu-Gln-Leu, containing the recognition site for the protease furin, was incorporated between the toxin and the ligand to generate restrictocin-spacer-anti-TFR(scFv) and anti-TFR(scFv)-spacer-restrictocin. The incorporation of the proteolytically cleavable spacer enhanced the cell-killing activity of both constructs by 2-30-fold depending on the target cell line. However, the introduction of linker improved the cytotoxic activity only for anti-TFR(scFv)-linker-restrictocin. The proteolytically cleavable spacer-containing chimaeric toxins had similar cytotoxic activities irrespective of the location of the ligand on the toxin and they were found to release the restrictocin fragment efficiently on proteolysis in vitro. PMID:10620501

  12. Novel application of PhastSystem polyacrylamide gel electrophoresis using restriction fragment length polymorphism--internal transcribed spacer patterns of individuals for molecular identification of entomopathogenic nematodes.

    PubMed

    Pamjav, H; Triga, D; Buzás, Z; Vellai, T; Lucskai, A; Adams, B; Reid, A P; Burnell, A; Griffin, C; Glazer, I; Klein, M G; Fodor, A

    1999-06-01

    différences! [editorial] [editorial]onomic way of identifying and assigning nematodes to taxons, which had already been determined either by comparative sequence analysis of nuclear rDNA internal transcribed spacer (ITS) region or by other methods of molecular or conventional taxonomy, is provided. Molecular identification of entomopathogenic nematodes (EPN) can be upgraded by basing it on PhastSystem polyacrylamide gel electrophoresis (PAGE) analysis of restriction fragment length polymorphism (RFLP) patterns of polymerase chain reaction (PCR)-amplified DNA derived from single nematodes of Steinernema or Heterorhabditis spp. Although analysis from single worms has previously been made on agarose gel, the resolution on PhastSystem PAGE gel is much higher. The DNA sequences selected for analysis were those constituting the internal transcribed spacer region between the 18S and 26S rDNA genes within the rRNA operon. RFLP analysis was carried out by gel electrophoresis on the PhastSystem (Pharmacia) as detailed elsewhere (Triga et al., Electrophoresis 1999, 20, 1272-1277. The downscaling from conventional agarose to PhastSystem gels resulted in pattern of DNA fragments differing from those obtained with agarose gel electrophoresis under conventional conditions by increasing the number of detected fragments. The approach supported previous species identifications and was able to identify several unclassified isolates, such as those from Hungary and Ireland, and provides a method for identification of previously unclassified strains. We confirmed that Heterorhabditis "Irish Type", represented by two strains of different geographical origin, comprise a species different from H. megidis. We also confirmed that strain IS5 belongs to the species H. indicus rather than to H. bacteriophora, as had been suggested previously. PMID:10380767

  13. Ultrasonic propagation in finite-length granular chains.

    PubMed

    Hutchins, D A; Yang, J; Akanji, O; Thomas, P J; Davis, L A J; Freear, S; Harput, S; Saffari, N; Gelat, P

    2016-07-01

    A narrowband ultrasound source has been used to generate solitary wave impulses in finite-length chains of spheres. Once the input signal is of sufficient amplitude, both harmonics and sub-harmonics of the input frequency can be generated as non-linear normal modes of the system, allowing a train of impulses to be established from a sinusoidal input. The characteristics of the response have been studied as a function of the physical properties of the chain, the input waveform and the level of static pre-compression. The results agree with the predictions of a theoretical model, based on a set of discrete dynamic equations for the spheres for finite-length chains. Impulses are only created for very small pre-compression forces of the order of 0.01N, where strongly non-linear behaviour is expected. PMID:26548524

  14. Increased Chain Length Promotes Pneumococcal Adherence and Colonization

    PubMed Central

    Rodriguez, Jesse L.; Dalia, Ankur B.

    2012-01-01

    Streptococcus pneumoniae is a mucosal pathogen that grows in chains of variable lengths. Short-chain forms are less likely to activate complement, and as a consequence they evade opsonophagocytic clearance more effectively during invasive disease. When grown in human nasal airway surface fluid, pneumococci exhibited both short- and long-chain forms. Here, we determined whether longer chains provide an advantage during colonization when the organism is attached to the epithelial surface. Chain-forming mutants and the parental strain grown under conditions to promote chain formation showed increased adherence to human epithelial cells (A549 cells) in vitro. Additionally, adherence to A549 cells selected for longer chains within the wild-type strain. In vivo in a murine model of colonization, chain-forming mutants outcompeted the parental strain. Together, our results demonstrate that morphological heterogeneity in the pneumococcus may promote colonization of the upper respiratory tract by enhancing the ability of the organism to bind to the epithelial surface. PMID:22825449

  15. A phylogenetic analysis of the genus Carica L. (Caricaceae) based on restriction fragment length variation in a cpDNA intergenic spacer region

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phylogenetic relationships among twelve wild and cultivated species of Carica (Caricaceae) were analyzed using restriction fragment length variation in a 3.2-kb PCR amplified intergenic spacer region of the chloroplast DNA. A total of 138 fragments representing 137 restriction sites accounting f...

  16. Para-aminobenzamidine linked regenerated cellulose membranes for plasminogen activator purification: Effect of spacer arm length and ligand density

    PubMed Central

    Fasoli, Ezio; Reyes, Yiaslin Ruiz; Guzman, Osiris Martinez; Rosado, Alexandra; Cruz, Vivian Rodriguez; Borges, Amaris; Martinez, Edmarie; Bansal, Vibha

    2013-01-01

    Despite membrane-based separations offering superior alternative to packed bed chromatographic processes, there has been a substantial lacuna in their actual application to separation processes. One of the major reasons behind this is the lack of availability of appropriately modified or end-group modifiable membranes. In this paper, an affinity membrane was developed using a commercially available serine protease inhibitor, para-aminobenzamidine (pABA). The membrane modification was optimized for protein binding capacity by varying: i) the length of the spacer arm (SA; 5-atoms, 7-atoms, and 14-atoms) linking the ligand to membrane surface; ii) the affinity ligand (pABA) density on membrane surface (5–25 nmoles per cm2). Resulting membranes were tested for their ability to bind plasminogen activators (PAs) from mono- and multi- component systems in batch mode. The membrane containing pABA linked through 7-atoms SA but similar ligand density as in the case of 5- or 14- atoms long SA was found to bind up to 1.6-times higher amounts of PA per nmole of immobilized ligand from conditioned HeLa cell culture media. However, membranes with similar ligand densities but different lengths of SA, showed comparable binding capacities in monocomponent system. In addition, the length of SA did not affect the selectivity of the ligand for PA. A clear inverse linear correlation was observed between ligand density and binding capacity until the point of PA binding optima was reached (11±1.0 nmoles per cm2) in mono- and multi- component systems for 7- as well as 14- atoms SA. Up to 200-fold purification was achieved in a single step separation of PA from HeLa conditioned media using these affinity membranes. The issues of ligand leaching and reuse of the membranes were also investigated. An extensive regeneration procedure allowed the preservation of approximately 95% of the PA binding capacity of the membranes even after five cycles of use. PMID:23703544

  17. Secretion Genes as Determinants of Bacillus anthracis Chain Length

    PubMed Central

    Nguyen-Mau, Sao-Mai; Oh, So-Young; Kern, Valerie J.; Missiakas, Dominique M.

    2012-01-01

    Bacillus anthracis grows in chains of rod-shaped cells, a trait that contributes to its escape from phagocytic clearance in host tissues. Using a genetic approach to search for determinants of B. anthracis chain length, we identified mutants with insertional lesions in secA2. All isolated secA2 mutants exhibited an exaggerated chain length, whereas the dimensions of individual cells were not changed. Complementation studies revealed that slaP (S-layer assembly protein), a gene immediately downstream of secA2 on the B. anthracis chromosome, is also a determinant of chain length. Both secA2 and slaP are required for the efficient secretion of Sap and EA1 (Eag), the two S-layer proteins of B. anthracis, but not for the secretion of S-layer-associated proteins or of other secreted products. S-layer assembly via secA2 and slaP contributes to the proper positioning of BslO, the S-layer-associated protein, and murein hydrolase, which cleaves septal peptidoglycan to separate chains of bacilli. SlaP was found to be both soluble in the bacterial cytoplasm and associated with the membrane. The purification of soluble SlaP from B. anthracis-cleared lysates did not reveal a specific ligand, and the membrane association of SlaP was not dependent on SecA2, Sap, or EA1. We propose that SecA2 and SlaP promote the efficient secretion of S-layer proteins by modifying the general secretory pathway of B. anthracis to transport large amounts of Sap and EA1. PMID:22609926

  18. Acyl Chain Length of Phosphatidylserine Is Correlated with Plant Lifespan

    PubMed Central

    Tian, Xuejun; Li, Weiqi

    2014-01-01

    Plant lifespan is affected by factors with genetic and environmental bases. The laws governing these two factors and how they affect plant lifespan are unclear. Here we show that the acyl chain length (ACL) of phosphatidylserine (PS) is correlated with plant lifespan. Among the detected eight head-group classes of membrane lipids with lipidomics based on triple quadrupole tandem mass spectrometry, the ACL of PS showed high diversity, in contrast to the ACLs of the other seven classes, which were highly conserved over all stages of development in all plant species and organs and under all conditions that we studied. Further investigation found that acyl chains of PS lengthened during development, senescence, and under environmental stresses and that increasing length was accelerated by promoted- senescence. The acyl chains of PS were limited to a certain carbon number and ceased to increase in length when plants were close to death. These findings suggest that the ACL of PS can count plant lifespan and could be a molecular scale ruler for measuring plant development and senescence. PMID:25058060

  19. 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.

  20. Micelle-Vesicle Transition by Cleavage of Disulfide Spacer Chain for Gemini Surfactant in Didodecyldimethylammonium Chloride Aqueous Solutions.

    PubMed

    Mizuhashi, Toshinari; Asakawa, Tsuyoshi; Ohta, Akio

    2015-01-01

    We examined the "micelle-vesicle transition" through the mixing effect of single-tailed thiol surfactants produced by the cleavage of gemini surfactants, [C12H25N(CH3)2CH2CH2SSCH2CH2N(CH3)2C12H25] 2Cl (C12SSC12), which have a disulfide bond in the spacer chain. Phase diagrams of C12H25N(CH3)2CH2CH2SHCl-didodecyldimethylammonium chloride (C12SH-DDAC) and C12SSC12-DDAC were determined by conductivity and pyrene fluorescence probe methods. The aggregate diameters were evaluated by dynamic light scattering (DLS). The critical vesicle concentration (CVC) was confirmed by the abrupt increase in the intensity of light scattering with excitation at 335 nm. Vesicle formation was confined to the DDAC-rich region of the C12SSC12-DDAC system, while the vesicle formation region for the C12SH-DDAC system spread out with the addition of dithiothreitol (DTT) to C12SSC12-DDAC. This implies that single-tailed surfactants can induce a more favorable environment for molecular packing of the vesicular surface. The micelle-vesicle transition occurs with disulfide spacer chain cleavage of gemini surfactants at a particular specific concentration range. PMID:26250426

  1. Glycogen with short average chain length enhances bacterial durability

    NASA Astrophysics Data System (ADS)

    Wang, Liang; Wise, Michael J.

    2011-09-01

    Glycogen is conventionally viewed as an energy reserve that can be rapidly mobilized for ATP production in higher organisms. However, several studies have noted that glycogen with short average chain length in some bacteria is degraded very slowly. In addition, slow utilization of glycogen is correlated with bacterial viability, that is, the slower the glycogen breakdown rate, the longer the bacterial survival time in the external environment under starvation conditions. We call that a durable energy storage mechanism (DESM). In this review, evidence from microbiology, biochemistry, and molecular biology will be assembled to support the hypothesis of glycogen as a durable energy storage compound. One method for testing the DESM hypothesis is proposed.

  2. Perfluorinated Surfactant Chain-Length Effects on Sonochemical Kinetics

    NASA Astrophysics Data System (ADS)

    Campbell, Tammy Y.; Vecitis, Chad D.; Mader, Brian T.; Hoffmann, Michael R.

    2009-08-01

    The sonochemical degradation kinetics of the aqueous perfluorochemicals (PFCs) perfluorobutanoate (PFBA), perfluorobutanesulfonate (PFBS), perfluorohexanoate (PFHA), and perfluorohexanesulfonate (PFHS) have been investigated. Surface tension measurements were used to evaluate chain-length effects on equilibrium air-water interface partitioning. The PFC air-water interface partitioning coefficients, KeqPF, and maximum surface concentrations, ΓmaxPF, were determined from the surface pressure equation of state for PFBA, PFBS, PFHA, and PFHS. Relative KeqPF values were dependent upon chain length KeqPFHS ≅ 2.1KeqPFHA ≅ 3.9KeqPFBS ≅ 5.0KeqPFBA, whereas relative ΓmaxPF values had minimal chain length dependence ΓmaxPFHS ≅ ΓmaxPFHA ≅ ΓmaxPFBS ≅ 2.2ΓmaxPFBA. The rates of sonolytic degradation were determined over a range of frequencies from 202 to 1060 kHz at dilute (<1 μM) initial PFC concentrations and are compared to previously reported results for their C8 analogs: perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA). Under all conditions, the time-dependent PFC sonolytic degradation was observed to follow pseudo-first-order kinetics, i.e., below kinetic saturation, suggesting bubble-water interface populations were significantly below the adsorption maximum. The PFHX (where X = A or S) sonolysis rate constant was observed to peak at an ultrasonic frequency of 358 kHz, similar to that for PFOX. In contrast, the PFBX degradation rate constants had an apparent maximum at 610 kHz. Degradation rates observed for PFHX are similar to previously determined PFOX rates, kapp,358PFOX ≅ kapp,358PFHX. PFOX is sonolytically pyrolyzed at the transiently cavitating bubble-water interface, suggesting that rates should be proportional to equilibrium interfacial partitioning. However, relative equilibrium air-water interfacial partitioning predicts that KeqPFOX ≅ 5KeqPFHX. This suggests that at dilute PFC concentrations, adsorption to the bubble

  3. 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.

  4. Hydrolysis of different chain length xylooliogmers by cellulase and hemicellulase.

    PubMed

    Qing, Qing; Wyman, Charles E

    2011-01-01

    Commercial cellulase complexes produced by cellulolytic fungi contain enzyme activities that are capable of hydrolyzing non-cellulosic polysaccharides in biomass, primarily hemicellulose and pectins, in addition to cellulose. However, xylanase activities detected in most commercial enzyme preparations have been shown to be insufficient to completely hydrolyze xylan, resulting in high xylooligomer concentrations remaining in the hydrolysis broth. Our recent research showed that these xylooligomers are stronger inhibitors of cellulase activity than others have previously established for glucose and cellobiose, making their removal of great importance. In this study, a HPLC system that can measure xylooligomers with degrees of polymerization (DP) up to 30 was applied to assess how Spezyme CP cellulase, Novozyme 188 β-glucosidase, Multifect xylanase, and non-commercial β-xylosidase enzymes hydrolyze different chain length xylooligomers derived from birchwood xylan. Spezyme CP cellulase and Multifect xylanase partially hydrolyzed high DP xylooligomers to lower DP species and monomeric xylose, while β-xylosidase showed the strongest ability to degrade both high and low DP xylooligomers. However, about 10-30% of the higher DP xylooligomers were difficult to be breakdown by cellulase or xylanase and about 5% of low DP xylooligomers (mainly xylobiose) proved resistant to hydrolysis by cellulase or β-glucosidase, possibly due to low β-xylosidase activity in these enzymes and/or the precipitation of high DP xylooligomers. PMID:20943381

  5. Enhanced target recognition of nanoparticles by cocktail PEGylation with chains of varying lengths.

    PubMed

    Ishii, Takehiko; Miyata, Kanjiro; Anraku, Yasutaka; Naito, Mitsuru; Yi, Yu; Jinbo, Takao; Takae, Seiji; Fukusato, Yu; Hori, Mao; Osada, Kensuke; Kataoka, Kazunori

    2016-01-25

    Monodispersed gold nanoparticles (AuNPs) were simultaneously decorated with lactosylated and non-modified shorter poly(ethylene glycol)s (PEGs) to enhance their target recognition. The decoration with sufficiently shorter PEGs dramatically enhanced the multivalent binding ability of lactosylated AuNPs to the lectin-fixed surface, possibly due to the enhanced mobility of the ligands via the spacer effect generated by the shorter PEG chains. PMID:26658952

  6. Evolutionary consequences of food chain length in kelp forest communities.

    PubMed Central

    Steinberg, P D; Estes, J A; Winter, F C

    1995-01-01

    Kelp forests are strongly influenced by macroinvertebrate grazing on fleshy macroalgae. In the North Pacific Ocean, sea otter predation on macroinvertebrates substantially reduces the intensity of herbivory on macroalgae. Temperate Australasia, in contrast, has no known predator of comparable influence. These ecological and biogeographic patterns led us to predict that (i) the intensity of herbivory should be greater in temperate Australasia than in the North Pacific Ocean; thus (ii) Australasian seaweeds have been under stronger selection to evolve chemical defenses and (iii) Australasian herbivores have been more strongly selected to tolerate these compounds. We tested these predictions first by measuring rates of algal tissue loss to herbivory at several locations in Australasian and North Pacific kelp forests. There were significant differences in grazing rates among sea otter-dominated locations in the North Pacific (0-2% day-1), Australasia (5-7% day-1), and a North Pacific location lacking sea otters (80% day-1). The expectations that chronically high rates of herbivory in Australasia have selected for high concentrations of defensive secondary metabolites (phlorotannins) in brown algae and increased tolerance of these defenses in the herbivores also were supported. Phlorotannin concentrations in kelps and fucoids from Australasia were, on average, 5-6 times higher than those in a comparable suite of North Pacific algae, confirming earlier findings. Furthermore, feeding rates of Australasian herbivores were largely unaffected by phlorotannins, regardless of the compounds' regional source. North Pacific herbivores, in contrast, were consistently deterred by phlorotannins from both Australasia and the North Pacific. These findings suggest that top-level consumers, acting through food chains of various lengths, can strongly influence the ecology and evolution of plantherbivore interactions. Images Fig. 1 Fig. 2 Fig. 3 PMID:11607573

  7. Phase behavior of polyion-surfactant ion complex salts: effects of surfactant chain length and polyion length.

    PubMed

    Svensson, Anna; Norrman, Jens; Piculell, Lennart

    2006-06-01

    The aqueous phase behavior of a series of complex salts, containing cationic surfactants with polymeric counterions, has been investigated by visual inspection and small-angle X-ray scattering (SAXS). The salts were alkyltrimethylammonium polyacrylates, CxTAPAy, based on all combinations of five surfactant chain lengths (C6, C8, C10, C12, and C16) and two lengths of the polyacrylate chain (30 and 6 000 repeating units). At low water contents, all complex salts except C6TAPA6000 formed hexagonal and/or cubic Pm3n phases, with the hexagonal phase being favored by lower water contents. The aggregate dimensions in the liquid crystalline phases changed with the surfactant chain length. The determined micellar aggregation numbers of the cubic phases indicated that the micelles were only slightly aspherical. At high water contents, the C6TAPAy salts were miscible with water, whereas the other complex salts featured wide miscibility gaps with a concentrated phase in equilibrium with a (sometimes very) dilute aqueous solution. Thus, the attraction between oppositely charged surfactant aggregates and polyions decreases with decreasing surfactant chain length, and with decreasing polyion length, resulting in an increased miscibility with water. The complex salt with the longest surfactant chains and polyions gave the widest miscibility gap, with a concentrated hexagonal phase in equilibrium with almost pure water. A decrease in the attraction led to cubic-micellar and micellar-micellar coexistence in the miscibility gap and to an increasing concentration of the complex salt in the dilute phase. For each polyion length, the mixtures for the various surfactant chain lengths were found to conform to a global phase diagram, where the surfactant chain length played the role of an interaction parameter. PMID:16722736

  8. 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.

  9. 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.

  10. Dependence on chain length of NMR relaxation times in mixtures of alkanes

    NASA Astrophysics Data System (ADS)

    Freed, Denise E.

    2007-05-01

    Many naturally occurring fluids, such as crude oils, consist of a very large number of components. It is often of interest to determine the composition of the fluids in situ. Diffusion coefficients and nuclear magnetic resonance (NMR) relaxation times can be measured in situ and depend on the size of the molecules. It has been shown [D. E. Freed et al., Phys. Rev. Lett. 94, 067602 (2005)] that the diffusion coefficient of each component in a mixture of alkanes follows a scaling law in the chain length of that molecule and in the mean chain length of the mixture, and these relations were used to determine the chain length distribution of crude oils from NMR diffusion measurements. In this paper, the behavior of NMR relaxation times in mixtures of chain molecules is addressed. The author explains why one would expect scaling laws for the transverse and longitudinal relaxation times of mixtures of short chain molecules and mixtures of alkanes, in particular. It is shown how the power law dependence on the chain length can be calculated from the scaling laws for the translational diffusion coefficients. The author fits the literature data for NMR relaxation in binary mixtures of alkanes and finds that its dependence on chain length agrees with the theory. Lastly, it is shown how the scaling laws in the chain length and the mean chain length can be used to determine the chain length distribution in crude oils that are high in saturates. A good fit is obtained between the NMR-derived chain length distributions and the ones from gas chromatography.

  11. 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. PMID:27244550

  12. Growth of Highly Oriented Ultrathin Crystalline Organic Microstripes: Effect of Alkyl Chain Length.

    PubMed

    Zhu, Tao; Xiao, Chengliang; Wang, Binghao; Hu, Xiaorong; Wang, Zi; Fan, Jian; Huang, Lizhen; Yan, Donghang; Chi, Lifeng

    2016-09-13

    The growth of organic semiconductor with controllable morphology is a crucial issue for achieving high-performance devices. Here we present the systematic study of the effect of the alkyl chain attached to the functional entity on controlling the growth of oriented microcrystals by dip-coating. Alkylated DTBDT-based molecules with variable chain lengths from n-butyl to n-dodecyl formed into one-dimensional micro- or nanostripe crystals at different pulling speeds. The alignment and ordering are significantly varied with alkyl chain length, as is the transistor performance. Highly uniform oriented and higher-molecular-order crystalline stripes with improved field-effect mobility can be achieved with an alkyl-chain length of around 6. We attribute this effect to the alkyl-chain-length-dependent packing, solubility, and self-assembly behavior. PMID:27548053

  13. Identification of cultured isolates of clinically important yeast species using fluorescent fragment length analysis of the amplified internally transcribed rRNA spacer 2 region

    PubMed Central

    De Baere, Thierry; Claeys, Geert; Swinne, Danielle; Massonet, Caroline; Verschraegen, Gerda; Muylaert, An; Vaneechoutte, Mario

    2002-01-01

    Background The number of patients with yeast infection has increased during the last years. Also the variety of species of clinical importance has increased. Correct species identification is often important for efficient therapy, but is currently mostly based on phenotypic features and is sometimes time-consuming and depends largely on the expertise of technicians. Therefore, we evaluated the feasibility of PCR-based amplification of the internally transcribed spacer region 2 (ITS2), followed by fragment size analysis on the ABI Prism 310 for the identification of clinically important yeasts. Results A rapid DNA-extraction method, based on simple boiling-freezing was introduced. Of the 26 species tested, 22 could be identified unambiguously by scoring the length of the ITS2-region. No distinction could be made between the species Trichosporon asteroides and T. inkin or between T. mucoides and T. ovoides. The two varieties of Cryptococcus neoformans (var. neoformans and var. gattii) could be differentiated from each other due to a one bp length difference of the ITS2 fragment. The three Cryptococcus laurentii isolates were split into two groups according to their ITS2-fragment lengths, in correspondence with the phylogenetic groups described previously. Since the obtained fragment lengths compare well to those described previously and could be exchanged between two laboratories, an internationally usable library of ITS2 fragment lengths can be constructed. Conclusions The existing ITS2 size based library enables identification of most of the clinically important yeast species within 6 hours starting from a single colony and can be easily updated when new species are described. Data can be exchanged between laboratories. PMID:12139769

  14. The effect of the length and flexibility of the side chain of basic amino acids on the binding of antimicrobial peptides to zwitterionic and anionic membrane model systems.

    PubMed

    Russell, Amanda L; Williams, Brittany C; Spuches, Anne; Klapper, David; Srouji, Antoine H; Hicks, Rickey P

    2012-03-01

    The intent of this investigation was to determine the effect of varying the side chain length of the basic amino acids residues on the binding of a series of antimicrobial peptides (AMPs) to zwitterionic and anionic LUVs, SUVs and micelles. These AMPs are based on the incorporation of three dipeptide units consisting of the unnatural amino acids Tic-Oic in the sequence, Ac-GF-Tic-Oic-GX-Tic-Oic-GF-Tic-Oic-GX-Tic-XXXX-CONH(2), where X (Spacer #2) may be one of the following amino acids, Lys, Orn, Dab, Dpr or Arg. A secondary focus of this study was to attempt to correlate the possible mechanisms of membrane binding of these AMPs to their bacterial strain potency and selectivity. These AMPs produced different CD spectra in the presence of zwitterionic DPC and anionic SDS micelles. This observation indicates that these AMPs adopt different conformations on binding to the surface of zwitterionic and anionic membrane model systems. The CD spectra of these AMPs in the presence of zwitterionic POPC and anionic 4:1 POPC/POPG LUVs and SUVs also were different, indicating that they adopt different conformations on interaction with the zwitterionic and anionic liposomes. This observation was supported by ITC and calcein leakage data that indicated that these AMPs interact via very different mechanisms with anionic and zwitterionic LUVs. The enthalpy for the binding of these AMPs to POPC directly correlates to the length of Spacer #2. The enthalpy of binding of these AMPs to 4:1 POPC/POPG, however do not correlate with the length of Spacer #2. Clear evidence exists that the AMP containing the Dpr residues (the shortest length spacer) interacts very differently with both POPC and 4:1 POPC/POPG LUVs compared to the other four compounds. Data indicates that both the hydrophobicity and the charge distribution of Spacer #2, contribute to defining antibacterial activity. These observations have major implications on the development of these analogs as potential therapeutic agents

  15. Thermoelectric transport through a zigzag like chain: Influence of the chain length, the interdot tunneling and the intradot Coulomb interaction

    NASA Astrophysics Data System (ADS)

    Li, Rui-Xue; Ni, Yun; Li, Hai-Dong; Tian, Xing-Ling; Yao, Kai-Lun; Fu, Hua-Hua

    2016-07-01

    We have studied the thermoelectric transport through a zigzaglike chain in the linear response regime using the non-equilibrium Green's function method. This model consists of the main zigzaglike chain and the side radicals coupled with the main chain at the next-near-neighbor sites. The finite-scale effect on the thermoelectric properties has been studied, our results show that thermoelectric efficiency can be enhanced by increasing the chain length. The thermopower and the figure of merit can be enhanced by strengthening the interdot tunneling coupling between the main chain and the side radicals. However, increase of the interdot tunneling coupling in the main chain can weaken the thermoelectric efficiency. Moreover, the thermoelectric efficiency is also strongly dependent on the intradot Coulomb interaction. These results can provide a guidance for the synthesis of thermal devices with high thermoelectric efficiency.

  16. Chain Length and Grafting Density Dependent Enhancement in the Hydrolysis of Ester-Linked Polymer Brushes.

    PubMed

    Melzak, Kathryn A; Yu, Kai; Bo, Deng; Kizhakkedathu, Jayachandran N; Toca-Herrera, José L

    2015-06-16

    Poly(N,N-dimethylacrylamide) (PDMA) brushes with different grafting density and chain length were grown from an ester group-containing initiator using surface-initiated polymerization. Hydrolysis of the PDMA chains from the surface was monitored by measuring thickness of the polymer layer by ellipsometry and extension length by atomic force microscopy. It was found that the initial rate of cleavage of one end-tethered PDMA chains was dependent on the grafting density and chain length; the hydrolysis rate was faster for high grafting density brushes and brushes with higher molecular weights. Additionally, the rate of cleavage of polymer chains during a given experiment changed by up to 1 order of magnitude as the reaction progressed, with a distinct transition to a lower rate as the grafting density decreased. Also, polymer chains undergo selective cleavage, with longer chains in a polydisperse brush being preferentially cleaved at one stage of the hydrolysis reaction. We suggest that the enhanced initial hydrolysis rates seen at high grafting densities and high chain lengths are due to mechanical activation of the ester bond connecting the polymer chains to the surface in association with high lateral pressure within the brush. These results have implications for the preparation of polymers brushes, their stability under harsh conditions, and the analysis of polymer brushes from partial hydrolysates. PMID:26010390

  17. 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.

  18. Biosynthesis and Elongation of Short- and Medium-Chain-Length Fatty Acids

    PubMed Central

    van der Hoeven, Rutger S.; Steffens, John C.

    2000-01-01

    Short- and medium-chain-length fatty acids (FAs) are important constituents of a wide array of natural products. Branched and straight short-chain-length FAs originate from branched chain amino acid metabolism, and serve as primers for elongation in FA synthase-like reactions. However, a recent model proposes that the one-carbon extension reactions that utilize 2-oxo-3-methylbutyric acid in leucine biosynthesis also catalyze a repetitive one-carbon elongation of short-chain primers to medium-chain-length FAs. The existence of such a mechanism would require a novel form of regulation to control carbon flux between amino acid and FA biosynthesis. A critical re-analysis of the data used to support this pathway fails to support the hypothesis for FA elongation by one-carbon extension cycles of α-ketoacids. Therefore, we tested the hypothesis experimentally using criteria that distinguish between one- and two-carbon elongation mechanisms: (a) isotopomer patterns in terminal carbon atom pairs of branched and straight FAs resulting from differential labeling with [13C]acetate; (b) [13C]threonine labeling patterns in odd- and even chain length FAs; and (c) differential sensitivity of elongation reactions to inhibition by cerulenin. All three criteria indicated that biosynthesis of medium-chain length FAs is mediated primarily by FA synthase-like reactions. PMID:10631271

  19. 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.

  20. Spacer fluids

    SciTech Connect

    Wilson, W.N.; Bradshaw, R.D.; Wilton, B.S.; Carpenter, R.B.

    1992-05-19

    This patent describes a method for cementing a wellbore penetrating an earth formation into which a conduit extends, the wellbore having a space occupied by a drilling fluid. It comprises displacing the drilling fluid from the space with a spacer fluid comprising: sulfonated styrene-maleic anhydride copolymer, bentonite, welan gum, surfactant and a weighting agent; and displacing the spacer composition and filling the wellbore space with a settable cement composition.

  1. Conformational changes of DNA in the presence of 12-s-12 gemini surfactants (s=2 and 10). Role of the spacer's length in the interaction surfactant-polynucleotide.

    PubMed

    García, J P; Marrón, E; Martín, V I; Moyá, M L; Lopez-Cornejo, P

    2014-06-01

    A multifaceted study on the interaction of calf-thymus DNA with two different cationic gemini surfactants alkanediyl-α-ω-bis(dodecyldimethyl-amonium)bromide, 12-s-12,2Br(-) (with s=2, G2, and 10, G10) was carried out. The measurements were done at different molar ratios X=[surfactant]/[DNA]. Results show two different conformational changes in DNA: a first compaction of the polynucleotide corresponding to a partial conformational (not total) change of DNA from an extended coil state to a globular state that happens at the lower molar ratio X. A second change corresponds to a breaking of the partial condensation, that is, the transition from the compacted state to a new more extended conformation (for the higher X values) different to the initial extension. According to circular dichroism spectra and dynamic light scattering measurements, this new state of DNA seems to be similar to a ψ-phase. Measurements confirm that interactions involved in the compaction are different to those previously obtained for the analog surfactant CTAB. X values at which the conformational changes happen depend on the length of the spacer in the surfactant along with the charge of the polar heads. PMID:24736044

  2. 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. PMID:20828705

  3. MAM3 catalyzes the formation of all aliphatic glucosinolate chain lengths in Arabidopsis.

    PubMed

    Textor, Susanne; de Kraker, Jan-Willem; Hause, Bettina; Gershenzon, Jonathan; Tokuhisa, James G

    2007-05-01

    Chain elongated, methionine (Met)-derived glucosinolates are a major class of secondary metabolites in Arabidopsis (Arabidopsis thaliana). The key enzymatic step in determining the length of the chain is the condensation of acetyl-coenzyme A with a series of omega-methylthio-2-oxoalkanoic acids, catalyzed by methylthioalkylmalate (MAM) synthases. The existence of two MAM synthases has been previously reported in the Arabidopsis ecotype Columbia: MAM1 and MAM3 (formerly known as MAM-L). Here, we describe the biochemical properties of the MAM3 enzyme, which is able to catalyze all six condensation reactions of Met chain elongation that occur in Arabidopsis. Underlining its broad substrate specificity, MAM3 also accepts a range of non-Met-derived 2-oxoacids, e.g. converting pyruvate to citramalate and 2-oxoisovalerate to isopropylmalate, a step in leucine biosynthesis. To investigate its role in vivo, we identified plant lines with mutations in MAM3 that resulted in a complete lack or greatly reduced levels of long-chain glucosinolates. This phenotype could be complemented by reintroduction of a MAM3 expression construct. Analysis of MAM3 mutants demonstrated that MAM3 catalyzes the formation of all glucosinolate chain lengths in vivo as well as in vitro, making this enzyme the major generator of glucosinolate chain length diversity in the plant. The localization of MAM3 in the chloroplast suggests that this organelle is the site of Met chain elongation. PMID:17369439

  4. Helical folding of conjugated oligo(phenyleneethynylene): chain-length dependence, solvent effects, and intermolecular assembly.

    PubMed

    Zhu, Ningbo; Yan, Qifan; Luo, Zhouyang; Zhai, You; Zhao, Dahui

    2012-10-01

    As a representative folding system that features a conjugated backbone, a series of monodispersed (o-phenyleneethynylene)-alt-(p-phenyleneethynylene) (PE) oligomers of varied chain length and different side chains were studied. Molecules with the same backbone but different side-chain structures were shown to exhibit similar helical conformations in respectively suitable solvents. Specifically, oligomers with dodecyloxy side chains folded into the helical structure in apolar aliphatic solvents, whereas an analogous oligomer with tri(ethylene glycol) (Tg) side chains adopted the same conformation in polar solvents. The fact that the oligomers with the same backbone manifested a similar folded conformation independent of side chains and the nature of the solvent confirmed the concept that the driving force for folding was the intramolecular aromatic stacking and solvophobic interactions. Although all were capable of inducing folding, different solvents were shown to bestow slightly varied folding stability. The chain-length dependence study revealed a nonlinear correlation between the folding stability with backbone chain length. A critical size of approximately 10 PE units was identified for the system, beyond which folding occurred. This observation corroborated the helical nature of the folded structure. Remarkably, based on the absorption and emission spectra, the effective conjugation length of the system extended more effectively under the folded state than under random conformations. Moreover, as evidenced by the optical spectra and dynamic light-scattering studies, intermolecular association took place among the helical oligomers with Tg side chains in aqueous solution. The demonstrated ability of such a conjugated foldamer in self-assembling into hierarchical supramolecular structures promises application potential for the system. PMID:22829335

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

    PubMed

    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. PMID:27627344

  6. Bottlebrush Copolymer Morphology Transition: Influence of Side Chain Length and Block Volume Fraction

    NASA Astrophysics Data System (ADS)

    Gai, Yue; Song, Dong-Po; Watkins, James

    Brush block copolymers synthesized via living ring-opening metathesis polymerization (ROMP) offer unique advantages as templates for functional hybrid materials. Unlike linear block copolymer, the bottlebrush polymer phase transition not only depends on volume fractions of the two blocks but also on side chain length. Here we report the morphology transitions of PS-b-PEO bottlebrush copolymer (BBCP) as a function of PEO side chain length and block volume fraction. For the BBCPs with similar side chain lengths, highly ordered lamellar morphologies were observed with PEO volume fractions in a wide range from 32 vol% to 72 vol%, which is significantly different from that of traditional linear block copolymers. This study will lay the groundwork for nanostructure fabrications using the BBCPs and provides new insights into the phase behavior of the new type of materials. This work was supported by NSF center for Hierarchical Manufacturing at the University of Massachusetts, Amherst.

  7. Interaction between DNA and Trimethyl-Ammonium Bromides with Different Alkyl Chain Lengths

    PubMed Central

    Cheng, Chao; Ran, Shi-Yong

    2014-01-01

    The interaction between λ—DNA and cationic surfactants with varying alkyl chain lengths was investigated. By dynamic light scattering method, the trimethyl-ammonium bromides-DNA complex formation was shown to be dependent on the length of the surfactant's alkyl chain. For surfactants with sufficient long alkyl chain (CTAB, TTAB, DTAB), the compacted particles exist with a size of ~60–110 nm at low surfactant concentrations. In contrast, high concentration of surfactants leads to aggregates with increased sizes. Atomic force microscope scanning also supports the above observation. Zeta potential measurements show that the potential of the particles decreases with the increase of surfactant concentration (CTAB, TTAB, DTAB), which contributes much to the coagulation of the particles. For OTAB, the surfactant with the shortest chain in this study, it cannot fully neutralize the charges of DNA molecules; consequently, the complex is looser than other surfactant-DNA structures. PMID:24574926

  8. Calmodulin Polymerase Chain Reaction-Restriction Fragment Length Polymorphism for Leishmania Identification and Typing.

    PubMed

    Miranda, Aracelis; Samudio, Franklyn; González, Kadir; Saldaña, Azael; Brandão, Adeilton; Calzada, Jose E

    2016-08-01

    A precise identification of Leishmania species involved in human infections has epidemiological and clinical importance. Herein, we describe a preliminary validation of a restriction fragment length polymorphism assay, based on the calmodulin intergenic spacer region, as a tool for detecting and typing Leishmania species. After calmodulin amplification, the enzyme HaeIII yielded a clear distinction between reference strains of Leishmania mexicana, Leishmania amazonensis, Leishmania infantum, Leishmania lainsoni, and the rest of the Viannia reference species analyzed. The closely related Viannia species: Leishmania braziliensis, Leishmania panamensis, and Leishmania guyanensis, are separated in a subsequent digestion step with different restriction enzymes. We have developed a more accessible molecular protocol for Leishmania identification/typing based on the exploitation of part of the calmodulin gene. This methodology has the potential to become an additional tool for Leishmania species characterization and taxonomy. PMID:27352873

  9. To Slip or Snap: Finite Length Chains and Yield Mechanisms in Polyethylene Fibers

    NASA Astrophysics Data System (ADS)

    O'Connor, Thomas; Robbins, Mark

    2015-03-01

    Understanding the microscopic mechanisms of yield in oriented polymer fibers is a long -standing problem. Advances in polymer processing have produced highly ordered polyethylene (PE) fibers with tensile strengths between 4-7 GPa, but these values are far less than the theoretical limiting strength of 25 Gpa due to C-C bond scission. This reduction in strength is caused by the presence of defects within the fiber. The simplest type of defect is chain ends which reflect the finite length of polymer chains. The presence of chain ends allows a polymer fiber to yield by chain slip without scission of covalent bonds. Here we present extensive united atom (UA) and all atom (AA) molecular dynamics simulations of crystalline PE fibers subjected to uniaxial tension. The fibers are fully aligned crystals constructed from chains of finite length N, with N spanning 3 orders of magnitude (101 -104 monomers). We explore the yield behavior of these systems and relate it to the dynamics of the underlying chain end defects. UA tensile strengths are systematically smaller than AA by a factor of about 3. Both show a saturation in tensile strength as N rises above 500 monomers. This reflects a saturation in the stress for chain ends to slip and implies a maximum tensile strength of 6 Gpa. Financial Support from: NSF IGERT-0801471; US Army Research Laboratory W911NF-12-2-0022.

  10. 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...

  11. 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. PMID:26461930

  12. 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.

  13. Effect of chain length on the formation and stability of synthetic alpha-helical coiled coils.

    PubMed

    Su, J Y; Hodges, R S; Kay, C M

    1994-12-27

    A series of polypeptides containing 9, 12, 16, 19, 23, 26, 30, 33, and 35 amino acid residues was designed to investigate the effects of peptide chain length on the formation and stability of two-stranded alpha-helical dimers or coiled coils. These peptides were synthesized by the solid-phase method, purified by reversed-phase high-performance liquid chromatography (RP-HPLC), and characterized by RP-HPLC, amino acid composition analysis, and mass spectrometry. The amphipathic alpha-helical peptides were designed to dimerize by interchain hydrophobic interactions at positions a and d and interchain salt bridges between lysine and glutamic acid residues at positions e and g of the repeating heptad sequence of Glu-Ile-Glu-Ala-Leu-Lys-Ala (g-a-b-c-d-e-f). The ability of these peptides to form alpha-helical structures in the presence and absence of a helix-inducing reagent (trifluoroethanol) was monitored by circular dichroism spectroscopy. The helicity of the peptides increased with increasing chain length in a cooperative manner. A minimum of three heptads corresponding to six helical turns was required for a peptide to adopt the two-stranded alpha-helical coiled coil conformation in aqueous medium. The increased stability of the peptides as a result of an increase in hydrophobic interactions (chain length) was demonstrated by the shift in the transitions of the guanidine hydrochloride (Gdn.HCl) denaturation and thermal unfolding profiles. The concentrations of denaturant (Gdn.HCl) required to achieve 50% denaturation are 3.2, 4.9, 6.9, and 7.5 M for peptides 23r, 26r, 30r, and 33r, respectively, in aqueous medium. However, the effect of a chain length increase on coiled-coil stability was not additive. The melting temperature, Tm, at which 50% of the helicity is lost, increased by 34 degrees C in changing the peptide chain length from 23 to 26; however, that shift was only 14 degrees C when the chain length was increased from 30 to 33 residues. These results are

  14. [Progress on the biosynthesis of medium-chain-length polyhydroxyalkanoates by microorganisms].

    PubMed

    Yan, Q; Li, Y; Chen, J; Du, G C

    2001-09-01

    Polyhydroxylkanoates(PHAs) are a class of polyesters produced as reserve materials by a large number of microorganisms under metabolic stress. The most fascinating feature of PHAs is its degradability, and which is supposed to take place of the traditional plastics made from petroleum in the future. PHAs are divided into two classes: short-chain-length PHAs(scl-PHAs) and medium-chain-length PHAs. mcl-PHAs is more welcome owing to its more wide crystallinity and higher extension to break than scl-PHAs, especially when some kind of new functional groups were incorporated into the side chain of the polyester. Since Psedumonas oleovorans is the most typical microorganism to produce mcl-PHAs, here the author summarized how P. oleovorans synthesize the mcl-PHAs and the production of mcl-PHAs by fermentation and give some of the idea about the future research of this field. PMID:11797205

  15. Free fatty acids chain length distribution affects the permeability of skin lipid model membranes.

    PubMed

    Uchiyama, Masayuki; Oguri, Masashi; Mojumdar, Enamul H; Gooris, Gert S; Bouwstra, Joke A

    2016-09-01

    The lipid matrix in the stratum corneum (SC) plays an important role in the barrier function of the skin. The main lipid classes in this lipid matrix are ceramides (CERs), cholesterol (CHOL) and free fatty acids (FFAs). The aim of this study was to determine whether a variation in CER subclass composition and chain length distribution of FFAs affect the permeability of this matrix. To examine this, we make use of lipid model membranes, referred to as stratum corneum substitute (SCS). We prepared SCS containing i) single CER subclass with either a single FFA or a mixture of FFAs and CHOL, or ii) a mixture of various CER subclasses with either a single FFA or a mixture of FFAs and CHOL. In vitro permeation studies were performed using ethyl-p-aminobenzoic acid (E-PABA) as a model drug. The flux of E-PABA across the SCS containing the mixture of FFAs was higher than that across the SCS containing a single FA with a chain length of 24 C atoms (FA C24), while the E-PABA flux was not effected by the CER composition. To select the underlying factors for the changes in permeability, the SCSs were examined by Fourier transform infrared spectroscopy (FTIR) and Small angle X-ray scattering (SAXS). All lipid models demonstrated a similar phase behavior. However, when focusing on the conformational ordering of the individual FFA chains, the shorter chain FFA (with a chain length of 16, 18 or 20 C atoms forming only 11m/m% of the total FFA level) had a higher conformational disordering, while the conformational ordering of the chains of the CER and FA C24 and FA C22 hardly did not change irrespective of the composition of the SCS. In conclusion, the conformational mobility of the short chain FFAs present only at low levels in the model SC lipid membranes has a great impact on the permeability of E-PABA. PMID:27287726

  16. Controlling the reversible thermochromism of polydiacetylene/zinc oxide nanocomposites by varying alkyl chain length.

    PubMed

    Chanakul, Amornsak; Traiphol, Nisanart; Traiphol, Rakchart

    2013-01-01

    In this work, polydiacetylene (PDA)/ZnO nanocomposites are successfully fabricated by using three types of monomers with different alkyl chain length, 5,7-hexadecadiynoic acid, 10,12-tricosadiynoic acid, and 10,12-pentacosadiynoic acid. The monomers dispersed in aqueous medium spontaneously assemble onto the surface of ZnO nanoparticles, promoted by strong interfacial interactions. The PDA/ZnO nanocomposites obtained via photopolymerization process are characterized by scanning electron microscopy, laser light scattering, infrared spectroscopy, and uv/vis absorption spectroscopy. The strength of interfacial interactions and morphologies of the nanocomposites are found to vary with alkyl chain length of the monomers. The PDA/ZnO nanocomposites also exhibit rather different thermochromic behaviors compared to their pure PDA counterparts. All nanocomposites show reversible blue/purple color transition upon multiple heating/cooling cycles, while the irreversible blue/red color transition is observed in the systems of pure PDAs. The shortening of alkyl side chain in PDA/ZnO nanocomposites leads to a systematic decrease in their color-transition temperatures. Colors of the nanocomposites at elevated temperature also vary with the alkyl chain length. Our results provide a simple route for controlling the reversible thermochromism of PDA-based materials, allowing their utilization in a wider range of applications. PMID:23058980

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

    PubMed

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

    2014-10-01

    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. PMID:25296310

  18. Chain-Length Heterogeneity Allows for the Assembly of Fatty Acid Vesicles in Dilute Solutions

    PubMed Central

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

    2014-01-01

    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. PMID:25296310

  19. How fatty acids of different chain length enter and leave cells by free diffusion.

    PubMed

    Kamp, Frits; Hamilton, James A

    2006-09-01

    Opposing views exist as to how unesterified fatty acids (FA) enter and leave cells. It is commonly believed that for short- and medium-chain FA free diffusion suffices whereas it is questioned whether proteins are required to facilitate transport of long-chain fatty acid (LCFA). Furthermore, it is unclear whether these proteins facilitate binding to the plasma membrane, trans-membrane movement, dissociation into the cytosol and/or transport in the cytosol. In this mini-review we approach the controversy from a different point of view by focusing on the membrane permeability constant (P) of FA with different chain length. We compare experimentally derived values of the P of short and medium-chain FA with values of apparent permeability coefficients for LCFA calculated from their dissociation rate constant (k(off)), flip-flop rate constant (k(flip)) and partition coefficient (Kp) in phospholipid bilayers. It was found that Overton's rule is valid as long as k(flip)chain length, the permeability increases according to increasing Kp and reaches a maximum for LCFA with chain length of 18 carbons or longer. For fast flip-flop (e.g. k(flip)=15s(-1)), the apparent permeability constant for palmitic acid is very high (P(app)=1.61 cm/s). Even for a slow flip-flop rate constant (e.g. k(flip)=0.3s(-1)), the permeability constant of LCFA is still several orders of magnitude larger than the P of water and other small non-electrolytes. Since polyunsaturated FA have basically the same physico-chemical properties as LCFA, they have similar membrane permeabilities. The implications for theories involving proteins to facilitate uptake of FA are discussed. PMID:16829065

  20. 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

    2016-01-01

    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. PMID:27323120

  1. On the path length of an excess electron interacted with optical phonons in a molecular chain

    NASA Astrophysics Data System (ADS)

    Lakhno, V. D.

    2008-08-01

    We show that in a molecular chain with dispersionless phonons at zero temperature, a “quasistationary” moving soliton state of an excess electron is possible. As the soliton velocity vanishes, the path length of the excess electron exponentially tends to infinity. It is demonstrated that in the presence of dispersion, when the soliton initial velocity exceeds the maximum group velocity of the chain, the soliton slows down until it reaches the maximum group velocity and then moves stationarily at this maximum group velocity. A conclusion is made of the fallacy of some works were the existence of moving polarons in a dispersionless medium is considered infeasible.

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

    DOE PAGESBeta

    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 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

  3. 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.

  4. Nicotine carboxylate insecticide emulsions: effect of the fatty acid chain length.

    PubMed

    Casanova, Herley; Araque, Pedronel; Ortiz, Carlos

    2005-12-28

    The effect of fatty acid chain length on nicotine carboxylate insecticide emulsions has been studied in terms of particle size, interfacial tension, nicotine encapsulation on emulsion droplets, and bioactivity. The particle size of the nicotine emulsion and the interfacial tension at the nicotine carboxylate oil phase (0.03 M)--Tween 80 aqueous phase (0.001 M) were affected in a similar way by the change in the fatty acid chain length, which was correlated by the packing conformation of Tween 80 and nicotine carboxylate molecules as obtained by AM1 theoretical calculations. The amount of encapsulated nicotine inside the nicotine carboxylate emulsion droplets influenced the insecticide bioactivity of nicotine; this relationship was explained in terms of the acid value of the different fatty acids used to prepare the nicotine formulation. PMID:16366679

  5. 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.

  6. 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. PMID:24026215

  7. 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

  8. 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.

  9. Effects of myosin light chain phosphorylation on length-dependent myosin kinetics in skinned rat myocardium.

    PubMed

    Pulcastro, Hannah C; Awinda, Peter O; Breithaupt, Jason J; Tanner, Bertrand C W

    2016-07-01

    Myosin force production is Ca(2+)-regulated by thin-filament proteins and sarcomere length, which together determine the number of cross-bridge interactions throughout a heartbeat. Ventricular myosin regulatory light chain-2 (RLC) binds to the neck of myosin and modulates contraction via its phosphorylation state. Previous studies reported regional variations in RLC phosphorylation across the left ventricle wall, suggesting that RLC phosphorylation could alter myosin behavior throughout the heart. We found that RLC phosphorylation varied across the left ventricle wall and that RLC phosphorylation was greater in the right vs. left ventricle. We also assessed functional consequences of RLC phosphorylation on Ca(2+)-regulated contractility as sarcomere length varied in skinned rat papillary muscle strips. Increases in RLC phosphorylation and sarcomere length both led to increased Ca(2+)-sensitivity of the force-pCa relationship, and both slowed cross-bridge detachment rate. RLC-phosphorylation slowed cross-bridge rates of MgADP release (∼30%) and MgATP binding (∼50%) at 1.9 μm sarcomere length, whereas RLC phosphorylation only slowed cross-bridge MgATP binding rate (∼55%) at 2.2 μm sarcomere length. These findings suggest that RLC phosphorylation influences cross-bridge kinetics differently as sarcomere length varies and support the idea that RLC phosphorylation could vary throughout the heart to meet different contractile demands between the left and right ventricles. PMID:26763941

  10. Fatty Acid Chain Length Dependence of Phase Separation Kinetics in Stratum Corneum Models by IR Spectroscopy.

    PubMed

    Mendelsohn, Richard; Rabie, Emann; Walters, Russel M; Flach, Carol R

    2015-07-30

    The main barrier to permeability in human skin resides in the stratum corneum (SC), a layered structure consisting of anucleated, flattened cells (corneocytes) embedded in a heterogeneous lamellar lipid matrix. While lipid structures and packing propensities in the SC and in SC models have been extensively investigated, only limited data are available concerning the kinetics and mechanism of formation of lamellar phases and particular lipid packing motifs. In our prior investigation, kinetic IR spectroscopy measurements probed the temporal sequence of phase separation leading to ordered structures in a three component SC model of equimolar structurally heterogeneous ceramide[NS], chain perdeuterated stearic acid, and cholesterol. In the current work, the phase separation kinetic effects of specific fatty acid chain lengths with a synthetic structurally homogeneous ceramide[NS] in similar ternary mixtures are examined. These are compared with a mixture containing ceramide[NS] with an unsaturated acid chain. The kinetic events are sensitive to the difference in chain lengths between the ceramide acid chain and the fatty acid as well as to the presence of unsaturation in the former. The observed kinetic behaviors span a wide range of phase separation times, ranging from the formation of a solid solution stable for at least 200 h, to a system in which an orthorhombic fatty acid structure is essentially completely formed within the time resolution of the experiment (15 min). The data seem to offer some features of a spinodal phase separation at relatively short times. Overall the approach offers a possible means for addressing several unanswered questions pertinent to skin pharmacology, such as the roles of a wide variety of ceramide and fatty acid species and the design of therapeutic interventions for repair of pathological conditions of the SC. PMID:26131756

  11. Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.

    PubMed

    Drake, Justin A; Harris, Robert C; Pettitt, B Montgomery

    2016-08-23

    Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains. PMID:27558719

  12. The Characterization of Modified Starch Branching Enzymes: Toward the Control of Starch Chain-Length Distributions

    PubMed Central

    Li, Cheng; Wu, Alex Chi; Go, Rob Marc; Malouf, Jacob; Turner, Mark S.; Malde, Alpeshkumar K.; Mark, Alan E.; Gilbert, Robert G.

    2015-01-01

    Starch is a complex branched glucose polymer whose branch molecular weight distribution (the chain-length distribution, CLD) influences nutritionally important properties such as digestion rate. Chain-stopping in starch biosynthesis is by starch branching enzyme (SBE). Site-directed mutagenesis was used to modify SBEIIa from Zea mays (mSBEIIa) to produce mutants, each differing in a single conserved amino-acid residue. Products at different times from in vitro branching were debranched and the time evolution of the CLD measured by size-exclusion chromatography. The results confirm that Tyr352, Glu513, and Ser349 are important for mSBEIIa activity while Arg456 is important for determining the position at which the linear glucan is cut. The mutant mSBEIIa enzymes have different activities and suggest the length of the transferred chain can be varied by mutation. The work shows analysis of the molecular weight distribution can yield information regarding the enzyme branching sites useful for development of plants yielding starch with improved functionality. PMID:25874689

  13. 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. PMID:9644597

  14. Diversion of phagosome trafficking by pathogenic Rhodococcus equi depends on mycolic acid chain length.

    PubMed

    Sydor, Tobias; von Bargen, Kristine; Hsu, Fong-Fu; Huth, Gitta; Holst, Otto; Wohlmann, Jens; Becken, Ulrike; Dykstra, Tobias; Söhl, Kristina; Lindner, Buko; Prescott, John F; Schaible, Ulrich E; Utermöhlen, Olaf; Haas, Albert

    2013-03-01

    Rhodococcus equi is a close relative of Mycobacterium spp. and a facultative intracellular pathogen which arrests phagosome maturation in macrophages before the late endocytic stage. We have screened a transposon mutant library of R. equi for mutants with decreased capability to prevent phagolysosome formation. This screen yielded a mutant in the gene for β-ketoacyl-(acyl carrier protein)-synthase A (KasA), a key enzyme of the long-chain mycolic acid synthesizing FAS-II system. The longest kasA mutant mycolic acid chains were 10 carbon units shorter than those of wild-type bacteria. Coating of non-pathogenic E. coli with purified wild-type trehalose dimycolate reduced phagolysosome formation substantially which was not the case with shorter kasA mutant-derived trehalose dimycolate. The mutant was moderately attenuated in macrophages and in a mouse infection model, but was fully cytotoxic.Whereas loss of KasA is lethal in mycobacteria, R. equi kasA mutant multiplication in broth was normal proving that long-chain mycolic acid compounds are not necessarily required for cellular integrity and viability of the bacteria that typically produce them. This study demonstrates a central role of mycolic acid chain length in diversion of trafficking by R. equi. PMID:23078612

  15. How does spacer length of imidazolium gemini surfactants control the fabrication of 2D-Langmuir films of silver-nanoparticles at the air-water interface?

    PubMed

    Datta, Sougata; Biswas, Joydeep; Bhattacharya, Santanu

    2014-09-15

    A series of gemini surfactants based on cationic imidazolium ring as polar headgroup, abbreviated as [Im-n-Im], 2Br(-) (n=2, 5, 6 and 12), was synthesized. Their ability to stabilize silver nanoparticles in aqueous media was investigated. The resulting suspensions were characterized by UV-Vis spectroscopy and transmission electron microscopy (TEM). They exhibit specific morphologies by adopting different supramolecular assemblies in aqueous media depending on the internal packing arrangements and on the number of spacer methylene units [-(CH2)n-]. Individual colloids were extracted from the aqueous to chloroform layer and spread at the air/water interface to allow the formation of well-defined Langmuir films. By analysis of the surface pressure-area isotherms, the details about the packing behavior and orientation of the imidazolium gemini surfactant capped silver nanoparticles were obtained. Morphological features of the dynamic process of monolayer compression at the air-water interface were elucidated using Brewster angle microscopy (BAM). These monolayers were further transferred on mica sheets by the Langmuir-Blodgett technique at their associated collapse pressure and the morphology of these monolayers was investigated by atomic force microscopy (AFM). The number of spacer methylene units [-(CH2)n-] of the gemini surfactants exerted critical influence in modulating the characteristics of the resulting Langmuir films. PMID:24998058

  16. 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.

  17. Effects of varying surfactant chain lengths on the magnetic, optical and hyperthermia properties of ferrofluids

    NASA Astrophysics Data System (ADS)

    Rablau, Corneliu; Vaishnava, Prem; Regmi, Rajesh; Sudakar, Chandran; Black, Correy; Lawes, Gavin; Naik, Ratna; Lavoie, Melissa; Kahn, David

    2009-03-01

    We report studies of the structural, magnetic, magneto-thermal and magneto-optic properties of dextran, oleic acid, lauric acid and myristic acid surfacted Fe3O4 nanoparticles of hydrodynamic sizes ranging from 32 nm to 92 nm. All the samples showed saturation magnetization of ˜50 emu/g, significantly smaller than the bulk value for Fe3O4, together with superparamagnetic behavior. The ac magnetization measurements on the dextran coated nanoparticles showed frequency dependent blocking temperature, consistent with superparamgnetic blocking. The ferrofluid heating rates in a 250 Gauss, 100 kHz ac magnetic field varied with the chain lengths of the surfactants, with higher heating rates for longer chains. DC-magnetic-field-induced light scattering patterns produced by two orthogonal He-Ne laser beams passing through the ferrofluid sample revealed different optical signatures for different surfactants.

  18. 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.

  19. 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.

  20. Triazatriangulenium adlayers on Au(111): Superstructure as a function of alkyl side chain length

    NASA Astrophysics Data System (ADS)

    Lemke, Sonja; Ulrich, Sandra; Claußen, Frauke; Bloedorn, Andreas; Jung, Ulrich; Herges, Rainer; Magnussen, Olaf M.

    2015-02-01

    The structure of organic adlayers, formed by self-assembly of molecular platforms of triazatriangulenium ions on Au(111), was systematically studied by scanning tunneling microscopy as a function of the length of the lateral ligands for alkyl side chains from propyl to dodecyl. A series of hexagonally-ordered adlayers with spacings from 10.7 Å (propyl) to 13.6 Å (dodecyl) was found which are commensurate to the Au(111) substrate lattice, indicating localized bonding of the molecules to the metal.

  1. Human 20S proteasome activity towards fluorogenic peptides of various chain lengths.

    PubMed

    Rut, Wioletta; Drag, Marcin

    2016-09-01

    The proteasome is a multicatalytic protease responsible for the degradation of misfolded proteins. We have synthesized fluorogenic substrates in which the peptide chain was systematically elongated from two to six amino acids and evaluated the effect of peptide length on all three catalytic activities of human 20S proteasome. In the cases of five- and six-membered peptides, we have also synthesized libraries of fluorogenic substrates. Kinetic analysis revealed that six-amino-acid substrates are significantly better for chymotrypsin-like and caspase-like activity than shorter peptidic substrates. In the case of trypsin-like activity, a five-amino-acid substrate was optimal. PMID:27176742

  2. 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.

  3. Self-structuring of lamellar bridged silsesquioxanes with long side spacers.

    PubMed

    Fernandes, Mariana; Nobre, Sónia S; Xu, Qinghong; Carcel, Carole; Cachia, Jean Nicolas; Cattoën, Xavier; Sousa, José M; Ferreira, Rute A S; Carlos, Luís D; Santilli, Celso V; Wong Chi Man, Michel; Bermudez, Verónica de Zea

    2011-09-22

    Diurea cross-linked bridged silsesquioxanes (BSs) C(10)C(n)C(10) derived from organosilane precursors, including decylene chains as side spacers and alkylene chains with variable length as central spacers (EtO)(3)Si-(CH(2))(10)-Y-(CH(2))(n)-Y-(CH(2))(10)-Si(OEt)(3) (n = 7, 9-12; Y = urea group and Et = ethyl), have been synthesized through the combination of self-directed assembly and an acid-catalyzed sol-gel route involving the addition of dimethylsulfoxide (DMSO) and a large excess of water. This new family of hybrids has enabled us to conclude that the length of the side spacers plays a unique role in the structuring of alkylene-based BSs, although their morphology remains unaffected. All the samples adopt a lamellar structure. While the alkylene chains are totally disordered in the case of the C(10)C(7)C(10) sample, a variable proportion of all-trans and gauche conformers exists in the materials with longer central spacers. The highest degree of structuring occurs for n = 9. The inclusion of decylene instead of propylene chains as side spacers leads to the formation of a stronger hydrogen-bonded urea-urea array as evidenced by two dimensional correlation Fourier transform infrared spectroscopic analysis. The emission spectra and emission quantum yields of the C(10)C(n)C(10) materials are similar to those reported for diurea cross-linked alkylene-based BSs incorporating propylene chains as side spacers and prepared under different experimental conditions. The emission of the C(10)C(n)C(10) hybrids is ascribed to the overlap of two distinct components that occur within the urea cross-linkages and within the siliceous nanodomains. Time-resolved photoluminescence spectroscopy has provided evidence that the average distance between the siliceous domains and the urea cross-links is similar in the C(10)C(n)C(10) BSs and in oxyethylene-based hybrid analogues incorporating propylene chains as side spacers (diureasils), an indication that the longer side chains in the

  4. Near-infrared optical-absorption behavior in high-beta nonlinear optical chromophore-polymer guest-host materials. II. Dye spacer length effects in an amorphous polycarbonate copolymer host

    NASA Astrophysics Data System (ADS)

    Barto, Richard R.; Frank, Curtis W.; Bedworth, Peter V.; Ermer, Susan; Taylor, Rebecca E.

    2005-06-01

    In the second of a three-part series, spectral absorption behavior of nonlinear optical (NLO) dyes incorporated into amorphous polycarbonate, comprised of a homologous series of dialkyl spacer groups extending from the midsection of the dye molecule, is characterized by UV-Vis and photothermal deflection spectroscopy. The dyes are structural analogs of the NLO dye FTC [2-(3-cyano-4-{2-[5-(2-{4-[ethyl-(2-methoxyethyl)amino]phenyl}vinyl)-3,4-diethylthiophen-2-yl]vinyl}-5,5-dimethyl-5H-furan-2-ylidene)malononitrile]. Previous Monte Carlo calculations [B. H. Robinson and L. R. Dalton, J. Phys. Chem. A 104, 4785 (2000)] predict a strong dependence of the macroscopic nonlinear optical susceptibility on the chromophore waist: length aspect ratio in electric-field-poled films arising from interactions between chromophores. It is expected that these interactions will play a role in the absorption characteristics of unpoled films, as well. The spacer groups range in length from diethyl to dihexyl, and each dye is studied over a wide range of concentrations. Among the four dyes studied, a universal dependence of near-IR loss on inhomogeneous broadening of the dye main absorption peak is found. The inhomogeneous width and its concentration dependence are seen to vary with spacer length in a manner characteristic of the near-IR loss-concentration slope at transmission wavelengths of 1.06 and 1.3μm, but not at 1.55μm. The lower wavelength loss behavior is assigned to purely Gaussian broadening, and is described by classical mixing thermodynamic quantities based on the Marcus theory of inhomogeneous broadening [R. A. Marcus, J. Chem. Phys. 43, 1261 (1965)], modeled as a convolution of dye-dye dipole broadening and dye-polymer van der Waals broadening. The Gaussian dipole interactions follow a Loring dipole-broadening description [R. F. Loring, J. Phys. Chem. 94, 513 (1990)] dominated by the excited-state dipole moment, and have a correlated homogeneous broadening contribution

  5. Dye-sensitized solar cells using a chlorophyll a derivative as the sensitizer and carotenoids having different conjugation lengths as redox spacers

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-Feng; Xiang, Junfeng; Wang, Peng; Koyama, Yasushi; Yanagida, Shozo; Wada, Yuji; Hamada, Kazunori; Sasaki, Shin-ichi; Tamiaki, Hitoshi

    2005-06-01

    Titania-based Grätzel-type solar cells were fabricated by the use of a chlorophyll a derivative (methyl 3-carboxy-3-devinyl-pyropheophorobide a) as the dye sensitizer. A 10% each of carotenoids, including neurosporene, spheroidene, lycopene, anhydrorhodovibrin and spirilloxanthin with numbers of conjugated double bonds, n = 9-13, was added as a conjugated spacer in order to neutralize the dye radical cation and to block the reverse electron transfer. The short-circuit current density ( Jsc) and the solar energy-to-electricity conversion efficiency ( η) systematically increased, with increasing n, from the values of 10.1 mA cm -2 and 3.1% (with no carotenoid) up to 11.5 mA cm -2 and 4.0% (with spirilloxanthin, n = 13), i.e., an enhancement of ≈30%.

  6. 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

  7. The effect of an increase in chain length on the mechanical properties of polyethylene glycols.

    PubMed

    Al-Nasassrah, M A; Podczeck, F; Newton, J M

    1998-07-01

    The mechanical properties of different molecular weights of polyethylene glycol (PEG) have been determined by formation of compacted tablets and beams, which were subjected to diametral compression and 3-point bending, respectively. From diametral compression, the tensile strength for the different grades of PEG was determined. Flat beams made from powder by compaction were used to determine Young's modulus of elasticity. Beams into which a notch had been introduced after formation allowed the fracture mechanical parameters of critical stress intensity factor, K(IC), and fracture toughness, R, to be determined. Evaluation of these parameters as a function of compact porosity allowed extrapolation to values at zero porosity, providing an estimate of the material properties. The increase in chain length of the PEG was found to have a non-linear effect on tensile strength and Young's modulus. The ductility of the polymer increased proportionally to the increase in chain length, reflected by the linear relationship between K(IC) and the molecular weight. Young's modulus and critical stress intensity factor allowed the estimation of the strain energy release rate, G(IC), which is the driving force in crack propagation. Consequently, the tensile strength at zero porosity was found to be predictable from the values of G(IC) and the molecular weight of the different grades of PEG. PMID:9700020

  8. 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.

  9. A coiled-coil domain acts as a molecular ruler in LPS chain length regulation

    PubMed Central

    Tuukkanen, Anne; Danciu, Iulia; Svergun, Dmitri I.; Hussain, Rohanah; Liu, Huanting; Whitfield, Chris; Naismith, James H.

    2014-01-01

    Long-chain bacterial polysaccharides play important roles in pathogenicity. In Escherichia coli O9a, a model for ABC transporter dependent polysaccharide assembly, a large extracellular carbohydrate with a narrow distribution of size is polymerized from monosaccharides by a complex of two proteins, WbdA (polymerase) and WbdD (terminating protein). Such careful control of polymerization is recurring theme in biology. Combining crystallography and small angle X-ray scattering, we show that the C-terminal domain of WbdD contains an extended coiled-coil that physically separates WbdA from the catalytic domain of WbdD. The effects of insertions and deletions within the coiled-coil region were analyzed in vivo, revealing that polymer size is controlled by varying the length of the coiled-coil domain. Thus, the coiled-coil domain of WbdD functions as a molecular ruler that, along with WbdA:WbdD stoichiometry, controls the chain length of a model bacterial polysaccharide. PMID:25504321

  10. 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

  11. Insect attachment on crystalline bioinspired wax surfaces formed by alkanes of varying chain lengths

    PubMed Central

    Böhm, Sandro; Jacky, Nadine; Maier, Louis-Philippe; Dening, Kirstin; Pechook, Sasha; Pokroy, Boaz; Gorb, Stanislav

    2014-01-01

    Summary The impeding effect of plant surfaces covered with three-dimensional wax on attachment and locomotion of insects has been shown previously in numerous experimental studies. The aim of this study was to examine the effect of different parameters of crystalline wax coverage on insect attachment. We performed traction experiments with the beetle Coccinella septempunctata and pull-off force measurements with artificial adhesive systems (tacky polydimethylsiloxane semi-spheres) on bioinspired wax surfaces formed by four alkanes of varying chain lengths (C36H74, C40H82, C44H90, and C50H102). All these highly hydrophobic coatings were composed of crystals having similar morphologies but differing in size and distribution/density, and exhibited different surface roughness. The crystal size (length and thickness) decreased with an increase of the chain length of the alkanes that formed these surfaces, whereas the density of the wax coverage, as well as the surface roughness, showed an opposite relationship. Traction tests demonstrated a significant, up to 30 fold, reduction of insect attachment forces on the wax surfaces when compared with the reference glass sample. Attachment of the beetles to the wax substrates probably relied solely on the performance of adhesive pads. We found no influence of the wax coatings on the subsequent attachment ability of beetles. The obtained data are explained by the reduction of the real contact between the setal tips of the insect adhesive pads and the wax surfaces due to the micro- and nanoscopic roughness introduced by wax crystals. Experiments with polydimethylsiloxane semi-spheres showed much higher forces on wax samples when compared to insect attachment forces measured on these surfaces. We explain these results by the differences in material properties between polydimethylsiloxane probes and tenent setae of C. septempunctata beetles. Among wax surfaces, force experiments showed stronger insect attachment and higher pull

  12. How does the spacer length of cationic gemini lipids influence the lipoplex formation with plasmid DNA? Physicochemical and biochemical characterizations and their relevance in gene therapy.

    PubMed

    Muñoz-Úbeda, Mónica; Misra, Santosh K; Barrán-Berdón, Ana L; Datta, Sougata; Aicart-Ramos, Clara; Castro-Hartmann, Pablo; Kondaiah, Paturu; Junquera, Elena; Bhattacharya, Santanu; Aicart, Emilio

    2012-12-10

    with HEK293T, HeLa, CHO, U343, and H460 cells. The α and ρeff values for each lipid mixture were optimized on HEK293T cells for transfection, and using these values, the remaining cells were also transfected in absence (-FBS-FBS) and presence (-FBS+FBS) of serum. The transfection efficiency was higher with the CLs of shorter gemini spacers (n=2 or 3). Each formulation expressed GFP on pDNA transfection and confocal fluorescence microscopy corroborated the results. C16C2C16/DOPE mixtures were the most efficient toward transfection among all the lipid mixtures and, in presence of serum, even better than the Lipofectamine2000, a commercial transfecting agent. Each lipid combination was safe and did not show any significant levels of toxicity. Probably, the presence of two coexisting lamellar structures in lipoplexes synergizes the transfection efficiency of the lipid mixtures which are plentiful in the lipoplexes formed by CLs with short spacer (n=2, 3) than those with the long spacer (n=5, 12). PMID:23130552

  13. Spacer-length dependence of programmed −1 or −2 ribosomal frameshifting on a U6A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting

    PubMed Central

    Lin, Zhaoru; Gilbert, Robert J. C.; Brierley, Ian

    2012-01-01

    Programmed −1 ribosomal frameshifting is employed in the expression of a number of viral and cellular genes. In this process, the ribosome slips backwards by a single nucleotide and continues translation of an overlapping reading frame, generating a fusion protein. Frameshifting signals comprise a heptanucleotide slippery sequence, where the ribosome changes frame, and a stimulatory RNA structure, a stem–loop or RNA pseudoknot. Antisense oligonucleotides annealed appropriately 3′ of a slippery sequence have also shown activity in frameshifting, at least in vitro. Here we examined frameshifting at the U6A slippery sequence of the HIV gag/pol signal and found high levels of both −1 and −2 frameshifting with stem–loop, pseudoknot or antisense oligonucleotide stimulators. By examining −1 and −2 frameshifting outcomes on mRNAs with varying slippery sequence-stimulatory RNA spacing distances, we found that −2 frameshifting was optimal at a spacer length 1–2 nucleotides shorter than that optimal for −1 frameshifting with all stimulatory RNAs tested. We propose that the shorter spacer increases the tension on the mRNA such that when the tRNA detaches, it more readily enters the −2 frame on the U6A heptamer. We propose that mRNA tension is central to frameshifting, whether promoted by stem–loop, pseudoknot or antisense oligonucleotide stimulator. PMID:22743270

  14. Ancestry inference in complex admixtures via variable-length Markov chain linkage models.

    PubMed

    Rodriguez, Jesse M; Bercovici, Sivan; Elmore, Megan; Batzoglou, Serafim

    2013-03-01

    Inferring the ancestral origin of chromosomal segments in admixed individuals is key for genetic applications, ranging from analyzing population demographics and history, to mapping disease genes. Previous methods addressed ancestry inference by using either weak models of linkage disequilibrium, or large models that make explicit use of ancestral haplotypes. In this paper we introduce ALLOY, an efficient method that incorporates generalized, but highly expressive, linkage disequilibrium models. ALLOY applies a factorial hidden Markov model to capture the parallel process producing the maternal and paternal admixed haplotypes, and models the background linkage disequilibrium in the ancestral populations via an inhomogeneous variable-length Markov chain. We test ALLOY in a broad range of scenarios ranging from recent to ancient admixtures with up to four ancestral populations. We show that ALLOY outperforms the previous state of the art, and is robust to uncertainties in model parameters. PMID:23421795

  15. A method for the determination of the carbon chain length composition of amine oxides.

    PubMed

    Langley, N A; Suddaby, D; Coupland, K

    1988-12-01

    Synopsis Alkylamine oxides and alkylamidopropyldimethylamine oxides belong to an important group of surfactant materials. They are used extensively in formulations for cosmetics, toiletries and household products. Although there are numerous analytical methods available to evaluate physical and chemical properties of these compounds, there remains a demand for a qualitative method for the determination of the carbon chain length composition. Amine oxides cannot be analysed directly by gas liquid chromatography (GLC) as they decompose at temperatures above 100 degrees C to give the terminal alkenes and tertiary amines. However, amine oxides can be analysed by GLC if they are first reduced to the tertiary amines. Examples of each type of amine oxide were reduced with triphenylphosphine in boiling glacial acetic acid between 1 and 1.5 h. In this paper a rapid qualitative analytical procedure is described. PMID:19456939

  16. Density fluctuations in saturated phospholipid bilayers increase as the acyl-chain length decreases.

    PubMed Central

    Ipsen, J H; Jørgensen, K; Mouritsen, O G

    1990-01-01

    A systematic computer simulation study is conducted for a model of the main phase transition of fully hydrated saturated diacyl phosphatidylcholine bilayers (DMPC, DPPC, and DSPC). With particular focus on the fluctuation effects on the thermal properties in the transition region, the study yields data for the specific heat, the lateral compressibility, and the lipid-domain size distribution. Via a simple model assumption the transmembrane passive ion permeability is derived from the lipid-domain interfacial measure. A comparative analysis of the various data shows, in agreement with a number of experiments, that the lateral density fluctuations and hence the response functions increase as the acyl-chain length is decreased. Images FIGURE 2 PMID:2291936

  17. Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models

    PubMed Central

    Bercovici, Sivan; Elmore, Megan; Batzoglou, Serafim

    2013-01-01

    Abstract Inferring the ancestral origin of chromosomal segments in admixed individuals is key for genetic applications, ranging from analyzing population demographics and history, to mapping disease genes. Previous methods addressed ancestry inference by using either weak models of linkage disequilibrium, or large models that make explicit use of ancestral haplotypes. In this paper we introduce ALLOY, an efficient method that incorporates generalized, but highly expressive, linkage disequilibrium models. ALLOY applies a factorial hidden Markov model to capture the parallel process producing the maternal and paternal admixed haplotypes, and models the background linkage disequilibrium in the ancestral populations via an inhomogeneous variable-length Markov chain. We test ALLOY in a broad range of scenarios ranging from recent to ancient admixtures with up to four ancestral populations. We show that ALLOY outperforms the previous state of the art, and is robust to uncertainties in model parameters. PMID:23421795

  18. 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.

  19. Normal and shear forces between charged solid surfaces immersed in cationic surfactant solution: the role of the alkyl chain length.

    PubMed

    Silbert, Gilad; Kampf, Nir; Klein, Jacob

    2014-05-13

    Using a surface force balance (SFB), we measured the boundary friction and the normal forces between mica surfaces immersed in a series of alkyltrimethylammonium chloride (TAC) surfactant solutions well above the critical micelle concentration (CMC). The surfactants that were used--C14TAC, C16TAC, and C18TAC--varied by the length of the alkyl chain. The structures of the adsorbed layers on the mica were obtained using AFM imaging and ranged from flat bilayers to rodlike micelles. Despite the difference in alkyl chain, all the surfactant solutions reduce the friction between the two mica surfaces enormously relative to immersion in water, and have similar friction coefficients (μ ≈ 0.001). The pressure at which such lubrication breaks down is higher for the surfactants with longer chain lengths and indicates that an important role of the chain length is to provide a more robust structure of the adsorbed layers which maintains its integrity to higher pressures. PMID:24720712

  20. Primitive models of chemical association. II. Polymerization into flexible chain molecules of prescribed length

    SciTech Connect

    Kalyuzhnyi, Y.V. |; Lin, C.; Stell, G.

    1997-02-01

    The structural properties of the totally flexible sticky two-point (S2P) model for polymerization into chain molecules of fixed length are studied. The model is represented by an n-component mixture of hard spheres of the same size with species 2,{hor_ellipsis},n{minus}1 bearing two attractive sticky sites A and B, randomly distributed on the surface. The hard spheres of species 1 and n have only one site per particle, site B for species 1 and site A for species n. Due to the specific choice for the attractive interaction, which is present only between site B of the particles of species a and site A of the particles of species a+1, this version of the S2P model represents an associating fluid that polymerizes into freely jointed tangent hard-sphere chain molecules. The correlation functions of this model are studied at all degrees of association using a recently obtained general solution of the polymer Percus{endash}Yevick (PPY) approximation [Yu. Kalyuzhnyi and P. Cummings, J. Chem. Phys. {bold 103}, 3265 (1995)]. Comparison of the results of the present theory in the complete association limit with corresponding computer-simulation results and results of other theories is presented and discussed. The complete-association results constitute a quantitatively successful theory of the mean monomer{endash}monomer distribution functions for n{le}16 but for n=50 these functions are no longer quantitatively accurate. {copyright} {ital 1997 American Institute of Physics.}

  1. Chain length, temperature and solvent effects on the structural properties of α-aminoisobutyric acid homooligopeptides.

    PubMed

    Grubišić, Sonja; Chandramouli, Balasubramanian; Barone, Vincenzo; Brancato, Giuseppe

    2016-07-27

    Non-coded α-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is α-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on α-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)n-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 310- and/or α-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i → i + 3 and i → i + 4 hydrogen bonds characterizing 310 and α-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides. PMID:27402118

  2. Dynamic Assessment of Bilayer Thickness by Varying Phospholipid and Hydraphile Synthetic Channel Chain Lengths

    PubMed Central

    Weber, Michelle E.; Schlesinger, Paul H.; Gokel, George W.

    2008-01-01

    A library of “hydraphile” synthetic ion channel analogues that differ in overall length from ∼28-58 Å has been prepared. A new and convenient ion-selective electrode (ISE) method was used to assay Na+ release. Liposomes were formed from three different phospholipids: 1,2-dimyristoleoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 1,2-dierucoyl-sn-glycero-3-phosphocholine (DEPC). The acyl chains of the lipids comprise cis-unsaturated 14:1, 18:1, or 22:1 residues, respectively. Sodium release was measured for each liposome system with each of the synthetic channels. Peak activity was observed for shorter channels in liposomes formed from DMPC and for longer channels in DEPC. A separate study was then conducted in DMPC liposomes in the presence of the putative membrane-thickening agents cholesterol and decane. Peak activity was clearly shifted to longer channel lengths upon addition of 20 or 40 mol % cholesterol or n-decane to the liposome preparation. PMID:15643888

  3. Effects of particle size and chain length on flotation of quaternary ammonium salts onto kaolinite

    NASA Astrophysics Data System (ADS)

    Longhua, Xu; Yuehua, Hu; Faqin, Dong; Hao, Jiang; Houqin, Wu; Zhen, Wang; Ruohua, Liu

    2015-06-01

    Effects of particle size and chain length on flotation of quaternary ammonium salts (QAS) onto kaolinite have been investigated by flotation tests. Dodecyltrimethylammonium chloride (DTAC) and cetyltrimethylammonium chloride (CTAC) were used as collectors for kaolinite in different particle size fractions (0.075 ~ 0.01 mm, 0.045 ~ 0.075 mm, 0 ~ 0.045 mm). The anomalous flotation behavior of kaolinite have been further explained based on crystal structure considerations by adsorption tests and molecular dynamics (MD) simulation. The results show that the flotation recovery of kaolinite in all different particle size fractions decreases with an increase in pH. As the concentration of collectors increases, the flotation recovery increases. The longer the carbon chain of QAS is, the higher the recoveries of coarse kaolinite (0.075 ~ 0.01 mm and 0.045 ~ 0.075 mm) are. But the flotation recovery of the finest kaolinite (0 ~ 0.045 mm) decreases with chain lengths of QAS collectors increasing, which is consistent with the flotation results of unscreened kaolinite (0 ~ 0.075 mm). It is explained by the froth stability related to the residual concentration of QAS collector in mineral pulp. In lower residual concentration, the froth stability becomes worse. Within the range of flotation collector concentration, it's easy of CTAC to be completely adsorbed by kaolinite in the particle size fraction (0-0.045 mm), which led to lower flotation recovery. Moreover, it is interesting that the coarser particle size of kaolinite is, the higher flotation recovery is. The anomalous flotation behavior of kaolinite is rationalized based on crystal structure considerations. The results of MD simulations show that the (001) kaolinite surface has the strongest interaction with DTAC, compared with the (00 1) face, (010) and (110) edges. On the other hand, when particle size of kaolinite is altered, the number of basal planes and edge planes is changed. It is observed that the finer kaolinite

  4. Effects of spacer parameters, modified monolayers, and patterned substrate on the capture efficiency of Escherichia coli-antibody based biosensing matrix

    NASA Astrophysics Data System (ADS)

    Cao, Ting

    2007-12-01

    To overcome the problem of losing bioactivity in covalent coupling in chemical sensor, a potential approach is to employ a long chain spacer to immobilize the antibody indirectly while maintaining separation of the biomolecule from the substrate. In this study, Poly (ethylene glycol) (PEG) spacers were employed for tethering E.Coli K99 pilus antibody to silicon wafer surfaces for the purpose of increasing the flexibility of antibody as well as reducing the steric hindrance. To illustrate the effect of spacer length, a series of spacer lengths were used to covalently attach the antibodies to silicon surfaces. XPS and AFM were used to characterize the surface morphology and chemical composition at each reaction step. The effect of spacer length in improving the specificity of immobilized antibody and the recognition process for bacteria-antibody was investigated by attaching E.Coli on the end of an AFM tip. Distribution of unbinding force and rupture distance from the force-distance curved obtained by AFM showed that the introduction of PEG spacer facilitates bacterial recognition which can improve the detected specific interaction up to 90%. J600 exhibited better flexibility in overcoming the steric hindrance experienced with direct immobilization than other spacer lengths. Moreover, binding efficiency, rupture distance and force distribution of bacteria-antibody pairs can be elucidated with AFM for measurement.

  5. Determination of locust bean gum and guar gum by polymerase chain reaction and restriction fragment length polymorphism analysis.

    PubMed

    Meyer, K; Rosa, C; Hischenhuber, C; Meyer, R

    2001-01-01

    A polymerase chain reaction (PCR) was developed to differentiate the thickening agents locust bean gum (LBG) and the cheaper guar gum in finished food products. Universal primers for amplification of the intergenic spacer region between trnL 3' (UAA) exon and trnF (GAA) gene in the chloroplast (cp) genome and subsequent restriction analysis were applied to differentiate guar gum and LBG. The presence of <5% (w/w) guar gum powder added to LBG powder was detectable. Based on data obtained from sequencing this intergenic spacer region, a second PCR method for the specific detection of guar gum DNA was also developed. This assay detected guar gum powder in LBG in amounts as low as 1% (w/w). Both methods successfully detected guar gum and/or LBG in ice cream stabilizers and in foodstuffs, such as dairy products, ice cream, dry seasoning mixes, a finished roasting sauce, and a fruit jelly product, but not in products with highly degraded DNA, such as tomato ketchup and sterilized chocolate cream. Both methods detected guar gum and LBG in ice cream and fresh cheese at levels <0.1%. PMID:11234856

  6. Use of Length Heterogeneity Polymerase Chain Reaction (LH-PCR) as Non-Invasive Approach for Dietary Analysis of Svalbard Reindeer, Rangifer tarandus platyrhynchus

    PubMed Central

    Joo, Sungbae; Han, Donguk; Lee, Eun Ju; Park, Sangkyu

    2014-01-01

    To efficiently investigate the forage preference of Svalbard reindeer (Rangifer tarandus platyrhynchus), we applied length-heterogeneity polymerase chain reaction (LH-PCR) based on length differences of internal transcribed spacer (ITS) regions of ribosomal RNA (rRNA) to fecal samples from R. tarandus platyrhynchus. A length-heterogeneity (LH) database was constructed using both collected potential food sources of Svalbard reindeer and fecal samples, followed by PCR, cloning and sequencing. In total, eighteen fecal samples were collected between 2011 and 2012 from 2 geographic regions and 15 samples were successfully amplified by PCR. The LH-PCR analysis detected abundant peaks, 18.6 peaks on an average per sample, ranging from 100 to 500 bp in size and showing distinct patterns associated with both regions and years of sample collection. Principal component analysis (PCA) resulted in clustering of 15 fecal samples into 3 groups by the year of collection and region with a statistically significant difference at 99.9% level. The first 2 principal components (PCs) explained 71.1% of the total variation among the samples. Through comparison with LH database and identification by cloning and sequencing, lichens (Stereocaulon sp. and Ochrolechia sp.) and plant species (Salix polaris and Saxifraga oppositifolia) were detected as the food sources that contributed most to the Svalbard reindeer diet. Our results suggest that the use of LH-PCR analysis would be a non-invasive and efficient monitoring tool for characterizing the foraging strategy of Svalbard reindeer. Additionally, combining sequence information would increase its resolving power in identification of foraged diet components. PMID:24618847

  7. Chain length dependence of non-surface activity and micellization behavior of cationic amphiphilic diblock copolymers.

    PubMed

    Ghosh, Arjun; Yusa, Shin-ichi; Matsuoka, Hideki; Saruwatari, Yoshiyuki

    2014-04-01

    The cationic and anionic amphiphilic diblock copolymers with a critical chain length and block ratio do not adsorb at the air/water interface but form micelles in solution, which is a phenomenon called "non-surface activity". This is primarily due to the high charge density of the block copolymer, which creates a strong image charge effect at the air/water interface preventing adsorption. Very stable micelle formation in bulk solution could also play an important role in the non-surface activity. To further confirm these unique properties, we studied the adsorption and micellization behavior of cationic amphiphilic diblock copolymers of poly(n-butyl acrylate)-b-poly(3-(methacryloyloxy)ethyl)trimethylammonium chloride) (PBA-b-PDMC) with different molecular weights of hydrophobic blocks but with the same ionic block length. These block copolymers were successfully prepared via consecutive reversible addition-fragmentation chain transfer (RAFT) polymerization. The block copolymer with the shortest hydrophobic block length was surface-active; the solution showed surface tension reduction and foam formation. However, above the critical block ratio, the surface tension of the solution did not decrease with increasing polymer concentration, and there was no foam formation, indicating lack of surface activity. After addition of 0.1 M NaCl, stable foam formation and slight reduction of surface tension were observed, which is reminiscent of the electrostatic nature of the non-surface activity. Fluorescence and dynamic and static light scattering measurements showed that the copolymer with the shortest hydrophobic block did not form micelles, while the block copolymers formed spherical micelles having radii of 25-30 nm. These observations indicate that micelle formation is also important for non-surface activity. Upon addition of NaCl, cmc did not decrease but rather increased as observed for non-surface-active block copolymers previously studied. The micelles formed were

  8. Utilization of medium-chain triglycerides by neonatal piglets: chain length of even- and odd-carbon fatty acids and apparent digestion/absorption and hepatic metabolism.

    PubMed

    Odle, J; Benevenga, N J; Crenshaw, T D

    1991-05-01

    Jugular plasma concentrations of medium-chain fatty acids (MCFA) and whole blood concentrations of D-beta-hydroxybutyrate (BHBA) were measured in 1-d-old pigs at 0, 1, 2, 4 and 8 h after forcefeeding 12 mL of one of four triglycerides: tri-7:0, 8:0, 9:0 or 10:0. Both BHBA and MCFA were highest at 1 h. The MCFA measured at 1 h decreased (P less than 0.01) with increasing chain length. The BHBA was not different in pigs given tri-7:0, 8:0 or 9:0 but was lower (P less than 0.05) for pigs given tri-10:0. Isolated hepatocytes converted [1-14C] C7 or C9 to CO2 and acid soluble products more than 40% faster than cells given 8:0 or 10:0 and consumed 7% more O2. Even- and odd-MCFA were oxidized faster (P less than 0.01) than 18:1 (n-9). Theoretical calculations from fatty acid oxidation accounted for 96 to 142% of measured O2 consumption for the various fatty acids. In all instances, L-carnitine had no effect. Appearance of 14C in lipid products increased progressively with chain length from 7:0 to 18:1 (n-9). Collectively, these data suggest that changes in chain length within the medium-chain family may dramatically influence the rate and extent of digestion and/or absorption and metabolism of medium-chain triglycerides by neonates. This may be a consequence of increased hydrophobicity with increasing chain length or, for odd-chain fatty acids, a reflection of anaplerotic carbon effects from propionyl-CoA metabolism. PMID:2019870

  9. Poly(2-aminoethyl methacrylate) with well-defined chain-length for DNA vaccine delivery to dendritic cells

    PubMed Central

    Ji, Weihang; Panus, David; Palumbo, R. Noelle; Tang, Rupei; Wang, Chun

    2011-01-01

    Poly(2-aminoethyl methacrylate) (PAEM) homopolymers with defined chain-length and narrow molecular weight distribution were synthesized using atom transfer radical polymerization (ATRP), and a comprehensive study was conducted to evaluate the colloidal properties of PAEM/plasmid DNA polyplexes, the uptake and subcellular trafficking of polyplexes in antigen-presenting dendritic cells (DCs), and the biological performance of PAEM as a potential DNA vaccine carrier. PAEM of different chain-length (45, 75 and 150 repeating units) showed varying strength in condensing plasmid DNA into narrowly dispersed nanoparticles with very low cytotoxicity. Longer polymer chain-length resulted in higher levels of overall cellular uptake and nuclear uptake of plasmid DNA, but shorter polymer chains favored intracellular and intra-nuclear release of free plasmid from the polyplexes. Despite its simple chemical structure, PAEM transfected DCs very efficiently in vitro in media with or without serum and led to phenotypic maturation of DCs. When a model antigen-encoding ovalbumin plasmid was used, transfected DCs stimulated the activation of naïve CD8+ T cells to produce high levels of interferon-γ. The efficiency of transfection, DC maturation, and CD8+ T cell activation showed varying degrees of polymer chain-length dependence. These structurally defined cationic polymers may have much potential as efficient DNA vaccine carriers and immunostimulatory adjuvants. They may also serve as a model material system for elucidating structural and intracellular mechanisms of polymer-mediated DNA vaccine delivery. PMID:22082257

  10. Plasmon-assisted photocurrent generation from silver nanoparticle monolayers combined with porphyrins via their different chain-length alkylcarboxylates.

    PubMed

    Kakuta, Takayoshi; Kon, Hiroki; Kajikawa, Azusa; Kanaizuka, Katsuhiko; Yagyu, Shigeta; Miyake, Ryosuke; Ishizakil, Manabu; Uruma, Keirei; Togashi, Takanari; Sakamoto, Masatomi; Kurihara, Masato

    2014-06-01

    Three-typed porphyrin derivatives with a different chain-length alkylcarboxylic acid as their peripheral anchor group have been prepared. Anodic photocurrents were observed in a simple system where the porphyrin derivatives were directly anchored on an indium tin oxide (ITO) electrode. Cathodic photocurrents and their plasmon-assisted enhancement appeared from an Ag nanoparticle (Ag NP) composite monolayer combined with the porphyrin derivatives on the ITO electrode. In the photocurrent generation mechanism, Ag NPs played both the roles as photon- and energy-transfer to the porphyrin derivatives. The plasmon-assisted enhancement was affected by the chain-lengths of the peripheral anchor groups. PMID:24738356

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

    NASA Astrophysics Data System (ADS)

    Polley, Anirban; Mayor, Satyajit; Rao, Madan

    2014-08-01

    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 (lo)-liquid disordered (ld) phases, while the composition of the lower leaflet is varied from the phase coexistence regime to the mixed ld phase, across a first-order phase boundary. In the regime of phase coexistence in each leaflet, we find strong transbilayer correlations of the lo 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 lo domains in the upper leaflet can induce phase segregation in the lower leaflet, when the latter is nominally in the mixed (ld) phase.

  12. 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.

  13. Fungal Polyketide Synthase Product Chain-Length Control by Partnering Thiohydrolase

    PubMed Central

    2015-01-01

    Fungal highly reducing polyketide synthases (HRPKSs) are an enigmatic group of multidomain enzymes that catalyze the biosynthesis of structurally diverse compounds. This variety stems from their intrinsic programming rules, which permutate the use of tailoring domains and determine the overall number of iterative cycles. From genome sequencing and mining of the producing strain Eupenicillium brefeldianum ATCC 58665, we identified an HRPKS involved in the biosynthesis of an important protein transport-inhibitor Brefeldin A (BFA), followed by reconstitution of its activity in Saccharomyces cerevisiae and in vitro. Bref-PKS demonstrated an NADPH-dependent reductive tailoring specificity that led to the synthesis of four different octaketide products with varying degrees of reduction. Furthermore, contrary to what is expected from the structure of BFA, Bref-PKS is found to be a nonaketide synthase in the absence of an associated thiohydrolase Bref-TH. Such chain-length control by the partner thiohydrolase was found to be present in other HRPKS systems and highlights the importance of including tailoring enzyme activities in predicting fungal HRPKS functions and their products. PMID:24845309

  14. Exploring the low temperature thermodynamics of lattice proteins and polymers with chain lengths > 1000

    NASA Astrophysics Data System (ADS)

    Wuest, Thomas

    2012-02-01

    Coarse-grained (lattice-) models have a long tradition in aiding to decipher the physical or biological complexity of polymers and proteins. Despite their simplicity however, numerical simulations of such models are often computationally very demanding and the quest for efficient algorithms is as old as the models themselves. I present a computational method based on Wang-Landau sampling in combination with suitable trial move sets which is particularly effective to study models such as the hydrophobic-polar (HP) lattice model of protein folding or its counterpart in polymer physics, the interactive self-avoiding walk (ISAW) at low temperatures. The approach provides a versatile and powerful mean for both the ground state search and the determination of the entire energy density of states (DOS) yielding reliable estimates of thermodynamic quantities for chain lengths > 4000 (ISAW) even in the very dense collapsed phase. The appearance of multiple low temperature pseudo-transitions for ISAWs will be elucidated. Further methodological improvements will be discussed.

  15. 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.

  16. 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

  17. 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. PMID:26153503

  18. 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. PMID:25609558

  19. 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. PMID:19202803

  20. Model and cell membrane partitioning of perfluorooctanesulfonate is independent of the lipid chain length.

    PubMed

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

    2010-03-01

    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 produced a concentration-dependent decrease of the main phase transition temperature (T(m)) and an increased peak width (DeltaT(w)) 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 4.4x10(4) to 8.8x10(4). 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

  1. PARTITIONING OF PERFLUOROOCTANOATE INTO PHOSPHATIDYLCHOLINE BILAYERS IS CHAIN LENGTH-INDEPENDENT

    PubMed Central

    Xie, Wei; Bothun, Geoffrey D.; Lehmler, Hans-Joachim

    2010-01-01

    The chain length dependence of the interaction of PFOA, a persistent environmental contaminant, with dimyristoyl- (DMPC), dipalmitoyl- (DPPC) and distearoylphosphatidylcholine (DSPC) was investigated using steady-state fluorescence anisotropy spectroscopy, differential scanning calorimetry (DSC) and dynamic light scattering (DLS). PFOA caused a linear depression of the main phase transition temperature Tm while increasing the width of the phase transition of all three phosphatidylcholines. Although PFOA’s effect on the on Tm and the transition width decreased in the order DMPC > DPPC > DSPC, its relative effect on the phase behavior was largely independent of the phosphatidylcholine. PFOA caused swelling of DMPC but not DPPC and DSPC liposomes at 37°C in the DLS experiments, which suggests that PFOA partitions more readily into bilayers in the fluid phase. These findings suggest that PFOA’s effect on the phase behavior of phosphatidylcholines depends on the cooperativity and state (i.e., gel versus liquid phase) of the membrane. DLS experiments are also consistent with partial liposome solubilization at PFOA/lipid molar ratios > 1, which suggests the formation of mixed PFOA-lipid micelles. PMID:20096277

  2. 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

  3. Embedding the outer chain movement for main partition of β-number with length [1, 0, 0,…

    NASA Astrophysics Data System (ADS)

    Mohommed, Eman F.; Ibrahim, Haslinda; Ahmad, Nazihah; Mahmood, Ammar

    2016-08-01

    One of the graphical representations for any partition of a non-negative integers in the modular representation theory of diagram algebra is James abacus using Beta numbers. In this work James abacus is divided positions into several chains. A new diagram Atco is introduced by employing on the outer chain with length [1, 0, 0,…] on the active James abacus. Finally a consecutive new diagram of b2, b3,…, be can be found from active diagram Atco which is found after applying chain movement.

  4. The horizontal transfer of antibiotic resistance genes is enhanced by ionic liquid with different structure of varying alkyl chain length

    PubMed Central

    Wang, Qing; Lu, Qian; Mao, Daqing; Cui, Yuxiao; Luo, Yi

    2015-01-01

    Antibiotic resistance genes (ARGs) have become a global health concern. In our previous study, an ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]) had been proven to facilitate the dissemination of ARGs in the environment. However, enhanced alkyl group chain length or the substitution of alkyl groups with the cation ring corresponded with increased antimicrobial effects. In this study, we investigated how different structures of ILs with 4, 6, and 8 C atoms in the longer alkyl chain on the imidazolium cations facilitated the dissemination of ARGs. The promotion of plasmid RP4 transfer frequency decreased with [CnMIM][BF4] increasing the alkyl chain length from 4 carbon atoms to 8 carbon atoms on the imidazolium cations, which is observed with [BMIM][BF4] (n = 4, 5.9 fold) > HMIM][BF4] (n = 6, 2.2 fold) > [OMIM][BF4] (n = 8, 1.7 fold). This illustrates that [CnMIM][BF4] with increasing the alkyl chain length exert decreasing ability in facilitating plasmid RP4 horizontal transfer, which is possibly related to IL-structure dependent toxicity. The IL-structure dependent plasmid RP4 transfer frequency was attributable to bacterial cell membrane permeability weaken with increasing alkyl chain length of [CnMIM][PF4], which was evidenced by flow cytometry. In freshwater microcosm, [CnMIm][BF4] promoted the relative abundance of the sulI and intI genes for 4.6 folds, aphA and traF for 5.2 folds higher than the untreated groups, promoting the propagation of ARGs in the aquatic environment. This is the first report that ILs with different structure of varying alkyl chain length facilitate horizontal transfer of plasmid RP4 which is widely distributed in the environment, and thus add the adverse effects of the environmental risk of ILs. PMID:26379641

  5. Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida

    PubMed Central

    2014-01-01

    Background Pseudomnas putida is a natural producer of medium chain length polyhydroxyalkanoates (mcl-PHA), a polymeric precursor of bioplastics. A two-fold increase of mcl-PHA production via inactivation of the glucose dehydrogenase gene gcd, limiting the metabolic flux towards side products like gluconate was achieved before. Here, we investigated the overproduction of enzymes catalyzing limiting steps of mcl-PHA precursor formation. Results A genome-based in silico model for P. putida KT2440 metabolism was employed to identify potential genetic targets to be engineered for the improvement of mcl-PHA production using glucose as sole carbon source. Here, overproduction of pyruvate dehydrogenase subunit AcoA in the P. putida KT2440 wild type and the Δgcd mutant strains led to an increase of PHA production. In controlled bioreactor batch fermentations PHA production was increased by 33% in the acoA overexpressing wild type and 121% in the acoA overexpressing Δgcd strain in comparison to P. putida KT2440. Overexpression of pgl-encoding 6-phosphoglucolactonase did not influence PHA production. Transcriptome analyses of engineered PHA producing P. putida in comparison to its parental strains revealed the induction of genes encoding glucose 6-phosphate dehydrogenase and pyruvate dehydrogenase. In addition, NADPH seems to be quantitatively consumed for efficient PHA synthesis, since a direct relationship between low levels of NADPH and high concentrations of the biopolymer were observed. In contrast, intracellular levels of NADH were found increased in PHA producing organisms. Conclusion Production of mcl-PHAs was enhanced in P. putida when grown on glucose via overproduction of a pyruvate dehydrogenase subunit (AcoA) in combination with a deletion of the glucose dehydrogenase (gcd) gene as predicted by in silico elementary flux mode analysis. PMID:24948031

  6. 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. PMID:24630613

  7. Adsorption of quinolone antibiotics in spherical mesoporous silica: Effects of the retained template and its alkyl chain length.

    PubMed

    Liang, Zhijie; Zhaob, Zhiwei; Sun, Tianyi; Shi, Wenxin; Cui, Fuyi

    2016-03-15

    In this study, mesoporous silica (meso-silica) MCM-41 and those with the templates retained were synthesized and characterized. Adsorption capacities of the synthesized materials towards typical quinolone antibiotic pollutants, enrofloxacin and norfloxacin as representative, were investigated, and effects of the alkyl chain length of the templates on the adsorption capacity were evaluated. The results of this study indicated that the retained templates enhanced the adsorption capacities (Qmax) of the meso-silica MCM-41 toward hydrophobic enrofloxacin, but had an inhibitory effect on that towards hydrophilic norfloxacin, which were attributed to the hydrophobic inter-environment created by the long alkyl chains of the retained templates. Importantly, the adsorption capacity increased with the increase of the alkyl chain length of the retained templates. PMID:26642441

  8. Effect of alkyl side-chain length on the photophysical, morphology and photoresponse properties of poly(3-alkylthiophene)

    NASA Astrophysics Data System (ADS)

    Xu, Wei-Long; Yang, Xiao-Yu; Zheng, Fei; Jin, Han-Dong; Hao, Xiao-Tao

    2015-12-01

    The effect of alkyl side-chain length on the photophysical, morphology and photoresponse properties of poly (3-alkylthiophene) (P3AT) has been investigated. Butyl, hexyl, octyl, decyl, and dodecyl side chains have been studied. In solution state, the average lifetime of poly (3-octylthiophene) (P3OT) is the shortest among P3AT solution owing to the strong intrachain interaction. The fluorescence lifetime of P3AT solution increases with the side-chain length increasing. A similar trend occurs in the P3AT films. This phenomenon illustrates conformation ‘memory’ property evolving from solution state to solid film. The four lifetimes represent different photophysical processes and have been systematically analyzed. The photodetector based on P3DDT is a suitable candidate for practical application owing to the fast, reversible photoresponse and photostability. The high performance of P3DDT-based photodetector is correlated to the optimized morphology and strong interchain interaction which promotes the exciton delocalization.

  9. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids.

    PubMed

    Hofbauer, Harald F; Schopf, Florian H; Schleifer, Hannes; Knittelfelder, Oskar L; Pieber, Bartholomäus; Rechberger, Gerald N; Wolinski, Heimo; Gaspar, Maria L; Kappe, C Oliver; Stadlmann, Johannes; Mechtler, Karl; Zenz, Alexandra; Lohner, Karl; Tehlivets, Oksana; Henry, Susan A; Kohlwein, Sepp D

    2014-06-23

    Membrane phospholipids typically contain fatty acids (FAs) of 16 and 18 carbon atoms. This particular chain length is evolutionarily highly conserved and presumably provides maximum stability and dynamic properties to biological membranes in response to nutritional or environmental cues. Here, we show that the relative proportion of C16 versus C18 FAs is regulated by the activity of acetyl-CoA carboxylase (Acc1), the first and rate-limiting enzyme of FA de novo synthesis. Acc1 activity is attenuated by AMPK/Snf1-dependent phosphorylation, which is required to maintain an appropriate acyl-chain length distribution. Moreover, we find that the transcriptional repressor Opi1 preferentially binds to C16 over C18 phosphatidic acid (PA) species: thus, C16-chain containing PA sequesters Opi1 more effectively to the ER, enabling AMPK/Snf1 control of PA acyl-chain length to determine the degree of derepression of Opi1 target genes. These findings reveal an unexpected regulatory link between the major energy-sensing kinase, membrane lipid composition, and transcription. PMID:24960695

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

    NASA Astrophysics Data System (ADS)

    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.

  11. 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. PMID:24483495

  12. 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 .

  13. Heterogeneity of lipopolysaccharides from Pseudomonas aeruginosa: analysis of lipopolysaccharide chain length.

    PubMed Central

    Rivera, M; Bryan, L E; Hancock, R E; McGroarty, E J

    1988-01-01

    Lipopolysaccharide (LPS) from smooth strains of Pseudomonas aeruginosa 503, PAZ1, PAO1715, PAO1716, and Z61 was fractionated by gel filtration chromatography. LPS samples from the first four strains, all PAO1 derivatives, separated into three major size populations, whereas LPS from strain Z61, a Pac K799/WT mutant strain, separated into two size populations. When column fractions were applied to sodium dodecyl sulfate-polyacrylamide gels in their order of elution, molecules of decreasing size were resolved, and the ladder of molecules with different-length O antigens formed a diagonal across the gel. The LPS from the PAO1 derivatives contained two distinct sets of bands, distinguished on the gels as two sets of diagonals. The set of bands with the faster mobility, the B bands, was found in column fractions comprising the three major amino sugar-containing peaks. In the sample from strain 503, a fourth minor peak which contained B bands was resolved. The slower-moving set of bands, the A bands, were recovered in a minor peak. LPS from strain Z61 contained only one set of bands, with the higher-molecular-weight molecules eluting from the column in a volume similar to that of the B bands of the PAO1 strains. Analysis of the fractions of LPS from all strains indicated that less than 8% of the LPS molecules had a long, attached O antigen. Analysis of the peak that contained mainly A bands indicated a lack of reactive amino sugar and phosphate, although heptose and 2-keto-3-deoxyoctulosonic acid were detected. Reaction of isolated fractions with monoclonal antibody specific for the PAO1 O-antigen side chain indicated that only the B bands from the PAO1 strains were antigenically reactive. The bands from strain Z61 showed no reactivity. The data suggest that the A and B bands from the PAO1 strains are antigenically distinct. We propose that PAO1 strains synthesize two types of molecules that are antigenically different. Images PMID:3123455

  14. Highly grafted polystyrene/polyvinylpyridine polymer gold nanoparticles in a good solvent: effects of chain length and composition.

    PubMed

    Posel, Zbyšek; Posocco, Paola; Lísal, Martin; Fermeglia, Maurizio; Pricl, Sabrina

    2016-04-21

    In this work, the structural features of spherical gold nanoparticles (NPs) decorated with highly grafted poly(styrene) (PS), poly(vinylpyridine) (PVP) and PS-PVP diblock copolymer brushes immersed in a good solvent are investigated by means of Dissipative Particle Dynamics (DPD) simulations as a function of grafted chain length and of homopolymer and copolymer chain composition. For NPs grafted either by PS or PVP homopolymer brushes (selected as a proof of concept), good agreement between the Daoud-Cotton theory, experimental evidence, and our DPD simulations is observed in the scaling behavior of single chain properties, especially for longer grafted chains, and in brush thickness prediction. On the other hand, for grafted chain lengths comparable to NP dimensions parabolic-like profiles of the end-monomer distributions are obtained. Furthermore, a region of high concentration of polymer segments is observed in the monomer density distribution for long homopolymers. In the case of copolymer-decorated NPs, the repulsion between PS and PVP blocks is found to substantially influence the radius of gyration and the shape of the end-monomer distribution of the relevant polymer shell. Moreover, for diblock chains, the un-swollen region is observed to be thinner (and, correspondingly, the swollen layer thicker) than that of a NP modified with a homopolymer of the same length. Finally, the lateral segregation of PS and PVP blocks is evidenced by our calculations and a detailed analysis of the corona behavior is reported, thus revealing the key parameters in controlling the surface properties and the response of diblock copolymer modified nanoparticles. PMID:26980360

  15. Comprehensive Study on the Impact of the Cation Alkyl Side Chain Length on the Solubility of Water in Ionic Liquids

    PubMed Central

    Kurnia, Kiki A.; Neves, Catarina M. S. S.; Freire, Mara G.; Santos, Luís M. N. B. F.; Coutinho, João A. P.

    2015-01-01

    A comprehensive study on the phase behaviour of two sets of ionic liquids (ILs) and their interactions with water is here presented through combining experimental and theoretical approaches. The impact of the alkyl side chain length and the cation symmetry on the water solubility in the asymmetric [CN-1C1im][NTf2] and symmetric [CN-1CN-1im][NTf2] series of ILs (N up to 22), from 288.15 K to 318.15 K and at atmospheric pressure, was studied. The experimental data reveal that the solubility of water in ILs with an asymmetric cation is higher than in those with the symmetric isomer. Several trend shifts on the water solubility as a function of the alkyl side chain length were identified, namely at [C6C1im][NTf2] for asymmetric ILs and at [C4C4im][NTf2] and [C7C7im][NTf2] for the symmetric ILs. To complement the experimental data and to further investigate the molecular-level mechanisms behind the dissolution process, Density Functional Theory calculations, using the Conductor-like Screening Model for Real Solvents (COSMO-RS) and the Electrostatic potential-derived CHelpG, were performed. The COSMO-RS model is able to qualitatively predict water solubility as function of temperature and alkyl chain lengths of both symmetric and asymmetric cations. Furthermore, the model is also capable to predict the somewhat higher water solubility in the asymmetric cation, as well as the trend shift as function of alkyl chain lengths experimentally observed. Both COSMO-RS and the electrostatic potential-derived CHelpG show that the interactions of water and the IL cation take place on the IL polar region, namely on the aromatic head and adjacent methylene groups what explains the differences in water solubility observed for cations with different chain lengths. Furthermore, the CHelpG calculations for the isolated cations in the gas phase indicates that the trend shift of water solubility as function of alkyl chain lengths and the difference of water solubility in symmetric may also

  16. APPLICATION OF POLYMERASE CHAIN REACTION (PCR) AND PCR BASED RESTRICTION FRAGMENT LENGTH POLYMORPHISM FOR DETECTION AND IDENTIFICATION OF DERMATOPHYTES FROM DERMATOLOGICAL SPECIMENS

    PubMed Central

    Bagyalakshmi, R; Senthilvelan, B; Therese, K L; Murugusundram, S; Madhavan, H N

    2008-01-01

    Objective: To develop and optimize polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) targeting 18S rDNA and internal transcribed spacer (ITS) region of fungi for rapid detection and identification of dermatophytes. Materials and Methods: Two PCR-RFLP methods targeting 18S rDNA and ITS regions of fungi were optimized using standard and laboratory isolates of dermatophytes and other fungi. Sixty-eight dermatological clinical specimens (nail clippings (56), material obtained from blisters (8), hair root (2), scraping from scaly plaque of foot (1) and skin scraping (1) collected by the dermatologist were subjected to both the optimized PCR-RFLP and conventional mycological (smear and culture) methods. Results: PCRs targeting 18S rDNA and the ITS region were sensitive to detect 10 picograms and 1 femtogram of T. rubrum DNA, respectively. PCR targeting 18S rDNA was specific for dermatophytes and subsequent RFLP identified them to species level. PCR-RFLP targeting the ITS region differentiated dermatophytes from other fungi with identification to species level. Among the 68 clinical specimens tested, both PCR-RFLP methods revealed the presence of dermatophytes in 27 cases (39.7%), whereas culture revealed the same only in 2 cases (7.40%), increasing the clinical sensitivity by 32.3%. Among 20 smear positive specimens, both PCR-RFLP methods detected dermatophytes in 12 (17.6%). Both the methods detected the presence of dermatophytes in 13 (19.11%) smear and culture negative specimens, increasing the clinical sensitivity by 36.1%. Conclusion: PCR-RFLP methods targeting 18S rDNA and the ITS regions of fungi were specific and highly sensitive for detection and speciation of dermatophytes. PMID:19967012

  17. Characterization of site-specific mutations in a short-chain-length/medium-chain-length polyhydroxyalkanoate synthase: in vivo and in vitro studies of enzymatic activity and substrate specificity.

    PubMed

    Chuah, Jo-Ann; Tomizawa, Satoshi; Yamada, Miwa; Tsuge, Takeharu; Doi, Yoshiharu; Sudesh, Kumar; Numata, Keiji

    2013-06-01

    Saturation point mutagenesis was carried out at position 479 in the polyhydroxyalkanoate (PHA) synthase from Chromobacterium sp. strain USM2 (PhaC(Cs)) with specificities for short-chain-length (SCL) [(R)-3-hydroxybutyrate (3HB) and (R)-3-hydroxyvalerate (3HV)] and medium-chain-length (MCL) [(R)-3-hydroxyhexanoate (3HHx)] monomers in an effort to enhance the specificity of the enzyme for 3HHx. A maximum 4-fold increase in 3HHx incorporation and a 1.6-fold increase in PHA biosynthesis, more than the wild-type synthase, was achieved using selected mutant synthases. These increases were subsequently correlated with improved synthase activity and increased preference of PhaC(Cs) for 3HHx monomers. We found that substitutions with uncharged residues were beneficial, as they resulted in enhanced PHA production and/or 3HHx incorporation. Further analysis led to postulations that the size and geometry of the substrate-binding pocket are determinants of PHA accumulation, 3HHx fraction, and chain length specificity. In vitro activities for polymerization of 3HV and 3HHx monomers were consistent with in vivo substrate specificities. Ultimately, the preference shown by wild-type and mutant synthases for either SCL (C(4) and C(5)) or MCL (C(6)) substrates substantiates the fundamental classification of PHA synthases. PMID:23584780

  18. The effect of the cation alkyl chain length on density and diffusion in dialkylpyrrolidinium bis(mandelato)borate ionic liquids.

    PubMed

    Filippov, Andrei; Taher, Mamoun; Shah, Faiz Ullah; Glavatskih, Sergei; Antzutkin, Oleg N

    2014-12-28

    The physicochemical properties of ionic liquids are strongly affected by the selective combination of the cations and anions comprising the ionic liquid. In particular, the length of the alkyl chains of ions has a clear influence on the ionic liquid's performance. In this paper, we study the self-diffusion of ions in a series of halogen-free boron-based ionic liquids (hf-BILs) containing bis(mandelato)borate anions and dialkylpyrrolidinium cations with long alkyl chains CnH2n+1 with n from 4 to 14 within a temperature range of 293-373 K. It was found that the hf-BILs with n = 4-7 have very similar diffusion coefficients, while hf-BILs with n = 10-14 exhibit two liquid sub-phases in almost the entire temperature range studied (293-353 K). Both liquid sub-phases differ in their diffusion coefficients, while values of the slower diffusion coefficients are close to those of hf-BILs with shorter alkyl chains. To explain the particular dependence of diffusion on the alkyl chain length, we examined the densities of the hf-BILs studied here. It was shown that the dependence of the density on the number of CH2 groups in long alkyl chains of cations can be accurately described using a "mosaic type" model, where regions of long alkyl chains of cations (named 'aliphatic' regions) and the residual chemical moieties in both cations and anions (named 'ionic' regions) give additive contributions. Changes in density due to an increase in temperature and the number of CH2 groups in the long alkyl chains of cations are determined predominantly by changes in the free volume of the 'ionic' regions, while 'aliphatic' regions are already highly compressed by van der Waals forces, which results in only infinitesimal changes in their free volumes with temperature. PMID:25372279

  19. Characterization of full-length and polymerase chain reaction-derived partial-length Gottfried and OSU gene 4 probes for serotypic differentiation of porcine rotaviruses.

    PubMed

    Rosen, B I; Parwani, A V; Gorziglia, M; Larralde, G; Saif, L J

    1992-10-01

    To determine the VP4 (P type) specificity of porcine rotaviruses, full- and partial-length gene 4 probes were produced from cloned Gottfried and OSU porcine rotavirus genomic segment 4 cDNAs. The gene 4 segments from the prototype Gottfried (VP7 serotype 4) and OSU (VP7 serotype 5) porcine rotavirus strains were selected for study because of their distinct P types and the occurrence of rotaviruses with similar serotypes among swine. Partial-length gene 4 cDNAs were produced and amplified by the polymerase chain reaction (PCR) and encompassed portions of the variable region (nucleotides 211 to 612) of VP8 encoded by genomic segment 4. The hybridization stringency conditions necessary for optimal probe specificity and sensitivity were determined by dot or Northern (RNA) blot hybridizations against a diverse group of human and animal rotaviruses of heterologous group A serotypes and against representative group B and C porcine rotaviruses. The PCR-derived gene 4 probes were more specific than the full-length gene 4 probes but demonstrated equivalent sensitivity. The Gottfried PCR-derived probe hybridized with Gottfried, SB2, SB3, and SB5 G serotype 4 porcine rotaviruses. The OSU PCR-derived probe hybridized with OSU, EE, A580, and SB-1A porcine rotaviruses and equine H1 rotavirus. Results of the hybridization reactions of the PCR-derived gene 4 probes with selected porcine rotavirus strains agreed with previous serological or genetic analyses, indicating their suitability as diagnostic reagents. PMID:1328281

  20. Atomistic Simulations of the Effects of Polyglutamine Chain Length and Solvent Quality on Conformational Equilibria and Spontaneous Homodimerization

    PubMed Central

    Vitalis, Andreas; Wang, Xiaoling; Pappu, Rohit V.

    2009-01-01

    Summary Aggregation of expanded polyglutamine tracts is associated with nine different neurodegenerative diseases, including Huntington’s disease. Experiments and computer simulations have demonstrated that monomeric forms of polyglutamine molecules sample heterogeneous sets of collapsed structures in water. The current work focuses on a mechanistic characterization of polyglutamine homodimerization as a function of chain length and temperature. These studies were carried out using molecular simulations based on a recently developed continuum solvation model that was designed for studying conformational and binding equilibria of intrinsically disordered molecules such as polyglutamine systems. The main results are as follows: Polyglutamine molecules form disordered, collapsed globules in aqueous solution. These molecules spontaneously associate at conditions approaching those of typical in vitro experiments for chains of length N ≥ 15. The spontaneity of these homotypic associations increases with increasing chain length and decreases with increasing temperature. Similar and generic driving forces govern both collapse and spontaneous homodimerization of polyglutamine in aqueous milieus. Collapse and dimerization maximize self-interactions and reduce the interface between polyglutamine molecules and the surrounding solvent. Other than these generic considerations, there do not appear to be any specific structural requirements for either chain collapse or chain dimerization, i.e., both collapse and dimerization are non-specific in that disordered globules form disordered dimers. In fact, it is shown that the driving force for intermolecular associations is governed by spontaneous conformational fluctuations within monomeric polyglutamine. These results suggest that polyglutamine aggregation is unlikely to follow a homogeneous nucleation mechanism with the monomer as the critical nucleus. Instead, the results support the formation of disordered, non beta

  1. 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. PMID:25529680

  2. Effect of chain length on physicochemical properties and cytotoxicity of cationic vesicles composed of phosphatidylcholines and dialkyldimethylammonium bromides.

    PubMed

    Liang, Chia-Hua; Chou, Tzung-Han

    2009-04-01

    This study investigated the physicochemical characteristics of cationic vesicles that were prepared from two phosphatidylcholines and three dialkyldimethylammonium bromides (DXDAB) with differing in dialkyl chain lengths, ranging from 2-C(14) to 2-C(18), by measuring particle size and zeta potential. The dependence of particle size, zeta potential and short-storage stability of mixed phosphatidylcholine/DXDAB vesicles on the chain length and composition were also elucidated. Transmission electron microscopy analysis verified that vesicles were formed as a phosphatidylcholine film to which DXDAB was added in a phosphate buffer saline (PBS, pH 7.4). Furthermore, the toxicity to the human keratinocytes (HaCaT) and squamous cell carcinomas (SCC25) cells that were incubated with these vesicles, evaluated by a cell viability assay, increased with the percentage of DXDAB that was incorporated and was inversely proportional to the chain length of DXDAB. The morphological features (round shape, chromatin condensation and apoptosis bodies) and results of flow cytometry analysis (increased sub-G(1) fraction) confirmed the induction of apoptosis in HaCaT and SCC25 cells by cationic vesicles. Apoptosis caused by cationic vesicles without the addition of any drugs was observed for the first time in HaCaT and SCC25 cells. The results of this investigation suggest that cytotoxicity is related to the zeta potential of the cationic vesicles. PMID:19428352

  3. Chain length affects pancreatic lipase activity and the extent and pH-time profile of triglyceride lipolysis.

    PubMed

    Benito-Gallo, Paloma; Franceschetto, Alessandro; Wong, Jonathan C M; Marlow, Maria; Zann, Vanessa; Scholes, Peter; Gershkovich, Pavel

    2015-06-01

    Triglycerides (TG) are one of the most common excipients used in oral lipid-based formulations. The chain length of the TG plays an important role in the oral bioavailability of the co-administered drug. Fatty acid (FA) chain-length specificity of porcine pancreatic lipase was studied by means of an in vitro lipolysis model under bio-relevant conditions at pH 6.80. In order to determine the total extent of lipolysis, back-titration experiments at pH 11.50 were performed. Results suggest that there is a specific chain length range (C2-C8) for which pancreatic lipase shows higher activity. This specificity could result from a combination of physicochemical properties of TGs, 2-monoglycerides (2-MGs) and FAs, namely the droplet size of the TGs, the solubility of 2-MGs within mixed micelles, and the relative stability of the FAs as leaving groups in the hydrolysis reaction. During experimentation, it was evident that an optimisation of lipolysis conditions was needed for tighter control over pH levels so as to better mimic in vivo conditions. 1M NaOH, 3.5 mL/min maximum dosing rate, and 3 μL/min minimum dosing rate were the optimised set of conditions that allowed better pH control, as well as the differentiation of the lipolysis of different lipid loads. PMID:25936853

  4. Photoinitiated electron transfer to selected physisorbed alkyl bromides: The effects of alkyl chain length on dissociation cross sections

    SciTech Connect

    Khan, K.A.; Camillone, N. III; Osgood, R.M. Jr.

    1999-06-01

    We report the results of measurements of the cross section as a function of wavelength (351, 248, and 193 nm) for photoinitiated dissociative electron attachment to three normal alkyl bromides [CH{sub 3}(CH{sub 2}){sub n{minus}1}Br, n=1, 2, and 3] physisorbed on GaAs(110). Upon UV exposure, the molecules undergo C{endash}Br bond cleavage due to a substrate-mediated electron-transfer process. The cross sections for all three molecules increase monotonically with decreasing wavelength. Our results suggest a {approximately}1 eV higher threshold for dissociation of ethyl and propyl bromide than for methyl bromide. A simple model of the electron-transfer process is employed to estimate the peak per-electron cross section for dissociative attachment in the monolayer. We find that the cross sections for the physisorbed molecules are approximately five times smaller than those for gas-phase molecules, due to a reduction in the lifetime of the molecular anion in the vicinity of the surface. In addition, we also find an increase in cross section with chain length very similar to that observed in the gas phase; the gas-phase behavior has been explained by an increase in the anion lifetime with chain length. Our results suggest that while quenching of the molecular anion at the surface is important, it does not eliminate the progression of anion lifetime with chain length. {copyright} {ital 1999 American Institute of Physics.}

  5. Role of the charge, carbon chain length, and content of surfactant on the skin penetration of meloxicam-loaded liposomes

    PubMed Central

    Duangjit, Sureewan; Pamornpathomkul, Boonnada; Opanasopit, Praneet; Rojanarata, Theerasak; Obata, Yasuko; Takayama, Kozo; Ngawhirunpat, Tanasait

    2014-01-01

    The objective of this study was to investigate the influence of surfactant charge, surfactant carbon chain length, and surfactant content on the physicochemical characteristics (ie, vesicle size, zeta potential, elasticity, and entrapment efficiency), morphology, stability, and in vitro skin permeability of meloxicam (MX)-loaded liposome. Moreover, the mechanism for the liposome-enhanced skin permeation of MX was determined by Fourier transform infrared spectroscopy and differential scanning calorimetry. The model formulation used in this study was obtained using a response surface method incorporating multivariate spline interpolation (RSM-S). Liposome formulations with varying surfactant charge (anionic, neutral, and cationic), surfactant carbon chain length (C4, C12, and C16), and surfactant content (10%, 20%, and 29%) were prepared. The formulation comprising 29% cationic surfactant with a C16 chain length was found to be the optimal liposome for the transdermal delivery of MX. The skin permeation flux of the optimal formulation was 2.69-fold higher than that of a conventional liposome formulation. Our study revealed that surfactants affected the physicochemical characteristics, stability, and skin permeability of MX-loaded liposomes. These findings provide important fundamental information for the development of liposomes as transdermal drug delivery systems. PMID:24851047

  6. New surfactants for EOR applications: Effect of chain length on performance

    NASA Astrophysics Data System (ADS)

    Mushtaq, Muhammad; Tan, Isa M.; Sagir, Muhammad

    2014-10-01

    Two surfactants were synthesized using natural oil derivative as raw material. The surfactants contained n-propoxy and n-hexoxy pendent chains. In this multistep synthesis, hydroxyl groups (OH) were successfully protected by the acetylation reaction and the subsequent sulfonation step produced sulfonated surfactants. The relative yield of sulfonation for hexoxy chain surfactant was found lower when compared to short chain propoxy surfactant. Steric hindrance and high viscosity were the factors which showed influence on the production yield. Both surfactants were found excellent performers in EOR evaluation tests. The surfactants were found tolerant against heat and mild salinity. Microemulsion was generated by both surfactants with crude oil resulting good solubilisation parameters. The surfactant with longer side chain (10-Acetoxy-9-hexoxy-2-sulfo-octadecanoic acid methyl ester) showed low interfacial tension (IFT) (0.019 mN/m) and high oil recovery (93.2%). The propoxy side chain surfactant (10-Acetoxy-9-propoxy-2-sulfo-octadecanoic acid methyl ester) showed 0.033 mN/m IFT and a recovery of 89.3 %. It is concluded that both surfactants are suitable for Chemical EOR applications.

  7. Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructanstructans.

    USGS Publications Warehouse

    Muller, Laura K.; Lorch, Jeffrey M.; Lindner, Daniel L.; O'Connor, Michael; Gargas, Andrea; Blehert, David S.

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg of genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was further qualified by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific, and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research.

  8. Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructans.

    PubMed

    Muller, Laura K; Lorch, Jeffrey M; Lindner, Daniel L; O'Connor, Michael; Gargas, Andrea; Blehert, David S

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was qualified further by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research. PMID:22962349

  9. Impact of chain length, temperature, and humidity on the growth of long alkyltrichlorosilane self-assembled monolayers.

    PubMed

    Desbief, Simon; Patrone, Lionel; Goguenheim, Didier; Guérin, David; Vuillaume, Dominique

    2011-02-21

    In this work, we have studied the growth of self-assembled monolayers (SAMs) on silicon dioxide (SiO(2)) made of various long alkyltrichlorosilane chains (16, 18, 20, 24, and 30 carbon atoms in the alkyl chain), at several values of temperature (11 and 20 °C in most cases) and relative humidity (18 and 45% RH). Using atomic force microscopy analysis, thickness measurements by ellipsometry, and contact angle measurements, we have built a model of growth behaviour of SAMs of those molecules according to the deposition conditions and the chain length. Particularly, this work brings not only a better knowledge of the less studied growth of triacontyltrichlorosilane (C(30)H(61)SiCl(3)) SAMs but also new results on SAMs of tetracosyltrichlorosilane (C(24)H(49)SiCl(3)) that have not already been studied to our knowledge. We have shown that the SAM growth behaviour of triacontyltrichlorosilane at 20 °C and 45% RH is similar to that obtained at 11 °C and 45% RH for shorter molecules of hexadecyltrichlorosilane (C(16)H(33)SiCl(3)), octadecyltrichlorosilane (C(18)H(37)SiCl(3)), eicosyltrichlorosilane (C(20)H(41)SiCl(3)) and tetracosyltrichlorosilane (C(24)H(49)SiCl(3)). We have also observed that the monolayers grow faster at 45% than at 18% RH, and surprisingly slower at 20 °C than at 11 °C. Another important result is that the growth time constant decreases with the number of carbon atoms in the alkyl chain except for C(24)H(49)SiCl(3) at 11 °C and 18% RH, and for C(30)H(61)SiCl(3). To our knowledge, such a chain length dependence of the growth time constant has never been reported. The latter and all the other results are interpreted by adapting a diffusion limited aggregation growth model. PMID:21161113

  10. 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. PMID:24398082

  11. Interplaying roles of native topology and chain length in marginally cooperative and noncooperative folding of small protein fragments

    NASA Astrophysics Data System (ADS)

    Badasyan, Artem; Liu, Zhirong; Chan, Hue Sun

    Coarse-grained chain simulations were used to study fragments of two homologous proteins of the peripheral subunit-binding domain (PSBD) family, Bacillus stearothermophilus PSBD (E3BD) and Escherichia coli 2-oxo-glutarate dehydrogenase PSBD (BBL). To ascertain a robust rank order of folding cooperativity, native-centric intraprotein interactions were modeled by (i) a common Gō;-like potential, and (ii) native-centric potentials with desolvation barriers or (iii) many-body terms. Homologous proteins can possess substantially different folding cooperativity. Consistent with experiment, our calculations indicated that E3BD fragments fold more cooperatively than BBL fragments of approximately the same chain length. For a given fragment, native contacts deduced from Protein Data Bank structures can vary significantly depending on the number of residues that the structure encompasses in addition to those of the fragment itself, resulting in variation in model folding cooperativity predicted using different native contact sets for the same fragment. This observation underscores that folding cooperativity of these fragments can be extremely sensitive to change in chain length. Thus, a ˜40-residue protein fragment's folding cooperativity, or lack thereof, does not necessarily imply essentially identical behaviors for super- or sub-fragments with only several residues more, or less, than the given fragment. Ramifications for experimental investigations of downhill folding are discussed.

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

    PubMed

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

    2014-12-01

    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 the liver but not in the adipose tissue or skeletal muscle of 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 [VH]-palmitate was also abrogated in the hepa- tocytes 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 the 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

  13. Elucidation and Control of an Intramolecular Charge Transfer Property of Fucoxanthin by a Modification of Its Polyene Chain Length.

    PubMed

    Kosumi, Daisuke; Kajikawa, Takayuki; Okumura, Satoshi; Sugisaki, Mitsuru; Sakaguchi, Kazuhiko; Katsumura, Shigeo; Hashimoto, Hideki

    2014-03-01

    Fucoxanthin is an essential pigment for the highly efficient light-harvesting function of marine algal photosynthesis. It exhibits excited state properties attributed to intramolecular charge transfer (ICT) in polar environments due to the presence of the carbonyl group in its polyene backbone. This report describes the excited state properties of fucoxanthin homologues with four to eight conjugated double bonds in various solvents using the femtosecond pump-probe technique. The results clarified that fucoxanthin homologues with longer polyene chains did not possess pronounced ICT spectroscopic signatures, while the shorter fucoxanthin homologues had a strong ICT character, even in a nonpolar solvent. On the basis of the observations, we quantitatively correlated the ICT character in the excited state to the conjugated polyene chain lengths of fucoxanthin molecules. PMID:26274069

  14. A simple HPLC-MS method for the quantitative determination of the composition of bacterial medium chain-length polyhydroxyalkanoates.

    PubMed

    Grubelnik, Andreas; Wiesli, Luzia; Furrer, Patrick; Rentsch, Daniel; Hany, Roland; Meyer, Veronika R

    2008-06-01

    Bacterial poly(hydroxyalkanoates) (PHAs) vary in the composition of their monomeric units. Besides saturated side-chains, unsaturated ones can also be found. The latter leads to unwanted by-products (THF ester, secondary alcohols) during acidic cleavage of the polymer backbone in the conventional analytical assays. To prevent these problems, we developed a new method for the reductive depolymerization of medium chain-length PHAs, leading to monomeric diols that can be separated and quantified by HPLC/MS. Reduction is performed at room temperature with lithium aluminum hydride within 5-15 min. The new method is faster and simpler than the previous ones and is quantitative. The results are consistent with the ones obtained by quantitative (1)H NMR. PMID:18461645

  15. Immobilization of Lipases on Alkyl Silane Modified Magnetic Nanoparticles: Effect of Alkyl Chain Length on Enzyme Activity

    PubMed Central

    Wang, Jiqian; Meng, Gang; Tao, Kai; Feng, Min; Zhao, Xiubo; Li, Zhen; Xu, Hai; Xia, Daohong; Lu, Jian R.

    2012-01-01

    Background Biocatalytic processes often require a full recycling of biocatalysts to optimize economic benefits and minimize waste disposal. Immobilization of biocatalysts onto particulate carriers has been widely explored as an option to meet these requirements. However, surface properties often affect the amount of biocatalysts immobilized, their bioactivity and stability, hampering their wide applications. The aim of this work is to explore how immobilization of lipases onto magnetite nanoparticles affects their biocatalytic performance under carefully controlled surface modification. Methodology/Principal Findings Magnetite nanoparticles, prepared through a co-precipitation method, were coated with alkyl silanes of different alkyl chain lengths to modulate their surface hydrophobicity. Candida rugosa lipase was then directly immobilized onto the modified nanoparticles through hydrophobic interaction. Enzyme activity was assessed by catalytic hydrolysis of p-nitrophenyl acetate. The activity of immobilized lipases was found to increase with increasing chain length of the alkyl silane. Furthermore, the catalytic activities of lipases immobilized on trimethoxyl octadecyl silane (C18) modified Fe3O4 were a factor of 2 or more than the values reported from other surface immobilized systems. After 7 recycles, the activities of the lipases immobilized on C18 modified nanoparticles retained 65%, indicating significant enhancement of stability as well through hydrophobic interaction. Lipase immobilized magnetic nanoparticles facilitated easy separation and recycling with high activity retaining. Conclusions/Significance The activity of immobilized lipases increased with increasing alkyl chain length of the alkyl trimethoxy silanes used in the surface modification of magnetite nanoparticles. Lipase stability was also improved through hydrophobic interaction. Alkyl silane modified magnetite nanoparticles are thus highly attractive carriers for enzyme immobilization

  16. 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. PMID:25917507

  17. On the possibility of using short chain length mono-carboxylic acids for stabilization of magnetic fluids

    NASA Astrophysics Data System (ADS)

    Avdeev, Mikhail V.; Bica, Doina; Vékás, Ladislau; Marinica, Oana; Balasoiu, Maria; Aksenov, Victor L.; Rosta, László; Garamus, Vasil M.; Schreyer, Andreas

    2007-04-01

    Short chain length mono-carboxylic acids (lauric and myristic acids) are used to coat magnetite nanoparticles in non-polar organic liquids, which results in highly stable magnetic fluids. The new fluids are compared with classical organic fluids stabilized by oleic acid (OA). Magnetic granulometry and small-angle neutron scattering (polarized mode) reveal a great difference in the particle size distribution function for the studied magnetic fluids, particularly a decrease in the characteristic particle radius of magnetite when lauric and myristic acids are used instead of OA.

  18. Aliphatic chain length by isotropic mixing (ALCHIM): determining composition of complex lipid samples by 1H NMR spectroscopy

    PubMed Central

    Yi, Ruiyang; Volden, Paul A.; Conzen, Suzanne D.

    2015-01-01

    Quantifying the amounts and types of lipids present in mixtures is important in fields as diverse as medicine, food science, and biochemistry. Nuclear magnetic resonance (NMR) spectroscopy can quantify the total amounts of saturated and unsaturated fatty acids in mixtures, but identifying the length of saturated fatty acid or the position of unsaturation by NMR is a daunting challenge. We have developed an NMR technique, aliphatic chain length by isotropic mixing, to address this problem. Using a selective total correlation spectroscopy technique to excite and transfer magnetization from a resolved resonance, we demonstrate that the time dependence of this transfer to another resolved site depends linearly on the number of aliphatic carbons separating the two sites. This technique is applied to complex natural mixtures allowing the identification and quantification of the constituent fatty acids. The method has been applied to whole adipocytes demonstrating that it will be of great use in studies of whole tissues. PMID:24831341

  19. Collapse of Langmuir monolayer at lower surface pressure: Effect of hydrophobic chain length

    NASA Astrophysics Data System (ADS)

    Das, Kaushik; Kundu, Sarathi

    2016-05-01

    Long chain fatty acid molecules (e.g., stearic and behenic acids) form a monolayer on water surface in the presence of Ba2+ ions at low subphase pH (≈ 5.5) and remain as a monolayer before collapse generally occurs at higher surface pressure (πc > 50 mN/m). Monolayer formation is verified from the surface pressure vs. area per molecule (π-A) isotherms and also from the atomic force microscopy (AFM) analysis of the films deposited by single upstroke of hydrophilic Si (001) substrate through the monolayer covered water surface. At high subphase pH (≈ 9.5), barium stearate molecules form multilayer structure at lower surface pressure which is verified from the π-A isotherms and AFM analysis of the film deposited at 25 mN/m. Such monolayer to multilayer structure formation or monolayer collapse at lower surface pressure is unusual as at this surface pressure generally fatty acid salt molecules form a monolayer on the water surface. Formation of bidentate chelate coordination in the metal containing headgroups is the reason for such monolayer to multilayer transition. However, for longer chain barium behenate molecules only monolayer structure is maintained at that high subphase pH (≈ 9.5) due to the presence of relatively more tail-tail hydrophobic interaction.

  20. Poly(ethylene glycol)-mediated molar mass control of short-chain- and medium-chain-length poly(hydroxyalkanoates) from Pseudomonas oleovorans.

    PubMed

    Ashby, R D; Solaiman, D K Y; Foglia, T A

    2002-10-01

    Three strains of Pseudomonas oleovorans, a well known poly(hydroxyalkanoate) (PHA) producer, were tested for the ability to control PHA molar mass and end group structure by addition of poly(ethylene glycol) (PEG) to the fermentation medium. Each strain of P. oleovorans - NRRL B-14682 (B-14682), NRRL B-14683 (B-14683), and NRRL B-778 (B-778) - synthesized a different type of PHA from oleic acid when cultured under identical growth conditions. Strain B-14682 produced poly(3-hydroxybutyrate) (PHB), while B-14683 synthesized a medium-chain-length PHA ( mcl-PHA) with a repeat unit composition ranging from C4 to C14 and some mono-unsaturation in the C14 alkyl side chains. Strain B-778 synthesized a mixture of PHB (95 mol%) and mcl-PHA (5 mol%). The addition of 0.5% (v/v) PEG (M(n) =200 g/mol, PEG-200) to the fermentation broth of strains B-14682 and B-778 resulted in chain termination through esterification at the carboxyl terminus of the PHB with PEG chain segments, thus reducing the molar mass by 54% and 23%, respectively. The molar mass of the mcl-PHA produced by strains B-14683 and B-778 also showed a 34% and 47% reduction in the presence of PEG-200, respectively, but no evidence of esterification was present. PEG-400 (M(n) =400 g/mol) had a reduced effect on PHA molar mass. In fact, the molar masses of the mcl-PHA derived from strain B-14683 and both the PHB and mcl-PHA from B-778 were unchanged by PEG-400. In contrast, the PHB produced by B-14682 showed a 35% reduction in molar mass in the presence of PEG-400. PMID:12382057

  1. 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.

  2. 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.

  3. How Alcohol Chain-Length and Concentration Modulate Hydrogen Bond Formation in a Lipid Bilayer

    PubMed Central

    Dickey, Allison N.; Faller, Roland

    2007-01-01

    Molecular dynamics simulations are used to measure the change in properties of a hydrated dipalmitoylphosphatidylcholine bilayer when solvated with ethanol, propanol, and butanol solutions. There are eight oxygen atoms in dipalmitoylphosphatidylcholine that serve as hydrogen bond acceptors, and two of the oxygen atoms participate in hydrogen bonds that exist for significantly longer time spans than the hydrogen bonds at the other six oxygen atoms for the ethanol and propanol simulations. We conclude that this is caused by the lipid head group conformation, where the two favored hydrogen-bonding sites are partially protected between the head group choline and the sn-2 carbonyl oxygen. We find that the concentration of the alcohol in the ethanol and propanol simulations does not have a significant influence on the locations of the alcohol/lipid hydrogen bonds, whereas the concentration does impact the locations of the butanol/lipid hydrogen bonds. The concentration is important for all three alcohol types when the lipid chain order is examined, where, with the exception of the high-concentration butanol simulation, the alcohol molecules having the longest hydrogen-bonding relaxation times at the favored carbonyl oxygen acceptor sites also have the largest order in the upper chain region. The lipid behavior in the high-concentration butanol simulation differs significantly from that of the other alcohol concentrations in the order parameter, head group rotational relaxation time, and alcohol/lipid hydrogen-bonding location and relaxation time. This appears to be the result of the system being very near to a phase transition, and one occurrence of lipid flip-flop is seen at this concentration. PMID:17218462

  4. Effect of bidispersity in grafted chain length on grafted chain conformations and potential of mean force between polymer grafted nanoparticles in a homopolymer matrix.

    PubMed

    Nair, Nitish; Wentzel, Nathaniel; Jayaraman, Arthi

    2011-05-21

    In efforts to produce polymeric materials with tailored physical properties, significant interest has grown around the ability to control the spatial organization of nanoparticles in polymer nanocomposites. One way to achieve controlled particle arrangement is by grafting the nanoparticle surface with polymers that are compatible with the matrix, thus manipulating the interfacial interactions between the nanoparticles and the polymer matrix. Previous work has shown that the molecular weight of the grafted polymer, both at high grafting density and low grafting density, plays a key role in dictating the effective inter-particle interactions in a polymer matrix. At high grafting density nanoparticles disperse (aggregate) if the graft molecular weight is higher (lower) than the matrix molecular weight. At low grafting density the longer grafts can better shield the nanoparticle surface from direct particle-particle contacts than the shorter grafts and lead to the dispersion of the grafted particles in the matrix. Despite the importance of graft molecular weight, and evidence of non-trivial effects of polydispersity of chains grafted on flat surfaces, most theoretical work on polymer grafted nanoparticles has only focused on monodisperse grafted chains. In this paper, we focus on how bidispersity in grafted chain lengths affects the grafted chain conformations and inter-particle interactions in an implicit solvent and in a dense homopolymer polymer matrix. We first present the effects of bidispersity on grafted chain conformations in a single polymer grafted particle using purely Monte Carlo (MC) simulations. This is followed by calculations of the potential of mean force (PMF) between two grafted particles in a polymer matrix using a self-consistent Polymer Reference Interaction Site Model theory-Monte Carlo simulation approach. Monte Carlo simulations of a single polymer grafted particle in an implicit solvent show that in the bidisperse polymer grafted particles

  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. Production of medium-chain-length polyhydroxyalkanoates by activated sludge enriched under periodic feeding with nonanoic acid.

    PubMed

    Lee, Sun Hee; Kim, Jae Hee; Mishra, Debaraj; Ni, Yu-Yang; Rhee, Young Ha

    2011-05-01

    The potential use of activated sludge for the production of medium-chain-length polyhydroxyalkanoates (MCL-PHAs) was investigated. The enrichment of bacterial populations capable of producing MCL-PHAs was achieved by periodic feeding with nonanoic acid in a sequencing batch reactor (SBR). Denaturing gradient gel electrophoresis analysis revealed Pseudomonas aeruginosa strains to be predominant in the bacterial community during the SBR process. The composition of PHA synthesized by the enriched biomass from nonanoic acid consisted of a large concentration (>89 mol%) of MCL monomer units and a small amount of short-chain-length monomer units. Under fed-batch fermentation with continuous feeding of nonanoic acid at a flow rate of 0.225 g/L/h and a C/N ratio of 40, a maximum PHA content of 48.6% dry cell weight and a conversion yield (Y(p/s)) of 0.94 g/g were achieved. These results indicate that MCL-PHA production by activated sludge is a promising alternative to typical pure culture approaches. PMID:21463934

  7. Impact of glucose polymer chain length on heat and physical stability of milk protein-carbohydrate nutritional beverages.

    PubMed

    Chen, Biye; O'Mahony, James A

    2016-11-15

    This study investigated the impact of glucose polymer chain length on heat and physical stability of milk protein isolate (MPI)-carbohydrate nutritional beverages containing 8.5% w/w total protein and 5% w/w carbohydrate. The maltodextrin and corn syrup solids glucose polymers used had dextrose equivalent (DE) values of 17 or 38, respectively. Increasing DE value of the glucose polymers resulted in a greater increase in brown colour development, ionic calcium, protein particle size, apparent viscosity and pseudoplastic rheological behaviour, and greater reduction in pH, hydration and heat stability on sterilisation at 120°C. Incorporation of glucose polymers with MPI retarded sedimentation of protein during accelerated physical stability testing, with maltodextrin DE17 causing a greater reduction in sedimentation velocity and compressibility of sediment formed than corn syrup solids DE38. The results demonstrate that chain length of the glucose polymer used strongly impacts heat and physical stability of MPI-carbohydrate nutritional beverages. PMID:27283657

  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. O-antigen chain-length distribution in Salmonella enterica serovar Enteritidis is regulated by oxygen availability.

    PubMed

    Silva-Valenzuela, Cecilia A; Velásquez, Felipe; Peñailillo, Johany; Garcias-Papayani, Héctor; Fernández, Paulina; Tobar, Pía; Contreras, Inés; Santiviago, Carlos A; Álvarez, Sergio A

    2016-09-01

    Lipopolysaccharide (LPS) consists of three covalently linked domains: the lipid A, the core region and the O antigen (OAg), consisting of repeats of an oligosaccharide. Salmonella enterica serovar Enteritidis (S. Enteritidis) produces a LPS with two OAg preferred chain lengths: a long (L)-OAg controlled by WzzSE and a very long (VL)-OAg controlled by WzzfepE. In this work, we show that OAg produced by S. Enteritidis grown in E minimal medium also presented two preferred chain-lengths. However, a simultaneous and opposing change in the production of L-OAg and VL-OAg was observed in response to oxygen availability. Biochemical and genetics analyses indicate that this process is regulated by transcriptional factors Fnr and ArcA by means of controlling the transcription of genes encoding WzzSE and WzzfepE in response to oxygen availability. Thus, our results revealed a sophisticated regulatory mechanism involved in the adaptation of S. Enteritidis to one of the main environmental cues faced by this pathogen during infection. PMID:27343553

  10. Stealth filaments: polymer chain length and conformation affect the in vivo fate of PEGylated potato virus X

    PubMed Central

    Lee, Karin L.; Shukla, Sourabh; Wu, Mengzhi; Ayat, Nadia R.; El Sanadi, Caroline E.; Wen, Amy M.; Edelbrock, John F.; Pokorski, Jonathan K.; Commandeur, Ulrich; Dubyak, George R.

    2015-01-01

    Nanoparticles hold great promise for delivering medical cargos to cancerous tissues to enhance contrast and sensitivity of imaging agents or to increase specificity and efficacy of therapeutics. A growing body of data suggests that nanoparticle shape, in combination with surface chemistry, affects their in vivo fates, with elongated filaments showing enhanced tumor targeting and tissue penetration, while promoting immune evasion. The synthesis of high aspect ratio filamentous materials at the nanoscale remains challenging using synthetic routes; therefore we turned toward nature’s materials, developing and studying the filamentous structures formed by the plant virus potato virus X (PVX). We recently demonstrated that PVX shows enhanced tumor homing in various preclinical models. Like other nanoparticle systems, the proteinaceous platform is cleared from circulation and tissues by the mononuclear phagocyte system (MPS). To increase bioavailability we set out to develop PEGylated stealth filaments and evaluate the effects of PEG chain length and conformation on pharmacokinetics, biodistribution, as well as potential immune and inflammatory responses. We demonstrate that PEGylation effectively reduces immune recognition while increasing pharmacokinetic profiles. Stealth filaments show biodistribution consistent with MPS clearance mechanisms; the protein:polymer hybrids are cleared from the body indicating biodegradability and biocompatibility. Tissue compatibility is indicated with no apparent inflammatory signaling in vivo. Tailoring PEG chain length and conformation (brush vs. mushroom) allows tuning of the pharmacokinetics, yielding long-circulating stealth filaments for applications in nanomedicine. PMID:25769228

  11. Stealth filaments: Polymer chain length and conformation affect the in vivo fate of PEGylated potato virus X.

    PubMed

    Lee, Karin L; Shukla, Sourabh; Wu, Mengzhi; Ayat, Nadia R; El Sanadi, Caroline E; Wen, Amy M; Edelbrock, John F; Pokorski, Jonathan K; Commandeur, Ulrich; Dubyak, George R; Steinmetz, Nicole F

    2015-06-01

    Nanoparticles hold great promise for delivering medical cargos to cancerous tissues to enhance contrast and sensitivity of imaging agents or to increase specificity and efficacy of therapeutics. A growing body of data suggests that nanoparticle shape, in combination with surface chemistry, affects their in vivo fates, with elongated filaments showing enhanced tumor targeting and tissue penetration, while promoting immune evasion. The synthesis of high aspect ratio filamentous materials at the nanoscale remains challenging using synthetic routes; therefore we turned toward nature's materials, developing and studying the filamentous structures formed by the plant virus potato virus X (PVX). We recently demonstrated that PVX shows enhanced tumor homing in various preclinical models. Like other nanoparticle systems, the proteinaceous platform is cleared from circulation and tissues by the mononuclear phagocyte system (MPS). To increase bioavailability we set out to develop PEGylated stealth filaments and evaluate the effects of PEG chain length and conformation on pharmacokinetics, biodistribution, as well as potential immune and inflammatory responses. We demonstrate that PEGylation effectively reduces immune recognition while increasing pharmacokinetic profiles. Stealth filaments show reduced interaction with cells of the MPS; the protein:polymer hybrids are cleared from the body tissues within hours to days indicating biodegradability and biocompatibility. Tissue compatibility is indicated with no apparent inflammatory signaling in vivo. Tailoring PEG chain length and conformation (brush vs. mushroom) allows tuning of the pharmacokinetics, yielding long-circulating stealth filaments for applications in nanomedicine. PMID:25769228

  12. A multisubstrate assay for lipases/esterases: assessing acyl chain length selectivity by reverse-phase high-performance liquid chromatography.

    PubMed

    Divakar, K; Gautam, Pennathur

    2014-03-01

    Lipases and esterases are hydrolytic enzymes and are known to hydrolyze esters with unique substrate specificity and acyl chain length selectivity. We have developed a simple competitive multiple substrate assay for determination of acyl chain length selectivity of lipases/esterases using RP-HPLC with UV detection. A method for separation and quantification of 4-nitrophenyl fatty acid esters (C4-C18) was developed and validated. The chain length selectivity of five lipases and two esterases was determined in a multisubstrate reaction system containing equimolar concentrations of 4-nitrophenyl esters (C4-C18). This assay is simple, reproducible, and a useful tool for determining chain length selectivity of lipases/esterases. PMID:24316114

  13. 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. PMID:24151777

  14. 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. PMID:16144421

  15. Effects of chlorine content and carbon chain length in the bioaccumulation of chlorinated paraffins by juvenile rainbow trout

    SciTech Connect

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

    1995-12-31

    Chlorinated paraffins (CPs) are C{sub 10{minus}30} chlorinated n-alkanes used as high pressure lubricants, flame retardants and plasticizers. Relatively little is known about their chemical-physical properties or bioaccumulation potential. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to three dietary concentrations (approximately 0, 20 and 200 ng/g) of two {sup 14}C- dodecane (56 and 69% Cl) and hexadecane (35 and 69% Cl) CPs. Assimilation efficiencies ranged from a mean of 11.3 {+-} 3.1 % for the high chlorinated hexadecane to 49.2 {+-} 27.8% for the low chlorinated dodecane. Half-lives varied from a mean of 21 {+-} 1.6 days in the low chlorinated dodecane to 404 {+-} 289 days in the high chlorinated dodecane. The high chlorinated dodecane was found to have a biomagnification factor (BMF) of 14.8 and 2.5 for the low and high concentration treatments respectively, implying a potential to biomagnify. Chlorine content and carbon chain length both appear to effect bioaccumulation. Higher chlorination was associated with longer half lives and lower elimination rates. Longer carbon chain lengths produced lower assimilation efficiencies and BMF values. Low assimilation efficiencies (8.2 to 1 4.4%) and elimination rate constants (0.008 to 0.009 days-{minus}) found for the high chlorinated hexadecane may be attributed to the large size (MW 668) of this molecule. Short chain, highly chlorinated CPs are the most likely to bioaccumulate, and need further assessment of risk to the aquatic environment.

  16. The chain length of biologically produced (R)-3-hydroxyalkanoic acid affects biological activity and structure of anti-cancer peptides.

    PubMed

    Szwej, Emilia; Devocelle, Marc; Kenny, Shane; Guzik, Maciej; O'Connor, Stephen; Nikodinovic-Runic, Jasmina; Radivojevic, Jelena; Maslak, Veselin; Byrne, Annete T; Gallagher, William M; Zulian, Qun Ren; Zinn, Manfred; O'Connor, Kevin E

    2015-06-20

    Conjugation of DP18L peptide with (R)-3-hydroxydecanoic acid, derived from the biopolymer polyhydroxyalkanoate, enhances its anti-cancer activity (O'Connor et al., 2013. Biomaterials 34, 2710-2718). However, it is unknown if other (R)-3-hydroxyalkanoic acids (R3HAs) can enhance peptide activity, if chain length affects enhancement, and what effect R3HAs have on peptide structure. Here we show that the degree of enhancement of peptide (DP18L) anti-cancer activity by R3HAs is carbon chain length dependent. In all but one example the R3HA conjugated peptides were more active against cancer cells than the unconjugated peptides. However, R3HAs with 9 and 10 carbons were most effective at improving DP18L activity. DP18L peptide variant DP17L, missing a hydrophobic amino acid (leucine residue 4) exhibited lower efficacy against MiaPaCa cells. Circular dichroism analysis showed DP17L had a lower alpha helix content and the conjugation of any R3HA ((R)-3-hydroxyhexanoic acid to (R)-3-hydroxydodecanoic acid) to DP17L returned the helix content back to levels of DP18L. However (R)-3-hydroxyhexanoic did not enhance the anti-cancer activity of DP17L and at least 7 carbons were needed in the R3HA to enhance activity of D17L. DP17L needs a longer chain R3HA to achieve the same activity as DP18L conjugated to an R3HA. As a first step to assess the synthetic potential of polyhydroxyalkanoate derived R3HAs, (R)-3-hydroxydecanoic acid was synthetically converted to (±)3-chlorodecanoic acid, which when conjugated to DP18L improved its antiproliferative activity against MiaPaCa cells. PMID:25820126

  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. PMID:25819752

  18. 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.

  19. 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

  20. 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.

  1. 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. PMID:27116996

  2. Insight from molecular modelling: does the polymer side chain length matter for transport properties of perfluorosulfonic acid membranes?

    SciTech Connect

    Devanathan, Ramaswami; Dupuis, Michel

    2012-08-28

    We present a detailed analysis of the nanostructure of short side chain (SSC) perfluorosulfonic acid membrane and its effect on H{sub 2}O network percolation, H{sub 3}O{sup +} and H{sub 2}O diffusion, and mean residence times of H{sub 3}O{sup +} and H{sub 2}O near SO{sub 3}{sup -} groups based on molecular dynamics simulations. We studied a range of hydration levels ({lambda}) at temperatures of 300 and 360 K, and compare the results to our previous findings in the benchmark Nafion membrane at 300 K. The water channel diameter is about 20% larger in Nafion, while the extent of SO3- clustering is more in SSC membrane. The calculated channel diameter is in excellent agreement with the recently proposed cylindrical water channel model of these membranes. The H{sub 2}O network percolation occurs at comparable hydration levels, and the diffusion coefficients of H{sub 2}O and H{sub 3}O{sup +} are similar in SSC and Nafion membranes. Raising the temperature of the SSC membrane from 300 to 360 K provides a much bigger increase in proton vehicular diffusion coefficient (by a factor of about 4) than changing the side chain length. H3O+ ions are found to exchange more frequently with SO{sub 3}{sup -} partners at the higher temperature. Our key findings are that (a) the hydrophobic-hydrophilic separation in the two membranes is surprisingly similar; (b) at all hydration levels studied, the longer side chain of Nafion is bent and is effectively equivalent to a short side chain in terms of extension into the water domain; and (c) proton transport along the centre of the channel is improbable and vehicular proton transport occurs between SO{sub 3}{sup -} groups. The simulations are validated by good agreement with corresponding experimental values for the simulated membrane density and diffusion coefficients of H{sub 2}O.

  3. Acyl chain length effects related to glycosphingolipid crypticity in phospholipid membranes: probed by 2H-NMR.

    PubMed

    Hamilton, K S; Briere, K; Jarrell, H C; Grant, C W

    1994-03-23

    Wideline 2H-NMR was used to consider the relationships amongst glycosphingolipid and phospholipid fatty acid chain length and glycosphingolipid receptor function, in a system classically associated with crypticity. Galactosyl ceramide (GalCer), having 18- or 24-carbon fatty acid, was deuterium labelled at the conformationally-restricted fatty acid alpha-carbon (C-2). 2H-NMR spectra of N-[2,2-2H2]stearoyl and N-[2,2-2H2]lignoceroyl GalCer (GalCer with 18-vs. 24-carbon selectively deuterated fatty acid) were then compared over a range of temperatures in phosphatidylcholine/cholesterol membranes in which the host phospholipid had dimyristoyl, dipalmitoyl, or distearoyl fatty acid composition. Findings were evaluated in the light of known sensitivity of antibody interaction with GalCer to temperature and to both glycolipid fatty acid chain length and host matrix fatty acid chain length. Under the conditions of experimentation, spectra were not obtainable for glycolipids having rigid body motions that were slow on the NMR timescale (10(-4)-10(-5) s)-i.e.. motions typical of non-fluid (gel phase) membranes. The systems, DPPC/cholesterol and DSPC/cholesterol, in which the original observation was made of increased antibody binding to GalCer with long fatty acid, proved to be characterised by receptor motions that were in this slow timescale for both 18:0 and 24:0 GalCer at 22-24 degrees C. Under conditions for which spectra could be obtained, those for GalCer with [2,2-2H2]lignoceroyl (24-carbon alpha-deuterated) fatty acid were qualitatively similar to those of its 18-carbon analogue in all (fluid) membranes examined. However, spectral splittings differed quantitatively between deuterated 18:0 and 24:0 GalCer at a given temperature, dependent upon host matrix. These differences were most marked at lower temperatures and in the longer chain (more ordered) matrices, DPPC/cholesterol and DSPC/cholesterol. This suggests that maximum effects of glycolipid chain length on

  4. Synthesis, Characterization and Biological Studies of New Linear Thermally Stable Schiff Base Polymers with Flexible Spacers.

    PubMed

    Qureshi, Farah; Khuhawar, Muhammad Yar; Jahangir, Taj Muhammad; Channar, Abdul Hamid

    2016-01-01

    Five new linear Schiff base polymers having azomethine structures, ether linkages and extended aliphatic chain lengths with flexible spacers were synthesized by polycondensation of dialdehyde (monomer) with aliphatic and aromatic diamines. The formation yields of monomer and polymers were obtained within 75-92%. The polymers with flexible spacers of n-hexane were somewhat soluble in acetone, chloroform, THF, DMF and DMSO on heating. The monomer and polymers were characterized by melting point, elemental microanalysis, FT-IR, (1)HNMR, UV-Vis spectroscopy, thermogravimetry (TG), differential thermal analysis (DTA), fluorescence emission, scanning electron microscopy (SEM) and viscosities and thermodynamic parameters measurements of their dilute solutions. The studies supported formation of the monomer and polymers and on the basis of these studies their structures have been assigned. The synthesized polymers were tested for their antibacterial and antifungal activities. PMID:26970795

  5. 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

  6. Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker's Yeast.

    PubMed

    Chen, Po-Wei; Fonseca, Luis L; Hannun, Yusuf A; Voit, Eberhard O

    2015-08-01

    The article demonstrates that computational modeling has the capacity to convert metabolic snapshots, taken sequentially over time, into a description of cellular, dynamic strategies. The specific application is a detailed analysis of a set of actions with which Saccharomyces cerevisiae responds to heat stress. Using time dependent metabolic concentration data, we use a combination of mathematical modeling, reverse engineering, and optimization to infer dynamic changes in enzyme activities within the sphingolipid pathway. The details of the sphingolipid responses to heat stress are important, because they guide some of the longer-term alterations in gene expression, with which the cells adapt to the increased temperature. The analysis indicates that all enzyme activities in the system are affected and that the shapes of the time trends in activities depend on the fatty-acyl CoA chain lengths of the different ceramide species in the system. PMID:26241868

  7. 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. PMID:24628189

  8. Identification and biochemical evidence of a medium-chain-length polyhydroxyalkanoate depolymerase in the Bdellovibrio bacteriovorus predatory hydrolytic arsenal.

    PubMed

    Martínez, Virginia; de la Peña, Fernando; García-Hidalgo, Javier; de la Mata, Isabel; García, José Luis; Prieto, María Auxiliadora

    2012-09-01

    The obligate predator Bdellovibrio bacteriovorus HD100 shows a large set of proteases and other hydrolases as part of its hydrolytic arsenal needed for its predatory life cycle. We present genetic and biochemical evidence that open reading frame (ORF) Bd3709 of B. bacteriovorus HD100 encodes a novel medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase (PhaZ(Bd)). The primary structure of PhaZ(Bd) suggests that this enzyme belongs to the α/β-hydrolase fold family and has a typical serine hydrolase catalytic triad (serine-histidine-aspartic acid) in agreement with other PHA depolymerases and lipases. PhaZ(Bd) has been extracellularly produced using different hypersecretor Tol-pal mutants of Escherichia coli and Pseudomonas putida as recombinant hosts. The recombinant PhaZ(Bd) has been characterized, and its biochemical properties have been compared to those of other PHA depolymerases. The enzyme behaves as a serine hydrolase that is inhibited by phenylmethylsulfonyl fluoride. It is also affected by the reducing agent dithiothreitol and nonionic detergents like Tween 80. PhaZ(Bd) is an endoexohydrolase that cleaves both large and small PHA molecules, producing mainly dimers but also monomers and trimers. The enzyme specifically degrades mcl-PHA and is inactive toward short-chain-length polyhydroxyalkanoates (scl-PHA) like polyhydroxybutyrate (PHB). These studies shed light on the potentiality of these predators as sources of new biocatalysts, such as an mcl-PHA depolymerase, for the production of enantiopure hydroxyalkanoic acids and oligomers as building blocks for the synthesis of biobased polymers. PMID:22706067

  9. Interaction and dynamics of (alkylamide + electrolyte) deep eutectics: Dependence on alkyl chain-length, temperature, and anion identity

    NASA Astrophysics Data System (ADS)

    Guchhait, Biswajit; Das, Suman; Daschakraborty, Snehasis; Biswas, Ranjit

    2014-03-01

    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 (Tg) 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 Tgs. 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.

  10. Effect of Sophorolipid n-Alkyl Ester Chain Length on Its Interfacial Properties at the Almond Oil-Water Interface.

    PubMed

    Koh, Amanda; Linhardt, Robert J; Gross, Richard

    2016-06-01

    Sophorolipids (SLs), produced by Candida bombicola, are of interest as potential replacements for hazardous commercial surfactants. For the first time, a series of molecularly edited SLs with ethyl (EE), n-hexyl (HE), and n-decyl (DE) esters were evaluated at an oil (almond oil)-water interface for their ability to reduce interfacial tension (IFT) and generate stable emulsions. An increase in the n-alkyl ester chain length from ethyl to hexyl resulted in a maximum % decrease in the IFT from 86.1 to 95.3, respectively. Furthermore, the critical aggregation concentrations (CACs) decreased from 0.035 to 0.011 and 0.006 mg/mL as the ester chain length was increased from ethyl to n-hexyl and n-decyl, respectively. In contrast, the CAC of natural SL, composed of 50/50 acidic and LSL, is 0.142 mg/mL. Dynamic IFT analysis showed significant differences in diffusion coefficients for all SLs studied. Almond oil emulsions with up to 200:1 (by weight) oil/SL-DE were stable against oil separation for up to 1 week with average droplet sizes below 5 μm. Emulsions of almond oil with natural SLs showed consistent oil separation 24 h after emulsification. A unique connection between IFT and emulsification was found as SL-DE has both the lowest CAC and the best emulsification performance of all natural and modified SLs studied herein. This connection between CAC and emulsification may be generally applicable, providing a tool for the prediction of optimal surfactants in other oil-water interfacial applications. PMID:27159768

  11. Influence of alkyl chain length and temperature on thermophysical properties of ammonium-based ionic liquids with molecular solvent.

    PubMed

    Kavitha, T; Attri, Pankaj; Venkatesu, Pannuru; Devi, R S Rama; Hofman, T

    2012-04-19

    Mixing of ionic liquids (ILs) with molecular solvent can expand the range of structural properties and the scope of molecular interactions between the molecules of the solvents. Exploiting of these phenomena essentially require a basic fundamental understanding of mixing behavior of ILs with molecular solvents. In this context, a series of protic ILs possessing tetra-alkyl ammonium cation [R(4)N](+) with commonly used anion hydroxide [OH](-) were synthesized and characterized by temperature dependent thermophysical properties. The ILs [R(4)N](+)[OH](-) are varying only in the length of alkyl chain (R is methyl, ethyl, propyl, or butyl) of tetra-alkyl ammonium on the cationic part. The ILs used for the present study included tetramethyl ammonium hydroxide [(CH(3))(4)N](+)[OH](-) (TMAH), tetraethyl ammonium hydroxide [(C(2)H(5))(4)N](+)[OH](-) (TEAH), tetrapropyl ammonium hydroxide [(C(3)H(7))(4)N](+)[OH](-) (TPAH) and tetrabutyl ammonium hydroxide [(C(4)H(9))(4)N](+)[OH](-) (TBAH). The alkyl chain length effect has been analyzed by precise measurements such as densities (ρ), ultrasonic sound velocity (u), and viscosity (η) of these ILs with polar solvent, N-methyl-2-pyrrolidone (NMP), over the full composition range as a function of temperature. The excess molar volume (V(E)), the deviation in isentropic compressibility (Δκ(s)) and deviation in viscosity (Δη) were predicted using these properties as a function of the concentration of ILs. Redlich-Kister polynomial was used to correlate the results. A qualitative analysis of the results is discussed in terms of the ion-dipole, ion-pair interactions, and hydrogen bonding between ILs and NMP molecules. Later, the hydrogen bonding features between ILs and NMP were also analyzed using a molecular modeling program with the help of HyperChem 7. PMID:22443087

  12. 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.

  13. 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

  14. Effect of the alkyl chain length of secondary amines on the phase transfer of gold nanoparticles from water to toluene.

    PubMed

    Soliwoda, Katarzyna; Tomaszewska, Emilia; Tkacz-Szczesna, Beata; Mackiewicz, Ewelina; Rosowski, Marcin; Bald, Adam; Blanck, Christian; Schmutz, Marc; Novák, Jiří; Schreiber, Frank; Celichowski, Grzegorz; Grobelny, Jaroslaw

    2014-06-17

    In the present paper we describe a phase transfer of aqueous synthesized gold nanoparticles (AuNPs) from water to toluene using secondary amines: dioctylamine, didodecylamine, and dioctadecylamine. The effect of the hydrocarbon chain length and amount of amines on the transfer efficiency were investigated in the case of nanoparticles (NPs) with three different sizes: 5, 9, and 13 nm. Aqueous colloids were precisely characterized before the transfer process using UV-vis spectroscopy, dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), and transmission electron microscopy (TEM). Nanoparticles were next transferred to toluene and characterized using UV-vis and DLS techniques. It was found that dioctadecylamine provides the most effective transfer of nanoparticles. No time-dependent changes in the NP size were observed after 12 days, showing that the dioctadecylamine-stabilized nanoparticles dispersed in toluene were stable. This indicates that long hydrocarbon chains of dioctadecylamine exhibit sufficiently hydrophobic properties of nanoparticles and consequently their good dispersibility in nonpolar solvent. PMID:24893068

  15. 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. PMID:21643581

  16. 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. PMID:21866943

  17. Synthesis of short-/medium-chain-length poly(hydroxyalkanoate) blends by mixed culture fermentation of glycerol.

    PubMed

    Ashby, Richard D; Solaiman, Daniel K Y; Foglia, Thomas A

    2005-01-01

    Glycerol was used as a substrate in the bio-production of poly(hydroxyalkanoates) (PHAs) in an effort to establish an alternative outlet for glycerol and produce value-added products. Pseudomonas oleovorans NRRL B-14682 and Pseudomonas corrugata 388 grew and synthesized poly(3-hydroxybutyrate) (P3HB) and medium-chain-length PHA (mcl-PHA) consisting primarily of 3-hydroxydecanoic acid (C(10:0); 44 +/- 2 mol %) and 3-hydroxydodecenoic acid (C(12:1); 31 +/- 2 mol %), respectively, from glycerol at concentrations up to 5% (v/v). Cellular productivity maximized at 40% for P. oleovorans in 5% (v/v) glycerol and 20% for P. corrugata in 2% (v/v) glycerol after 72 h. Increasing the glycerol media concentration from 1% to 5% (v/v) caused a 61% and 72% reduction in the molar mass (M(n)) of the P3HB and mcl-PHA polymers, respectively. Proton-NMR analysis of the glycerol-derived P3HB revealed that the M(n) decrease was the result of esterification of glycerol onto the polymer in a chain terminating position. However, no evidence of glycerol-based chain termination was present in the mcl-PHA. The growth patterns of P. oleovorans and P. corrugata on glycerol permitted their use as mixed cultures to produce natural blends of P3HB and mcl-PHA. By incorporating a staggered inoculation pattern and varying the duration of the fermentations, P3HB/mcl-PHA ratios were achieved that varied from 34:66 to 96:4. PMID:16004451

  18. 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. PMID:23616516

  19. ε-Poly-L-lysine peptide chain length regulated by the linkers connecting the transmembrane domains of ε-Poly-L-lysine synthetase.

    PubMed

    Hamano, Yoshimitsu; Kito, Naoko; Kita, Akihiro; Imokawa, Yuuki; Yamanaka, Kazuya; Maruyama, Chitose; Katano, Hajime

    2014-08-01

    ε-Poly-l-lysine (ε-PL), consisting of 25 to 35 l-lysine residues with linkages between the α-carboxyl groups and ε-amino groups, is produced by Streptomyces albulus NBRC14147. ε-PL synthetase (Pls) is a membrane protein with six transmembrane domains (TM1 to TM6) as well as both an adenylation domain and a thiolation domain, characteristic of the nonribosomal peptide synthetases. Pls directly generates ε-PL chain length diversity (25- to 35-mer), but the processes that control the chain length of ε-PL during the polymerization reaction are still not fully understood. Here, we report on the identification of Pls amino acid residues involved in the regulation of the ε-PL chain length. From approximately 12,000 variants generated by random mutagenesis, we found 8 Pls variants that produced shorter chains of ε-PL. These variants have one or more mutations in two linker regions connecting the TM1 and TM2 domains and the TM3 and TM4 domains. In the Pls catalytic mechanism, the growing chain of ε-PL is not tethered to the enzyme, implying that the enzyme must hold the growing chain until the polymerization reaction is complete. Our findings reveal that the linker regions are important contributors to grasp the growing chain of ε-PL. PMID:24907331

  20. Comparison of Chain-Length Preferences and Glucan Specificities of Isoamylase-Type α-Glucan Debranching Enzymes from Rice, Cyanobacteria, and Bacteria.

    PubMed

    Kobayashi, Taiki; Sasaki, Satoshi; Utsumi, Yoshinori; Fujita, Naoko; Umeda, Kazuhiro; Sawada, Takayuki; Kubo, Akiko; Abe, Jun-Ichi; Colleoni, Christophe; Ball, Steven; Nakamura, Yasunori

    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

  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. Radionuclide migration through fractured rock for arbitrary-length decay chain: Analytical solution and global sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Shahkarami, Pirouz; Liu, Longcheng; Moreno, Luis; Neretnieks, Ivars

    2015-01-01

    This study presents an analytical approach to simulate nuclide migration through a channel in a fracture accounting for an arbitrary-length decay chain. The nuclides are retarded as they diffuse in the porous rock matrix and stagnant zones in the fracture. The Laplace transform and similarity transform techniques are applied to solve the model. The analytical solution to the nuclide concentrations at the fracture outlet is governed by nine parameters representing different mechanisms acting on nuclide transport through a fracture, including diffusion into the rock matrices, diffusion into the stagnant water zone, chain decay and hydrodynamic dispersion. Furthermore, to assess how sensitive the results are to parameter uncertainties, the Sobol method is applied in variance-based global sensitivity analyses of the model output. The Sobol indices show how uncertainty in the model output is apportioned to the uncertainty in the model input. This method takes into account both direct effects and interaction effects between input parameters. The simulation results suggest that in the case of pulse injections, ignoring the effect of a stagnant water zone can lead to significant errors in the time of first arrival and the peak value of the nuclides. Likewise, neglecting the parent and modeling its daughter as a single stable species can result in a significant overestimation of the peak value of the daughter nuclide. It is also found that as the dispersion increases, the early arrival time and the peak time of the daughter decrease while the peak value increases. More importantly, the global sensitivity analysis reveals that for time periods greater than a few thousand years, the uncertainty of the model output is more sensitive to the values of the individual parameters than to the interaction between them. Moreover, if one tries to evaluate the true values of the input parameters at the same cost and effort, the determination of priorities should follow a certain

  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. Structure-activity relationship studies on acremomannolipin A, the potent calcium signal modulator with a novel glycolipid structure 3: role of the length of alditol side chain.

    PubMed

    Tsutsui, Nozomi; Tanabe, Genzoh; Morita, Nao; Okayama, Yoshitomo; Kita, Ayako; Sugiura, Reiko; Muraoka, Osamu

    2015-07-01

    Five homologs of a novel glycolipid acremomannolipin A (1a), the potential Ca(2+) signal modulator isolated from Acremonium strictum, bearing alditols of different length (1g-1k) were synthesized by a stereoselective β-mannosylation of appropriately protected mannosyl sulfoxide (2) with five alditols (1g: C2, 1h: C3, 1i: C4, 1j: C5 and 1k: C7 units), and their potential in modulating Ca(2+) signaling were evaluated. Homologs with alditols of more than 4 carbons (1i, 1j and 1k) were equally or more potent than the parent compound (1a) regardless of the length of the alditol chain. Whereas activities of two homologs with shorter chains (1g and 1h) decreased to a considerable extent. The results indicated that the length of the alditol side chain was a crucial determinant for the potent calcium signal modulating activity. PMID:25910586

  5. Effects of different fatty acid chain lengths on fatty acid oxidation-related protein expression levels in rat skeletal muscles.

    PubMed

    Ishizawa, Rie; Masuda, Kazumi; Sakata, Susumu; Nakatani, Akira

    2015-01-01

    Skeletal muscles can adapt to dietary interventions that affect energy metabolism. Dietary intake of medium-chain fatty acids (MCFAs) enhances mitochondrial oxidation of fatty acids (FAO) in type IIa skeletal muscle fibers. However, the effect of MCFAs diet on mitochondrial or cytoplasmic FAO-related protein expression levels in different types of muscle fibers remains unclear. This study aims to examine the effects of a high-fat diet, containing MCFAs, on mitochondrial enzyme activities and heart-type fatty acid-binding protein (H-FABP) levels in different types of skeletal muscle fibers. Five-week-old male Wistar rats were assigned to one of the following three dietary conditions: standard chow (SC, 12% of calories from fat), high-fat MCFA, or high-fat long-chain fatty acids (LCFAs) diet (60% of calories from fat for both). The animals were provided food and water ad libitum for 4 weeks, following which citrate synthase (CS) activity and H-FABP concentration were analyzed. The epididymal fat pads (EFP) were significantly smaller in the MCFA group than in the LCFA group (p < 0.05). MCFA-fed group displayed an increase in CS activity compared with that observed in SC-fed controls in all types of skeletal muscle fibers (triceps, surface portion of gastrocnemius (gasS), deep portion of gastrocnemius (gasD), and soleus; p < 0.05,). H-FABP concentration was significantly higher in the LCFA group than in both the SC-fed and MCFA-fed groups (triceps, gasS, gasD, and soleus; p < 0.05,). However, no significant difference was observed in the H-FABP concentrations between the SC-fed and MCFA-fed groups. The results of this study showed that the MCFA diet can increase the expression of the mitochondrial enzyme CS, but not that of H-FABP, in both fast- and slow-twitch muscle fibers, suggesting that H-FABP expression is dependent on the chain length of fatty acids in the cytoplasm of skeletal muscles cells. PMID:25766930

  6. Effect of carbon chain length in acyl coenzyme A on the efficiency of enzymatic transformation of okadaic acid to 7-O-acyl okadaic acid.

    PubMed

    Furumochi, Sachie; Onoda, Tatsuya; Cho, Yuko; Fuwa, Haruhiko; Sasaki, Makoto; Yotsu-Yamashita, Mari; Konoki, Keiichi

    2016-07-01

    Okadaic acid (OA), a product of dinoflagellate Prorocentrum spp., is transformed into 7-O-acyl OA in various bivalve species. The structural transformation proceeds enzymatically in vitro in the presence of the microsomal fraction from the digestive gland of bivalves. We have been using LC-MS/MS to identify OA-transforming enzymes by detecting 7-O-acyl OA, also known as dinophysistoxin 3 (DTX3). However, an alternative assay for DTX3 is required because the OA-transforming enzyme is a membrane protein, and surfactants for solubilizing membrane proteins decrease the sensitivity of LC-MS/MS. The present study examined saturated fatty acyl CoAs with a carbon chain length of 10 (decanoyl), 12 (dodecanoyl), 14 (tetradecanoyl), 16 (hexadecanoyl) and 18 (octadecanoyl) as the substrate for the in vitro acylation reaction. Saturated fatty acyl CoAs with a carbon chain length of 14, 16 and 18 exhibited higher yields than those with a carbon chain length of 10 or 12. Acyl CoAs with carbon chain lengths from 14 to 18 and containing either a diene unit, an alkyne unit, or an azide unit in the carbon chain were synthesized and shown to provide the corresponding DTX3 with a yield comparable to that of hexadecanoyl CoA. The three functional units can be conjugated with fluorescent reagents and are applicable to the development of a novel assay for DTX3. PMID:27231127

  7. 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. PMID:24929502

  8. Limits of a rapid identification of common Mediterranean sandflies using polymerase chain reaction-restriction fragment length polymorphism.

    PubMed

    Bounamous, Azzedine; Lehrter, Véronique; Hadj-Henni, Leila; Delecolle, Jean-Claude; Depaquit, Jérôme

    2014-07-01

    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

  9. Fed-batch production of unsaturated medium-chain-length polyhydroxyalkanoates with controlled composition by Pseudomonas putida KT2440.

    PubMed

    Sun, Zhiyong; Ramsay, Juliana A; Guay, Martin; Ramsay, Bruce A

    2009-03-01

    Unsaturated medium-chain-length polyhydroxyalkanoates (MCL-PHA) were produced at a productivity of 0.63-1.09 g PHA l(-1) h(-1) with final PHA content ranging from 42.6 to 55.8% in single-stage, carbon-limited, fed-batch fermentations of Pseudomonas putida KT2440. A mixture of nonanoic acid (NA) and 10-undecenoic acid (UDA=) was fed exponentially to control growth rate. Varying the specific growth rate (0.14 h(-1) vs. 0.23 h(-1)) at similar substrate feed ratios (NA:UDA= = 5:1) had little effect on the final PHA content and relative composition. However, decreasing the NA:UDA= ratio decreased the final amount of PHA produced from 56% with NA:UDA= = 5.07:1 to only 42% at NA:UDA= = 2.47:1. The molar fraction of all 3-hydroxyalkanoate monomers in the PHA product was relatively constant throughout each fermentation, indicating that the final product was homogeneous rather than a mixture of different copolymers. A linear relationship between unsaturation of the PHA produced and unsaturation of the carbon feed was found, which demonstrates the feasibility of producing unsaturated MCL-PHAs with controlled polymeric composition in a fed-batch process. PMID:19050862

  10. Metabolic engineering for microbial production and applications of copolyesters consisting of 3-hydroxybutyrate and medium-chain-length 3-hydroxyalkanoates.

    PubMed

    Zou, Xiang Hui; Chen, Guo-Qiang

    2007-02-12

    Poly(hydroxyalkanoate)s (PHAs) are a class of microbially synthesized polyesters that combine biological properties, such as biocompatibility and biodegradability, and non-bioproperties such as thermoprocessability, piezoelectricity, and nonlinear optical activity. PHA monomer structures and their contents strongly affect the PHA properties. Using metabolic engineering approaches, PHA structures and contents can be manipulated to achieve controllable monomer and PHA cellular contents. This paper focuses on metabolic engineering methods to produce PHA consisting of 3-hydroxybutyrate (3HB) and medium-chain-length 3-hydroxyalkanoates (3HA) in recombinant microbial systems. This type of copolyester has mechanical and thermal properties similar to conventional plastics such as poly(propylene) and poly(ethylene terephthalate) (PET). In addition, pathways containing engineered PHA synthases have proven to be useful for enhanced PHA production with adjustable PHA monomers and contents. The applications of PHA as implant biomaterials are briefly discussed here. In the very near term, metabolic engineering will help solve many problems in promoting PHA as a new type of plastic material for many applications. PMID:17295404

  11. 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

  12. Discovery of Two β-1,2-Mannoside Phosphorylases Showing Different Chain-Length Specificities from Thermoanaerobacter sp. X-514

    PubMed Central

    Suzuki, Erika; Nishimoto, Mamoru; Kitaoka, Motomitsu; Ohtsubo, Ken'ichi; Nakai, Hiroyuki

    2014-01-01

    We characterized Teth514_1788 and Teth514_1789, belonging to glycoside hydrolase family 130, from Thermoanaerobacter sp. X-514. These two enzymes catalyzed the synthesis of 1,2-β-oligomannan using β-1,2-mannobiose and d-mannose as the optimal acceptors, respectively, in the presence of the donor α-d-mannose 1-phosphate. Kinetic analysis of the phosphorolytic reaction toward 1,2-β-oligomannan revealed that these enzymes followed a typical sequential Bi Bi mechanism. The kinetic parameters of the phosphorolysis of 1,2-β-oligomannan indicate that Teth514_1788 and Teth514_1789 prefer 1,2-β-oligomannans containing a DP ≥3 and β-1,2-Man2, respectively. These results indicate that the two enzymes are novel inverting phosphorylases that exhibit distinct chain-length specificities toward 1,2-β-oligomannan. Here, we propose 1,2-β-oligomannan:phosphate α-d-mannosyltransferase as the systematic name and 1,2-β-oligomannan phosphorylase as the short name for Teth514_1788 and β-1,2-mannobiose:phosphate α-d-mannosyltransferase as the systematic name and β-1,2-mannobiose phosphorylase as the short name for Teth514_1789. PMID:25500577

  13. 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

  14. An improved polymerase chain reaction-restriction fragment length polymorphism assay for the detection of a PON2 gene polymorphism

    PubMed Central

    DUAN, XIAORAN; YANG, YONGLI; WANG, TUANWEI; FENG, XIAOLEI; YAO, WU; YAN, ZHEN; WANG, WEI

    2016-01-01

    In recent research, it has been shown that there have been variants of rs12026 within the paraoxonase 2 (PON2) gene, which have been associated with cardiovascular disease, cerebrovascular disease, diabetes and other diseases. The isochizomers, such as the BsoFI enzyme, required for the detection of this polymorphism are expensive. Therefore, an improved and less expensive polymerase chain reaction (PCR)-restriction fragment length polymorphism method was established for the detection of the single-nucleotide polymorphism rs12026 in the exon 5 of chromosome 7 of the human PON2 gene using the method of amplification-created restriction site. Subsequent to assessing 302 individuals, the genotype frequencies were 68.9% for CC, 29.8% for CG and 1.3% for GG, and the allelic frequencies were 83.8% for C and 16.2% for G. The PCR results were confirmed by DNA sequencing. The χ2 test showed that the genotype and allele frequencies of PON2-148 do not deviate from Hardy-Weinberg equilibrium, and the sequences of amplified products were consistent with the sequence published in GenBank with the exception of a mismatched base. PMID:27330753

  15. Medium chain length polyhydroxyalkanoate (mcl-PHA) production from volatile fatty acids derived from the anaerobic digestion of grass.

    PubMed

    Cerrone, Federico; Choudhari, Santosh K; Davis, Reeta; Cysneiros, Denise; O'Flaherty, Vincent; Duane, Gearoid; Casey, Eoin; Guzik, Maciej W; Kenny, Shane T; Babu, Ramesh P; O'Connor, Kevin

    2014-01-01

    A two step biological process for the conversion of grass biomass to the biodegradable polymer medium chain length polyhydroxyalkanoate (mcl-PHA) was achieved through the use of anaerobic and aerobic microbial processes. Anaerobic digestion (mixed culture) of ensiled grass was achieved with a recirculated leach bed bioreactor resulting in the production of a leachate, containing 15.3 g/l of volatile fatty acids (VFAs) ranging from acetic to valeric acid with butyric acid predominating (12.8 g/l). The VFA mixture was concentrated to 732.5 g/l with a 93.3 % yield of butyric acid (643.9 g/l). Three individual Pseudomonas putida strains, KT2440, CA-3 and GO16 (single pure cultures), differed in their ability to grow and accumulate PHA from VFAs. P. putida CA-3 achieved the highest biomass and PHA on average with individual fatty acids, exhibited the greatest tolerance to higher concentrations of butyric acid (up to 40 mM) compared to the other strains and exhibited a maximum growth rate (μMAX = 0.45 h⁻¹). Based on these observations P. putida CA-3 was chosen as the test strain with the concentrated VFA mixture derived from the AD leachate. P. putida CA-3 achieved 1.56 g of biomass/l and accumulated 39 % of the cell dry weight as PHA (nitrogen limitation) in shake flasks. The PHA was composed predominantly of 3-hydroxydecanoic acid (>65 mol%). PMID:24162086

  16. Evaluation of medium-chain-length polyhydroxyalkanoate production by Pseudomonas putida LS46 using biodiesel by-product streams.

    PubMed

    Fu, Jilagamazhi; Sharma, Umesh; Sparling, Richard; Cicek, Nazim; Levin, David B

    2014-07-01

    Medium-chain-length polyhydroxyalkanoate (mcl-PHA) production by Pseudomonas putida LS46 was analyzed in shake-flask-based batch reactions, using pure chemical-grade glycerol (PG), biodiesel-derived "waste" glycerol (WG), and biodiesel-derived "waste" free fatty acids (WFA). Cell growth, substrate consumption, mcl-PHA accumulation within the cells, and the monomer composition of the synthesized biopolymers were monitored. The patterns of mcl-PHA synthesis in P. putida LS46 cells grown on PG and WG were similar but differed from that of cells grown with WFA. Polymer accumulation in glycerol-based cultures was stimulated by nitrogen limitation and plateaued after 48 h in both PG and WG cultures, with a total accumulation of 17.9% cell dry mass and 16.3% cell dry mass, respectively. In contrast, mcl-PHA synthesis was independent of nitrogen concentration in P. putida LS46 cells cultured with WFA, which accumulated to 29% cell dry mass. In all cases, the mcl-PHAs synthesized consisted primarily of 3-hydroxyoctanoate (C(8)) and 3-hydroxydecanoate (C(10)). WG and WFA supported similar or greater cell growth and mcl-PHA accumulation than PG under the experimental conditions used. These results suggest that biodiesel by-product streams could be used as low-cost carbon sources for sustainable mcl-PHA production. PMID:24983445

  17. Fruit pomace and waste frying oil as sustainable resources for the bioproduction of medium-chain-length polyhydroxyalkanoates.

    PubMed

    Follonier, Stéphanie; Goyder, Miriam S; Silvestri, Anne-Claire; Crelier, Simon; Kalman, Franka; Riesen, Roland; Zinn, Manfred

    2014-11-01

    Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) are biobased and biodegradable alternatives to petrol-derived polymers, whose break-through has been prevented by high production cost. Therefore we investigated whether wastes from the food industry (nine types of fruit pomace including apricots, cherries and grapes, and waste frying oil) could replace the costly sugars and fatty acids typically used as carbon substrates for the bacterial fermentations. A selection of enzyme preparations was tested for converting the residual polysaccharides from the pomaces into fermentable monosaccharides. From the pomace of apricots, cherries and Solaris grapes, 47, 49 and 106gL(-1) glucose were recovered, respectively. Solaris grapes had the highest sugar content whereas apricots contained the fewest growth inhibitors. These two pomaces were assessed for their suitability to produce mcl-PHA in bioreactor. A 2-step fermentation was established with Pseudomonas resinovorans, hydrolyzed pomace as growth substrate and WFO as mcl-PHA precursor. Solaris grapes proved to be a very promising growth substrate, resulting in the production of 21.3gPHA(Lpomace)(-1) compared to 1.4g PHA (L pomace)(-1) for apricots. Finally, capillary zone electrophoresis analyses allowed monitoring of sugar and organic acid uptake during the fermentation on apricots, which led to the discovery of reverse diauxie in P. resinovorans. PMID:24882726

  18. The effect of chain length and unsaturation on Mtb Dxr inhibition and antitubercular killing activity of FR900098 analogs.

    PubMed

    Jackson, Emily R; San Jose, Géraldine; Brothers, Robert C; Edelstein, Emma K; Sheldon, Zachary; Haymond, Amanda; Johny, Chinchu; Boshoff, Helena I; Couch, Robin D; Dowd, Cynthia S

    2014-01-15

    Inhibition of the nonmevalonate pathway (NMP) of isoprene biosynthesis has been examined as a source of new antibiotics with novel mechanisms of action. Dxr is the best studied of the NMP enzymes and several reports have described potent Dxr inhibitors. Many of these compounds are structurally related to natural products fosmidomycin and FR900098, each bearing retrohydroxamate and phosphonate groups. We synthesized a series of compounds with two to five methylene units separating these groups to examine what linker length was optimal and tested for inhibition against Mtb Dxr. We synthesized ethyl and pivaloyl esters of these compounds to increase lipophilicity and improve inhibition of Mtb growth. Our results show that propyl or propenyl linker chains are optimal. Propenyl analog 22 has an IC50 of 1.07 μM against Mtb Dxr. The pivaloyl ester of 22, compound 26, has an MIC of 9.4 μg/mL, representing a significant improvement in antitubercular potency in this class of compounds. PMID:24360562

  19. Investigation of the structure of anti-human seminal plasma protein single-chain antibody and its association with linker peptide length

    PubMed Central

    JIANG, XIN; ZHAI, JUN; SONG, DONGKUI; QU, QINGSHAN; LI, MING; XING, LI; MIAO, SHUZHAI

    2015-01-01

    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. PMID:26099852

  20. Correlation of chain length compatibility and surface properties of mixed foaming agents with fluid displacement efficiency and effective air mobility in porous media

    SciTech Connect

    Sharma, M.K.; Bringham, W.E.; Shah, D.O.

    1984-05-01

    The effects of chain length compatibility and surface properties of mixed foaming agents on fluid displacement efficiency and effective air mobility in porous media were investigated. Sodium dodecyl sulfate (C/sub 12/H/sub 25/SO/sub 4/Na) and various alkyl alcohols (e.g., C/sub 8/OH,C/sub 10/OH,C/sub 12/OH,C/sub 14/OH, and C/sub 16/OH) were used as mixed foaming agents. It was observed that the surface properties of surfactant solutions and flow behavior of foams through porous media were influenced by the chain length compatibility of the surfactant molecules. The increase in the length of porous media improved fluid displacement efficiency while breakthrough time per unit length decreased slightly with increase in the length of porous media. For mixed surfactant systems, a minimum in surface tension, a maximum in surface viscosity, a minimum in bubble size, a maximum in breakthrough time, a maximum in fluid displacement efficiency, and a minimum in effective air mobility were observed when the two components of the surfactant system had the same chain length. These results indicate that the surface properties of foaming solutions and molecular packing at interfaces exhibit a striking correlation with breakthrough time, fluid displacement efficiency, and effective air mobility in porous media.

  1. Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin.

    PubMed

    Kuo, Hsiou-Ting; Liu, Shing-Lung; Chiu, Wen-Chieh; Fang, Chun-Jen; Chang, Hsien-Chen; Wang, Wei-Ren; Yang, Po-An; Li, Jhe-Hao; Huang, Shing-Jong; Huang, Shou-Ling; Cheng, Richard P

    2015-05-01

    β-Sheet is one of the major protein secondary structures. Oppositely charged residues are frequently observed across neighboring strands in antiparallel sheets, suggesting the importance of cross-strand ion pairing interactions. The charged amino acids Asp, Glu, Arg, and Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on lateral cross-strand ion pairing interactions at non-hydrogen-bonded positions, β-hairpin peptides containing Zbb-Agx (Zbb = Asp, Glu, Aad in increasing length; Agx = Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by NMR methods. The fraction folded population and folding energy were derived from the chemical shift deviation data. Peptides with high fraction folded populations involved charged residue side chain lengths that supported high strand propensity. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Minimal interaction was observed between residues with short side chains, most likely due to the diffused positive charge on the guanidinium group, which weakened cross-strand electrostatic interactions with the carboxylate side chain. Only the Aad-Arg/Agh interactions with long side chains clearly exhibited stabilizing energetics, possibly relying on hydrophobics. A survey of a non-redundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Arg < Glu-Arg, implying the need for matching long side chains. This suggested the need for long side chains on both guanidinium-bearing and carboxylate-bearing residues to stabilize the β-hairpin motif. PMID:25646959

  2. Structural and Biochemical Analysis of a Single Amino-Acid Mutant of WzzBSF That Alters Lipopolysaccharide O-Antigen Chain Length in Shigella flexneri.

    PubMed

    Chang, Chiung-Wen; Tran, Elizabeth N H; Ericsson, Daniel J; Casey, Lachlan W; Lonhienne, Thierry; Benning, Friederike; Morona, Renato; Kobe, Bostjan

    2015-01-01

    Lipopolysaccharide (LPS), a surface polymer of Gram-negative bacteria, helps bacteria survive in different environments and acts as a virulence determinant of host infection. The O-antigen (Oag) component of LPS exhibits a modal chain-length distribution that is controlled by polysaccharide co-polymerases (PCPs). The molecular basis of the regulation of Oag chain-lengths remains unclear, despite extensive mutagenesis and structural studies of PCPs from Escherichia coli and Shigella. Here, we identified a single mutation (A107P) of the Shigella flexneri WzzBSF, by a random mutagenesis approach, that causes a shortened Oag chain-length distribution in bacteria. We determined the crystal structures of the periplasmic domains of wild-type WzzBSF and the A107P mutant. Both structures form a highly similar open trimeric assembly in the crystals, and show a similar tendency to self-associate in solution. Binding studies by bio-layer interferometry reveal cooperative binding of very short (VS)-core-plus-O-antigen polysaccharide (COPS) to the periplasmic domains of both proteins, but with decreased affinity for the A107P mutant. Our studies reveal that subtle and localized structural differences in PCPs can have dramatic effects on LPS chain-length distribution in bacteria, for example by altering the affinity for the substrate, which supports the role of the structure of the growing Oag polymer in this process. PMID:26378781

  3. DATA COLLECTION CONSTRAINTS FOR THE USE OF LENGTH HETEROGENEITY POLYMERASE CHAIN REACTION (LH-PCR) AS AN INDICATOR OF STREAM SANITARY AND ECOLOGICAL CONDITION

    EPA Science Inventory

    This study is part of a larger project for the development of bacterial indicators of stream sanitary and ecological condition. Here we report preliminary research on the use of Length Heterogeneity Polymerase Chain Reaction (LH-PCR), which discriminates among 16S rRNA genes bas...

  4. Structural and Biochemical Analysis of a Single Amino-Acid Mutant of WzzBSF That Alters Lipopolysaccharide O-Antigen Chain Length in Shigella flexneri

    PubMed Central

    Casey, Lachlan W.; Lonhienne, Thierry; Benning, Friederike; Morona, Renato; Kobe, Bostjan

    2015-01-01

    Lipopolysaccharide (LPS), a surface polymer of Gram-negative bacteria, helps bacteria survive in different environments and acts as a virulence determinant of host infection. The O-antigen (Oag) component of LPS exhibits a modal chain-length distribution that is controlled by polysaccharide co-polymerases (PCPs). The molecular basis of the regulation of Oag chain-lengths remains unclear, despite extensive mutagenesis and structural studies of PCPs from Escherichia coli and Shigella. Here, we identified a single mutation (A107P) of the Shigella flexneri WzzBSF, by a random mutagenesis approach, that causes a shortened Oag chain-length distribution in bacteria. We determined the crystal structures of the periplasmic domains of wild-type WzzBSF and the A107P mutant. Both structures form a highly similar open trimeric assembly in the crystals, and show a similar tendency to self-associate in solution. Binding studies by bio-layer interferometry reveal cooperative binding of very short (VS)-core-plus-O-antigen polysaccharide (COPS) to the periplasmic domains of both proteins, but with decreased affinity for the A107P mutant. Our studies reveal that subtle and localized structural differences in PCPs can have dramatic effects on LPS chain-length distribution in bacteria, for example by altering the affinity for the substrate, which supports the role of the structure of the growing Oag polymer in this process. PMID:26378781

  5. LISA telescope spacer design investigations

    NASA Astrophysics Data System (ADS)

    Sanjuan, Josep; Mueller, Guido; Livas, Jeffrey; Preston, Alix; Arsenovic, Petar; Castellucci, Kevin; Generie, Joseph; Howard, Joseph; Stebbins, Robin

    The Laser Interferometer Space Antenna (LISA) is a space-based gravitational wave observa-tory with the goal of observing Gravitational Waves (GWs) from astronomical sources in a frequency range from 30 µHz to 0.1 Hz. The detection of GWs at such low frequency requires measurements of distances at the pico-meter level between bodies separated by 5 million kilo-meters. The LISA mission consists of three identical spacecraft (SC) separated by 5 × 106 km forming an equilateral triangle. Each SC contains two optical assemblies and two vacuum en-closures housing one proof mass (PM) in geodesic (free fall) motion each. The two assemblies on one SC are each pointing towards an identical assembly on each of the other two SC to form a non-equal arm interferometer. The measurement of the GW strain is done by measuring the change in the length of the optical path between the PMs of one arm relative to the other arms caused by the pass of a GW. An important element of the Interferometric Measurement System (IMS) is the telescope which, on one hand, gathers the light coming from the far SC (˜100 pW) and, on the other hand, expands and collimates the small outgoing beam ( 1 W) and sends it to the far SC. Due to the very demanding sensitivity requirements care must be taken in the design and validation of the telescope not to degrade the IMS performance. For instance, the diameter of the telescope sets the the shot noise of the IMS and depends critically on the diameter of the primary and the divergence angle of the outgoing beam. As the telescope is rather fast telescope, the divergence angle is a critical function of the overall separation between the primary and secondary. Any long term changes of the distance of more than a a few micro-meter would be detrimental to the LISA mission. Similarly challenging are the requirements on the in-band path-length noise for the telescope which has to be kept below 1 pm Hz-1/2 in the LISA band. Different configurations (on-axis/off axis

  6. Effects of added oligoguluronate on mechanical properties of Ca - alginate - oligoguluronate hydrogels depend on chain length of the alginate.

    PubMed

    Padoł, Anna Maria; Draget, Kurt Ingar; Stokke, Bjørn Torger

    2016-08-20

    The effect of adding shorter alginate fragments highly enriched in α-l-guluronic acid (oligoG) on the Young's modulus of the Ca-induced alginate hydrogels were determined using nanoindentation. Ca-alginate gels using two low and one high molecular weight alginate, with increasing amount of added oligoG, were prepared at constant 20mM total Ca(2+) by in situ release of the cation. Differences in the effect on the mechanical properties of increasing amount of oligoG to the various alginate samples were attributed to their different capability to support network connectivity by junction zone formation. Upon decreasing the fractional Ca-saturation of all the α-l-guluronic acid residues (G) present, Fsat, by increasing the oligoG concentration, the lower molecular weight alginates displayed the largest reduction in Young's modulus. This was suggested to be due to the few sequences of α-l-guluronic acid residues making up potential zones engaging in network connectivity of this alginate. Similar trends were observed for a low molecular weight alginate with larger fraction of G. The higher molecular weight sample displayed less reduction of Young's modulus associated with increasing concentration of oligoG. The consequences of reduction in effective, mean junction zone functionality and associated increase in sol fraction with added oligoG on the elastic properties thus depend on the chain length of the alginates. These finding suggest that effects of added oligoG on Ca-induced alginate gelation should connect the effect on junction zone formation to those mediating network connectivity. PMID:27178929

  7. Biosynthesis of medium chain length poly(3-hydroxyalkanoates) (mcl-PHAs) by Comamonas testosteroni during cultivation on vegetable oils.

    PubMed

    Thakor, Nehal; Trivedi, Ujjval; Patel, K C

    2005-11-01

    Comamonas testosteroni has been studied for its ability to synthesize and accumulate medium chain length poly(3-hydroxyalkanoates) (mcl-PHAs) during cultivation on vegetable oils available in the local market. Castor seed oil, coconut oil, mustard oil, cotton seed oil, groundnut oil, olive oil and sesame oil were supplemented in the mineral medium as a sole source of carbon for growth and PHAs accumulation. The composition of PHAs was analysed by a coupled gas chromatography/mass spectroscopy (GC/MS). PHAs contained C6 to C14 3-hydroxy acids, with a strong presence of 3-hydroxyoctanoate when coconut oil, mustard oil, cotton seed oil and groundnut oil were supplied. 3-hydroxydecanoate was incorporated at higher concentrations when castor seed oil, olive oil and sesame oil were the substrates. Purified PHAs samples were characterized by Fourier Transform Infrared (FTIR) and 13C NMR analysis. During cultivation on various vegetable oils, C. testosteroni accumulated PHAs up to 78.5-87.5% of the cellular dry material (CDM). The efficiency of the culture to convert oil to PHAs ranged from 53.1% to 58.3% for different vegetable oils. Further more, the composition of the PHAs formed was not found to be substrate dependent as PHAs obtained from C. testosteroni during growth on variety of vegetable oils showed similar compositions; 3-hydroxyoctanoic acid and/or 3-hydroxydecanoic acid being always predominant. The polymerizing system of C. testosteroni showed higher preference for C8 and C10 monomers as longer and smaller monomers were incorporated less efficiently. PMID:16084364

  8. Effects of quaternary ammonium chain length on the antibacterial and remineralizing effects of a calcium phosphate nanocomposite.

    PubMed

    Zhang, Ke; Cheng, Lei; Weir, Michael D; Bai, Yu-Xing; Xu, Hockin H K

    2016-03-01

    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 caries

  9. 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

  10. Two-stage continuous process development for the production of medium-chain-length poly(3-hydroxyalkanoates).

    PubMed

    Jung, K; Hazenberg, W; Prieto, M; Witholt, B

    2001-01-01

    Pseudomonas oleovorans forms medium-chain-length poly(3-hydroxyalkanoate) (PHA) most effectively at growth rates below the maximum specific growth rate. Under adequate conditions, PHA accumulates in inclusion bodies in cells up to levels higher than half of the cell mass, which is a time-consuming process. For PHA production, a two-stage continuous cultivation system with two fermentors connected in series is a potentially useful system. It offers production of cells at a specific growth rate in a first compartment at conditions that lead cells to generate PHA at higher rates in a second compartment, with a relatively long residence time. In such a system, dilution rates of 0.21 h(-1) in the first fermentor (D(1)) and 0.16 h(-1) in the second fermentor (D(2)) were found to yield the highest volumetric PHA productivity. Transient-state experiments allowed investigation of D(1) and D(2) over a wide dilution rate range at high resolution in time-saving experiments. Furthermore, the influence of temperature, pH, nutrient limitation, and carbon source on PHA productivity was investigated and results similar to optimum conditions in single-stage chemostat cultivations of P. oleovorans were found. With all culture parameters optimized, a volumetric PHA productivity of 1.06 g L(-1) h(-1) was determined. Under these conditions, P. oleovorans cells contained 63% (dry weight) PHA in the effluent of the second fermentor. This is the highest PHA productivity and PHA content reported thus far for P. oleovorans cultures grown on alkanes. PMID:11084589

  11. 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

  12. Photochemical Modification of Single Crystalline GaN Film Using n-Alkene with Different Carbon Chain Lengths as Biolinker.

    PubMed

    Wang, Chun; Zhuang, Hao; Huang, Nan; Heuser, Steffen; Schlemper, Christoph; Zhai, Zhaofeng; Liu, Baodan; Staedler, Thorsten; Jiang, Xin

    2016-06-14

    As a potential material for biosensing applications, gallium nitride (GaN) films have attracted remarkable attention. In order to construct GaN biosensors, a corresponding immobilization of biolinkers is of great importance in order to render a surface bioactive. In this work, two kinds of n-alkenes with different carbon chain lengths, namely allylamine protected with trifluoroacetamide (TFAAA) and 10-aminodec-1-ene protected with trifluoroacetamide (TFAAD), were used to photochemically functionalize single crystalline GaN films. The successful linkage of both TFAAA and TFAAD to the GaN films is confirmed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurement. With increased UV illumination time, the intensity of the secondary ions corresponding to the linker molecules initially increases and subsequently decreases in both cases. Based on the SIMS measurements, the maximum coverage of TFAAA is achieved after 14 h of UV illumination, while only 2 h is required in the case of TFAAD to reach the situation of a fully covered GaN surface. This finding leads to the conclusion that the reaction rate of TFAAD is significantly higher compared to TFAAA. Measurements by atomic force microscopy (AFM) indicate that the coverage of GaN films by a TFAAA layer leads to an increased surface roughness. The atomic terraces, which are clearly observable for the pristine GaN films, disappear once the surface is fully covered by a TFAAA layer. Such TFAAA layers will feature a homogeneous surface topography even for reaction times of 24 h. In contrast to this, TFAAD shows strong cross-polymerization on the surface, this is confirmed by optical microscopy. These results demonstrate that TFAAA is a more suitable candidate as biolinker in context of the GaN surfaces due to its improved controllability. PMID:27217218

  13. Organization of spacer DNA in chromatin.

    PubMed Central

    Lohr, D; Van Holde, K E

    1979-01-01

    Detailed analysis of the DNA fragment patterns produced by DNase I digestion of yeast, HeLa, and chicken erythrocyte nuclei reveals surprising features of nucleosome phasing. First, the spacer regions in phased yeast chromatin must be of lengths (10m + 5) base pairs, where m = 0, 1, 2,....This feature is not seen in parallel studies of chicken erythrocyte chromatin. The 5-base pair increment in the yeast spacer imposes interesting restraints on the higher order structure of yeast chromatin. Second, we have been able to simulate the DNase I cutting patterns and get good agreement with the observed yeast patterns. Third, three different chromatins show a long range periodicity in the DNase I digest pattern, with a period half that of the staphylococcal nuclease repeat. These results suggest that the amount of chromatin observed in discrete extended-ladder bands is a minimum estimate of phasing and in fact phasing may be a more general feature. Images PMID:392519

  14. The effect of side-chain length on the solid-state structure and optoelectronic properties of fluorene-alt-benzothiadiazole based conjugated polymers--a DFT study.

    PubMed

    Eslamibidgoli, Mohammad J; Lagowski, Jolanta B

    2012-11-01

    Using the dispersion corrected density functional theory (DFT-D/B97D) approach, we have performed bulk solid-state calculations to investigate the influence of side-chain length on the molecular packing and optoelectronic properties of poly (9,9-di-n-alkylfluorene-alt-benzothiadiazole) or FnBT's where n is the number of CH(2) units in the alkyl side-chains. Our results indicate that the FnBT's with longer side-chains in their most stable configurations, due to the significant intermolecular interactions between the side-chains, form lamellar crystal structures. On the other hand, for the FnBT's with shorter side-chains, two nearly degenerate stable crystal structures with nearly hexagonal symmetries have been found. These different packing structures can be attributed to the microphase separations between the flexible side-chains and the rigid backbones whose existence has been discussed in previous investigations for other hairy rod polymers. As a result of the efficient interchain interactions for the lamellar structures, the dihedral angle between the F and BT units is reduced by about 30°, providing a more planar configuration for the backbone. In turn, a more planar backbone leads to a decrease, about 0.2 and 0.3 eV, of the band gaps of the lamellar structures relative to the gap values for the gas and the nearly hexagonal phases, respectively. Time-dependent DFT (TD-DFT) was used to study the excited states of the monomers of FnBT's with various lengths of side-chains. TD-DFT study suggests that the absorption spectrum of the polymers with longer side-chains is red-shifted relative to the polymers with shorter side-chains and the gas phase. PMID:23050864

  15. 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.

  16. Thermodynamic and fibril formation studies of full length immunoglobulin light chain AL-09 and its germline protein using scan rate dependent thermal unfolding.

    PubMed

    Blancas-Mejía, Luis M; Horn, Timothy J; Marin-Argany, Marta; Auton, Matthew; Tischer, Alexander; Ramirez-Alvarado, Marina

    2015-12-01

    Light chain (AL) amyloidosis is a fatal disease where monoclonal immunoglobulin light chains deposit as insoluble amyloid fibrils. For many years it has been considered that AL amyloid deposits are formed primarily by the variable domain, while its constant domain has been considered not to be amyloidogenic. However recent studies identify full length (FL) light chains as part of the amyloid deposits. In this report, we compare the stabilities and amyloidogenic properties of two light chains, an amyloid-associated protein AL-09 FL, and its germline protein κ I O18/O8 FL (IGKV 1-33). We demonstrate that the thermal unfolding for both proteins is irreversible and scan rate dependent, with similar stability parameters compared to their VL counterparts. In addition, the constant domain seems to modulate their amyloidogenic properties and affect the morphology of the amyloid fibrils. These results allow us to understand the role of the kappa constant domain in AL amyloidosis. PMID:26263488

  17. 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.

  18. 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.

  19. Selenium Chain Length Distribution in GexSe100-x Glasses: Insights from (77)Se NMR Spectroscopy and Quantum Chemical Calculations.

    PubMed

    Kaseman, Derrick C; Oliveira, Karina Moreira; Palazzo, Teresa; Sen, Sabyasachi

    2016-05-19

    The statistics of selenium chain length distribution in GexSe100-x glasses with 5 ≤ x ≤ 20 are investigated using a combination of high-resolution, two-dimensional (77)Se nuclear magnetic resonance (NMR) spectroscopy and quantum chemical calculations. This combined approach allows for the distinction of various selenium chain environments on the basis of subtle but systematic effects of next-nearest neighbors of Se atoms in -Se-Se-Se- linkages on the (77)Se chemical shift tensor parameters. Simulation of the experimental (77)Se NMR spectral line shapes indicates that Se chain speciation in these chalcogenide glasses follows the Flory-Schulz distribution, originally developed for organic chain polymers. PMID:27129100

  20. Beware of Cocktails: Chain-Length Bidispersity Triggers Explosive Self-Assembly of Poly-l-Glutamic Acid β2-Fibrils.

    PubMed

    Hernik-Magoń, Agnieszka; Puławski, Wojciech; Fedorczyk, Bartłomiej; Tymecka, Dagmara; Misicka, Aleksandra; Szymczak, Piotr; Dzwolak, Wojciech

    2016-04-11

    Chain-length polydispersity is among the least understood factors governing the fibrillation propensity of homopolypeptides. For monodisperse poly-l-glutamic acid (PLGA), the tendency to form fibrils depends of the main-chain length. Long-chained PLGA, so-called (Glu)200, fibrillates more readily than short (Glu)5 fragments. Here we show that conversion of α-helical (Glu)200 into amyloid-like β-fibrils is dramatically accelerated in the presence of intrinsically disordered (Glu)5. While separately self-assembled fibrils of (Glu)200 and (Glu)5 reveal distinct morphological and infrared characteristics, accelerated fibrillation in mixed (Glu)200 and (Glu)5 leads to aggregates similar to neat (Glu)200 fibrils, even in excess of (Glu)5. According to molecular dynamics simulations and circular dichroism measurements, local events of "misfolding transfer" from (Glu)5 to (Glu)200 may play a key role in the initial stages of conformational dynamics underlying the observed phenomenon. Our results highlight chain-length polydispersity as a potent, although so-far unrecognized factor profoundly affecting the fibrillation propensity of homopolypeptides. PMID:26909651

  1. 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. PMID:21975541

  2. X-ray spectroscopy characterization of self-assembled monolayers of nitrile-substituted oligo(phenylene ethynylene)s with variable chain length

    PubMed Central

    Hamoudi, Hicham; Kao, Ping; Nefedov, Alexei; Allara, David L

    2012-01-01

    Summary Self-assembled monolayers (SAMs) of nitrile-substituted oligo(phenylene ethynylene) thiols (NC-OPEn) with a variable chain length n (n ranging from one to three structural units) on Au(111) were studied by synchrotron-based high-resolution X-ray photoelectron spectroscopy and near-edge absorption fine-structure spectroscopy. The experimental data suggest that the NC-OPEn molecules form well-defined SAMs on Au(111), with all the molecules bound to the substrate through the gold–thiolate anchor and the nitrile tail groups located at the SAM–ambient interface. The packing density in these SAMs was found to be close to that of alkanethiolate monolayers on Au(111), independent of the chain length. Similar behavior was found for the molecular inclination, with an average tilt angle of ~33–36° for all the target systems. In contrast, the average twist of the OPEn backbone (planar conformation) was found to depend on the molecular length, being close to 45° for the films comprising the short OPE chains and ~53.5° for the long chains. Analysis of the data suggests that the attachment of the nitrile moiety, which served as a spectroscopic marker group, to the OPEn backbone did not significantly affect the molecular orientation in the SAMs. PMID:22428092

  3. Quantizing Open Spin Chains with Variable Length and Giant Gravitons in the Anti-de Sitter-Space/Conformal Field-Theory Correspondence

    SciTech Connect

    Berenstein, David; Correa, Diego H.; Vazquez, Samuel E.

    2005-11-04

    We study an XXX open spin chain with variable number of sites, where the variability is introduced only at the boundaries. This model arises naturally in the study of giant gravitons in the anti-de Sitter-space/conformal field-theory correspondence. We show how to quantize the spin chain by mapping its states to a bosonic lattice of finite length with sources and sinks of particles at the boundaries. Using coherent states, we show how the Hamiltonian for the bosonic lattice gives the correct description of semiclassical open strings ending on giant gravitons.

  4. Effects of molecular and lattice structure on the thermal behaviours of some long chain length potassium(I) n-alkanoates

    NASA Astrophysics Data System (ADS)

    Nelson, Peter N.; Ellis, Henry A.; Taylor, Richard A.

    2014-01-01

    Lattice structures and thermal behaviours for some long chain potassium carboxylates (nc = 8-18, inclusive) are investigated using Fourier Transform Infrared spectroscopy, X-ray Powder Diffraction, Solid State spin decoupled 13C NMR spectroscopy, Differential Scanning Calorimetry and Thermogravimetry. The measurements show that the carboxyl groups are coordinated to potassium atoms via asymmetric chelating bidentate bonding, with extensive carboxyl intermolecular interactions to yield tetrahedral metal centers, irrespective of chain length. Furthermore, the hydrocarbon chains are crystallized in the fully extended all-trans configuration and are arranged as non-overlapping lamellar bilayer structures with closely packed methyl groups from opposite layers. Additionally, odd-even alternation, observed in density and methyl group chemical shift, is ascribed to the relative vertical distances between layers in the bilayer, that are not in the same plane. Therefore, for even chain homologues, where this distances is less than for odd chain adducts, more intimate packing is indicated. The phase sequences for all compounds show several reversible crystal-crystal transition associated with kinetically controlled gauche-trans isomerism of the polymethylene chains which undergo incomplete fusion when heated to the melt. The compounds degrade above 785 K to yield carbon dioxide, water, potassium oxide and an alkene.

  5. 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.

  6. Effect of alkane chain length and counterion on the freezing transition of cationic surfactant adsorbed film at alkane mixture - water interfaces.

    PubMed

    Tokiwa, Yuhei; Sakamoto, Hiroyasu; Takiue, Takanori; Aratono, Makoto; Matsubara, Hiroki

    2015-05-21

    Penetration of alkane molecules into the adsorbed film gives rise to a surface freezing transition of cationic surfactant at the alkane-water interface. To examine the effect of the alkane chain length and counterion on the surface freezing, we employed interfacial tensiometry and ellipsometry to study the interface of cetyltrimethylammonium bromide and cetyltrimethylammonium chloride aqueous solutions against dodecane, tetradecane, hexadecane, and their mixtures. Applying theoretical equations to the experimental results obtained, we found that the alkane molecules that have the same chain length as the surfactant adsorb preferentially into the surface freezing film. Furthermore, we demonstrated that the freezing transition temperature of cationic surfactant adsorbed film was independent of the kind of counterion. PMID:25932500

  7. Top-Down 193-nm Ultraviolet Photodissociation Mass Spectrometry for Simultaneous Determination of Polyubiquitin Chain Length and Topology

    PubMed Central

    2016-01-01

    Protein ubiquitin modifications present a vexing analytical challenge, because of the dynamic changes in the site of modification on the substrate, the number of ubiquitin moieties attached, and the diversity of linkage patterns in which they are attached. Presented here is a method to confidently assign size and linkage type of polyubiquitin modifications. The method combines intact mass measurement to determine the number of ubiquitin moieties in the chain with backbone fragmentation by 193-nm ultraviolet photodissociation (UVPD) to determine the linkage pattern. UVPD fragmentation of proteins leads to reproducible backbone cleavage at almost every inter-residue position, and in polyubiquitin chains, the N-terminally derived fragments from each constituent monomer are identical, up to the site of conjugation. The N-terminal ubiquitin fragment ions are superimposed to create a diagnostic pattern that allows easy recognition of the dominant chain linkages. The method is demonstrated by achieving almost-complete fragmentation of monoubiquitin and then, subsequently, fragmentation of dimeric, tetrameric, and longer Lys48- and Lys63-linked ubiquitin chains. The utility of the method for the analysis of mixed linkage chains is confirmed for mixtures of Lys48 and Lys63 tetramers with known relative concentrations and for an in vitro-formulated ubiquitin chain attached to a substrate protein. PMID:25559986

  8. Structural and Rotational Dynamics of Carbon Dioxide in 1-Alkyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ionic Liquids: The Effect of Chain Length.

    PubMed

    Giammanco, Chiara H; Yamada, Steven A; Kramer, Patrick L; Tamimi, Amr; Fayer, Michael D

    2016-07-14

    Ionic liquids (ILs) have been proposed as possible carbon dioxide (CO2) capture media; thus, it is useful to understand the dynamics of both the dissolved gas and its IL environment as well as how altering an IL affects these dynamics. With increasing alkyl chain length, it is well-established that ILs obtain a mesoscopic structural feature assigned to polar-apolar segregation, and the change in structure with chain length affects the dynamics. Here, the dynamics of CO2 in a series of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ILs, in which the alkyl group is ethyl, butyl, hexyl, or decyl, were investigated using ultrafast infrared spectroscopy by measuring the reorientation and spectral diffusion of carbon dioxide in the ILs. It was found that reorientation of the carbon dioxide occurs on three time scales, which correspond to two different time scales of restricted wobbling-in-a-cone motions and a long-time complete diffusive reorientation. Complete reorientation slows with increasing chain length but less than the increases in viscosity of the bulk liquids. Spectral diffusion, measured with two-dimensional IR spectroscopy, is caused by a combination of the liquids' structural fluctuations and reorientation of the CO2. The data were analyzed using a recent theory that takes into account both contributions to spectral diffusion and extracts the structural spectral diffusion. Different components of the structural fluctuations have distinct dependences on the alkyl chain length. All of the dynamics are fast compared to the complete orientational randomization of the bulk ILs, as measured with optical heterodyne-detected optical Kerr effect measurements. The results indicate a hierarchy of constraint releases in the liquids that give rise to increasingly slower dynamics. PMID:27264965

  9. Complexation of carboxylate anions with the arginine gas-phase amino acid: Effects of chain length on the geometry of extended ion binding

    NASA Astrophysics Data System (ADS)

    Luxford, Thomas F. M.; Milner, Edward M.; Yoshikawa, Naruo; Bullivant, Chad; Dessent, Caroline E. H.

    2013-07-01

    Complexation of deprotonated carboxylic acids with arginine was investigated using collision-induced dissociation to probe the nature of isolated carboxylate-amino acid interactions as a function of anion size. Monocarboxylic CH3(CH2)nCOO-·Arg (n = 3-7, 9, 10) and dicarboxylic acid COOH(CH2)nCOO-·Arg (n = 3-5, 7-10) complexes were investigated. For the dicarboxylic acid clusters, chain length has a significant effect on the %fragmentation energies with the n = 9, 10 systems fragmenting at significantly lower energies than the corresponding shorter chain systems. Molecular mechanics calculations suggest that this fragmentation energy shift is associated with the longer-chain dicarboxylic acid-Arg clusters switching to ring structures.

  10. 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

    2015-07-01

    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. PMID:26062868

  11. Mechanisms by which saturated triacylglycerols elevate the plasma low density lipoprotein-cholesterol concentration in hamsters. Differential effects of fatty acid chain length.

    PubMed Central

    Woollett, L A; Spady, D K; Dietschy, J M

    1989-01-01

    These studies were designed to elucidate how shorter (MCT) and longer (HCO) chain-length saturated triacylglycerols and cholesterol interact to alter steady-state plasma LDL-cholesterol levels. When either MCT or HCO was fed in the absence of cholesterol, there was little effect on receptor-dependent LDL transport but a 36-43% increase in LDL-cholesterol production. Cholesterol feeding in the absence of triacylglycerol led to significant suppression of receptor-dependent LDL transport and a 26-31% increase in LDL-cholesterol production. However, when the longer chain-length saturated triacylglycerol was fed together with cholesterol there was a marked increase in the suppression of receptor-dependent LDL transport and an 82% increase in production rate. Together, these two alterations accounted for the observed eightfold increase in plasma LDL-cholesterol concentration. In contrast, feeding the shorter chain-length saturated triacylglycerol with cholesterol actually enhanced receptor-dependent LDL transport while also causing a smaller increase (52%) in the LDL-cholesterol production rate. As a result of these two opposing events, MCT feeding had essentially no net effect on plasma LDL-cholesterol levels beyond that induced by cholesterol feeding alone. PMID:2738148

  12. Ultrasonic Relaxation Study of 1-Alkyl-3-methylimidazolium-Based Room-Temperature Ionic Liquids: Probing the Role of Alkyl Chain Length in the Cation.

    PubMed

    Zorębski, Michał; Zorębski, Edward; Dzida, Marzena; Skowronek, Justyna; Jężak, Sylwia; Goodrich, Peter; Jacquemin, Johan

    2016-04-14

    Ultrasound absorption spectra of four 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imides were determined as a function of the alkyl chain length on the cation from 1-propyl to 1-hexyl from 293.15 to 323.15 K at ambient pressure. Herein, the ultrasound absorption measurements were carried out using a standard pulse technique within a frequency range from 10 to 300 MHz. Additionally, the speed of sound, density, and viscosity have been measured. The presence of strong dissipative processes during the ultrasound wave propagation was found experimentally, i.e., relaxation processes in the megahertz range were observed for all compounds over the whole temperature range. The relaxation spectra (both relaxation amplitude and relaxation frequency) were shown to be dependent on the alkyl side chain length of the 1-alkyl-3-methylimidazolium ring. In most cases, a single-Debye model described the absorption spectra very well. However, a comparison of the determined spectra with the spectra of a few other imidazolium-based ionic liquids reported in the literature (in part recalculated in this work) shows that the complexity of the spectra increases rapidly with the elongation of the alkyl chain length on the cation. This complexity indicates that both the volume viscosity and the shear viscosity are involved in relaxation processes even in relatively low frequency ranges. As a consequence, the sound velocity dispersion is present at relatively low megahertz frequencies. PMID:26982480

  13. Nuclear reactor spacer grid and ductless core component

    DOEpatents

    Christiansen, David W.; Karnesky, Richard A.

    1989-01-01

    The invention relates to a nuclear reactor spacer grid member for use in a liquid cooled nuclear reactor and to a ductless core component employing a plurality of these spacer grid members. The spacer grid member is of the egg-shell type and is constructed so that the walls of the cell members of the grid member are formed of a single thickness of metal to avoid tolerance problems. Within each cell member is a hydraulic spring which laterally constrains the nuclear material bearing rod which passes through each cell member against a hardstop in response to coolant flow through the cell member. This hydraulic spring is also suitable for use in a water cooled nuclear reactor. A core component constructed of, among other components, a plurality of these spacer grid members, avoids the use of a full length duct by providing spacer sleeves about the sodium tubes passing through the spacer grid members at locations between the grid members, thereby maintaining a predetermined space between adjacent grid members.

  14. 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. PMID:26773489

  15. Influence of acid chain length on the properties of TiO2 prepared by sol-gel method and LC-MS studies of methylene blue photodegradation.

    PubMed

    Bakre, Pratibha V; Volvoikar, Prajesh S; Vernekar, Amit A; Tilve, S G

    2016-07-15

    Nano-sized titanium dioxide photocatalysts were synthesized by hybrid hydrolytic nonhydrolytic sol-gel method using aliphatic organic acid templates to study the effect of chain length on their properties. X-ray diffraction pattern indicated crystalline anatase phase. The Barrett-Joyner-Halenda surface area measurement gave surface area ranging from 98.4 to 205.5m(2)/g and was found to be dependent on the chain length of the aliphatic acid. The longer chain acids rendered the material with high surface area. The organic acids acted as bidentate ligand and a surfactant in controlling the size and the mesoporosity. The size of the TiO2 nanoparticulate was found to be in the range of 10-18nm. The catalyst prepared by employing long chain acids octanoic acid and palmitic acid had smaller size, narrow pore radius, higher surface area and showed better photocatalytic activity than the commercially available Degussa P25 catalyst for the degradation of methylene blue dye. A new intermediate was identified by tandem liquid chromatography mass spectrometry studies during the degradation of methylene blue solution. PMID:27100905

  16. 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

    2015-04-01

    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. PMID:25652263

  17. 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.

  18. Bond length and electric current oscillation of long linear carbon chains: Density functional theory, MpB model, and quantum spin transport studies

    NASA Astrophysics Data System (ADS)

    Oeiras, R. Y.; da Silva, E. Z.

    2014-04-01

    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.

  19. 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.

  20. Regioselective enzymatic acylation of methyl shikimate. Influence of acyl chain length and solvent polarity on enzyme specificity.

    PubMed

    Armesto, Nuria; Ferrero, Miguel; Fernández, Susana; Gotor, Vicente

    2002-07-12

    Candida antarctica lipase A (CAL-A) selectively catalyzes the acylation at the secondary C-4 hydroxyl group of methyl shikimate (2), which possesses three secondary hydroxyl groups, the C-3 allylic one being chemically more reactive. The effect both of the acyl group of the acylating agents and of the solvent polarity has been studied. The selectivity of CAL-A is almost complete with acyl donors that possess short chains. However, when acyl donors have longer chains, better results are obtained by C. antarctica lipase B (CAL-B). PMID:12098318

  1. Crystal Structures of Ligand-Bound Octaprenyl Pyrophosphate Synthase from Escherichia coli Reveal the Catalytic and Chain-Length Determining Mechanisms*

    PubMed Central

    Han, Xu; Chen, Chun-Chi; Kuo, Chih-Jung; Huang, Chun-Hsiang; Zheng, Yingying; Ko, Tzu-Ping; Zhu, Zhen; Feng, Xinxin; Wang, Ke; Oldfield, Eric; Wang, Andrew H.-J.; Liang, Po-Huang; Guo, Rey-Ting; Ma, Yanhe

    2014-01-01

    Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of one allylic substrate farnesyl pyrophosphate (FPP) and five homoallylic substrate isopentenyl pyrophosphate (IPP) molecules to form a C40 long-chain product OPP, which serves as a side chain of ubiquinone and menaquinone. OPPs belongs to the trans-prenyltransferase class of proteins. The structures of OPPs from Escherichia coli were solved in the apo-form as well as in complexes with IPP and a FPP thio-analog, FsPP, at resolutions of 2.2 to 2.6 Å, and revealed the detailed interactions between the ligands and enzyme. At the bottom of the active-site tunnel, M123 and M135 act in concert to form a wall which determines the final chain length. These results represent the first ligand-bound crystal structures of a long-chain trans-prenyltransferase and provide new information on the mechanisms of catalysis and product chain elongation. PMID:24895191

  2. Binding of the Cationic Peptide (KL)4K to Lipid Monolayers at the Air-Water Interface: Effect of Lipid Headgroup Charge, Acyl Chain Length, and Acyl Chain Saturation.

    PubMed

    Hädicke, André; Blume, Alfred

    2016-04-28

    The binding of the cationic peptide (KL)4K to monolayers of different anionic lipids was determined by adsorption experiments. The chemical structure of the anionic phospholipids was changed in different ways. First, the hydrophobic region of phosphatidylglycerols was altered by elongation of the acyl chain length. Second, an unsaturated chain was introduced. Third, lipids with negatively charged headgroups of different chemical structure were compared. (KL)4K itself shows no surface activity and does not bind to monolayers of zwitterionic lipids. Analysis of (KL)4K binding to anionic lipid monolayers reveals a competition between two binding processes: (i) incorporation of the peptide into the acyl chain region (surface pressure increase) and (ii) electrostatic interaction screening the negative charges with reduction of charge repulsion (surface pressure decrease due to monolayer condensation). The lipid acyl chain length and the chemical structure of the headgroup have minor effects on the binding properties. However, a strong dependence on the phase state of the monolayer was observed. In the liquid-expanded (LE) phase, the fluid monolayer provides enough space, so that peptide insertion due to hydrophobic interactions dominates. For monolayers in the liquid-condensed (LC) phase, peptide binding followed by monolayer condensation is the main effect. PMID:27049846

  3. 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. PMID:22112024

  4. The mitogenic activities of phosphatidate are acyl-chain-length dependent and calcium independent in C3H/10T1/2 cells.

    PubMed Central

    Krabak, M J; Hui, S W

    1991-01-01

    Phosphatidates (PA or phosphatidic acid) were shown to have mitogenic properties, including the stimulation of DNA synthesis and calcium mobilization in C3H/10T1/2 cells. Their continuous presence for a minimum of 7 h induced DNA synthesis with kinetics similar to that observed when 10% fetal bovine serum was used as a mitogen. PAs with long chain saturated fatty acid moieties were more mitogenic, in a dose-dependent fashion, than PAs with short saturated or unsaturated fatty acid moieties. When compared with lysostearoyl-PA (LSPA), distearoyl-PA (DSPA) was as potent with respect to the induction of DNA synthesis. Lysooleoyl-PA (LOPA) was slightly more potent than dioleoyl-PA (DOPA), but much weaker than DSPA and LSPA. Preincubation with dilauroyl-PA (DLPA) reduces the mitogenic effect of DSPA by 85%. The pattern of mitogenic inhibition suggests that a chain-length-independent, yet PA-specific, mechanism is involved. Both DSPA and DLPA are equally taken up by the cells after 30 min. LOPA, but not LSPA, produced a large calcium transient (1.3 microM), which we found to be derived from intracellular sources. DSPA, the most mitogenic PA tested, produced a weaker transient (0.6 microM). Interestingly, LSPA did not produce any detectable calcium transient. These results suggest that the chain-length-specific step in the signaling mechanism of PA occurs after the initial chain-length-independent partitioning and/or binding to the membrane and that the induction of DNA synthesis is not related to the observed calcium transients. PMID:2007185

  5. PEG-g-poly(GdDTPA-co-L-cystine): effect of PEG chain length on in vivo contrast enhancement in MRI.

    PubMed

    Mohs, Aaron M; Zong, Yuda; Guo, Junyu; Parker, Dennis L; Lu, Zheng-Rong

    2005-01-01

    Biodegradable macromolecular Gd(III) complexes, Gd-DTPA cystine copolymers (GDCP), were grafted with PEG of different sizes to modify the physicochemical properties and in vivo MRI contrast enhancement of the agents and to study the effect of PEG chain length on these properties. Three new PEG-grafted biodegradable macromolecular gadolinium(III) complexes were synthesized and characterized as blood pool MRI contrast agents. One of three different lengths of MPEG-NH(2) (MW = 550, 1000, and 2000) was grafted to the backbone of GDCP to yield PEG(n)()-g-poly(GdDTPA-co-l-cystine), PEG(n)()-GDCP. The PEG chain length did not dramatically alter the T(1) relaxivity, r(1), of the modified agents. The MRI enhancement profile of PEG(n)()-GDCP with different PEG sizes was significantly different in mice with respect to both signal intensity and clearance profiles. PEG(2000)-GDCP showed more prominent enhancement in the blood pool for a longer period of time than either PEG(1000)-GDCP or PEG(550)-GDCP. In the kidney, PEG(2000)-GDCP had less enhancement at 2 min than PEG(1000)-GDCP, but both PEG(550)-GDCP and PEG(1000)-GDCP showed a more pronounced signal decay thereafter. The three agents behaved similarly in the liver, as compared to that in the heart. All three agents showed little enhancement in the muscle. Chemical grafting with PEG of different chain lengths is an effective approach to modify the physiochemistry and in vivo contrast enhancement dynamics of the biodegradable macromolecular contrast agents. The novel agents are promising for further clinical development for cardiovascular and cancer MR imaging. PMID:16004476

  6. Characterization of alkylphenol degradation gene cluster in Pseudomonas putida MT4 and evidence of oxidation of alkylphenols and alkylcatechols with medium-length alkyl chain.

    PubMed

    Takeo, Masahiro; Prabu, Subbuswamy K; Kitamura, Chitoshi; Hirai, Makoto; Takahashi, Hana; Kato, Dai-Ichiro; Negoro, Seiji

    2006-10-01

    Alkylphenols (APs) are ubiquitous contaminants in aquatic environments and have endocrine disrupting and toxic effects on aquatic organisms. To investigate biodegradation mechanisms of APs, an AP degradation gene cluster was cloned from a butylphenol (BP)-degrading bacterium, Pseudomonas putida MT4. The gene cluster consisted of 13 genes named bupBA1A2A3A4A5A6CEHIFG. From the nucleotide sequences, bupA1A2A3A4A5A6 were predicted to encode a multicomponent phenol hydroxylase (PH), whereas bupBCEHIFG were expected to encode meta-cleavage pathway enzymes. A partial sequence of a putative NtrC-type regulatory gene, bupR, was also found upstream of the gene bupB. This result indicates that APs can be initially oxidized into alkylcatechols (ACs), followed by the meta-cleavage of the aromatic rings. To confirm this pathway, AP degradation tests were carried out using the recombinant P. putida KT2440 harboring the PH genes (bupA1A2A3A4A5A6). The recombinant strain oxidized 4-n-APs with an alkyl chain of up to C7 (< or = C7) efficiently and also several BPs including those with an alkyl chain with some degree of branching. Therefore, it was found that PH had a broad substrate specificity for APs with a medium-length alkyl chain (C3-C7). Moreover, the cell extract of a recombinant Escherichia coli harboring bupB (a catechol 2,3-dioxygenase gene) converted 4-n-ACs with an alkyl chain of < or = C9 into yellow meta-cleavage products with a maximum absorbance at 379 nm, indicating that the second step enzyme in this pathway is also responsible for the degradation of ACs with a medium-length alkyl chain. These results suggest that MT4 is a very useful strain in the biodegradation of a wide range of APs with a medium-length alkyl chain, which known nonylphenol-degrading Sphingomonas strains have never degraded. PMID:17116584

  7. 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. PMID:25830631

  8. Polar and azimuthal alignment of a nematic liquid crystal by alkylsilane self-assembled monolayers: effects of chain-length and mechanical rubbing.

    PubMed

    Malone, Stephanie M; Schwartz, Daniel K

    2008-09-01

    Alkylsilane self-assembled monolayers (SAMs) on oxide substrates are commonly used as liquid crystal (LC) alignment layers. We have studied the effects of alkyl chain length, photolytic degradation, and mechanical rubbing on polar and azimuthal LC anchoring. Both gradient surfaces (fabricated using photolytic degradation of C18 SAMs) and unirradiated SAMs composed of short alkyl chains show abrupt transitions from homeotropic to tilted alignment as a function of degradation or chain length. In both cases, the transition from homeotropic to tilted anchoring corresponds to increasing wettability of the SAM surfaces. However, there is an offset in the critical contact angle for the transition on gradient vs unirradiated SAMs, suggesting that layer thickness is more relevant than wettability for LC alignment. Mechanical rubbing can induce azimuthal alignment along the rubbing direction for alignment layers sufficiently near the homeotropic-to-planar transition. Notably, mechanical rubbing causes a small but significant shift in the homeotropic-to-tilted transition, e.g., unrubbed C5 SAMs induce homeotropic anchoring, but the same surface after rubbing induces LC pretilt. PMID:18686979

  9. 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. PMID:27276499

  10. Influence of chain length and polymer concentration on the gelation of (amidated) low-methoxyl pectin induced by calcium.

    PubMed

    Capel, François; Nicolai, Taco; Durand, Dominique; Boulenguer, Patrick; Langendorff, Virginie

    2005-01-01

    The gelation of low-methoxyl pectin (LMP) induced by addition of Ca2+ was studied by measuring the storage modulus as a function of temperature during cooling. Samples with different molar masses were prepared by mechanical degradation. The effect of the molar mass and the pectin concentration on the gelation properties was investigated. The effect of partial amidation was studied by comparing LMP and partially amidated LMP with the same molar mass and degree of methylation. The results are compared to those from a model developed for Ca2+-induced pectin gelation, and good agreement is found except at low concentrations and low molar masses where the gels are weaker than predicted. At low concentrations intrachain bonding weakens the gel, while the presence of small pectin chains weakens the gel because it neutralizes binding sites on larger chains. PMID:16283714

  11. Structure and Mechanism of an Arabidopsis Medium/Long-Chain-Length Prenyl Pyrophosphate Synthase1[W][OA

    PubMed Central

    Hsieh, Fu-Lien; Chang, Tao-Hsin; Ko, Tzu-Ping; Wang, Andrew H.-J.

    2011-01-01

    Prenyltransferases (PTSs) are involved in the biosynthesis of terpenes with diverse functions. Here, a novel PTS from Arabidopsis (Arabidopsis thaliana) is identified as a trans-type polyprenyl pyrophosphate synthase (AtPPPS), which forms a trans-double bond during each homoallylic substrate condensation, rather than a homomeric C10-geranyl pyrophosphate synthase as originally proposed. Biochemical and genetic complementation analyses indicate that AtPPPS synthesizes C25 to C45 medium/long-chain products. Its close relationship to other long-chain PTSs is also uncovered by phylogenetic analysis. A mutant of contiguous surface polar residues was produced by replacing four charged surface amino acids with alanines to facilitate the crystallization of the enzyme. The crystal structures of AtPPPS determined here in apo and ligand-bound forms further reveal an active-site cavity sufficient to accommodate the medium/long-chain products. The two monomers in each dimer adopt different conformations at the entrance of the active site depending on the binding of substrates. Taken together, these results suggest that AtPPPS is endowed with a unique functionality among the known PTSs. PMID:21220764

  12. 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. PMID:25108512

  13. 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. PMID:26945646

  14. Tailoring aqueous solubility of functionalized single-wall carbon nanotubes over a wide pH range through substituent chain length.

    PubMed

    Zeng, Liling; Zhang, Lei; Barron, Andrew R

    2005-10-01

    Carboxylic acid-functionalized SWNTs prepared via the reaction of an amino acid, NH2(CH2)nCO2H, with fluoronanotubes show similar levels of sidewall functionalization; however, the solubility in water is controlled by the length of the hydrocarbon side chain (i.e., n). The 6-aminohexanoic acid derivative is soluble in aqueous solution (0.5 mg mL(-1)) between pH 4 and 11, whereas the glysine and 11-aminoundecanoic acid derivatives are insoluble across all pH values. PMID:16218726

  15. Distinction of deep versus superficial clinical and nonclinical isolates of Trichosporon beigelii by isoenzymes and restriction fragment length polymorphisms of rDNA generated by polymerase chain reaction.

    PubMed Central

    Kemker, B J; Lehmann, P F; Lee, J W; Walsh, T J

    1991-01-01

    Fifteen clinical and environmental strains of Trichosporon beigelii were analyzed for similarities by using morphological features, biochemical profiles based on carbon compound assimilation and uric acid utilization, isoenzyme electrophoresis, and restriction fragment length polymorphisms of a segment of genes coding for rRNA expanded with the polymerase chain reaction. The findings suggest that strains that cause invasive disease are distinct from the superficial and the nonclinical isolates and that isolates from the skin and mucosae represent a number of different organisms, including some environmental forms. The study shows that T. beigelii is a complex of genetically distinct organisms and that more than one type is found in clinical samples. Images PMID:1684798

  16. A polymerase chain reaction method for the amplification of full-length envelope genes of HIV-1 from DNA samples containing single molecules of HIV-1 provirus.

    PubMed

    McClure, P; Curran, R; Boneham, S; Ball, J K

    2000-07-01

    Polymerase chain reaction (PCR) amplification of full-length envelope genes from the human immunodeficiency virus type 1 (HIV-1) directly from uncultured clinical samples is difficult. This paper describes a comparative assessment of the performance of three thermostable polymerases in an HIV-1 full-length envelope gene PCR. The PCR method utilising Expand HiFi polymerase was successful when using DNA samples extracted from a variety of sources including blood, semen and various tissues. This method generated high and specific yields of product from samples containing as little as one copy of HIV-1 proviral DNA. The resulting PCR products were suitable for a variety of downstream analytical methods including DNA sequence analysis. PMID:10921844

  17. Phytochelatins in Cadmium-Sensitive and Cadmium-Tolerant Silene vulgaris (Chain Length Distribution and Sulfide Incorporation).

    PubMed Central

    De Knecht, J. A.; Van Dillen, M.; Koevoets, PLM.; Schat, H.; Verkleij, JAC.; Ernst, WHO.

    1994-01-01

    In response to a range of Cd concentrations, the root tips of Cd-tolerant plants of Silene vulgaris exhibit a lower rate of PC production accompanied by a lower rate of longer chain PC synthesis than those of Cd-sensitive plants. At the same Cd exposure level, stable PC-Cd complexes are more rapidly formed in the roots of Cd-sensitive plants than in those of tolerant plants. At an equal PC concentration in the roots, the PC composition and the amount of sulfide incorporated per unit of PC-thiol is the same in both populations. Although these compounds might play some role in mechanisms that contribute to Cd detoxification, the ability to produce these compounds in greater amounts is not, itself, the mechanism that produces increased Cd tolerance in tolerant S. vulgaris plants. PMID:12232077

  18. Aquatic Macrophytes Inputs of Middle Chain Length n-alkyl Lipids into Lake Sediments: a Linear Algebra Approach

    NASA Astrophysics Data System (ADS)

    Gao, L.; Huang, Y.

    2009-12-01

    Quantitatively delineating multiple source inputs is a common but often difficult task in geological and environmental researches. Binary mixing model works well for simple two-component mixing problems when the two end members can be accurately defined. However, real world mixing problems usually involve more than two source components, and each component may have many composite profiles. Therefore, binary model is inadequate to provide an accurate estimate of contribution of all the end member sources. In such cases, linear combination model by solving linear algebra equations will have to be developed. In this study, we demonstrate the application of the linear algebra method to accurately calculate the percentage inputs of leaf waxes from different plant groups to lake sediments of Blood Pond and Rocky Pond in Massachusetts. We systematically sampled 28 species, including 6 tree species, 6 grass species, 7 emergent plants, 4 floating and 3 submerged aquatic plants around Blood Pond as well as 6 sediments samples of different depth. The distributions of these plants leaf waxes (n-alkanes and n-alkanoic acids) show distinctively different patterns, but also significant overlaps. To accurately quantify the percentage source inputs, we develop the 4-end member linear combination model. As we have an equation for each of the total 6 n-alkane compounds we use (C23 alkane ~C33 alkane), a 'least square fitting' is applied to solved the overdetermined linear system. Our results show that 91.7% of the total C23 alkane in sediments is derived from floating and submerged plants. We also applied our approach to Rocky Pond in southeastern Massachusetts and found >92 % of mid chain n-alkyl lipids are contributed by floating and submerged plants. Our results provide critical basis for using D/H ratios of mid-chain n-alkyl lipids (such as behenic acid) in lake sediments for reconstructing lake water D/H ratios.

  19. A feeding strategy for incorporation of canola derived medium-chain-length monomers into the PHA produced by wild-type Cupriavidus necator.

    PubMed

    Rathinasabapathy, Arthi; Ramsay, Bruce A; Ramsay, Juliana A; Pérez-Guevara, Fermín

    2014-04-01

    The aim of this study was to increase the density of wild type Cupriavidus necator H16 biomass grown on fructose in order to produce sufficient copolymer of short-chain-length (scl) and medium-chain-length (mcl) polyhydroxyalkanoate (PHA) from canola oil for mechanical testing of the PHA. Initial batch cultivation on fructose was followed by exponential feeding of fructose at a predetermined μ to achieve 44.4 g biomass/l containing only 20 % w/w of polyhydroxybutyrate (PHB) with a Y(x/fructose) of 0.44 g/g. In a third stage, canola oil was added under N-limited conditions to produce 92 g/l of biomass with 48 % w/w scl-mcl PHA. Using known standards, the PHA composition was confirmed by GC-MS analysis as 99.81 % 3-hydroxybutyrate, 0.06 % 3-hydroxyvalerate, 0.09 % 3-hydroxyhexanoate and 0.04 % 3-hydroxyoctanoate. The melting temperature (179 °C), crystallinity (54 %), tensile stress (25.1 Mpa) and Young's modulus (698 Mpa) for a PHB standard decreased to 176 °C, 52 %, 19.1 and 443 Mpa respectively for C. necator PHA produced in the 3-stage process. PMID:24287944

  20. Somatic mutation and CDR3 lengths of immunoglobulin kappa light chains expressed in patients with rheumatoid arthritis and in normal individuals.

    PubMed Central

    Bridges, S L; Lee, S K; Johnson, M L; Lavelle, J C; Fowler, P G; Koopman, W J; Schroeder, H W

    1995-01-01

    Immunoglobulin secretion by plasma cells infiltrating synovial membranes is a prominent feature of RA. Previous analyses of a cDNA library generated from synovium of RA patient BC revealed immunoglobulin kappa light chain transcripts with extensive somatic mutation, frequent N region addition, and unexpected variation in the lengths of CDR3 regions which form the center of the antigen binding site. To determine if these characteristics are present in other individuals, we performed reverse transcription-polymerase chain reaction amplification and sequenced > or = 10 V kappa-containing amplicons from nine tissue samples: synovia of three individuals with long-standing RA (including patient BC), PBLs of two of these individuals, and PBLs or splenocytes of four normal individuals. Increased levels of somatic mutation in PBLs appeared to correlate with increased age, which may reflect accumulation of circulating memory cells and/or decreased bone marrow production of naive B lymphocytes. Two of three RA synovial samples and both RA PBL samples exhibited increased proportions of clones with unusual CDR3 lengths. Enrichment for these antibody binding sites could be due to abnormal regulation of the emerging repertoire or to selection for B lymphocytes bearing antibodies of unusual specificity, and may play a role in the pathogenesis of RA. Images PMID:7635977

  1. A Unique Primer with an Inosine Chain at the 5′-Terminus Improves the Reliability of SNP Analysis Using the PCR-Amplified Product Length Polymorphism Method

    PubMed Central

    Shojo, Hideki; Tanaka, Mayumi; Takahashi, Ryohei; Kakuda, Tsuneo; Adachi, Noboru

    2015-01-01

    Polymerase chain reaction-amplified product length polymorphism (PCR-APLP) is one of the most convenient and reliable methods for single nucleotide polymorphism (SNP) analysis. This method is based on PCR, but uses allele-specific primers containing SNP sites at the 3′-terminus of each primer. To use this method at least two allele-specific primers and one “counter-primer”, which serves as a common forward or reverse primer of the allele-specific primers, are required. The allele-specific primers have SNP sites at the 3′-terminus, and another primer should have a few non-complementary flaps at the 5′-terminus to detect SNPs by determining the difference of amplicon length by PCR and subsequent electrophoresis. A major disadvantage of the addition of a non-complementary flap is the non-specific annealing of the primer with non-complementary flaps. However, a design principle for avoiding this undesired annealing has not been fully established, therefore, it is often difficult to design effective APLP primers. Here, we report allele-specific primers with an inosine chain at the 5′-terminus for PCR-APLP analysis. This unique design improves the competitiveness of allele-specific primers and the reliability of SNP analysis when using the PCR-APLP method. PMID:26381262

  2. Quantum chemical clarification of the alkyl chain length threshold of nonionic surfactants for monolayer formation at the air/water interface.

    PubMed

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

    2016-03-21

    A theoretical basis is provided for the experimental fact that for various surfactant classes the alkyl chain length threshold varies for the formation of condensed monolayers. The existence of the alkyl chain length threshold for a surfactant enabling the formation of monolayers is determined by the entropy increment to the Gibbs' energy, assessed by using the quantum chemical semiempiric method PM3. The value of the clusterization threshold is not stipulated by the surfactant solubility in water, rather by the electron-donor and electron-seeking properties of the head groups. These properties in turn impact the value of the solubility threshold for surfactants. The value of the clusterization threshold depends quadratically on the substituent constants, i.e. it is independent of whether the functional group is a donor or an acceptor of electrons. Rather it depends only on the donor or the acceptor 'force' of the substituent. The square-law dependence of the surface clusterization threshold of the amphiphile on the solubility threshold is evidenced. PMID:26957020

  3. Anti-spacer double patterning

    NASA Astrophysics Data System (ADS)

    Hyatt, Michael; Huang, Karen; DeVilliers, Anton; Slezak, Mark; Liu, Zhi

    2014-03-01

    With extreme UV not ready for HVM for the 20nm and 14nm nodes, double patterning options that extend the use of 193nm immersion lithography beyond the optical resolution limits, such as LELE (Litho-Etch-Litho-Etch) and SADP (Self Aligned Double Patterning), are being used for critical layers for these nodes. LELE requires very stringent overlay capability of the optical exposure tool. The spacer scheme of SADP starts with a conformal film of material around the mandrels and etched along the mandrel sidewalls to form patterns with doubled frequency. SADP, while having the advantage of being a self-aligned process, adds a number of process steps and strict control of the mandrel profile is required. In this paper, we will demonstrate a novel technique - ASDP (Anti-Spacer Double Patterning), which uses only spin-on materials to achieve self-aligned double patterning. After initial resist patterning, an Anti-Spacer Generator (ASG) material is coated on the resist pattern to create the developable spacer region. Another layer of material is then coated and processed to generate the second pattern in between the first resist pattern. We were able to define 37.5nm half pitch pattern features using this technique as well as sub-resolution features for an asymmetric pattern. In this paper we will review the capability of the process in terms of CD control and LWR (line width roughness) and discuss the limitations of the process.

  4. Contribution of the Distal Pocket Residue to the Acyl-Chain-Length Specificity of (R)-Specific Enoyl-Coenzyme A Hydratases from Pseudomonas spp.

    PubMed Central

    Sato, Shun; Hiroe, Ayaka; Ishizuka, Koya; Kanazawa, Hiromi; Shiro, Yoshitsugu

    2015-01-01

    (R)-Specific enoyl-coenzyme A (enoyl-CoA) hydratases (PhaJs) are capable of supplying monomers from fatty acid β-oxidation to polyhydroxyalkanoate (PHA) biosynthesis. PhaJ1Pp from Pseudomonas putida showed broader substrate specificity than did PhaJ1Pa from Pseudomonas aeruginosa, despite sharing 67% amino acid sequence identity. In this study, the substrate specificity characteristics of two Pseudomonas PhaJ1 enzymes were investigated by site-directed mutagenesis, chimeragenesis, X-ray crystallographic analysis, and homology modeling. In PhaJ1Pp, the replacement of valine with isoleucine at position 72 resulted in an increased preference for enoyl-coenzyme A (CoA) elements with shorter chain lengths. Conversely, at the same position in PhaJ1Pa, the replacement of isoleucine with valine resulted in an increased preference for enoyl-CoAs with longer chain lengths. These changes suggest a narrowing and broadening in the substrate specificity range of the PhaJ1Pp and PhaJ1Pa mutants, respectively. However, the substrate specificity remains broader in PhaJ1Pp than in PhaJ1Pa. Additionally, three chimeric PhaJ1 enzymes, composed from PhaJ1Pp and PhaJ1Pa, all showed significant hydratase activity, and their substrate preferences were within the range exhibited by the parental PhaJ1 enzymes. The crystal structure of PhaJ1Pa was determined at a resolution of 1.7 Å, and subsequent homology modeling of PhaJ1Pp revealed that in the acyl-chain binding pocket, the amino acid at position 72 was the only difference between the two structures. These results indicate that the chain-length specificity of PhaJ1 is determined mainly by the bulkiness of the amino acid residue at position 72, but that other factors, such as structural fluctuations, also affect specificity. PMID:26386053

  5. Solute transport through fractured rock: Radial diffusion into the rock matrix with several geological layers for an arbitrary length decay chain

    NASA Astrophysics Data System (ADS)

    Mahmoudzadeh, Batoul; Liu, Longcheng; Moreno, Luis; Neretnieks, Ivars

    2016-05-01

    The paper presents a model development to derive a semi-analytical solution to describe reactive solute transport through a single channel in a fracture with cylindrical geometry. The model accounts for advection through the channel, radial diffusion into the adjacent heterogeneous rock matrix comprising different geological layers, adsorption on both the channel surface, and the geological layers of the rock matrix and radioactive decay chain. Not only an arbitrary-length decay chain, but also as many number of the rock matrix layers with different properties as observed in the field can be handled. The solution, which is analytical in the Laplace domain, is transformed back to the time domain numerically e.g. by use of de Hoog algorithm. The solution is verified against experimental data and analytical solutions of limiting cases of solute transport through porous media. More importantly, the relative importance and contribution of different processes on solute transport retardation in fractured rocks are investigated by simulating several cases of varying complexity. The simulation results are compared with those obtained from rectangular model with linear matrix diffusion. It is found that the impact of channel geometry on breakthrough curves increases markedly as the transport distance along the flow channel and away into the rock matrix increase. The effect of geometry is more pronounced for transport of a decay chain when the rock matrix consists of a porous altered layer.

  6. Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids

    SciTech Connect

    Touchette, Megan H.; Bommineni, Gopal R.; Delle Bovi, Richard J.; Gadbery, John; Nicora, Carrie D.; Shukla, Anil K.; Kyle, Jennifer E.; Metz, Thomas O.; Martin, Dwight W.; Sampson, Nicole S.; Miller, W. T.; Tonge, Peter J.; Seeliger, Jessica C.

    2015-09-08

    Although classified as Gram-positive bacteria, Corynebacterineae possess an asymmetric outer membrane that imparts structural and thereby physiological similarity to more distantly related Gram-negative bacteria. Like lipopolysaccharide in Gram-negative bacteria, lipids in the outer membrane of Corynebacterineae have been associated with the virulence of pathogenic species such as Mycobacterium tuberculosis (Mtb). For example, Mtb strains that lack long, branched-chain alkyl esters known as dimycocerosates (DIMs) are significantly attenuated in model infections. The resultant interest in the biosynthetic pathway of these unusual virulence factors has led to the elucidation of many of the steps leading to the final esterification of the alkyl beta-diol, phthiocerol, with branched-chain fatty acids know as mycocerosates. PapA5 is an acyltransferase implicated in these final reactions. We here show that PapA5 is indeed the terminal enzyme in DIM biosynthesis by demonstrating its dual esterification activity and chain-length preference using synthetic alkyl beta-diol substrate analogues. Applying these analogues to a series of PapA5 mutants, we also revise a model for the substrate binding within PapA5. Finally, we demonstrate that the Mtb Ser/Thr kinase PknB modifies PapA5 on three Thr residues, including two (T196, T198) located on an unresolved loop. These results clarify the DIM biosynthetic pathway and suggest possible mechanisms by which DIM biosynthesis may be regulated by the post-translational modification of PapA5.

  7. Double Gene Targeting Multiplex Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Assay Discriminates Beef, Buffalo, and Pork Substitution in Frankfurter Products.

    PubMed

    Hossain, M A Motalib; Ali, Md Eaqub; Abd Hamid, Sharifah Bee; Asing; Mustafa, Shuhaimi; Mohd Desa, Mohd Nasir; Zaidul, I S M

    2016-08-17

    Beef, buffalo, and pork adulteration in the food chain is an emerging and sensitive issue. Current molecular techniques to authenticate these species depend on polymerase chain reaction (PCR) assays involving long and single targets which break down under natural decomposition and/or processing treatments. This novel multiplex polymerase chain reaction-restriction fragment length polymorphism assay targeted two different gene sites for each of the bovine, buffalo, and porcine materials. This authentication ensured better security, first through a complementation approach because it is highly unlikely that both sites will be missing under compromised states, and second through molecular fingerprints. Mitochondrial cytochrome b and ND5 genes were targeted, and all targets (73, 90, 106, 120, 138, and 146 bp) were stable under extreme boiling and autoclaving treatments. Target specificity and authenticity were ensured through cross-amplification reaction and restriction digestion of PCR products with AluI, EciI, FatI, and CviKI-1 enzymes. A survey of Malaysian frankfurter products revealed rampant substitution of beef with buffalo but purity in porcine materials. PMID:27501408

  8. Chain-length dependence of the dissociation dynamics of oriented molecular adsorbates: n-alkyl bromides on GaAs(110)

    SciTech Connect

    Khan, K.A.; Camillone, N. III; Osgood, R.M. Jr.

    1999-07-01

    Brominated hydrocarbons adsorbed on semiconductor surfaces serve as ideal model systems for investigating the photoinduced chemistry of oriented molecules in the condensed phase. Under UV irradiation these adsorbates dissociate via attachment of photoexcited substrate electrons giving rise to energetic alkyl and surface-bound bromine fragments. In this report the authors describe the effect on the fragmentation dynamics due to systematic variation of the complexity (alkyl chain length) of the adsorbate. Increasing the length of the alkyl chain leads to distinct changes in the alkyl fragment angular distributions. For methyl bromide, the angular distribution is dominated by a focused beam of directly ejected hyperthermal methyl radicals at 44{degree} (in the [0{bar 1}] direction) from the surface normal. While a similar direct beam is observed for ethyl and propyl bromide, inelastic scattering of these fragments is found to result in increased importance of a slower diffuse cos{sup n} {theta} desorption. In addition, significant retention of alkyl fragments is detected by postirradiation thermal desorption measurements for these longer-chain homologues. Increasing the number of degrees of freedom of the adsorbate is also observed to dramatically alter the energetics of the ejection of the photofragments from the surface. As the number of carbons in the fragment is increased from one to three, the average energy of the directly ejected radicals decreases from 1.48 to 1.1 to 0.69 eV (UV incident at {lambda} = 193 nm). Variations in the energy and angular distributions are discussed in terms of initial adsorbate orientation, energy partitioning into rovibrational modes, and influence of radical-surface interactions.

  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. Self-Assembly of Amphiphilic Dendrimers: The Role of Generation and Alkyl Chain Length in siRNA Interaction.

    PubMed

    Márquez-Miranda, Valeria; Araya-Durán, Ingrid; Camarada, María Belén; Comer, Jeffrey; Valencia-Gallegos, Jesús A; González-Nilo, Fernando Danilo

    2016-01-01

    An ideal nucleic-acid transfection system should combine the physical and chemical characteristics of cationic lipids and linear polymers to decrease cytotoxicity and uptake limitations. Previous research described new types of carriers termed amphiphilic dendrimers (ADs), which are based on polyamidoamine dendrimers (PAMAM). These ADs display the cell membrane affinity advantage of lipids and preserve the high affinity for DNA possessed by cationic dendrimers. These lipid/dendrimer hybrids consist of a low-generation, hydrophilic dendron (G2, G1, or G0) bonded to a hydrophobic tail. The G2-18C AD was reported to be an efficient siRNA vector with significant gene silencing. However, shorter tail ADs (G2-15C and G2-13C) and lower generation (G0 and G1) dendrimers failed as transfection carriers. To date, the self-assembly phenomenon of this class of amphiphilic dendrimers has not been molecularly explored using molecular simulation methods. To gain insight into these systems, the present study used coarse-grained molecular dynamics simulations to describe how ADs are able to self-assemble into an aggregate, and, specifically, how tail length and generation play a key role in this event. Finally, explanations are given for the better efficiency of G2/18-C as gene carrier in terms of binding of siRNA. This knowledge could be relevant for the design of novel, safer ADs with well-optimized affinity for siRNA. PMID:27377641

  11. Self-Assembly of Amphiphilic Dendrimers: The Role of Generation and Alkyl Chain Length in siRNA Interaction

    PubMed Central

    Márquez-Miranda, Valeria; Araya-Durán, Ingrid; Camarada, María Belén; Comer, Jeffrey; Valencia-Gallegos, Jesús A.; González-Nilo, Fernando Danilo

    2016-01-01

    An ideal nucleic-acid transfection system should combine the physical and chemical characteristics of cationic lipids and linear polymers to decrease cytotoxicity and uptake limitations. Previous research described new types of carriers termed amphiphilic dendrimers (ADs), which are based on polyamidoamine dendrimers (PAMAM). These ADs display the cell membrane affinity advantage of lipids and preserve the high affinity for DNA possessed by cationic dendrimers. These lipid/dendrimer hybrids consist of a low-generation, hydrophilic dendron (G2, G1, or G0) bonded to a hydrophobic tail. The G2-18C AD was reported to be an efficient siRNA vector with significant gene silencing. However, shorter tail ADs (G2-15C and G2-13C) and lower generation (G0 and G1) dendrimers failed as transfection carriers. To date, the self-assembly phenomenon of this class of amphiphilic dendrimers has not been molecularly explored using molecular simulation methods. To gain insight into these systems, the present study used coarse-grained molecular dynamics simulations to describe how ADs are able to self-assemble into an aggregate, and, specifically, how tail length and generation play a key role in this event. Finally, explanations are given for the better efficiency of G2/18-C as gene carrier in terms of binding of siRNA. This knowledge could be relevant for the design of novel, safer ADs with well-optimized affinity for siRNA. PMID:27377641

  12. 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.

  13. Revisiting the influence of chain length on the α- and β-relaxations in oligomeric glass formers

    NASA Astrophysics Data System (ADS)

    Ngai, K. L.

    2013-12-01

    Dielectric relaxation measurements of a series of oligo(propylene glycol) dimethyl ethers, CH3-O-[CH2-CH(CH3)-O]N-CH3, including samples with the number of PG units N = 1, 2, 3, 7, 17, 34, and 69, were made by Mattsson et al. [Phys. Rev. Lett. 94, 165701 (2005)] at ambient pressure. The objective of the study was to relate the change of properties of the glass transition dynamics to the number of monomer units N in the chain. Not examined in the previous publication is how the change of the width of the frequency dispersion of the α-relaxation with N is related to the observed change in the α-β bifurcation characterized by the ratio, τα(Tg)/τβ(Tg). In this paper, the frequency dispersion of the dimer, trimer, and heptamer are fitted by the Fourier transform of the Kohlrausch stretched exponential function, ϕ(t) = exp[-(t/τα)1-n]. Determined from experimental data, both τα(Tg)/τβ(Tg) and n increase with N. More interestingly, we find τα(Tg)/τβ(Tg) has approximately the same value as [τα(Tg)/tc]n with tc = 2 ps, in accordance with the prediction of the Coupling Model of approximate relation between τα and τβ given by τβ ≈ (tc)n(τα)1-n. Considered also are previously unpublished dielectric loss spectra of the heptamer taken at different combinations of T and P with τα(T,P) fixed by Roland et al. [Phys. Rev. B 77, 012201 (2008)]. The dielectric loss data show not only the α-loss peaks superpose but also the high frequency flank including the barely resolved JG β-relaxation superposes approximately. This is again consistent with the approximate relation between τα and τβ from the Coupling Model because n is unchanged on varying P and T with τα(T,P) kept constant, and tc is a constant. The additional advance made herein has the benefit of enhancing the impact of the earlier experimental studies of the oligo(propylene glycol) dimethyl ethers on current understanding of the dynamics of glass transition.

  14. Spacer grid assembly and locking mechanism

    DOEpatents

    Snyder, Jr., Harold J.; Veca, Anthony R.; Donck, Harry A.

    1982-01-01

    A spacer grid assembly is disclosed for retaining a plurality of fuel rods in substantially parallel spaced relation, the spacer grids being formed with rhombic openings defining contact means for engaging from one to four fuel rods arranged in each opening, the spacer grids being of symmetric configuration with their rhombic openings being asymmetrically offset to permit inversion and relative rotation of the similar spacer grids for improved support of the fuel rods. An improved locking mechanism includes tie bars having chordal surfaces to facilitate their installation in slotted circular openings of the spacer grids, the tie rods being rotatable into locking engagement with the slotted openings.

  15. Generator stator core vent duct spacer posts

    DOEpatents

    Griffith, John Wesley; Tong, Wei

    2003-06-24

    Generator stator cores are constructed by stacking many layers of magnetic laminations. Ventilation ducts may be inserted between these layers by inserting spacers into the core stack. The ventilation ducts allow for the passage of cooling gas through the core during operation. The spacers or spacer posts are positioned between groups of the magnetic laminations to define the ventilation ducts. The spacer posts are secured with longitudinal axes thereof substantially parallel to the core axis. With this structure, core tightness can be assured while maximizing ventilation duct cross section for gas flow and minimizing magnetic loss in the spacers.

  16. Chain-length dependency of interactions of medium-chain fatty acids with glucose metabolism in acini isolated from lactating rat mammary glands. A putative feed-back to control milk lipid synthesis from glucose.

    PubMed Central

    Heesom, K J; Souza, P F; Ilic, V; Williamson, D H

    1992-01-01

    The effects of a series of medium-chain fatty acids (C6-C12) on glucose metabolism in isolated acini from lactating rat mammary glands have been studied. Hexanoate (C6) octanoate (C8) and decanoate (C10), but not laurate (C12), decreased [1-14C]glucose conversion into [14C]lipid and the production of 14CO2 (an index of the pentose phosphate pathway). With hexanoate and octanoate, glucose utilization was decreased, whereas decanoate had a slight stimulatory effect on glucose utilization, but there was a large accumulation of lactate. Addition of dichloroacetate (an inhibitor of pyruvate dehydrogenase kinase) decreased this accumulation of lactate and stimulated the conversion of [1-14C]glucose into [14C]lipid and 14CO2. Insulin had no effect on the rate of glucose utilization in the presence of hexanoate. It stimulated the rate in the presence of octanoate and laurate and increased the conversion of [1-14C]glucose into [14C]lipid in the presence of octanoate, decanoate or laurate. The major fate of 1-14C-labelled medium-chain fatty acids (C6, C8 and C12) was conversion into [14C]lipid. The proportion converted into 14CO2 decreased with increasing chain length, whereas the rate of [14C]lipid formation increased. It is concluded that the interactions between medium-chain fatty acids and glucose metabolism represent a feed-back mechanism to control milk lipid synthesis, and this may be important when milk accumulates in the gland. PMID:1731763

  17. Carbon-limited fed-batch production of medium-chain-length polyhydroxyalkanoates by a phaZ-knockout strain of Pseudomonas putida KT2440.

    PubMed

    Vo, Minh Tri; Ko, Kenton; Ramsay, Bruce

    2015-04-01

    A medium-chain-length poly-3-hydroxyalkanote (MCL-PHA) depolymerase knockout mutant of Pseudomonas putida KT2440 was produced by double homologous recombination. A carbon-limited shake-flask study confirmed that depolymerase activity was eliminated. Lysis of both mutant and wild-type strains occurred under these conditions. In carbon-limited, fed-batch culture, the yield of unsaturated monomers from unsaturated substrate averaged only 0.62 mol mol(-1) for the phaZ minus strain compared to 0.72 mol mol(-1) for the wild type. The mutant strain also produced more CO2 and less residual biomass from the same amount of carbon substrate. However, most results indicated that elimination of PHA depolymerase activity had little impact on the overall yield of biomass and PHA. PMID:25563970

  18. Examination of meat components in commercial dog and cat feed by using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) technique.

    PubMed

    Wang, Hsien-Chi; Lee, Shu-Hwae; Chang, Tien-Jye; Wong, Min-Liang

    2004-07-01

    It has been shown that certain slow neurological diseases such as bovine spongiform encephalopathy (also known as "mad cow" disease) could be transmitted through contaminated food intake by animals; therefore, the examination of meat components in commercial feeds is important for the control of the disease in public health. The combination of polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) technique was applied to examine the meat components in dog and cat commercial feeds. The partial nucleotide sequence (359 bp) of animal mitochondrial cytochrome b (cytb, CYT) gene was amplified by PCR and then digested with restriction enzyme Alu I or Mbo I. In this work, eight brands of commercial dog and cat feeds available in Taiwan were examined. All brands of dog feeds that were tested contained meat from four different animals (cattle, pig, goat and chicken). In cat feeds, the chicken meat was found in five out of eight brands. PMID:15297759

  19. Effect of polyethyleneglycol (PEG) chain length on the bio-nano-interactions between PEGylated lipid nanoparticles and biological fluids: from nanostructure to uptake in cancer cells

    NASA Astrophysics Data System (ADS)

    Pozzi, Daniela; Colapicchioni, Valentina; Caracciolo, Giulio; Piovesana, Susy; Capriotti, Anna Laura; Palchetti, Sara; de Grossi, Stefania; Riccioli, Anna; Amenitsch, Heinz; Laganà, Aldo

    2014-02-01

    When nanoparticles (NPs) enter a physiological environment, medium components compete for binding to the NP surface leading to formation of a rich protein shell known as the ``protein corona''. Unfortunately, opsonins are also adsorbed. These proteins are immediately recognized by the phagocyte system with rapid clearance of the NPs from the bloodstream. Polyethyleneglycol (PEG) coating of NPs (PEGylation) is the most efficient anti-opsonization strategy. Linear chains of PEG, grafted onto the NP surface, are able to create steric hindrance, resulting in a significant inhibition of protein adsorption and less recognition by macrophages. However, excessive PEGylation can lead to a strong inhibition of cellular uptake and less efficient binding with protein targets, reducing the potential of the delivery system. To reach a compromise in this regard we employed a multi-component (MC) lipid system with uncommon properties of cell uptake and endosomal escape and increasing length of PEG chains. Nano liquid chromatography coupled with tandem mass spectrometry (nanoLC-MS/MS) analysis allowed us to accurately determine the corona composition showing that apolipoproteins are the most abundant class in the corona and that increasing the PEG length reduced the protein adsorption and the liposomal surface affinity for apolipoproteins. Due to the abundance of apolipoproteins, we exploited the ``protein corona effect'' to deliver cationic liposome-human plasma complexes to human prostate cancer PC3 cells that express a high level of scavenger receptor class B type 1 in order to evaluate the cellular uptake efficiency of the systems used. Combining laser scanning confocal microscopy with flow cytometry analysis in PC3 cells we demonstrated that MC-PEG2k is the best compromise between an anti-opsonization strategy and active targeting and could be a promising candidate to treat prostate cancer in vivo.When nanoparticles (NPs) enter a physiological environment, medium components

  20. Effects of pH-sensitive chain length on release of doxorubicin from mPEG-b-PH-b-PLLA nanoparticles

    PubMed Central

    Liu, Rong; He, Bin; Li, Dong; Lai, Yusi; Chang, Jing; Tang, James Z; Gu, Zhongwei

    2012-01-01

    Background Two methoxyl poly(ethylene glycol)-poly(L-histidine)-poly(L-lactide) (mPEG-PH-PLLA) triblock copolymers with different poly(L-histidine) chain lengths were synthesized. The morphology and biocompatibility of these self-assembled nanoparticles was investigated. Methods Doxorubicin, an antitumor drug, was trapped in the nanoparticles to explore their drug-release behavior. The drug-loaded nanoparticles were incubated with HepG2 cells to evaluate their antitumor efficacy in vitro. The effects of poly(L-histidine) chain length on the properties, drug-release behavior, and antitumor efficiency of the nanoparticles were investigated. Results The nanoparticles were pH-sensitive. The mean diameters of the two types of mPEG-PH- PLLA nanoparticle were less than 200 nm when the pH values were 5.0 and 7.4. The nanoparticles were nontoxic to NIH 3T3 fibroblasts and HepG2 cells. The release of doxorubicin at pH 5.0 was much faster than that at pH 7.4. The release rate of mPEG45-PH15-PLLA82 nanoparticles was much faster than that of mPEG45-PH30-PLLA82 nanoparticles at pH 5.0. Conclusion The inhibition effect of mPEG45-PH15-PLLA82 nanoparticles on the growth of HepG2 cells was greater than that of mPEG45-PH30-PLLA82 nanoparticles when the concentration of encapsulated doxorubicin was less than 15 μg/mL. PMID:22923987

  1. The synthesis of short- and medium-chain-length poly(hydroxyalkanoate) mixtures from glucose- or alkanoic acid-grown Pseudomonas oleovorans.

    PubMed

    Ashby, R D; Solaiman, D K Y; Foglia, T A

    2002-03-01

    Pseudomonas oleovorans NRRL B-778 accumulated mixtures of poly-3-hydroxybutyrate (PHB) and medium-chain-length poly(hydroxyalkanoates) (mcl-PHAs) when grown on glucose, octanoic acid or oleic acid, whereas growth on nonanoic acid or undecanoic acid resulted in copolymers of poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHB-co-HV). Acetone fractionation verified the presence of PHB/mcl-PHA mixtures. The acetone-insoluble (AIS) fractions of the polymers derived from glucose (PHA-glucose), octanoic acid (PHA-octanoic) and oleic acid (PHA-oleic) were exclusively PHB while the acetone-soluble (AS) fractions contained mcl-PHA composed of differing ratios of 3-hydroxy-acid monomer units, which ranged in chain length from 6 to 14 carbon atoms. In contrast, both the AIS and AS fractions from the polymers derived from nonanoic acid (PHA-nonanoic) and undecanoic acid (PHA-undecanoic) were composed of comparable ratios of 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV). The unfractionated PHA-glucose, PHA-octanoic and PHA-oleic polymers had melting temperatures (Tm) between 177 and 179 degrees C, enthalpies of fusion (AHf) of 20 cal/g and glasstransition temperatures (Tg) of 3-4 degrees C. This was due to the large PHB content in the polymer mixtures. On the other hand, the PHA-nonanoic and PHA-undecanoic polymers had thermal properties that supported their copolymer nature. In both cases, the Tm values were 161 degrees C, deltaHf values were 7 cal/g and Tg values were - 3 degrees C. PMID:12074088

  2. Influence of trehalose 6,6'-diester (TDX) chain length on the physicochemical and immunopotentiating properties of DDA/TDX liposomes.

    PubMed

    Kallerup, Rie Selchau; Madsen, Cecilie Maria; Schiøth, Mikkel Lohmann; Franzyk, Henrik; Rose, Fabrice; Christensen, Dennis; Korsholm, Karen Smith; Foged, Camilla

    2015-02-01

    Linking physicochemical characterization to functional properties is crucial for defining critical quality attributes during development of subunit vaccines toward optimal safety and efficacy profiles. We investigated how the trehalose 6,6'-diester (TDX) chain length influenced the physicochemical and immunopotentiating properties of the clinically tested liposomal adjuvant composed of dimethyldioctadecylammonium (DDA) bromide and analogues of trehalose-6,6'-dibehenate (TDB). TDB analogues with symmetrically shortened acyl chains [denoted X: arachidate (A), stearate (S), palmitate (P), myristate (Myr) and laurate (L)] were incorporated into DDA liposomes and characterized with respect to size, polydispersity index, charge, thermotropic phase behavior and lipid-lipid interactions. Incorporation of 11 mol% TDX into DDA liposomes significantly decreased the polydispersity index when TDA, TDS, TDP and TDMyr were incorporated, whereas both the initial size and the charge of the liposomes were unaffected. The long-term colloidal stability was only decreased when including TDL in DDA liposomes. The fatty acid length of TDX affected the phase transition of the liposomes, and for the DDA/TDP and DDA/TDS liposomes a homogeneous distribution of the lipids in the bilayer was indicated. The membrane packing was studied further by using the Langmuir monolayer technique. Incorporation of TDS improved the packing of the lipid monolayer, as compared to the other analogues, suggesting the most favorable stability. Finally, immunization of mice with the recombinant tuberculosis fusion antigen Ag85B-ESAT-6-Rv2660c (H56) and the physicochemically most optimal formulations (DDA/TDB, DDA/TDS and DDA/TDP) induced comparable T-cell responses. In conclusion, of the investigated TDB analogues, incorporation of 11 mol% TDS or TDP into DDA liposomes resulted in an adjuvant system with the most favorable physicochemical properties and an immunological profile comparable to that of DDA/TDB. PMID

  3. Mechanical behaviour of standardized, endoskeleton-including hip spacers implanted into composite femurs

    PubMed Central

    Thielen, T.; Maas, S.; Zuerbes, A.; Waldmann, D.; Anagnostakos, K.; Kelm, J.

    2009-01-01

    Two-stage reconstruction using an antibiotic loaded cement spacer is the preferred treatment method of late hip joint infections. Hip spacers maintain stability of the joint and length of the limb during treatment period. However, as the material strength of bone cement (PMMA) is limited, spacer fractures led to serious complications in the past. This study investigated the load capacity of custom made hip spacers, developed at the 'Klinik für Orthopädie und Orthopädische Chirurgie' (Universitätsklinikum des Saarlandes, Homburg / Saar, Germany), and implanted into composite femurs. In a quasi-static test, non-reinforced spacers tolerated hip joint loads of about 3000 N, whereas reinforced spacers with titanium-grade-two endoskeletons doubled this load up to 6000 N. Even for cyclic loading, endoskeleton-including hip spacers tolerated loads of >4500 N with 500,000 load cycles. Thus, an endoskeleton-including spacer should provide a mobile and functional joint through the treatment course. A generated FE-model was used to determine the fracture stresses and allows for further sensitivity analysis. PMID:19834594

  4. Investigating the Influence of Alkyl Chain Length in Poly(3-alkylthiophene)s Over the Thin Film Morphology by Optical and Electrical Characterization.

    PubMed

    Bhargava, Kshitij; Bilgaiyan, Anubha; Mohan, S Raj; Itoop, M O; Joshi, Mukesh P; Kukreja, L M; Singh, Vipul

    2016-04-01

    This paper studies the influence of alkyl-chain length in poly(3-alkylthiophene)s over the morphology of thin films and electrical parameters of the devices based on it. Regioregular poly(3-hexylthiophene) and poly(3-octylthiophene) were chosen as the semiconducting materials for the study. The morphological variations were studied by absorption spectroscopy, photoluminescence spectroscopy and X-ray diffraction study. The absorption and photoluminescence showed decreased coplanarity of main chain in poly(3-octylthiophene) over poly(3-hexylthiophene) and which was later confirmed using X-ray diffraction studies which clearly showed increased interchain spacing in case of poly(3-octylthiophene). The schottky diodes fabricated using these materials showed decreased mobility in poly(3-octylthiophene) based diodes as measured by space-charge limiting current method and photo-induced charge carrier extraction by linearly increasing voltage technique. Moreover, we observed a negative field dependence of mobility at room temperature in both the devices and attributed this to the presence of dominant positional disorder in poly(3-alkylthiophene)s. Furthermore, the photocurrent dependence on electric field too showed inferior mobility of poly(3-octylthiophene) based diodes. PMID:27451611

  5. Overcoming the equivalent-chain-length rule with pH-zone-refining countercurrent chromatography for the preparative separation of fatty acids.

    PubMed

    Englert, Michael; Vetter, Walter

    2015-07-01

    Purification of individual fatty acids from vegetable oils by preparative liquid chromatography techniques such as countercurrent chromatography (CCC) is a challenging task due to the equivalent-chain-length (ECL) rule. It implies that one double bond equals two carbon atoms in the alkyl chain of a fatty acid and therefore causes co-elutions of saturated and unsaturated fatty acids. Accordingly, existing methods for the purification of individual fatty acids are cumbersome and time-consuming as two or more steps with different conditions are required. To avoid additional purification steps, we report a method utilizing pH-zone-refining CCC which enabled the purification of all major fatty acids from sunflower oil (purities >95 %) in one step by circumventing co-elutions caused by the ECL rule. This method is based on the involvement of acid strength and hydrophobicity of fatty acids during the separation process. By exploiting the preparative character of the pH-zone-refining mode, a tenfold sample amount of free fatty acids from sunflower oil could be separated in comparison to regular CCC. PMID:25943261

  6. Complex coacervation of hyaluronic acid and chitosan: effects of pH, ionic strength, charge density, chain length and the charge ratio.

    PubMed

    Kayitmazer, A B; Koksal, A F; Kilic Iyilik, E

    2015-11-28

    Hyaluronic acid (HA) and chitosan (CH) can form nanoparticles, hydrogels, microspheres, sponges, and films, all with a wide range of biomedical applications. This variety of phases reflects the multiple pathways available to HA/CH complexes. Here, we use turbidimetry, dynamic light scattering, light microscopy and zeta potential measurements to show that the state of the dense phase depends on the molar ratio of HA carboxyl to CH amines, and is strongly dependent on their respective degrees of ionization, α and β. Due to the strong charge complementarity between HA and CH, electrostatic self-assembly takes place at very acidic pH, but is almost unobservable at ionic strength (I) ≥ 1.5 M NaCl. All systems display discontinuity in the I-dependence of the turbidity, corresponding to a transition from coacervates to flocculates. An increase in either polymer chain length or charge density enhances phase separation. Remarkably, non-stoichiometric coacervate suspensions form at zeta potentials far away from zero. This result is attributed to the entropic effects of chain semi-flexibility as well as to the charge mismatch between the two biopolymers. PMID:26406548

  7. Effects of stereochemistry, saturation, and hydrocarbon chain length on the ability of synthetic constrained azacyclic sphingolipids to trigger nutrient transporter down-regulation, vacuolation, and cell death.

    PubMed

    Perryman, Michael S; Tessier, Jérémie; Wiher, Timothy; O'Donoghue, Heather; McCracken, Alison N; Kim, Seong M; Nguyen, Dean G; Simitian, Grigor S; Viana, Matheus; Rafelski, Susanne; Edinger, Aimee L; Hanessian, Stephen

    2016-09-15

    Constrained analogs containing a 2-hydroxymethylpyrrolidine core of the natural sphingolipids sphingosine, sphinganine, N,N-dimethylsphingosine and N-acetyl variants of sphingosine and sphinganine (C2-ceramide and dihydro-C2-ceramide) were synthesized and evaluated for their ability to down-regulate nutrient transporter proteins and trigger cytoplasmic vacuolation in mammalian cells. In cancer cells, the disruptions in intracellular trafficking produced by these sphingolipids lead to cancer cell death by starvation. Structure activity studies were conducted by varying the length of the hydrocarbon chain, the degree of unsaturation and the presence or absence of an aryl moiety on the appended chains, and stereochemistry at two stereogenic centers. In general, cytotoxicity was positively correlated with nutrient transporter down-regulation and vacuolation. This study was intended to identify structural and functional features in lead compounds that best contribute to potency, and to develop chemical biology tools that could be used to isolate the different protein targets responsible for nutrient transporter loss and cytoplasmic vacuolation. A molecule that produces maximal vacuolation and transporter loss is expected to have the maximal anti-cancer activity and would be a lead compound. PMID:27475534

  8. Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids.

    PubMed

    Touchette, Megan H; Bommineni, Gopal R; Delle Bovi, Richard J; Gadbery, John E; Nicora, Carrie D; Shukla, Anil K; Kyle, Jennifer E; Metz, Thomas O; Martin, Dwight W; Sampson, Nicole S; Miller, W Todd; Tonge, Peter J; Seeliger, Jessica C

    2015-09-01

    Although they are classified as Gram-positive bacteria, Corynebacterineae possess an asymmetric outer membrane that imparts structural and thereby physiological similarity to more distantly related Gram-negative bacteria. Like lipopolysaccharide in Gram-negative bacteria, lipids in the outer membrane of Corynebacterineae have been associated with the virulence of pathogenic species such as Mycobacterium tuberculosis (Mtb). For example, Mtb strains that lack long, branched-chain alkyl esters known as dimycocerosates (DIMs) are significantly attenuated in model infections. The resultant interest in the biosynthetic pathway of these unusual virulence factors has led to the elucidation of many of the steps leading to the final esterification of the alkyl β-diol, phthiocerol, with branched-chain fatty acids known as mycocerosates. PapA5 is an acyltransferase implicated in these final reactions. Here, we show that PapA5 is indeed the terminal enzyme in DIM biosynthesis by demonstrating its dual esterification activity and chain-length preference using synthetic alkyl β-diol substrate analogues. By applying these analogues to a series of PapA5 mutants, we also revise a model for the substrate binding within PapA5. Finally, we demonstrate that the Mtb Ser/Thr kinases PknB and PknE modify PapA5 on three overlapping Thr residues and that a fourth Thr is unique to PknE phosphorylation. These results clarify the DIM biosynthetic pathway and indicate post-translational modifications that warrant further elucidation for their roles in the regulation of DIM biosynthesis. PMID:26271001

  9. Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl Beta-Diol Lipids

    PubMed Central

    Touchette, Megan H.; Bommineni, Gopal R.; Delle Bovi, Richard J.; Gadbery, John E.; Nicora, Carrie D.; Shukla, Anil K.; Kyle, Jennifer E.; Metz, Thomas O.; Martin, Dwight W.; Sampson, Nicole S.; Miller, W. Todd; Tonge, Peter J.; Seeliger, Jessica C.

    2015-01-01

    Although classified as Gram-positive bacteria, Corynebacterineae possess an asymmetric outer membrane that imparts structural and thereby physiological similarity to more distantly related Gram-negative bacteria. Like lipopolysaccharide in Gram-negative bacteria, lipids in the outer membrane of Corynebacterineae have been associated with the virulence of pathogenic species such as Mycobacterium tuberculosis (Mtb). For example, Mtb strains that lack long, branched-chain alkyl esters known as dimycocerosates (DIMs) are significantly attenuated in model infections. The resultant interest in the biosynthetic pathway of these unusual virulence factors has led to the elucidation of many of the steps leading to the final esterification of the alkyl beta-diol, phthiocerol, with branched-chain fatty acids known as mycocerosates. PapA5 is an acyltransferase implicated in these final reactions. We here show that PapA5 is indeed the terminal enzyme in DIM biosynthesis by demonstrating its dual esterification activity and chain-length preference using synthetic alkyl beta-diol substrate analogues. Applying these analogues to a series of PapA5 mutants, we also revise a model for the substrate binding within PapA5. Finally, we demonstrate that the Mtb Ser/Thr kinases PknB and PknE modify PapA5 on three overlapping Thr residues and a fourth Thr is unique to PknE phosphorylation. These results clarify the DIM biosynthetic pathway and indicate post-translational modifications that warrant further elucidation for their roles in regulation DIM biosynthesis. PMID:26271001

  10. 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

  11. Immunochemical characterization of synthetic hexa-, octa- and decasaccharide conjugate vaccines for Vibrio cholerae O:1 Serotype Ogawa with emphasis on antigenic density and chain length

    PubMed Central

    Ftacek, Peter; Nelson, Victor; Szu, Shousun C.

    2013-01-01

    Cholera remains to be a global health problem without suitable vaccines for endemic control or outbreak relief. Here we describe a new parenteral vaccine based on neoglyco-conjugate of synthetic fragments of O-specific polysaccharide (O-SP) of Vibrio cholerae O1, serotype Ogawa. Hexa-, octa- and decasaccharides of the O-SP with carboxylic acid at the reducing end were chemically synthesized and conjugated to tetanus toxoid (TT). The conjugates prepared by a novel linking scheme consisted of 17-atom linker of hydrazide and alkyl bonds elicited robust serum IgG anti-LPS responses with vibriocidal activities in mice. There is a length dependence in immune response with decasaccharide conjugates elicited the highest anti-LPS IgG. There seems to be an indication that regardless of the carbohydrate chain length, a molar ratio of 230±10 monosaccharide units per TT induced high antibody response. The conjugates also elicited cross-reactive antibodies to serotype Inaba. The formulation of the proposed cholera conjugate vaccine, similar to other licensed polysaccharide vaccine, is suitable for children immunization. A parenteral cholera vaccine could overcome the diminishing immunogenicity in most of oral vaccines due to the gastrointestinal complexity and environmental enteropathy in children living in impoverished environment and could be considered for global cholera immunization. PMID:23955520

  12. Long chain polyunsaturated fatty acid supplementation in infancy increases length- and weight-for-age but not BMI to 6 years when controlling for effects of maternal smoking.

    PubMed

    Currie, L M; Tolley, E A; Thodosoff, J M; Kerling, E H; Sullivan, D K; Colombo, J; Carlson, S E

    2015-07-01

    Long chain polyunsaturated fatty acids (LCPUFA) are added to infant formula but their effect on long-term growth of children is under studied. We evaluated the effects of feeding LCPUFA-supplemented formula (n = 54) compared to control formula (n = 15) throughout infancy on growth from birth-6 years. Growth was described using separate models developed with the MIXED procedure of SAS(®) that included maternal smoking history and gender. Compared to children fed control formula, children who consumed LCPUFA supplemented formula had higher length-/stature-/and weight-for-age percentiles but not body mass index (BMI) percentile from birth to 6 years. Maternal smoking predicted lower stature (2-6 years), higher weight-for-length (birth-18 months) and BMI percentile (2-6 years) independent of LCPUFA effects. Gender interacted with the effect of LCPUFA on stature, and the relationship between smoking and BMI, with a larger effect for boys. Energy intake did not explain growth differences. A relatively small control sample is a limitation. PMID:25936840

  13. Immunochemical characterization of synthetic hexa-, octa- and decasaccharide conjugate vaccines for Vibrio cholerae O:1 serotype Ogawa with emphasis on antigenic density and chain length.

    PubMed

    Ftacek, Peter; Nelson, Victor; Szu, Shousun C

    2013-12-01

    Cholera remains to be a global health problem without suitable vaccines for endemic control or outbreak relief. Here we describe a new parenteral vaccine based on neoglyco-conjugate of synthetic fragments of O-specific polysaccharide (O-SP) of Vibrio cholerae O1, serotype Ogawa. Hexa-, octa- and decasaccharides of the O-SP with carboxylic acid at the reducing end were chemically synthesized and conjugated to tetanus toxoid (TT). The conjugates prepared by a novel linking scheme consisted of 17-atom linker of hydrazide and alkyl bonds elicited robust serum IgG anti-LPS responses with vibriocidal activities in mice. There is a length dependence in immune response with decasaccharide conjugates elicited the highest anti-LPS IgG. There seems to be an indication that regardless of the carbohydrate chain length, a molar ratio of 230 ± 10 monosaccharide units per TT induced high antibody response. The conjugates also elicited cross-reactive antibodies to serotype Inaba. The formulation of the proposed cholera conjugate vaccine, similar to other licensed polysaccharide vaccine, is suitable for children immunization. A parenteral cholera vaccine could overcome the diminishing immunogenicity in most of oral vaccines due to the gastrointestinal complexity and environmental enteropathy in children living in impoverished environment and could be considered for global cholera immunization. PMID:23955520

  14. Cloning of a coconut endosperm cDNA encoding a 1-acyl-sn-glycerol-3-phosphate acyltransferase that accepts medium-chain-length substrates.

    PubMed Central

    Knutzon, D S; Lardizabal, K D; Nelsen, J S; Bleibaum, J L; Davies, H M; Metz, J G

    1995-01-01

    Immature coconut (Cocos nucifera) endosperm contains a 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPAAT) activity that shows a preference for medium-chain-length fatty acyl-coenzyme A substrates (H.M. Davies, D.J. Hawkins, J.S. Nelsen [1995] Phytochemistry 39:989-996). Beginning with solubilized membrane preparations, we have used chromatographic separations to identify a polypeptide with an apparent molecular mass of 29 kD, whose presence in various column fractions correlates with the acyltransferase activity detected in those same fractions. Amino acid sequence data obtained from several peptides generated from this protein were used to isolate a full-length clone from a coconut endosperm cDNA library. Clone pCGN5503 contains a 1325-bp cDNA insert with an open reading frame encoding a 308-amino acid protein with a calculated molecular mass of 34.8 kD. Comparison of the deduced amino acid sequence of pCGN5503 to sequences in the data banks revealed significant homology to other putative LPAAT sequences. Expression of the coconut cDNA in Escherichia coli conferred upon those cells a novel LPAAT activity whose substrate activity profile matched that of the coconut enzyme. PMID:8552723

  15. Genotypic Characterization of Bradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing

    PubMed Central

    Vinuesa, Pablo; Rademaker, Jan L. W.; de Bruijn, Frans J.; Werner, Dietrich

    1998-01-01

    We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata. PMID:9603820

  16. Effect of alkyl chain length on the conformation and order of simple ionic surfactants adsorbed at the D{sub 2}O/CCl{sub 4} interface as studied by sum-frequency vibrational spectroscopy

    SciTech Connect

    Conboy, J.C.; Messmer, M.C.; Richmond, G.L.

    1998-11-10

    The conformational order of three alkanesulfonates, sodium hexanesulfonate (HS), sodium undecanesulfonate (UDS), and sodium dodecanesulfonate (DDS), adsorbed at the D{sub 2}O/CCl{sub 4} interface are examined in detail by sum-frequency vibrational spectroscopy. An increase in surfactant concentration at the interface results in the reduction of gauche defects in the hydrocarbon chains as determined from the intensity ratio of the methyl to methylene symmetric stretch vibrational modes. The degree of disorder in the alkyl chains varies greatly with alkyl chain length. The alkyl chain of HS displays the fewest gauche defects while DDS and UDS display more disorder in their hydrocarbon chains at similar surface concentrations. This observation is interpreted as a reduction in the possible number of gauche conformations for the shorter alkyl chain.

  17. Penam sulfones and β-lactamase inhibition: SA2-13 and the importance of the C2 side chain length and composition.

    PubMed

    Rodkey, Elizabeth A; Winkler, Marisa L; Bethel, Christopher R; Pagadala, Sundar Ram Reddy; Buynak, John D; Bonomo, Robert A; van den Akker, Focco

    2014-01-01

    β-Lactamases are the major reason β-lactam resistance is seen in Gram-negative bacteria. To combat this resistance mechanism, β-lactamase inhibitors are currently being developed. Presently, there are only three that are in clinical use (clavulanate, sulbactam and tazobactam). In order to address this important medical need, we explored a new inhibition strategy that takes advantage of a long-lived inhibitory trans-enamine intermediate. SA2-13 was previously synthesized and shown to have a lower k(react) than tazobactam. We investigated here the importance of the carboxyl linker length and composition by synthesizing three analogs of SA2-13 (PSR-4-157, PSR-4-155, and PSR-3-226). All SA2-13 analogs yielded higher turnover numbers and k(react) compared to SA2-13. We next demonstrated using protein crystallography that increasing the linker length by one carbon allowed for better capture of a trans-enamine intermediate; in contrast, this trans-enamine intermediate did not occur when the C2 linker length was decreased by one carbon. If the linker was altered by both shortening it and changing the carboxyl moiety into a neutral amide moiety, the stable trans-enamine intermediate in wt SHV-1 did not form; this intermediate could only be observed when a deacylation deficient E166A variant was studied. We subsequently studied SA2-13 against a relatively recently discovered inhibitor-resistant (IR) variant of SHV-1, SHV K234R. Despite the alteration in the mechanism of resistance due to the K→R change in this variant, SA2-13 was effective at inhibiting this IR enzyme and formed a trans-enamine inhibitory intermediate similar to the intermediate seen in the wt SHV-1 structure. Taken together, our data reveals that the C2 side chain linker length and composition profoundly affect the formation of the trans-enamine intermediate of penam sulfones. We also show that the design of SA2-13 derivatives offers promise against IR SHV β-lactamases that possess the K234R

  18. Chain-Length Distribution and Hydrogen Isotopic Fraction of n-alkyl Lipids in Aquatic and Terrestrial Plants: Implications for Paleoclimate Reconstructions

    NASA Astrophysics Data System (ADS)

    Gao, L.; Littlejohn, S.; Hou, J.; Toney, J.; Huang, Y.

    2008-12-01

    Recent studies demonstrate that in lacustrine sediments, aquatic plant lipids (e.g., C22-fatty acid) record lake water D/H ratio variation, while long-chain fatty acids (C26-C32, major components of terrestrial plant leaf waxes), record D/H ratios of precipitation (especially in arid regions). However, there are insufficient literature data for the distribution and hydrogen isotopic fractionation of n-alkyl lipids in aquatic and terrestrial plants. In this study, we determined the chain-length distributions and D/H ratios of n-alkyl lipids from 17 aquatic plant species (9 emergent, 4 floating and 4 submerge species) and 13 terrestrial plant species (7 grasses and 6 trees) from Blood Pond, Massachusetts. Our results are consistent with previous studies and provide a solid basis for the paleoclimatic reconstruction using D/H ratios of aquatic and terrestrial plant biomarkers. In addition, systematic hydrogen isotopic analyses on leaf waxes, leaf, stem and soil waters from trees and grasses significantly advance our understanding of our previously observed large D/H ratio difference between tree and grass leaf waxes. Our data indicate that the observed difference is not due to differences in leaf water D/H ratios. In comparison with grasses, trees use greater proportion of D-enriched residual or stored carbohydrates (as opposed to current photosynthetic carbohydrates) for leaf wax biosynthesis, resulting in higher leaf wax D/H ratios. The residual carbohydrates are enriched in deuterium because of the preferential consumption of light-hydrogen substrates during plant metabolism.

  19. Alkylphenol Xenoestrogens with Varying Carbon Chain Lengths Differentially and Potently Activate Signaling and Functional Responses in GH3/B6/F10 Somatomammotropes

    PubMed Central

    Kochukov, Mikhail Y.; Jeng, Yow-Jiun; Watson, Cheryl S.

    2009-01-01

    Background Alkylphenols varying in their side-chain lengths [ethyl-, propyl-, octyl-, and nonylphenol (EP, PP, OP, and NP, respectively)] and bisphenol A (BPA) represent a large group of structurally related xenoestrogens that have endocrine-disruptive effects. Their rapid nongenomic effects that depend on structure for cell signaling and resulting functions are unknown. Objectives We compared nongenomic estrogenic activities of alkylphenols with BPA and 17β-estradiol (E2) in membrane estrogen receptor-α–enriched GH3/B6/F10 pituitary tumor cells. These actions included calcium (Ca) signaling, prolactin (PRL) release, extracellular-regulated kinase (ERK) phosphorylation, and cell proliferation. Methods We imaged Ca using fura-2, measured PRL release via radioimmunoassay, detected ERK phosphorylation by fixed cell immunoassay, and estimated cell number using the crystal violet assay. Results All compounds caused increases in Ca oscillation frequency and intracellular Ca volume at 100 fM to 1 nM concentrations, although long-chain alkylphenols were most effective. All estrogens caused rapid PRL release at concentrations as low as 1 fM to 10 pM; the potency of EP, PP, and NP exceeded that of E2. All compounds at 1 nM produced similar increases in ERK phosphorylation, causing rapid peaks at 2.5–5 min, followed by inactivation and additional 60-min peaks (except for BPA). Dose–response patterns of ERK activation at 5 min were similar for E2, BPA, and PP, whereas EP caused larger effects. Only E2 and NP increased cell number. Some rapid estrogenic responses showed correlations with the hydrophobicity of estrogenic molecules; the more hydrophobic OP and NP were superior at Ca and cell proliferation responses, whereas the less hydrophobic EP and PP were better at ERK activations. Conclusions Alkylphenols are potent estrogens in evoking these nongenomic responses contributing to complex functions; their hydrophobicity can largely predict these behaviors. PMID

  20. Effect of alkyl chain length, head group and nature of the surfactant on the hydrolysis of 1,3-benzoxazine-2,4-dione and its derivatives.

    PubMed

    Al-Ayed, Abdullah S; Ali, Mohd Sajid; Al-Lohedan, Hamad A; Al-Sulaim, Adel M; Issa, Zuheir A

    2011-09-01

    The alkaline hydrolysis of carsalam (2H-1,3-benzoxazine-2,4(3H)-dione), denoted as I, and its N-substituted derivatives i.e., N-methyl-1,3-benzoxazine-2,4-dione (II) and N-benzoyl-1,3-benzoxazine-2,4-dione (III) was studied spectrophotometrically at physiological temperature. The rate of hydrolysis was found to be independent on the substrate concentration. In case of I, the reaction was fractional order with respect to [OH(-)] while for II and III, reaction obeyed the first order kinetics. Effect of cationic surfactants with varying hydrophobic chains (cetyltrimethylammonium bromide, CTAB, tetradecyltrimethylammonium bromide, TTAB and dodecyltrimethylammonium bromide, DTAB) and with different head-group (cetyl pyridinium chloride, CPC) and anionic surfactant (sodium dodecyl sulfate, SDS) was also seen on the rate of alkaline hydrolysis of the carsalam and its derivatives. Cationic surfactants first catalyzed the rate of hydrolysis at lower concentrations followed by the inhibition at higher concentrations. The length of the alkyl chain had remarkable effect on the catalytic efficiency of the surfactants. Similarly N-substitution on substrate also increased the catalysis by micelles. The anionic surfactant SDS inhibited the rate of hydrolysis at all of the concentrations studied. The catalysis by cationic micelles followed by inhibition was treated in terms of the pseudophase ion-exchange model, while for the inhibition by SDS micelles the Menger-Portnoy model was used to fit the data. The effect of salts (NaCl, NaBr and (CH(3))(4)NBr) was also seen on the hydrolysis of II and it was found that all salts inhibited the rate of reaction. The inhibition follows the trend NaCl

  1. In vitro analysis of the effect of alkyl-chain length of anionic surfactants on the skin by using a reconstructed human epidermal model.

    PubMed

    Yamaguchi, Fumiko; Watanabe, Shin-Ichi; Harada, Fusae; Miyake, Miyuki; Yoshida, Masaki; Okano, Tomomichi

    2014-01-01

    We investigated the effect of the alkyl-chain length of anionic surfactants on the skin using an in vitro model. The evaluated anionic surfactants were sodium alkyl sulfate (AS) and sodium fatty acid methyl ester sulfonate (MES), which had different alkyl-chain lengths (C8-C14). Skin tissue damage and permeability were examined using a reconstructed human epidermal model, LabCyte EPI-MODEL24. Skin tissue damage was examined by measuring cytotoxicity with an MTT assay. Liquid chromatography/tandem mass spectrometry (LC/MS-MS) and liquid chromatography/mass spectrometry (LC/MS) were used to detect surfactants that permeated into the assay medium through an epidermal model. To assess the permeation mechanism and cell damage caused by the surfactants through the epidermis, we evaluated the structural changes of Bovine Serum Albumin (BSA), used as a simple model protein, and the fluidity of 1,2-dipalmitoyl-sn-glycero-3-phosphpcholine (DPPC) liposome, which serves as one of the most abundant phospholipid models of living cell membranes in the epidermis. The effects of the surfactants on the proteins were measured using Circular Dichroism (CD) spectroscopy, while the effects on membrane fluidity were investigated by electron spin resonance (ESR) spectroscopy. ET50 (the 50% median effective time) increased as follows: C10 < C12 < C8 < C14 in AS and C8, C10 < C12 < C14 in MES. The order of permeation through the LabCyte EPI-MODEL24 was C10 > C12 > C14, for both AS and MES. For both AS and MES, the order parameter, which is the criteria for the microscopic viscosity of lipid bilayers, increased as follows: C10 < C12 < C14, which means the membrane fluidity is C10 > C12 > C14. It was determined that the difference in skin tissue damage in the LabCyte EPI-MODEL24 with C10 to C14 AS and MES was caused by the difference in permeation and cell membrane fluidity through the lipid bilayer path in the epidermis. PMID:25213449

  2. Mechanical evaluation of unipolar hip spacer constructs.

    PubMed

    Kummer, Frederick J; Strauss, Eric; Wright, Kevin; Kubiak, Erik N; Di Cesare, Paul E

    2008-10-01

    The strengths of 3 hip spacer constructs--Steinmann pins, a short intramedullary nail (both cement-incorporated), and a Charnley prosthesis--were determined and compared with the strength of a commercially available hip spacer. The hip prosthesis construct was more than twice as strong as the other 2 constructs and was equivalent in strength to the commercial spacer. For spacer applications in which limited weight-bearing is anticipated, the hip prosthesis construct appears more efficacious, but its pros and cons should be compared with those of the commercial product. PMID:19081880

  3. PEGylation of phytantriol-based lyotropic liquid crystalline particles--the effect of lipid composition, PEG chain length, and temperature on the internal nanostructure.

    PubMed

    Nilsson, Christa; Østergaard, Jesper; Larsen, Susan Weng; Larsen, Claus; Urtti, Arto; Yaghmur, Anan

    2014-06-10

    Poly(ethylene glycol)-grafted 1,2-distearoyl-sn-glycero-3-phosphoethanolamines (DSPE-mPEGs) are a family of amphiphilic lipopolymers attractive in formulating injectable long-circulating nanoparticulate drug formulations. In addition to long circulating liposomes, there is an interest in developing injectable long-circulating drug nanocarriers based on cubosomes and hexosomes by shielding and coating the dispersed particles enveloping well-defined internal nonlamellar liquid crystalline nanostructures with hydrophilic PEG segments. The present study attempts to shed light on the possible PEGylation of these lipidic nonlamellar liquid crystalline particles by using DSPE-mPEGs with three different block lengths of the hydrophilic PEG segment. The effects of lipid composition, PEG chain length, and temperature on the morphology and internal nanostructure of these self-assembled lipidic aqueous dispersions based on phytantriol (PHYT) were investigated by means of synchrotron small-angle X-ray scattering and Transmission Electron Cryo-Microscopy. The results suggest that the used lipopolymers are incorporated into the water-PHYT interfacial area and induce a significant effect on the internal nanostructures of the dispersed submicrometer-sized particles. The hydrophilic domains of the internal liquid crystalline nanostructures of these aqueous dispersions are functionalized, i.e., the hydrophilic nanochannels of the internal cubic Pn3m and Im3m phases are significantly enlarged in the presence of relatively small amounts of the used DSPE-mPEGs. It is evident that the partial replacement of PHYT by these PEGylated lipids could be an attractive approach for the surface modification of cubosomal and hexosomal particles. These PEGylated nanocarriers are particularly attractive in designing injectable cubosomal and hexosomal nanocarriers for loading drugs and/or imaging probes. PMID:24833115

  4. Screening for JH1 genetic defect carriers in Jersey cattle by a polymerase chain reaction and restriction fragment length polymorphism assay.

    PubMed

    Zhang, Yi; Guo, Gang; Huang, Hetian; Lu, Lu; Wang, Lijie; Fang, Lingzhao; Liu, Lin; Wang, Yachun; Zhang, Shengli

    2015-09-01

    An autosomal recessive genetic defect termed JH1 has been associated with early embryonic loss in the Jersey cattle breed. The genetic basis has been identified as a cytosine to thymine mutation in the CWC15 gene that changes an amino acid from arginine to a stop code. To screen for JH1 carriers in an imported Jersey population in China, a method based on a polymerase chain reaction amplification followed by a restriction fragment length polymorphism assay (PCR-RFLP) was developed for the accurate diagnosis of the JH1 allele. A total of 449 randomly chosen cows were examined with the PCR-RFLP assay, and 31 were identified as JH1 carriers, corresponding to a carrier frequency of 6.9%. The PCR-RFLP method was validated by DNA sequencing of 8 positive and 13 negative samples, with all 21 samples giving the expected DNA sequence. In addition, 3 negative and 3 positive samples were confirmed by a commercial microarray-based single nucleotide polymorphism assay. Finally, samples from 9 bulls in the United States of known status were correctly identified as carriers (5 bulls) or noncarriers (4 bulls). As the JH1 defect has most likely spread worldwide, implementing routine screening is necessary to avoid the risk of carrier-to-carrier matings and to gradually eradicate the deleterious gene. PMID:26179100

  5. Identification of blood meal sources of Lutzomyia longipalpis using polymerase chain reaction-restriction fragment length polymorphism analysis of the cytochrome B gene

    PubMed Central

    Soares, Vítor Yamashiro Rocha; da Silva, Jailthon Carlos; da Silva, Kleverton Ribeiro; Cruz, Maria do Socorro Pires e; Santos, Marcos Pérsio Dantas; Ribolla, Paulo Eduardo Martins; Alonso, Diego Peres; Coelho, Luiz Felipe Leomil; Costa, Dorcas Lamounier; Costa, Carlos Henrique Nery

    2014-01-01

    An analysis of the dietary content of haematophagous insects can provide important information about the transmission networks of certain zoonoses. The present study evaluated the potential of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mitochondrial cytochrome B (cytb) gene to differentiate between vertebrate species that were identified as possible sources of sandfly meals. The complete cytb gene sequences of 11 vertebrate species available in the National Center for Biotechnology Information database were digested with Aci I, Alu I, Hae III and Rsa I restriction enzymes in silico using Restriction Mapper software. The cytb gene fragment (358 bp) was amplified from tissue samples of vertebrate species and the dietary contents of sandflies and digested with restriction enzymes. Vertebrate species presented a restriction fragment profile that differed from that of other species, with the exception of Canis familiaris and Cerdocyon thous. The 358 bp fragment was identified in 76 sandflies. Of these, 10 were evaluated using the restriction enzymes and the food sources were predicted for four: Homo sapiens (1), Bos taurus (1) and Equus caballus (2). Thus, the PCR-RFLP technique could be a potential method for identifying the food sources of arthropods. However, some points must be clarified regarding the applicability of the method, such as the extent of DNA degradation through intestinal digestion, the potential for multiple sources of blood meals and the need for greater knowledge regarding intraspecific variations in mtDNA. PMID:24821056

  6. Polyester hydrolytic and synthetic activity catalyzed by the medium-chain-length poly(3-hydroxyalkanoate) depolymerase from Streptomyces venezuelae SO1.

    PubMed

    Santos, Marta; Gangoiti, Joana; Keul, Helmut; Möller, Martin; Serra, Juan L; Llama, María J

    2013-01-01

    The extracellular medium-chain-length polyhydroxyalkanote (MCL-PHA) depolymerase from an isolate identified as Streptomyces venezuelae SO1 was purified to electrophoretic homogeneity and characterized. The molecular mass and pI of the purified enzyme were approximately 27 kDa and 5.9, respectively. The depolymerase showed its maximum activity in the alkaline pH range and 50 °C and retained more than 70 % of its initial activity after 8 h at 40 °C. The MCL-PHA depolymerase hydrolyzes various p-nitrophenyl-alkanoates and polycaprolactone but not polylactide, poly-3-hydroxybutyrate, and polyethylene succinate. The enzymatic activity was markedly enhanced by the presence of low concentrations of detergents and organic solvents, being inhibited by dithiothreitol and EDTA. The potential of using the enzyme to produce (R)-3-hydroxyoctanoate in aqueous media or to catalyze ester-forming reactions in anhydrous media was investigated. In this sense, the MCL-PHA depolymerase catalyzes the hydrolysis of poly-3-hydroxyoctanoate to monomeric units and the ring-opening polymerization of β-butyrolactone and lactides, while ε-caprolactone and pentadecalactone were hardly polymerized. PMID:22695803

  7. Polymerase chain reaction-restriction fragment length polymorphism assays to distinguish Liriomyza huidobrensis (Diptera: Agromyzidae) from associated species on lettuce cropping systems in Italy.

    PubMed

    Masetti, Antonio; Luchetti, Andrea; Mantovani, Barbara; Burgio, Giovanni

    2006-08-01

    The pea leafminer, Liriomyza huidobrensis (Blanchard) (Diptera: Agromyzidae), is a serious insect pest infesting open field lettuce plantings in northern Italy. In these cropping systems, it coexists with several other agromyzid species that have negligible economic importance on open field vegetables. The rapid detection of L. huidobrensis is crucial for effective management strategies, but the identification of agromyzids to species can be very difficult at adult as well at immature stages. In this study, a polymerase chain reaction (PCR)-restriction fragment length polymorphism assay is proposed to separate L. huidobrensis from Liriomyza bryoniae (Kaltenbach), Liriomyza trifolii (Burgess), and Chromatomyia horticola (Goureau), which usually occur in the same lettuce plantings. An approximately 1,031-bp region of the mitochondrial genome encompassing the 3' region of cytochrome oxidase I, the whole leucine tRNA, and all of the cytochrome oxidase II was amplified by PCR and digested using the enzymes PvuII and SnaBI separately. Both endonucleases cut the amplicons of L. huidobrensis in two fragments, whereas the original band was not cleaved in the other analyzed species. The presence of Dacnusa spp. DNA does not bias the assay, because the PCR conditions and the primer set here described do not amplify any tract of this endoparasitic wasp genome. PMID:16937681

  8. Thermodynamic characterization of the interaction behavior of a hydrophobically modified polyelectrolyte and oppositely charged surfactants in aqueous solution: effect of surfactant alkyl chain length.

    PubMed

    Bai, Guangyue; Nichifor, Marieta; Lopes, António; Bastos, Margarida

    2005-01-13

    We have used a precision isothermal titration microcalorimeter (ITC) to measure the enthalpy curves for the interaction of a hydrophobically modified polyelectrolyte (D40OCT30) with oppositely charged surfactants (SC(n)S) in aqueous solution. D40OCT30 is a newly synthesized polymer based on dextran having pendant N-(2-hydroxypropyl)-N,N-dimethyl-N-octylammonium chloride groups randomly distributed along the polymer backbone with degree of substitution of 28.1%. The employed anionic surfactants are sodium octyl sulfate (SC(8)S) and sodium tetradecyl sulfate (SC(14)S). Microcalorimetric results along with turbidity and kinematic viscosity measurements demonstrate systematically the thermodynamic characterization of the interaction of D40OCT30/SC(n)S. A three-dimensional diagram with the derived phase boundaries is drawn to describe the effect of the alkyl chain length of surfactant and of the ratio between surfactant and pendant groups on the interaction. A more complete picture of the interaction mechanism for D40OCT30/SC(n)S systems is proposed here. PMID:16851043

  9. Biosynthesis from gluconate of a random copolyester consisting of 3-hydroxybutyrate and medium-chain-length 3-hydroxyalkanoates by Pseudomonas sp. 61-3.

    PubMed

    Abe, H; Doi, Y; Fukushima, T; Eya, H

    1994-06-01

    Pseudomonas sp. 61-3 isolated from soil was found to produce a polyester consisting of 3-hydroxyalkanoic acids of even carbon numbers C4, C6, C8, C10 and C12 when sodium gluconate was fed as the sole carbon source. The polyester produced was fractionated with boiling acetone. The acetone-insoluble fraction (28 wt%) of the polyester was a poly(3-hydroxybutyrate) homopolymer, while the acetone-soluble fraction (72 wt%) was composed of seven different 3-hydroxyalkanoate (3HA) units ranging from C4 to C12: 40 mol% 3-hydroxybutyrate (3HB), 5 mol% 3-hydroxyhexanoate (3HH), 20 mol% 3-hydroxyoctanoate (3HO), 24 mol% 3-hydroxydecanoate (3HD), 1 mol% 3-hydroxy-5-cis-decenoate (3H5D), 4 mol% 3-hydroxydodecanoate (3HDD) and 6 mol% 3-hydroxy-5-cis- dodecenoate (3H5DD). The copolymer was characterized by nuclear magnetic resonance (NMR) spectroscopy, gel permeation chromatography and differential scanning calorimetry. The acetone-soluble fraction of this amorphous copolymer was shown to have a random sequence distribution of the seven 3HA units of C4 to C12 by analysis of the 150 MHz 13C-NMR spectrum. This is the first example of microbial synthesis of a random copolyester consisting of 3HB and medium-chain-length 3HA units. PMID:7981156

  10. Rapid diagnosis and genotyping of Leishmania isolates from cutaneous and visceral leishmaniasis by microcapillary cultivation and polymerase chain reaction-restriction fragment length polymorphism of miniexon region.

    PubMed

    Serin, Mehmet S; Daglioglu, Kenan; Bagirova, Melahat; Allahverdiyev, Adil; Uzun, Soner; Vural, Zeynep; Kayar, Begum; Tezcan, Seda; Yetkin, Mesut; Aslan, Gonul; Emekdas, Gurol; Koksal, Fatih

    2005-11-01

    We have performed a combination of microcapillary cultivation method and restriction fragment length polymorphism (RFLP) analysis of amplified products by 1 single PCR of miniexon region of Leishmania for molecular diagnosis and genotyping of different Leishmania species isolated from cutaneous leishmaniasis (CL) and visceral leishmaniasis. We have analyzed 10 microcapillary cultivated isolates from cutaneous cases and 5 microcapillary cultivated isolates from visceral cases (totally 15) by polymerase chain reaction-RFLP (PCR-RFLP). Of 10 isolates, 3 (30%) were genotyped as Leishmania infantum and 7 (70%) of 10 isolates were genotyped as Leishmania tropica from the microcapillary cultivated isolates of cutaneous cases. On the other hand, all 5 isolates (100%) were genotyped as L. infantum from microcapillary cultivated visceral cases. Our most interesting finding is the presence of 3 L. infantum isolates in CL cases without kala-azar history. Therefore, we suggest that further investigations must be done about this subject. On the other hand, we suggest the combination of microcapillary culture method and PCR-RFLP of miniexon region of leishmaniae can be used in routine laboratory experimentation because of their simple, cheap, and rapid benefits (within a week), whereas other different approaches offer a multitude of valid taxonomic characters for species identification. PMID:16249065

  11. Comparison of detection platforms and post-polymerase chain reaction DNA purification methods for use in conjunction with Cleavase fragment length polymorphism analysis.

    PubMed

    Sander, T; Olson, S; Hall, J; Siebert, M; Grooms, K; Heisler, L; de Arruda, M; Neri, B

    1999-06-01

    The removal of impurities and contaminants from PCR-amplified fragments is important for mutation detection methods which identify mutations based on shifts in electrophoretic mobility. This is particularly critical for assays and detection methods which use target DNA that is labeled prior to analysis and electrophoretic detection. We examined several procedures for purifying DNA amplified by the polymerase chain reaction (PCR) and their use in conjunction with a novel DNA scanning method, the Cleavase fragment length polymorphism (CFLP)* assay. In this study, a 480 bp DNA fragment, fluorescently labeled on the 5'-end of one strand, was amplified and subjected to various widely used purification procedures, including several commercially available clean-up kits. We demonstrate that visualization of the fluorescent label, as opposed to simple ethidium bromide staining, reveals the presence of considerable levels of labeled, truncated, amplification products. The various procedures were evaluated on the basis of their ability to remove these unwanted DNA fragments as well as on the degree to which they inhibited or promoted the CFLP reaction. Several procedures are recommended for use with CFLP analysis, including isopropanol precipitation, gel excision, and several commercially available spin columns. Concurrently, we evaluated (compared) a number of commonly used visualization platforms, including fluorescence imaging, chemiluminescence, and post-electrophoretic staining, for the ability to detect CFLP pattern changes. The advantages and disadvantages of different methods are discussed and amounts of DNA to be used for CFLP analysis on different detection platforms are recommended. PMID:10380752

  12. Development of Fok-I based nested polymerase chain reaction-restriction fragment length polymorphism analysis for detection of hepatitis B virus X region V5M mutation

    PubMed Central

    Kim, Hong; Hong, Seok-Hyun; Lee, Seoung-Ae; Gong, Jeong-Ryeol; Kim, Bum-Joon

    2015-01-01

    AIM: To develop a Fok-I nested polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) method for the detection of hepatitis B virus X region (HBx) V5M mutation. METHODS: Nested PCR was applied into DNAs from 198 chronic patients at 2 different stages [121 patients with hepatocellular carcinoma (HCC) and 77 carrier patients]. To identify V5M mutants, digestion of nested PCR amplicons by the restriction enzyme Fok-I (GGA TGN9↓) was done. For size comparison, the enzyme-treated products were analyzed by electrophoresis on 2.5% agarose gels, stained with ethidium bromide, and visualized on a UV transilluminator. RESULTS: The assay enabled the identification of 69 patients (sensitivity of 34.8%; 46 HCC patients and 23 carrier patients). Our data also showed that V5M prevalence in HCC patients was significantly higher than in carrier patients (47.8%, 22/46 patients vs 0%, 0/23 patients, P < 0.001), suggesting that HBxAg V5M mutation may play a pivotal role in HCC generation in chronic patients with genotype C infections. CONCLUSION: The Fok-I nested PRA developed in this study is a reliable and cost-effective method to detect HBxAg V5M mutation in chronic patients with genotype C2 infection. PMID:26715821

  13. Chain-length-dependent impact of band broadening on the molar-mass determination of synthetic polymers via size-exclusion chromatography.

    PubMed

    Wolpers, Arne; Vana, Philipp

    2016-08-01

    The impact of band-broadening (BB) on the molar-mass determination of synthetic polymers via size-exclusion chromatography (SEC) is systematically studied. BB is simulated using the exponentially modified Gaussian (EMG) model, which combines the two inherent and distinct characteristics contributing to BB in SEC: symmetric Gaussian broadening and asymmetric skewing. It is demonstrated that BB both during the measurement of the analyte itself and during the calibration process has an individual impact on molar-mass determination. In this context, particularly skewing leads to a chain-length-dependent underestimation of molar masses, with deviations of the apparent from the true ones of only a few percent for low molar masses to up to 20% for high ones for reasonable extents of BB. The impact is shown to be independent of the shape of the analyte⬢s molar-mass distribution (MMD) and affects broad and multimodal MMDs similarly to narrow and unimodal ones. As a consequence, strategies are presented for a comprehensive quantitative correction of the observed effects, which may find their application in refined SEC software packages. The potential impact of the findings on general conceptions of repeatability and reproducibility within SEC experiments is discussed. PMID:27393628

  14. Identification of Echinococcus granulosus strains using polymerase chain reaction-restriction fragment length polymorphism amongst livestock in Moroto district, Uganda.

    PubMed

    Chamai, Martin; Omadang, Leonard; Erume, Joseph; Ocaido, Michael; Oba, Peter; Othieno, Emmanuel; Bonaventure, Straton; Kitibwa, Annah

    2016-01-01

    A descriptive study was conducted to identify the different strains of Echinococcus granulosus occurring in livestock in Moroto district, Uganda. Echinococcus cysts from 104 domestic animals, including cattle, sheep, goats and camels, were taken and examined by microscopy, polymerase chain reaction with restriction fragment length polymorphism and Sanger DNA sequencing. Echinococcus granulosus genotypes or strains were identified through use of Bioinformatics tools: BioEdit, BLAST and MEGA6. The major finding of this study was the existence of a limited number of E. granulosus genotypes from cattle, goats, sheep and camels. The most predominant genotype was G1 (96.05%), corresponding to the common sheep strain. To a limited extent (3.95%), the study revealed the existence of Echinococcus canadensis G6/7 in three (n = 3) of the E. granulosus-positive samples. No other strains of E. granulosus were identified. It was concluded that the common sheep strain of Echinococcus sensu stricto and G6/7 of E. canadensis were responsible for echinococcal disease in Moroto district, Uganda. PMID:27543147

  15. The effect of chain length on the thermal stability of 2-alkylimidazoles on copper and 2-alkylimidazolato copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Yoshida, Shuji; Ishida, Hatsuo

    1985-02-01

    The molecular structure and thermal stability of imidazole, 2-methylimidazole, 2-ethylimidazole, 2-propylimidazole, 2-undecylimidazole, and 2-heptadecylimidazole on copper are studied using FT-IR reflection—absorption spectroscopy. As model compounds of these complexes formed on copper, corresponding imidazole copper(II) complexes are synthesized in solution. The complexes appear to be the semicrystalline or crystalline structure. The series of imidazoles employed on copper indicates the same oxidation and degradation process at high temperatures even though imidazole, 2-methylimidazole and 2-ethylimidazole possess better thermal stability below 150°C. The synthesized complexes indicate poor thermal stability as the chain length of the alkyl substituent increases and the enhanced oxidation by the addition of copper powder. The difference in oxidation between imidazoles on copper and synthesized imidazole complexes are due to the presence of copper ion migrating from the copper substrate to catalyze oxidation and different morphological structure. The difference in oxidation among the imidazole derivatives depend on the melting points and the fraction of the imidazole ring which occupies the molecule.

  16. Effect of polyethyleneglycol (PEG) chain length on the bio-nano-interactions between PEGylated lipid nanoparticles and biological fluids: from nanostructure to uptake in cancer cells

    NASA Astrophysics Data System (ADS)

    Pozzi, Daniela; Colapicchioni, Valentina; Caracciolo, Giulio; Piovesana, Susy; Capriotti, Anna Laura; Palchetti, Sara; de Grossi, Stefania; Riccioli, Anna; Amenitsch, Heinz; Laganà, Aldo

    2014-02-01

    When nanoparticles (NPs) enter a physiological environment, medium components compete for binding to the NP surface leading to formation of a rich protein shell known as the ``protein corona''. Unfortunately, opsonins are also adsorbed. These proteins are immediately recognized by the phagocyte system with rapid clearance of the NPs from the bloodstream. Polyethyleneglycol (PEG) coating of NPs (PEGylation) is the most efficient anti-opsonization strategy. Linear chains of PEG, grafted onto the NP surface, are able to create steric hindrance, resulting in a significant inhibition of protein adsorption and less recognition by macrophages. However, excessive PEGylation can lead to a strong inhibition of cellular uptake and less efficient binding with protein targets, reducing the potential of the delivery system. To reach a compromise in this regard we employed a multi-component (MC) lipid system with uncommon properties of cell uptake and endosomal escape and increasing length of PEG chains. Nano liquid chromatography coupled with tandem mass spectrometry (nanoLC-MS/MS) analysis allowed us to accurately determine the corona composition showing that apolipoproteins are the most abundant class in the corona and that increasing the PEG length reduced the protein adsorption and the liposomal surface affinity for apolipoproteins. Due to the abundance of apolipoproteins, we exploited the ``protein corona effect'' to deliver cationic liposome-human plasma complexes to human prostate cancer PC3 cells that express a high level of scavenger receptor class B type 1 in order to evaluate the cellular uptake efficiency of the systems used. Combining laser scanning confocal microscopy with flow cytometry analysis in PC3 cells we demonstrated that MC-PEG2k is the best compromise between an anti-opsonization strategy and active targeting and could be a promising candidate to treat prostate cancer in vivo.When nanoparticles (NPs) enter a physiological environment, medium components

  17. Uncoupling and Toxic Action of Alkyltriphenylphosphonium Cations on Mitochondria and the Bacterium Bacillus subtilis as a Function of Alkyl Chain Length.

    PubMed

    Khailova, L S; Nazarov, P A; Sumbatyan, N V; Korshunova, G A; Rokitskaya, T I; Dedukhova, V I; Antonenko, Yu N; Skulachev, V P

    2015-12-01

    A series of permeating cations based on alkyl derivatives of triphenylphosphonium (C(n)-TPP(+)) containing linear hydrocarbon chains (butyl, octyl, decyl, and dodecyl) was investigated in systems of isolated mitochondria, bacteria, and liposomes. In contrast to some derivatives (esters) of rhodamine-19, wherein butyl rhodamine possessed the maximum activity, in the case of C(n)-TPP a stimulatory effect on mitochondrial respiration steadily increased with growing length of the alkyl radical. Tetraphenylphosphonium and butyl-TPP(+) at a dose of several hundred micromoles exhibited an uncoupling effect, which might be related to interaction between C(n)-TPP(+) and endogenous fatty acids and induction of their own cyclic transfer, resulting in transport of protons across the mitochondrial membrane. Such a mechanism was investigated by measuring efflux of carboxyfluorescein from liposomes influenced by C(n)-TPP(+). Experiments with bacteria demonstrated that dodecyl-TPP(+), decyl-TPP(+), and octyl-TPP(+) similarly to quinone-containing analog (SkQ1) inhibited growth of the Gram-positive bacterium Bacillus subtilis, wherein the inhibitory effect was upregulated with growing lipophilicity. These cations did not display toxic effect on growth of the Gram-negative bacterium Escherichia coli. It is assumed that the difference in toxic action on various bacterial species might be related to different permeability of bacterial coats for the examined triphenylphosphonium cations. PMID:26638684

  18. Dextran Sodium Sulfate (DSS) Induces Colitis in Mice by Forming Nano-Lipocomplexes with Medium-Chain-Length Fatty Acids in the Colon

    PubMed Central

    Laroui, Hamed; Ingersoll, Sarah A.; Liu, Hong Chun; Baker, Mark T.; Ayyadurai, Saravanan; Charania, Moiz A.; Laroui, Famina; Yan, Yutao; Sitaraman, Shanthi V.; Merlin, Didier

    2012-01-01

    Inflammatory bowel diseases (IBDs), primarily ulcerative colitis and Crohn's disease, are inflammatory disorders caused by multiple factors. Research on IBD has often used the dextran sodium sulfate (DSS)-induced colitis mouse model. DSS induces in vivo but not in vitro intestinal inflammation. In addition, no DSS-associated molecule (free glucose, sodium sulfate solution, free dextran) induces in vitro or in vivo intestinal inflammation. We find that DSS but not dextran associated molecules established linkages with medium-chain-length fatty acids (MCFAs), such as dodecanoate, that are present in the colonic lumen. DSS complexed to MCFAs forms nanometer-sized vesicles ∼200 nm in diameter that can fuse with colonocyte membranes. The arrival of nanometer-sized DSS/MCFA vesicles in the cytoplasm may activate intestinal inflammatory signaling pathways. We also show that the inflammatory activity of DSS is mediated by the dextran moieties. The deleterious effect of DSS is localized principally in the distal colon, therefore it will be important to chemically modify DSS to develop materials beneficial to the colon without affecting colon-targeting specificity. PMID:22427817

  19. The properties of mesoporous silica nanoparticles functionalized with different PEG-chain length via the disulfide bond linker and drug release in glutathione medium.

    PubMed

    Xie, Zhifei; Gong, Huameng; Liu, Mingxing; Zhu, Hongda; Sun, Honghao

    2016-01-01

    In this paper, a novel drug-loaded material (MSNs-SS-PEG) was obtained by grafting the thiol-linked methoxy polyethylene glycol (MeOPEG-SH) onto the thiol-functionalized mesoporous silica nanoparticles (MSNs-SH) via the disulfide bond linker. In our designed experiment, three different chain lengths of PEG (PEG(1000), PEG(5000), and PEG(1000)-PEG(5000)) were used. The silica materials were characterized by Fourier transform infrared spectroscopy (FT-IR), dynamic light scattering, field emission scanning electron microscopy, transmission electron microscopy, nitrogen adsorption-desorption measurements, and X-ray diffraction. The morphology of the MSNs-SS-PEG was spherical with an average diameter of about 150 nm. Due to the covalent modification of hydrophilic MeOPEG, the MSNs-SS-PEG was coated by a thin polymer shell, showing stable and inerratic MCM-41 type mesoporous structure as well as high specific surface areas and large pore volumes. Moreover, the releases of doxorubicin hydrochloride (DOX) from these materials at 10 mM of glutathione were investigated. The PEG functionalization could effectively cap drugs in the mesoporous channels. The release of DOX from the MSNs-SS-PEG(n) revealed redox-responsive characteristic. The obtained results showed that the MSNs-SS-PEG might be promising drug delivery carrier materials, which could play an important role in the development of drug delivery. PMID:26540096

  20. Highly efficient editing of the actinorhodin polyketide chain length factor gene in Streptomyces coelicolor M145 using CRISPR/Cas9-CodA(sm) combined system.

    PubMed

    Zeng, Hu; Wen, Shishi; Xu, Wei; He, Zhaoren; Zhai, Guifa; Liu, Yunkun; Deng, Zixin; Sun, Yuhui

    2015-12-01

    The current diminishing returns in finding useful antibiotics and the occurrence of drug-resistant bacteria call for the need to find new antibiotics. Moreover, the whole genome sequencing revealed that the biosynthetic potential of Streptomyces, which has produced the highest numbers of approved and clinical-trial drugs, has been greatly underestimated. Considering the known gene editing toolkits were arduous and inefficient, novel and efficient gene editing system are desirable. Here, we developed an engineered CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR-associated protein) combined with the counterselection system CodA(sm), the D314A mutant of cytosine deaminase, to rapidly and effectively edit Streptomyces genomes. In-frame deletion of the actinorhodin polyketide chain length factor gene actI-ORF2 was created in Streptomyces coelicolor M145 as an illustration. This CRISPR/Cas9-CodA(sm) combined system strikingly increased the frequency of unmarked mutants and shortened the time required to generate them. We foresee the system becoming a routine laboratory technique for genome editing to exploit the great biosynthetic potential of Streptomyces and perhaps for other medically and economically important actinomycetes. PMID:26318449

  1. Stationary cell size distributions and mean protein chain length distributions of Archaea, Bacteria and Eukaryotes described with an increment model in terms of irreversible thermodynamics

    NASA Astrophysics Data System (ADS)

    Kilian, H. G.; Gruler, H.; Bartkowiak, D.; Kaufmann, D.

    2005-07-01

    In terms of an increment model irreversible thermodynamics allows to formulate general relations of stationary cell size distributions observed in growing colonies. The treatment is based on the following key postulates: i) The growth dynamics covers a broad spectrum of fast and slow processes. ii) Slow processes are considered to install structural patterns that operate in short periods as temporary stationary states of reference in the sense of irreversible thermodynamics. iii) Distortion during growth is balanced out via the many fast processes until an optimized stationary state is achieved. The relation deduced identifies the numerous different stationary patterns as equivalents, predicting that they should fall on one master curve. Stationary cell size distributions of different cell types, like Hyperphilic archaea, E. coli (Prokaryotes) and S. cerevisiae (Eukaryotes), altogether taken from the literature, are in fact consistently described. As demanded by the model they agree together with the same master curve. Considering the “protein factories” as subsystems of cells the mean protein chain length distributions deduced from completely sequenced genomes should be optimized. In fact, the mean course can be described with analogous relations as used above. Moreover, the master curve fits well to the patterns of different species of Archaea, Bacteria and Eukaryotes. General consequences are discussed.

  2. New FadB homologous enzymes and their use in enhanced biosynthesis of medium-chain-length polyhydroxyalkanoates in FadB mutant Escherichia coli.

    PubMed

    Park, Si Jae; Yup Lee, Sang

    2004-06-20

    Recombinant Escherichia coli harboring the medium-chain-length (MCL) polyhydroxyalkanoate (PHA) synthase gene has been shown to accumulate MCL-PHAs from fatty acids when FadB is inactive. However, the enzymes in fadB mutant E. coli responsible for channeling the beta-oxidation intermediates to PHA biosynthesis have not been fully elucidated. Only recently, two enzymes encoded by yfcX and maoC have been found to be partially responsible for this. In this study, we identified five new FadB homologous enzymes in E. coli: PaaG, PaaF, BhbD, SceH, and YdbU, by protein database search, and examined their roles in the biosynthesis of MCL-PHAs in an fadB mutant E. coli strain. Coexpression of each of these genes along with the Pseudomonas sp. 61-3 phaC2 gene did not allow synthesis of MCL-PHA from fatty acid in recombinant E. coli W3110, which has a fully functional beta-oxidation pathway, but allowed MCL-PHA accumulation in an fadB mutant E. coli WB101. In particular, coexpression of the paaG, paaF, and ydbU genes resulted in a MCL-PHA production up to 0.37, 0.25, and 0.33 g/L, respectively, from 2 g/L of sodium decanoate, which is more than twice higher than that obtained with E. coli WB101 expressing only the phaC2 gene (0.16 g/L). These results suggest that the newly found FadB homologous enzymes, or at least the paaG, paaF, and ydbU genes, are involved in MCL-PHA biosynthesis in an fadB mutant E. coli strain and can be employed for the enhanced production of MCL-PHA. PMID:15137080

  3. Investigation of the role of hydrophilic chain length in amphiphilic perfluoropolyether/poly(ethylene glycol) networks: towards high-performance antifouling coatings

    SciTech Connect

    Wang, Yapei; Pitet, Louis M.; Finlay, John A.; Brewer, Lenora H.; Cone, Gemma; Betts, Douglas E.; Callow, Maureen E.; Callow, James A.; Wendt, Dean E.; Hillmyer, Marc A.; DeSimone, Joseph M.

    2013-03-07

    The facile preparation of amphiphilic network coatings having a hydrophobic dimethacryloxy-functionalized perfluoropolyether (PFPE-DMA; M{sub w} = 1500 g mol{sup -1}) crosslinked with hydrophilic monomethacryloxy functionalized poly(ethylene glycol) macromonomers (PEG-MA; M{sub w} = 300, 475, 1100 g mol{sup -1}), intended as non-toxic high-performance marine coatings exhibiting antifouling characteristics is demonstrated. The PFPE-DMA was found to be miscible with the PEG-MA. Photo-cured blends of these materials containing 10 wt% of PEG-MA oligomers did not swell significantly in water. PFPE-DMA crosslinked with the highest molecular weight PEG oligomer (ie PEG1100) deterred settlement (attachment) of algal cells and cypris larvae of barnacles compared to a PFPE control coating. Dynamic mechanical analysis of these networks revealed a flexible material. Preferential segregation of the PEG segments at the polymer/air interface resulted in enhanced antifouling performance. The cured amphiphilic PFPE/PEG films showed decreased advancing and receding contact angles with increasing PEG chain length. In particular, the PFPE/PEG1100 network had a much lower advancing contact angle than static contact angle, suggesting that the PEG1100 segments diffuse to the polymer/water interface quickly. The preferential interfacial aggregation of the larger PEG segments enables the coating surface to have a substantially enhanced resistance to settlement of spores of the green seaweed Ulva, cells of the diatom Navicula and cypris larvae of the barnacle Balanus amphitrite as well as low adhesion of sporelings (young plants) of Ulva, adhesion being lower than to a polydimethyl elastomer, Silastic T2.

  4. Characterization of infectious laryngotracheitis virus (ILTV) isolates from commercial poultry by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP).

    PubMed

    Oldoni, Ivomar; Rodríguez-Avila, Andrés; Riblet, Sylva; García, Maricarmen

    2008-03-01

    Infectious laryngotracheitis (ILT) is a highly contagious, acute respiratory disease of chickens, of worldwide distribution, that affects growth and egg production and leads to significant economic losses during periodic outbreaks of the disease. Live attenuated vaccines (chicken embryo origin [CEO] and tissue-culture origin [TCO]) have been widely used to control the disease in the United States. It is believed that most of the outbreaks in the United States are caused by vaccine-related isolates that persist in the field and spill over into naïve poultry populations. The objective of this study was to utilize the previously developed polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis to genotype recent ILT virus (ILTV) isolates from commercial poultry. Forty-six samples were collected during January 2006 to April 2007 from five poultry production regions of the United States and were characterized within PCR-RFLP groups III-VI. Sixty-three percent of the samples analyzed were categorized as closely related to the vaccine strains (groups III-V), whereas 33% were categorized as group VI viruses that differed in six and nine PCR-RFLP patterns from the CEO and TCO vaccines; a mixture of group IV and V viruses was detected in two samples (4%). In general, groups V and VI were the most prevalent viruses, found in 52% and 33% of the samples tested respectively. Both types of viruses were detected in vaccinated and nonvaccinated flocks. Although genetically different, both viruses produced severe disease in the field. PMID:18459297

  5. Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene

    PubMed Central

    Hadifar, Shima; Moghim, Sharareh; Fazeli, Hossein; GhasemianSafaei, Hajieh; Havaei, Seyed Asghar; Farid, Fariba; Esfahani, Bahram Nasr

    2015-01-01

    Background: Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region. Materials and Methods: Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes. Results: In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates. Conclusion: Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species. PMID:26380237

  6. The D3 bacteriophage α-polymerase inhibitor (Iap) peptide disrupts O-antigen biosynthesis through mimicry of the chain length regulator Wzz in Pseudomonas aeruginosa.

    PubMed

    Taylor, Véronique L; Udaskin, Molly L; Islam, Salim T; Lam, Joseph S

    2013-10-01

    Lysogenic bacteriophage D3 causes seroconversion of Pseudomonas aeruginosa PAO1 from serotype O5 to O16 by inverting the linkage between O-specific antigen (OSA) repeat units from α to β. The OSA units are polymerized by Wzy to modal lengths regulated by Wzz1 and Wzz2. A key component of the D3 seroconversion machinery is the inhibitor of α-polymerase (Iap) peptide, which is able to solely suppress α-linked long-chain OSA production in P. aeruginosa PAO1. To establish the target specificity of Iap for Wzyα, changes in OSA phenotypes were examined via Western immunoblotting for wzz1 and wzz2 single-knockout strains, as well as a wzz1 wzz2 double knockout, following the expression of iap from a tuneable vector. Increased induction of Iap expression completely abrogated OSA production in the wzz1 wzz2 double mutant, while background levels of OSA production were still observed in either of the single mutants. Therefore, Iap inhibition of OSA biosynthesis was most effective in the absence of both Wzz proteins. Sequence alignment analyses revealed a high degree of similarity between Iap and the first transmembrane segment (TMS) of either Wzz1 or Wzz2. Various topology prediction analyses of the Iap sequence consistently predicted the presence of a single TMS, suggesting a propensity for Iap to insert itself into the inner membrane (IM). The compromised ability of Iap to abrogate Wzyα function in the presence of Wzz1 or Wzz2 provides compelling evidence that inhibition occurs after Wzyα inserts itself into the IM and is achieved through mimicry of the first TMS from the Wzz proteins of P. aeruginosa PAO1. PMID:23955007

  7. Spacers' role in the dynamics of hyperbranched polymers

    NASA Astrophysics Data System (ADS)

    Satmarel, C.; von Ferber, C.; Blumen, A.

    2006-05-01

    We investigate hyperbranched polymers (HBPs) and highlight the relation between their architecture and their viscoelastic behavior, while paying special attention to the role of the chainlike spacer segments between branching points. For this we study the dynamics of HBP in solution, based on the generalized Gaussian structure formalism, an extension of the Rouse model, which disregards hydrodynamical and excluded volume effects. For HBP the dynamical effects display, beside the obvious contributions of localized modes on the spacers, also remarkable features, as we highlight based on the exact renormalization procedure recently developed by us in J. Chem. Phys. 123, 034907 (2005). We exemplify these features by analyzing the dynamics of randomly linked star polymers and study the impact both of the length and of the spacers' mobility on the normal modes' spectra. We compute these modes both by numerical diagonalization and also by employing our renormalization procedure; the excellent agreement between these methods allows us to extend the range of investigations to very large HBP.

  8. Restriction fragment length polymorphism species-specific patterns in the identification of white truffles.

    PubMed

    Bertini, L; Potenza, L; Zambonelli, A; Amicucci, A; Stocchi, V

    1998-07-15

    A molecular method for the identification of ectomycorrhizae belonging to five species of white truffle is described. The polymerase chain reaction (PCR) and universal primers were used to amplify internal transcribed spacers and 5.8S rDNA, target sequences present in a high number of copies. The amplified products were digested with restriction enzymes in order to detect interspecific polymorphisms. Species-specific restriction fragment length polymorphism patterns were determined for all five species. The use of PCR in conjunction with restriction enzymes provides a sensitive and efficient tool for use in distinguishing ectomycorrhizal species and monitoring inoculated seedlings or field mycorrhizal populations. PMID:9682488

  9. Adjustable spacer with rotational lock

    SciTech Connect

    Bowyer, M.L.

    1984-02-28

    A spacing apparatus for tubing conduit in a subterranean well, normally for use with an electric component with a longitudinally extending external electrical cable, permits irrotational adjustment of the length of the tubing conduit. The spacing apparatus comprises telescoping members which are keyed to prevent rotation therebetween. A threaded member, longitudinally fixed relative to one longitudinal member, normally engages threads extending substantially along the entire length of the other telescoping member. Movement of a retaining sleeve permits disengagement of the threaded segments which ratchet along the threads during telescoping movement. The length of the conduit can thus be irrotationally adjusted to remove slack from the electrical cable.

  10. Hole-transfer induced energy transfer in perylene diimide dyads with a donor-spacer-acceptor motif.

    PubMed

    Kölle, Patrick; Pugliesi, Igor; Langhals, Heinz; Wilcken, Roland; Esterbauer, Andreas J; de Vivie-Riedle, Regina; Riedle, Eberhard

    2015-10-14

    We investigate the photoinduced dynamics of perylene diimide dyads based on a donor-spacer-acceptor motif with polyyne spacers of varying length by pump-probe spectroscopy, time resolved fluorescence, chemical variation and quantum chemistry. While the dyads with pyridine based polyyne spacers undergo energy transfer with near-unity quantum efficiency, in the dyads with phenyl based polyyne spacers the energy transfer efficiency drops below 50%. This suggests the presence of a competing electron transfer process from the spacer to the energy donor as the excitation sink. Transient absorption spectra, however, reveal that the spacer actually mediates the energy transfer dynamics. The ground state bleach features of the polyyne spacers appear due to the electron transfer decay with the same time constant present in the rise of the ground state bleach and stimulated emission of the perylene energy acceptor. Although the electron transfer process initially quenches the fluorescence of the donor it does not inhibit energy transfer to the perylene energy acceptor. The transient signatures reveal that electron and energy transfer processes are sequential and indicate that the donor-spacer electron transfer state itself is responsible for the energy transfer. Through the introduction of a Dexter blocker unit into the spacer we can clearly exclude any through bond Dexter-type energy transfer. Ab initio calculations on the donor-spacer and the donor-spacer-acceptor systems reveal the existence of a bright charge transfer state that is close in energy to the locally excited state of the acceptor. Multipole-multipole interactions between the bright charge transfer state and the acceptor state enable the energy transfer. We term this mechanism coupled hole-transfer FRET. These dyads represent a first example that shows how electron transfer can be connected to energy transfer for use in novel photovoltaic and optoelectronic devices. PMID:26347443

  11. Quantitative ‘Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids

    PubMed Central

    Fu, Jilagamazhi; Sharma, Parveen; Spicer, Vic; Krokhin, Oleg V.; Zhang, Xiangli; Fristensky, Brian; Cicek, Nazim; Sparling, Richard; Levin, David. B.

    2015-01-01

    Transcriptomes and proteomes of Pseudomonas putida LS46 cultured with biodiesel-derived waste glycerol or waste free fatty acids, as sole carbon sources, were compared under conditions that were either permissive or non-permissive for synthesis of medium chain length polyhydroxyalkanoates (mcl-PHA). The objectives of this study were to elucidate mechanisms that influence activation of biopolymer synthesis, intra-cellular accumulation, and monomer composition, and determine if these were physiologically specific to the carbon sources used for growth of P. putida LS46. Active mcl-PHA synthesis by P. putida LS46 was associated with high expression levels of key mcl-PHA biosynthesis genes and/or gene products including monomer-supplying proteins, PHA synthases, and granule-associated proteins. ‘Omics data suggested that expression of these genes were regulated by different genetic mechanisms in P. putida LS46 cells in different physiological states, when cultured on the two waste carbon sources. Optimal polymer production by P. putida LS46 was primarily limited by less efficient glycerol metabolism during mcl-PHA synthesis on waste glycerol. Mapping the ‘Omics data to the mcl-PHA biosynthetic pathway revealed significant variations in gene expression, primarily involved in: 1) glycerol transportation; 2) enzymatic reactions that recycle reducing equivalents and produce key mcl-PHA biosynthesis pathway intermediates (e.g. NADH/NADPH, acetyl-CoA). Active synthesis of mcl-PHAs was observed during exponential phase in cultures with waste free fatty acids, and was associated with the fatty acid beta-oxidation pathway. A putative Thioesterase in the beta-oxidation pathway that may regulate the level of fatty acid beta-oxidation intermediates, and thus carbon flux to mcl-PHA biosynthesis, was highly up-regulated. Finally, the data suggested that differences in expression of selected fatty acid metabolism and mcl-PHA monomer-supplying enzymes may play a role in determining

  12. Nonideal mixing and phase separation in phosphatidylcholine-phosphatidic acid mixtures as a function of acyl chain length and pH.

    PubMed Central

    Garidel, P; Johann, C; Blume, A

    1997-01-01

    The miscibilities of phosphatidic acids (PAs) and phosphatidylcholines (PCs) with different chain lengths (n = 14, 16) at pH 4, pH 7, and pH 12 were examined by differential scanning calorimetry. Simulation of heat capacity curves was performed using a new approach that incorporates changes of cooperativity of the transition in addition to nonideal mixing in the gel and the liquid-crystalline phase as a function of composition. From the simulations of the heat capacity curves, first estimates for the nonideality parameters for nonideal mixing as a function of composition were obtained, and phase diagrams were constructed using temperatures for onset and end of melting, which were corrected for the broadening effect caused by a decrease in cooperativity. In all cases the composition dependence of the nonideality parameters indicated nonsymmetrical mixing behavior. The phase diagrams were therefore further refined by simulations of the coexistence curves using a four-parameter approximation to account for nonideal and nonsymmetrical mixing in the gel and the liquid-crystalline phase. The mixing behavior was studied at three different pH values to investigate how changes in headgroup charge of the PA influences the miscibility. The experiments showed that at pH 7, where the PA component is negatively charged, the nonideality parameters are in most cases negative, indicating that electrostatic effects favor a mixing of the two components. Partial protonation of the PA component at pH 4 leads to strong changes in miscibility; the nonideality parameters for the liquid-crystalline phase are now in most cases positive, indicating clustering of like molecules. The phase diagram for 1,2-dimyristoyl-sn-glycero-3-phosphatidic acid:1,2-dipalmitoyl-sn-glycero-3-phosphorylcholine mixtures at pH 4 indicates that a fluid-fluid immiscibility is likely. The results show that a decrease in ionization of PAs can induce large changes in mixing behavior. This occurs because of a

  13. Deletion of 1-43 amino acids in cardiac myosin essential light chain blunts length dependency of Ca(2+) sensitivity and cross-bridge detachment kinetics.

    PubMed

    Michael, John Jeshurun; Gollapudi, Sampath K; Ford, Steven J; Kazmierczak, Katarzyna; Szczesna-Cordary, Danuta; Chandra, Murali

    2013-01-15

    The role of cardiac myosin essential light chain (ELC) in the sarcomere length (SL) dependency of myofilament contractility is unknown. Therefore, mechanical and dynamic contractile properties were measured at SL 1.9 and 2.2 μm in cardiac muscle fibers from two groups of transgenic (Tg) mice: 1) Tg-wild-type (WT) mice that expressed WT human ventricular ELC and 2) Tg-Δ43 mice that expressed a mutant ELC lacking 1-43 amino acids. In agreement with previous studies, Ca(2+)-activated maximal tension decreased significantly in Tg-Δ43 fibers. pCa(50) (-log(10) [Ca(2+)](free) required for half maximal activation) values at SL of 1.9 μm were 5.64 ± 0.02 and 5.70 ± 0.02 in Tg-WT and Tg-Δ43 fibers, respectively. pCa(50) values at SL of 2.2 μm were 5.70 ± 0.01 and 5.71 ± 0.01 in Tg-WT and Tg-Δ43 fibers, respectively. The SL-mediated increase in the pCa(50) value was statistically significant only in Tg-WT fibers (P < 0.01), indicating that the SL dependency of myofilament Ca(2+) sensitivity was blunted in Tg-Δ43 fibers. The SL dependency of cross-bridge (XB) detachment kinetics was also blunted in Tg-Δ43 fibers because the decrease in XB detachment kinetics was significant (P < 0.001) only at SL 1.9 μm. Thus the increased XB dwell time at the short SL augments Ca(2+) sensitivity at short SL and thus blunts SL-mediated increase in myofilament Ca(2+) sensitivity. Our data suggest that the NH(2)-terminal extension of cardiac ELC not only augments the amplitude of force generation, but it also may play a role in mediating the SL dependency of XB detachment kinetics and myofilament Ca(2+) sensitivity. PMID:23144314

  14. Quantitative 'Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids.

    PubMed

    Fu, Jilagamazhi; Sharma, Parveen; Spicer, Vic; Krokhin, Oleg V; Zhang, Xiangli; Fristensky, Brian; Cicek, Nazim; Sparling, Richard; Levin, David B

    2015-01-01

    Transcriptomes and proteomes of Pseudomonas putida LS46 cultured with biodiesel-derived waste glycerol or waste free fatty acids, as sole carbon sources, were compared under conditions that were either permissive or non-permissive for synthesis of medium chain length polyhydroxyalkanoates (mcl-PHA). The objectives of this study were to elucidate mechanisms that influence activation of biopolymer synthesis, intra-cellular accumulation, and monomer composition, and determine if these were physiologically specific to the carbon sources used for growth of P. putida LS46. Active mcl-PHA synthesis by P. putida LS46 was associated with high expression levels of key mcl-PHA biosynthesis genes and/or gene products including monomer-supplying proteins, PHA synthases, and granule-associated proteins. 'Omics data suggested that expression of these genes were regulated by different genetic mechanisms in P. putida LS46 cells in different physiological states, when cultured on the two waste carbon sources. Optimal polymer production by P. putida LS46 was primarily limited by less efficient glycerol metabolism during mcl-PHA synthesis on waste glycerol. Mapping the 'Omics data to the mcl-PHA biosynthetic pathway revealed significant variations in gene expression, primarily involved in: 1) glycerol transportation; 2) enzymatic reactions that recycle reducing equivalents and produce key mcl-PHA biosynthesis pathway intermediates (e.g. NADH/NADPH, acetyl-CoA). Active synthesis of mcl-PHAs was observed during exponential phase in cultures with waste free fatty acids, and was associated with the fatty acid beta-oxidation pathway. A putative Thioesterase in the beta-oxidation pathway that may regulate the level of fatty acid beta-oxidation intermediates, and thus carbon flux to mcl-PHA biosynthesis, was highly up-regulated. Finally, the data suggested that differences in expression of selected fatty acid metabolism and mcl-PHA monomer-supplying enzymes may play a role in determining the

  15. Toll-like receptor 2 activation by β2→1-fructans protects barrier function of T84 human intestinal epithelial cells in a chain length-dependent manner.

    PubMed

    Vogt, Leonie M; Meyer, Diederick; Pullens, Gerdie; Faas, Marijke M; Venema, Koen; Ramasamy, Uttara; Schols, Henk A; de Vos, Paul

    2014-07-01

    Dietary fiber intake is associated with lower incidence and mortality from disease, but the underlying mechanisms of these protective effects are unclear. We hypothesized that β2→1-fructan dietary fibers confer protection on intestinal epithelial cell barrier function via Toll-like receptor 2 (TLR2), and we studied whether β2→1-fructan chain-length differences affect this process. T84 human intestinal epithelial cell monolayers were incubated with 4 β2→1-fructan formulations of different chain-length compositions and were stimulated with the proinflammatory phorbol 12-myristate 13-acetate (PMA). Transepithelial electrical resistance (TEER) was analyzed by electric cell substrate impedance sensing (ECIS) as a measure for tight junction-mediated barrier function. To confirm TLR2 involvement in barrier modulation by β2→1-fructans, ECIS experiments were repeated using TLR2 blocking antibody. After preincubation of T84 cells with short-chain β2→1-fructans, the decrease in TEER as induced by PMA (62.3 ± 5.2%, P < 0.001) was strongly attenuated (15.2 ± 8.8%, P < 0.01). However, when PMA was applied first, no effect on recovery was observed during addition of the fructans. By blocking TLR2 on the T84 cells, the protective effect of short-chain β2→1-fructans was substantially inhibited. Stimulation of human embryonic kidney human TLR2 reporter cells with β2→1-fructans induced activation of nuclear factor kappa-light-chain-enhancer of activated B cells, confirming that β2→1-fructans are specific ligands for TLR2. To conclude, β2→1-fructans exert time-dependent and chain length-dependent protective effects on the T84 intestinal epithelial cell barrier mediated via TLR2. These results suggest that TLR2 located on intestinal epithelial cells could be a target of β2→1-fructan-mediated health effects. PMID:24790027

  16. Mechanics of semiflexible chains formed by poly(ethylene glycol)-linked paramagnetic particles.

    PubMed

    Biswal, Sibani Lisa; Gast, Alice P

    2003-08-01

    Magnetorheological particles, permanently linked into chains, provide a magnetically actuated means to manipulate microscopic fluid flow. Paramagnetic colloidal particles form reversible chains by acquiring dipole moments in the presence of an external magnetic field. By chemically connecting paramagnetic colloidal particles, flexible magnetoresponsive chains can be created. We link the paramagnetic microspheres using streptavidin-biotin binding. Streptavidin coated microspheres are placed in a flow cell and a magnetic field is applied, causing the particles to form chains. Then a solution of polymeric linkers of bis-biotin-poly(ethylene glycol) molecules is added in the presence of the field. These linked chains remain responsive to a magnetic field; however, in the absence of an external magnetic field these chains bend and flex due to thermal motion. The chain flexibility is determined by the length of the spacer molecule between particles and is quantified by the flexural rigidity or bending stiffness. To understand the mechanical properties of the chains, we use a variety of optical trapping experiments to measure the flexural rigidity. Increasing the length of the poly(ethylene glycol) chain in the linker increases the flexibility of the chains. PMID:14524968

  17. The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers

    PubMed Central

    Luo, Michelle L.; Jackson, Ryan N.; Denny, Steven R.; Tokmina-Lukaszewska, Monika; Maksimchuk, Kenneth R.; Lin, Wayne; Bothner, Brian; Wiedenheft, Blake; Beisel, Chase L.

    2016-01-01

    Bacteria and archaea acquire resistance to foreign genetic elements by integrating fragments of foreign DNA into CRISPR (clustered regularly interspaced short palindromic repeats) loci. In Escherichia coli, CRISPR-derived RNAs (crRNAs) assemble with Cas proteins into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade recognizes DNA targets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairing between the crRNA spacer and the DNA target. Previously determined structures of Cascade showed that the crRNA is stretched along an oligomeric protein assembly, leading us to ask how crRNA length impacts the assembly and function of this complex. We found that extending the spacer portion of the crRNA resulted in larger Cascade complexes with altered stoichiometry and preserved in vitro binding affinity for target DNA. Longer spacers also preserved the in vivo ability of Cascade to repress target gene expression and to recruit the Cas3 endonuclease for target degradation. Finally, longer spacers exhibited enhanced silencing at particular target locations and were sensitive to mismatches within the extended region. These findings demonstrate the flexibility of the Type I-E CRISPR machinery and suggest that spacer length can be modified to fine-tune Cascade activity. PMID:27174938

  18. Frequent N addition and clonal relatedness among immunoglobulin lambda light chains expressed in rheumatoid arthritis synovia and PBL, and the influence of V lambda gene segment utilization on CDR3 length.

    PubMed Central

    Bridges, S. L.

    1998-01-01

    BACKGROUND: In rheumatoid arthritis (RA), B-lineage cells in the synovial membrane secrete large amounts of immunoglobulin that contribute to tissue destruction. The CDR3 of an immunoglobulin light chain is formed by rearrangements of VL and JL gene segments. Addition of non-germline-encoded (N) nucleotides at V(D)J joins by the enzyme terminal deoxynucleotidyl transferase (TdT) enhances antibody diversity. TdT was previously thought to be active in B cells only during heavy chain rearrangement, but we and others reported unexpectedly high levels of N addition in kappa light chains. We also found clonally related kappa chains bearing unusually long CDR3 intervals in RA synovium, suggesting oligoclonal expansion of a set of atypical B lymphocytes. In this study, we analyzed lambda light chain expression to determine if N addition occurs throughout immunoglobulin gene rearrangement and to compare CDR3 lengths of lambda and kappa light chains in RA patients and normal individuals. MATERIALS AND METHODS: Reverse transcription-polymerase chain reaction (RT-PCR) amplification of V lambda III transcripts was performed on RA synovia and peripheral blood lymphocytes (PBL) and normal PBL for which kappa repertoires were previously analyzed. Representative lambda + PCR products were cloned and sequenced. RESULTS: Analysis of 161 cDNA clones revealed that N addition occurs in lambda light chains of RA patients and normal controls. The lambda light chain repertoires in RA were enriched for long CDR3 intervals. In both RA and controls, CDR3 lengths were strongly influenced by which V lambda gene segment was present in the rearrangement. Five sets of clonally related sequences were found in RA synovia and PBL; one set was found in normal PBL. CONCLUSIONS: In humans, unlike mice, N addition enhances antibody diversity at all stages of immunoglobulin assembly, and the structural diversity of lambda CDR3 intervals is greater than that of kappa light chains. Clonally related V lambda

  19. A preliminary trial using multi-target polymerase chain reaction (multiplex PCR) and restriction fragment length polymorphism (PCR-RFLP) on the same feedstuffs to detect tissues of animal origin.

    PubMed

    Colombo, F; Marchisio, E; Trezzi, I E; Peri, V; Pinotti, L; Baldi, A; Soncini, G

    2004-08-01

    A preliminary study using multi-target polymerase chain reaction (multiplex PCR) and restriction fragment length polymorphism (PCR-RFLP) was done on the same feedstuffs to detect animal tissues. The results of the two methods differ somewhat: PCR-RFLP did not detect any signal in any sample, but multiplex PCR detected a signal in one sample. These findings could be a basis for further investigations. PMID:15509020

  20. Structure-Antibacterial Activity Relationships of Imidazolium-Type Ionic Liquid Monomers, Poly(ionic liquids) and Poly(ionic liquid) Membranes: Effect of Alkyl Chain Length and Cations.

    PubMed

    Zheng, Zhiqiang; Xu, Qiming; Guo, Jiangna; Qin, Jing; Mao, Hailei; Wang, Bin; Yan, Feng

    2016-05-25

    The structure-antibacterial activity relationship between the small molecular compounds and polymers are still elusive. Here, imidazolium-type ionic liquid (IL) monomers and their corresponding poly(ionic liquids) (PILs) and poly(ionic liquid) membranes were synthesized. The effect of chemical structure, including carbon chain length of substitution at the N3 position and charge density of cations (mono- or bis-imidazolium) on the antimicrobial activities against both Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) was investigated by determination of minimum inhibitory concentration (MIC). The antibacterial activities of both ILs and PILs were improved with the increase of the alkyl chain length and higher charge density (bis-cations) of imidazolium cations. Moreover, PILs exhibited lower MIC values relative to the IL monomers. However, the antibacterial activities of PIL membranes showed no correlation to those of their analogous small molecule IL monomers and PILs, which increased with the charge density (bis-cations) while decreasing with the increase of alkyl chain length. The results indicated that antibacterial property studies on small molecules and homopolymers may not provide a solid basis for evaluating that in corresponding polymer membranes. PMID:27145107

  1. The ribosomal gene spacer region in archaebacteria

    NASA Technical Reports Server (NTRS)

    Achenbach-Richter, L.; Woese, C. R.

    1988-01-01

    Sequences for the spacer regions that separate the 16S and 23S ribosomal RNA genes have been determined for four more (strategically placed) archaebacteria. These confirm the general rule that methanogens and extreme halophiles have spacers that contain a single tRNAala gene, while tRNA genes are not found in the spacer region of the true extreme thermophiles. The present study also shows that the spacer regions from the sulfate reducing Archaeglobus and the extreme thermophile Thermococcus (both of which cluster phylogenetically with the methanogens and extreme halophiles) contain each a tRNAala gene. Thus, not only all methanogens and extreme halophiles show this characteristic, but all organisms on the "methanogen branch" of the archaebacterial tree appear to do so. The finding of a tRNA gene in the spacer region of the extreme thermophile Thermococcus celer is the first known phenotypic property that links this organism with its phylogenetic counterparts, the methanogens, rather than with its phenotypic counterparts, the sulfur-dependent extreme thermophiles.

  2. Primitive models of chemical association. III. Totally flexible sticky two-point model for multicomponent heteronuclear fixed-chain-length polymerization

    SciTech Connect

    Lin, C.; Kalyuzhnyi, Y.V. |; Stell, G.

    1998-04-01

    A multidensity integral-equation theory for polymerization into freely jointed hard-sphere homonuclear chain fluids proposed earlier [J. Chem. Phys. {bold 106}, 1940 (1997)] is extended to the case of multicomponent heteronuclear chain polymerization. The theory is based on the analytical solution of the polymer Percus{endash}Yevick (PPY) approximation for the totally flexible sticky two-point (S2P) model of associating fluids. The model consists of an n-component mixture of hard spheres of different sizes with species 2,{hor_ellipsis},n{minus}1 bearing two sticky sites A and B, randomly distributed on its surface, and species 1 and n with only one B and A site per particle, respectively. Due to some specific restrictions imposed on the possibility of forming bonds between particles of various species, the present version of the S2P model represents an associating fluid that is able to polymerize into a mixture of heteronuclear chain macromolecules. The structural properties of such a model are studied in the complete-association limit and compared with computer-simulation results for homonuclear hard-sphere chain mixtures, symmetrical diblock copolymers, alternating copolymers, and homonuclear hard-sphere chains in a hard-sphere solvent. Some results for the case of partial association are also presented. The PPY theory represents a quantitatively successful theory for the mixtures of short homonuclear chains and the short copolymer systems studied here. We also expect that the theory will prove to be of the same order of accuracy in investigating the case of partial association. {copyright} {ital 1998 American Institute of Physics.}

  3. Aggregation behavior of a gemini surfactant with a tripeptide spacer.

    PubMed

    Wang, Meina; Han, Yuchun; Qiao, Fulin; Wang, Yilin

    2015-02-28

    A peptide gemini surfactant, 12-G(NH2)LG(NH2)-12, has been constructed with two dodecyl chains separately attached to the two terminals of a glutamic acid-lysine-glutamic acid peptide and the aggregation behavior of the surfactant was studied in aqueous solution. The 12-G(NH2)LG(NH2)-12 molecules form fiber-like precipitates around pH 7.0, and the precipitation range is widened on increasing the concentration. At pHs 3.0 and 11.0, 12-G(NH2)LG(NH2)-12 forms soluble aggregates because each molecule carries two positively charged amino groups at the two ends of the peptide spacer at pH 3.0, while each molecule carries one negatively charged carboxyl group in the middle of the peptide spacer at pH 11.0. 12-G(NH2)LG(NH2)-12 displays a similar concentration-dependent process at these two pHs: forming small micelles above the critical micelle concentration and transferring to fibers at pH 3.0 or twisted ribbons at pH 11.0 above the second critical concentration. The fibers formed at pH 3.0 tend to aggregate into bundles with twisted structure. Both the twisted fibers at pH 3.0 and the twisted ribbons at pH 11.0 contain β-sheet structure formed by the peptide spacer. PMID:25588349

  4. Probing the effects of the ester functional group, alkyl side chain length and anions on the bulk nanostructure of ionic liquids: a computational study.

    PubMed

    Fakhraee, Mostafa; Gholami, Mohammad Reza

    2016-04-14

    The effects of ester addition on nanostructural properties of biodegradable ILs composed of 1-alkoxycarbonyl-3-alkyl-imidazolium cations ([C1COOCnC1im](+), n = 1, 2, 4) combined with [Br](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) were explored by using the molecular dynamics (MD) simulations and quantum theory of atoms in molecules (QTAIM) analysis at 400 K. Various thermodynamic properties of these ILs were extensively computed in our earlier work (Ind. Eng. Chem. Res., 2015, 54, 11678-11700). Nano-scale segregation analysis demonstrates the formation of a small spherical island-like hydrocarbon within the continuous ionic domain for ILs with short alkyl side chain ([C1COOC1C1im]), and a sponge-like nanostructure for the compound with long alkyl side chain ([C1COOC4C1im]). Ester-functionalized ILs with ethyl side chain ([C1COOC2C1im]) are the turning point between two different morphologies. Non-polar channels were observed for [C1COOC4C1im] ILs composed of smaller anions such as [Br] and [NO3], whereas clustering organization was found for the other anions. Formation of the spherical micelle-like nanostructure was seen for lengthened cations. Finally, the incorporation of an ester group into the alkyl side chain of the cation leads to stronger segregation between charged and uncharged networks, which consequently increased the possibility of self-assembly and micelle formation. PMID:27001746

  5. Conformation of the Poly(ethylene Glycol) Chains in DiPEGylated Hemoglobin Specifically Probed by SANS: Correlation with PEG Length and in Vivo Efficiency.

    PubMed

    Le Cœur, Clémence; Combet, Sophie; Carrot, Géraldine; Busch, Peter; Teixeira, José; Longeville, Stéphane

    2015-08-01

    Cell-free hemoglobin (Hb)-based oxygen carriers have long been proposed as blood substitutes but their clinical use remains tricky due to problems of inefficiency and/or toxicity. Conjugation of Hb with the biocompatible polymer poly(ethylene glycol) (PEG) greatly improved their performance. However, physiological data suggested a polymer molecular weight (Mw) threshold of about 10 kDa, beyond which the grafting of two PEG chains no longer improves efficiency and nontoxicity of diPEG/Hb conjugates. We used small-angle neutron scattering and contrast variation, which are the only techniques able to probe separately the conformation of PEG chains and Hb protein within the complex, to investigate the role of PEG chain conformation in diPEGylated Hb conjugates as a function of the polymer Mw. We found out that the structure of Hb tetramer is not modified by the polymer grafting. Similarly, with a constant grafting of two chains per protein, there is no significant change of the Gaussian conformation between free and grafted PEG below ∼10 kDa, the complex being well described by the "dumbbell" model. However, beyond that threshold, the radius of gyration of grafted PEG is significantly smaller than that of the free polymer, showing a compaction of the PEG chains, either in the "dumbbell" model or in the "shroud" one. In the latter model, the polymer may be wrapped on the surface of the protein spreading a protective "shielding" effect over a larger fraction of the protein. Both proposed models are in good agreement with the physiological data reported in the literature. PMID:26153251

  6. New titanium spacer for cervical laminoplasty: initial clinical experience. Technical note.

    PubMed

    Tani, Satoshi; Suetsua, Futoshi; Mizuno, Junichi; Uchikado, Hisaaki; Nagashima, Hiroyasu; Akiyama, Masahiko; Isoshima, Akira; Ohashi, Hiroki; Hirano, Yoshitaka; Abe, Toshiaki

    2010-01-01

    Many commercially available hydroxyapatite (HA) spacers for cervical laminoplasty have been introduced but have disadvantages such as lack of plasticity, easy cracking, and occasional difficulty in fixation by sutures. Here we present the short-term results of a newly designed titanium spacer (Laminoplasty Basket) in open-door cervical laminoplasty, and evaluated clinically and radiologically. The titanium box-shaped spacer with two arms for fixation was easily inserted and fixed into the laminoplasty space with 4-mm or 5-mm length screws after the posterior cervical arch was repositioned for the canal expansion. Twenty-one patients with cervical myelopathy due to spondylosis or ossification of the longitudinal ligament or developmental narrow canal observed for more than 6 months postoperatively were enrolled in this study. The neurological condition of these patients improved from 9.4 points on the Japanese Orthopaedic Association scale preoperatively to 13.5 points at 6 months after surgery. Postoperative radiological evaluation showed no laminar closure or implant failure and cervical spine curvature was maintained. These results seemed to have no significant difference compared with those using HA spacers. This titanium spacer is a potential substitute for conventional HA or other similar devices in cervical laminoplasty. PMID:21206196

  7. Identification of raw and heat-processed meats from game bird species by polymerase chain reaction-restriction fragment length polymorphism of the mitochondrial D-loop region.

    PubMed

    Rojas, M; González, I; Fajardo, V; Martín, I; Hernández, P E; García, T; Martín, R

    2009-03-01

    Polymerase chain reaction-RFLP analysis has been applied to the identification of meats from quail (Coturnix coturnix), pheasant (Phasianus colchicus), red-legged partridge (Alectoris rufa), chukar partridge (Alectoris chukar), guinea fowl (Numida meleagris), capercaillie (Tetrao urogallus), Eurasian woodcock (Scolopax rusticola), and woodpigeon (Columba palumbus). Polymerase chain reaction amplification was carried out using a set of primers flanking a conserved region of approximately 310 bp from the mitochondrial D-loop region. Restriction site analysis based on sequence data from this DNA fragment permitted the selection of HinfI, MboII, and Hpy188III 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. Consistent results were obtained with both raw and heat-processed meats. PMID:19211540

  8. The non-signaling extracellular spacer domain of chimeric antigen receptors is decisive for in vivo antitumor activity

    PubMed Central

    Hudecek, Michael; Sommermeyer, Daniel; Kosasih, Paula L.; Silva-Benedict, Anne; Liu, Lingfeng; Rader, Christoph; Jensen, Michael C.; Riddell, Stanley R.

    2015-01-01

    The use of synthetic chimeric antigen receptors (CAR) to redirect T cells to recognize tumor provides a powerful new approach to cancer immunotherapy; however the attributes of CARs that ensure optimal in vivo tumor recognition remain to be defined. Here, we analyze the influence of length and composition of IgG-derived extracellular spacer domains on the function of CARs. Our studies demonstrate that CD19-CARs with a long spacer from IgG4 hinge-CH2-CH3 are functional in vitro but lack antitumor activity in vivo due to interaction between the Fc domain within the spacer and the Fc receptor-bearing myeloid cells, leading to activation-induced T-cell death. We demonstrate that in vivo persistence and antitumor effects of CAR-T-cells with a long spacer can be restored by modifying distinct regions in the CH2 domain that are essential for Fc receptor binding. Our studies demonstrate that modifications that abrogate binding to Fc receptors are crucial for CARs in which a long spacer is obligatory for tumor recognition as shown here for a ROR1-specific CAR. These results demonstrate that the length and composition of the extracellular spacer domain that lacks intrinsic signaling function can be decisive in the design of CARs for optimal in vivo activity. PMID:25212991

  9. Adsorption of sterically stabilized latex particles at liquid surfaces: effects of steric stabilizer surface coverage, particle size, and chain length on particle wettability.

    PubMed

    Reed, K M; Borovicka, J; Horozov, T S; Paunov, V N; Thompson, K L; Walsh, A; Armes, S P

    2012-05-01

    A series of five near-monodisperse sterically stabilized polystyrene (PS) latexes were synthesized using three well-defined poly(glycerol monomethacrylate) (PGMA) macromonomers with mean degrees of polymerization (DP) of 30, 50, or 70. The surface coverage and grafting density of the PGMA chains on the particle surface were determined using XPS and (1)H NMR spectroscopy, respectively. The wettability of individual latex particles adsorbed at the air-water and n-dodecane-water interfaces was studied using both the gel trapping technique and the film calliper method. The particle equilibrium contact angle at both interfaces is relatively insensitive to the mean DP of the PGMA stabilizer chains. For a fixed stabilizer DP of 30, particle contact angles were only weakly dependent on the particle size. The results are consistent with a model of compact hydrated layers of PGMA stabilizer chains at the particle surface over a wide range of grafting densities. Our approach could be utilized for studying the adsorption behavior of a broader range of sterically stabilized inorganic and polymeric particles of practical importance. PMID:22502638

  10. Separator-spacer for electrochemical systems

    DOEpatents

    Grimes, Patrick G.; Einstein, Harry; Newby, Kenneth R.; Bellows, Richard J.

    1983-08-02

    An electrochemical cell construction features a novel co-extruded plastic electrode in an interleaved construction with a novel integral separator-spacer. Also featured is a leak and impact resistant construction for preventing the spill of corrosive materials in the event of rupture.

  11. Bioaffinity sensor based on nanoarchitectonic films: control of the specific adsorption of proteins through the dual role of an ethylene oxide spacer.

    PubMed

    Davila, Johanna; Toulemon, Delphine; Garnier, Tony; Garnier, Aurélie; Senger, Bernard; Voegel, Jean-Claude; Mésini, Philippe J; Schaaf, Pierre; Boulmedais, Fouzia; Jierry, Loïc

    2013-06-18

    The identification and quantification of biomarkers or proteins is a real challenge in allowing the early detection of diseases. The functionalization of the biosensor surface has to be properly designed to prevent nonspecific interactions and to detect the biomolecule of interest specifically. A multilayered nanoarchitecture, based on polyelectrolyte multilayers (PEM) and the sequential immobilization of streptavidin and a biotinylated antibody, was elaborated as a promising platform for the label-free sensing of targeted proteins. We choose ovalbumin as an example. Thanks to the versatility of PEM films, the platform was built on two types of sensor surface and was evaluated using both optical- and viscoelastic-based techniques, namely, optical waveguide lightmode spectroscopy and the quartz crystal microbalance, respectively. A library of biotinylated poly(acrylic acids) (PAAs) was synthesized by grafting biotin moieties at different grafting ratios (GR). The biotin moieties were linked to the PAA chains through ethylene oxide (EO) spacers of different lengths. The adsorption of the PAA-EOn-biotin (GR) layer on a PEM precursor film allows tuning the surface density in biotin and thus the streptavidin adsorption mainly through the grafting ratio. The nonspecific adsorption of serum was reduced and even suppressed depending on the length of the EO arms. We showed that to obtain an antifouling polyelectrolyte the grafting of EO9 or EO19 chains at 25% in GR is sufficient. Thus, the spacer has a dual role: ensuring the antifouling property and allowing the accessibility of biotin moieties. Finally, an optimized platform based on the PAA-EO9-biotin (25%)/streptavidin/biotinylated-antibody architecture was built and demonstrated promising performance as interface architecture for bioaffinity sensing of a targeted protein, in our case, ovalbumin. PMID:23346932

  12. A conformation and orientation model of the carboxylic group of fatty acids dependent on chain length in a Langmuir monolayer film studied by polarization-modulation infrared reflection absorption spectroscopy.

    PubMed

    Muro, Maiko; Itoh, Yuki; Hasegawa, Takeshi

    2010-09-01

    The conformation of the carboxylic group of fatty acids in a Langmuir (L) monolayer film on water is described in relation to the aggregation property of the hydrocarbon chain. Polarization-modulation infrared reflection absorption spectra (PM-IRRAS) of L films of heptadecanoic acid (C(17)), octadecanoic acid (C(18)), and nonadecanoic acid (C(19)) exhibit systematic spectral changes in both the C-H and C=O stretching vibration regions. Through a stabilization analysis of the L films at a high surface pressure, the C(19) L film has been found outstandingly stable exhibiting no film shrink, while the other two compounds exhibit a large shrink at high surface pressure. By taking into account the uniquely high aggregation property of the hydrocarbon chains of C(19), the three major bands arising from the C=O stretching vibration mode propose three types of molecular conformations about the carboxylic group, which are elucidated by a balance of the hydration of the carboxylic group, the chain length of the hydrocarbon chain, and the surface pressure. PMID:20718412

  13. PCR amplification of the 3' external transcribed and intergenic spacers of the ribosomal DNA repeat unit in three species of Saccharomyces.

    PubMed

    Molina, F I; Jong, S C; Huffman, J L

    1993-04-15

    Two spacer regions outside the ribosomal DNA (rDNA) transcriptional unit in three species of Saccharomyces, S. cerevisiae, S. carlsbergensis and S. pastorianus, were amplified using the polymerase chain reaction. These regions were composed of the 3' external transcribed spacer (ETS) and the intergenic spacer (IGS). Primers were developed from sequence alignments and by taking the reverse complement of a previously described sequence. The region amplified spanned base position 3110 on the 26S rRNA to base position 27 on the 5S rRNA of S. cerevisiae. Nine of the twelve strains used in this study exhibited different restriction profiles, showing that the spacers are highly variable between species. The results suggest that PCR fingerprinting of the non-coding spacer regions can be used to distinguish between closely related Saccharomyces species and may have potential in DNA profiling of other yeasts. PMID:8099889

  14. BIODEGRADABLE BRANCHED POLYCATIONIC POLYMERS WITH VARYING HYDROPHILIC SPACERS FOR NON-VIRAL GENE DELIVERY

    PubMed Central

    Chew, Sue Anne; Hacker, Michael C.; Saraf, Anita; Raphael, Robert M.; Kasper, F. Kurtis; Mikos, Antonios G.

    2009-01-01

    Biodegradable branched polycationic polymers with varying hydrophilic spacer lengths were synthesized from different triacrylate monomers and the amine monomer 1-(2-aminoethyl)piperazine by Michael addition polymerization. The hydrophilic spacers were varied by the number of ethyleneoxy groups in the triacrylate monomer (E/M) that ranged from 0 to 14. The polymer degradation depended on the spacer length and pH; the amount of ester degraded as determined by 1H-NMR after 14 days was 43.4 ± 2.1% (pH 5.0) and 89.7 ± 1.3% (pH 7.4) for the polymer with 0 E/M compared to 55.7 ± 2.6% (pH 5.0) and 98.5 ± 1.6% (pH 7.4) for the polymer with 14 E/M. Cell viability of rat fibroblasts after exposure to polymer solutions of concentrations up to 1000 μg/mL remained high (above 66.9 ± 12.1% compared to below 7.6 ± 1.1% for polyethylenimine at a concentration of 50 μg/mL or higher) and increased with the spacer length. The polyplexes made with all the synthesized polymers showed higher transfection efficiency (4.5 ± 1.7% to 9.4 ± 2.0%, dependent on the polymer/pDNA weight ratio) with an enhanced green fluorescent protein reporter gene compared to naked pDNA (0.8 ± 0.4%) as quantified by flow cytometry. This study demonstrates that hydrophilic spacers can be incorporated into polycationic polymers to reduce their cytotoxicity and enhance their degradability for non-viral gene delivery. PMID:19678696

  15. Inter-Ring and Hexyl Chain Torsional Potentials in Poly (3-HEXYLTHIOPHENE) Oligomers: Scaling with the Length of the Conjugted Polymer Backbone

    NASA Astrophysics Data System (ADS)

    Bhatta, Ram S.; Perry, David S.; Yimer, Yeneneh; Tsige, Mesfin

    2011-06-01

    Density functional theory calculations are presented for the equilibrium structures and torsional potentials for isolated Poly (3-Hexylthiophene) (P3HT) oligomers up to 12 monomer units (up to 302 atoms). Calculations were performed at B3LYP/6-31++G(d,p) treating both the backbone of thiophene rings and the hexyl chains explicitly. One-dimensional inter-ring torsional potentials were calculated by rotating backbone around the central inter-ring bond and hexyl torsional potentials were calculated rotating n-hexyl group adjacent to the central inter-ring bond for each oligomer. The torsional and electronic properties change significantly for oligomers with 2 to 8 units but reach asymptotic values for a 10 unit P3HT chain, thereby suggesting the 10 unit long oligomer as a molecular model for the extended polymer. For P3HT oligomers having 10 or more units, all the rings and the hexyl groups are approximately coplanar except for one hexyl group at head end. The principal interaction that promotes the coplanarity of the hexyl groups is the attraction of the proximal methylene hydrogens to the sulfur on the adjacent thiophene ring. The cis conformation of the backbone is about 2kT higher than the trans minimum at room temperature. The gauche conformation of the hexyl group is within about half kT of the planar minimum. Therefore conformational polymorphisms of both types will likely be significant in the heterogeneous environment of photovoltaic devices.

  16. Conserved-residue mutations in Wzy affect O-antigen polymerization and Wzz-mediated chain-length regulation in Pseudomonas aeruginosa PAO1

    NASA Astrophysics Data System (ADS)

    Islam, Salim T.; Huszczynski, Steven M.; Nugent, Timothy; Gold, Alexander C.; Lam, Joseph S.

    2013-12-01

    O antigen (O-Ag) in many bacteria is synthesized via the Wzx/Wzy-dependent pathway in which Wzy polymerizes lipid-linked O-Ag subunits to modal lengths regulated by Wzz. Characterization of 83 site-directed mutants of Wzy from Pseudomonas aeruginosa PAO1 (WzyPa) in topologically-mapped periplasmic (PL) and cytoplasmic loops (CL) verified the functional importance of PL3 and PL5, with the former shown to require overall cationic properties. Essential Arg residues in the RX10G motifs of PL3 and PL5 were found to be conserved in putative homologues of WzyPa, as was the overall sequence homology between these two periplasmic loops in each protein. Amino acid substitutions in CL6 were found to alter Wzz-mediated O-antigen modality, with evidence suggesting that these changes may perturb the C-terminal WzyPa tertiary structure. Together, these data suggest that the catch-and-release mechanism of O-Ag polymerization is widespread among bacteria and that regulation of polymer length is affected by interaction of Wzz with Wzy.

  17. Influence of the ester chain length on the mesogenic behavior and optical anisotropy of 4-[[4-(butoxy)phenyl]diazenyl]phenyl alkanoates

    NASA Astrophysics Data System (ADS)

    Niezgoda, Izabela; Szypszak, Ewelina; Dardas, Dorota; Galewski, Zbigniew

    2016-04-01

    In this manuscript, we report synthesis and physico-chemical characterization of 4-[[4-(butoxy)phenyl]diazenyl]phenyl alkanoates homologous series. For the first time, nineteen derivatives are described here. The enantiotropic nematic phase is typically observed among all members of this series. However, in the case of 4-[[4-(butoxy)phenyl]diazenyl]phenyl stearate, the nematic phase shows a monotropic character. In addition to liquid-crystalline polymorphism, a second crystalline form was observed in some homologs. Furthermore, using a photoelastic modulator, the optical anisotropy in the nematic phase was determined in the first nine compounds of this series. Temperature dependence of optical anisotropy at significantly lower values of reduced temperature is relatively weak. In contrast, optical anisotropy shows a strong temperature effect near isotropization. Moreover, the influence of the ester chain elongation on liquid crystalline and optical properties was established.

  18. Expression of poly-3-(R)-hydroxyalkanoate (PHA) polymerase and acyl-CoA-transacylase in plastids of transgenic potato leads to the synthesis of a hydrophobic polymer, presumably medium-chain-length PHAs.

    PubMed

    Romano, Andrea; van der Plas, Linus H W; Witholt, Bernard; Eggink, Gerrit; Mooibroek, Hans

    2005-01-01

    Medium-chain-length poly-3-(R)-hydroxyalkanoates (mcl-PHAs) belong to the group of microbial polyesters. The minimum gene-set for the accumulation of mcl-PHAs from de novo fatty acid biosynthesis has been identified in prokaryotes as consisting of the Pha-C1 polymerase and the ACP-CoA-transacylase. In this paper, the synthesis of mcl-PHAs has been attempted in transgenic potato (Solanum tuberosum L.) using the same set of genes that were introduced into potato by particle bombardment. Polymer contents of transgenic lines were analysed by gas chromatography and by a new simple method employing a size-exclusion filter column. The expression of the Pha-C1 polymerase and the ACP-CoA-transacylase in the plastids of transgenic potato led to the synthesis of a hydrophobic polymer composed of mcl-hydroxy-fatty acids with carbon chain lengths ranging from C-6 to C-12 in leaves of the selected transgenic lines. We strongly suggest that the polymer observed consists of mcl-PHAs and that this report establishes for the first time a possible route for the production of mcl-PHAs from de novo fatty acid biosynthesis in plants. PMID:15351883

  19. Tube support grid and spacer therefor

    DOEpatents

    Ringsmuth, Richard J.; Kaufman, Jay S.

    1986-01-01

    A tube support grid and spacers therefor provide radially inward preloading of heat exchange tubes to minimize stress upon base welds due to differential thermal expansion. The grid comprises a concentric series of rings and spacers with opposing concave sides for conforming to the tubes and V-shaped ends to provide resilient flexibility. The flexibility aids in assembly and in transmitting seismic vibrations from the tubes to a shroud. The tube support grid may be assembled in place to achieve the desired inwardly radial preloading of the heat exchange tubes. Tab and slot assembly further minimizes stresses in the system. The radii of the grid rings may be preselected to effect the desired radially inward preloading.

  20. Honeycomb spacer crush stength test results

    SciTech Connect

    Leader, D.R.

    1993-09-15

    This report discusses aluminum honeycomb spacers, which are used as an energy absorbent material in shipping packages for off site shipment of radioactive materials and which were ordered in two crush strengths, 1,000 psi and 2,000 psi for use in drop tests requested by the Packaging and Transportation group as part of the shipping container rectification process. Both the group as part of the shipping container rectification process. Both the vendor and the SRTC Materials Laboratory performed crush strength measurements on test samples made from the material used to fabricate the actual spacers. The measurements of crush strength made in the SRTC Materials Laboratory are within 100 psi of the measurements made by the manufacturer for all samples tested and all test measurements are within 10% of the specified crush strength, which is acceptable to the P&T group for the planned tests.

  1. Heterogeneous diversity of spacers within CRISPR

    NASA Astrophysics Data System (ADS)

    Deem, Michael; He, Jiankui

    2011-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of anti-viral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face. 1) J. He and M. W. Deem, Phys. Rev. Lett. 105 (2010) 128102

  2. Improved nuclear fuel assembly grid spacer

    DOEpatents

    Marshall, John; Kaplan, Samuel

    1977-01-01

    An improved fuel assembly grid spacer and method of retaining the basic fuel rod support elements in position within the fuel assembly containment channel. The improvement involves attachment of the grids to the hexagonal channel and of forming the basic fuel rod support element into a grid structure, which provides a design which is insensitive to potential channel distortion (ballooning) at high fluence levels. In addition the improved method eliminates problems associated with component fabrication and assembly.

  3. Selective Ni-P electroless plating on photopatterned cationic adsorption films influenced by alkyl chain lengths of polyelectrolyte adsorbates and additive surfactants.

    PubMed

    Nakagawa, Masaru; Nawa, Nozomi; Iyoda, Tomokazu

    2004-10-26

    We demonstrated that the photopatterned single-layer adsorption film of poly(1-dodecyl-4-pyridinium bromide) on a silica surface was available for a template of nickel-phosphorus (Ni-P) electroless plating through sensitization with a SnCl(2) aqueous solution and activation with a PdCl(2) aqueous solution. Four kinds of poly(1-alkyl-4-vinylpyridinium halide)s bearing methyl, propyl, hexyl, and dodecyl groups were prepared. The cationic polymers were adsorbed by a negatively charged silica surface from their solutions, to form single-layer adsorption films exhibiting desorption-resistance toward deionized water and ethanol. The organic adsorption films could be decomposed completely by exposure to 172 nm deep-UV light. The formation and decomposition of the single-layer films were confirmed by deep-UV absorption spectral measurement and zeta-potential measurement. Ni-P electroless plating was carried out on the photopatterned adsorption films, using three types of SnO(x) colloidal materials without and with cationic or anionic surfactant as catalyst precursors in the sensitization step. In the case of the negatively charged SnO(x) colloids surrounded by anionic surfactant, Ni-deposition took place preferentially on the cationic adsorption films remaining in unexposed regions. The Ni-deposition was accelerated significantly on the cationic adsorption film bearing dodecyl groups. It was obvious by ICP-AES analyses that the hydrophobic long-chain dodecyl groups in the adsorption film could promote the adsorption of the negative SnO(x) colloids on the film surface, followed by much nucleus formation of zerovalent Pd catalysts useful for the electroless plating. The result of our experiment clearly showed that, in addition to electrostatic interaction, van der Waals interaction generating between the hydrophobic long-chain hydrocarbons of the adsorption film and the surfactant improved significantly the adsorption stability of the SnO(x) colloids, resulting in highly

  4. Effect of Structure on Transport Properties (Viscosity, Ionic Conductivity, and Self-Diffusion Coefficient) of Aprotic Heterocyclic Anion (AHA) Room Temperature Ionic Liquids. 2. Variation of Alkyl Chain Length in the Phosphonium Cation.

    PubMed

    Sun, Liyuan; Morales-Collazo, Oscar; Xia, Han; Brennecke, Joan F

    2016-06-30

    A series of room-temperature ionic liquids (ILs) composed of triethyl(alkyl)phosphonium cations paired with three different aprotic heterocyclic anions (AHAs) (alkyl = butyl ([P2224](+)) and octyl ([P2228](+))) were prepared to investigate the effect of cationic alkyl chain length on transport properties. The transport properties and density of these ILs were measured from 283.15 to 343.15 K at ambient pressure. The dependence of the transport properties (viscosity, ionic conductivity, diffusivity, and molar conductivity) on temperature can be described by the Vogel-Fulcher-Tamman (VFT) equation. The ratio of the molar conductivity obtained from the molar concentration and ionic conductivity measurements to that calculated from self-diffusion coefficients (measured by pulsed gradient spin-echo nuclear magnetic resonance spectroscopy) using the Nernst-Einstein equation was used to quantify the ionicity of these ILs. The molar conductivity ratio decreases with increasing number of carbon atoms in the alkyl chain, indicating that the reduced Coulombic interactions resulting from lower density are more than balanced by the increased van der Waals interactions between the alkyl chains. The results of this study may provide insight into the design of ILs with enhanced dynamics that may be suitable as electrolytes in lithium ion batteries and other electrochemical applications. PMID:27243107

  5. Influence of the length and positioning of the antiestrogenic side chain of endoxifen and 4-hydroxytamoxifen on gene activation and growth of estrogen receptor positive cancer cells.

    PubMed

    Maximov, Philipp Y; Fernandes, Daphne J; McDaniel, Russell E; Myers, Cynthia B; Curpan, Ramona F; Jordan, V Craig

    2014-06-12

    Tamoxifen has biologically active metabolites: 4-hydroxytamoxifen (4OHT) and endoxifen. The E-isomers are not stable in solution as Z-isomerization occurs. We have synthesized fixed ring (FR) analogues of 4OHT and endoxifen as well as FR E and Z isomers with methoxy and ethoxy side chains. Pharmacologic properties were documented in the MCF-7 cell line, and prolactin synthesis was assessed in GH3 rat pituitary tumor cells. The FR Z-isomers of 4OHT and endoxifen were equivalent to 4OHT and endoxifen. Other test compounds used possessed partial estrogenic activity. The E-isomers of FR 4OHT and endoxifen had no estrogenic activity at therapeutic serum concentrations. None of the newly synthesized compounds were able to down-regulate ER levels. Molecular modeling demonstrated that some compounds would each create a best fit with a novel agonist conformation of the ER. The results demonstrate modulation by the ER complex of cell replication or gene transcription in cancer. PMID:24805199

  6. Giardia duodenalis in Damascus, Syria: Identification of Giardia genotypes in a sample of human fecal isolates using polymerase chain reaction and restriction fragment length polymorphism analyzing method.

    PubMed

    Skhal, Dania; Aboualchamat, Ghalia; Al Nahhas, Samar

    2016-02-01

    Giardia duodenalis is a common gastrointestinal parasite that infects humans and many other mammals. It is most prevalent in many developing and industrialized countries. G. duodenalis is considered to be a complex species. While no morphological distinction among different assemblages exist, it can be genetically differentiated into eight major assemblages: A to H. The aim of this study was to determine the genetic heterogeneity of G. duodenalis in human isolates (a study conducted for the first time in Syria). 40 fecal samples were collected from three different hospitals during the hot summer season of 2014. Extraction of genomic DNA from all Giardia positive samples (based on a microscopic examination) was performed using QIAamp DNA Stool Mini Kit. β-giardin gene was used to differentiate between different Giardia assemblages. The 514 bp fragment was amplified using the Polymerase Chain Reaction method, followed by digestion in HaeIII restriction enzyme. Our result showed that genotype A was more frequent than genotype B, 27/40 (67.5%); 4/40 (10%) respectively. A mixed genotype of A+B was only detected in 9 isolates (22.5%). This is the first molecular study performed on G. duodenalis isolates in Syria in order to discriminate among the different genotypes. Further expanded studies using more genes are needed to detect and identify the Giardia parasite at the level of assemblage and sub-assemblage. PMID:26524628

  7. Influence of the Length and Positioning of the Antiestrogenic Side Chain of Endoxifen and 4-Hydroxytamoxifen on Gene Activation and Growth of Estrogen Receptor Positive Cancer Cells

    PubMed Central

    2015-01-01

    Tamoxifen has biologically active metabolites: 4-hydroxytamoxifen (4OHT) and endoxifen. The E-isomers are not stable in solution as Z-isomerization occurs. We have synthesized fixed ring (FR) analogues of 4OHT and endoxifen as well as FR E and Z isomers with methoxy and ethoxy side chains. Pharmacologic properties were documented in the MCF-7 cell line, and prolactin synthesis was assessed in GH3 rat pituitary tumor cells. The FR Z-isomers of 4OHT and endoxifen were equivalent to 4OHT and endoxifen. Other test compounds used possessed partial estrogenic activity. The E-isomers of FR 4OHT and endoxifen had no estrogenic activity at therapeutic serum concentrations. None of the newly synthesized compounds were able to down-regulate ER levels. Molecular modeling demonstrated that some compounds would each create a best fit with a novel agonist conformation of the ER. The results demonstrate modulation by the ER complex of cell replication or gene transcription in cancer. PMID:24805199

  8. Radiological evaluation of acetabular erosion after antibiotic-impregnated polymethylmethacrylate spacer (Spacer-G).

    PubMed

    García-Oltra, Ester; Bori, Guillem; Tomas, Xavier; Gallart, Xavier; Garcia, Sebastian; Soriano, Alex

    2013-06-01

    Different types of hip spacers have been described (hand-made, custom-molded or prefabricated) for treatment of a chronic hip infection. A potential disadvantage of monoblock prefabricated spacer is that it may cause acetabular bone loss. This study assesses the radiological acetabular erosion using an antibiotic-impregnated pre-fabricated polymethylmethacrylate Spacer-G. We retrospectively reviewed the radiographs of thirty five patients who were managed with Spacer-G to treat chronic hip infection. No acetabular erosion were observed in thirty two patients with a mean time from the first to second stage and from the first to the last radiograph of 5.09 and 3.77 months respectively. In three patients the time between the radiographs was more than one year and the second stage was not performed; two developed a protrusion acetabuli whereas the other one a destruction of the acetabular roof. Using a Spacer-G in chronic hip infection treatment for less than one year is not associated with radiological acetabular erosion if the patient is maintained at partial weight bearing. PMID:23142448

  9. Genotypic characterization of Indian isolates of infectious bursal disease virus strains by reverse transcription-polymerase chain reaction combined with restriction fragment length polymorphism analysis.

    PubMed

    Priyadharsini, C V; Senthilkumar, T M A; Raja, P; Kumanan, K

    2016-03-01

    The reverse transcription PCR (RT-PCR) combined with restriction fragment length polymorphism (RFLP) is used for the differentiation of classical virulent (cv), virulent (v) and very virulent (vv) strains of infectious bursal disease virus (IBDV) isolates from chicken bursal tissues in southern states of India. In the present study, six different isolates (MB11, HY12, PY12, BGE14, VCN14 and NKL14) of IBDV strains were subjected for genotyping along with vaccine virus (Georgia, intermediate strain) using RT-PCR for amplification of a 743 bp sequence in the hypervariable region of VP2 gene followed by restriction enzyme digestion with 5 different restriction enzymes (BspMI, SacI, HhaI, StuI and SspI). The RT-PCR products obtained from vvIBDV strains were digested by SspI enzyme except PY12, BGE14 and MB11 isolates. The SacI digested the isolate MB11, PY12 and the vaccine strain, but it did not cleave the very virulent isolates of IBDV. HhaI cleaved all the isolates with different restriction profile patterns. StuI digested all the vvIBDV isolates and BspMI was not able to differentiate field isolates from vaccine strain. Though RT-PCR combined with RFLP is a genotypic method, further confirmation of serotypes to distinguish the vvIBDV from cvIBDV has to be carried out using pathogenicity studies. PMID:26982465

  10. Engineering a Disulfide Bond in the Lid Hinge Region of Rhizopus chinensis Lipase: Increased Thermostability and Altered Acyl Chain Length Specificity

    PubMed Central

    Yu, Xiao-Wei; Tan, Nian-Jiang; Xiao, Rong; Xu, Yan

    2012-01-01

    The key to enzyme function is the maintenance of an appropriate balance between molecular stability and structural flexibility. The lid domain which is very important for “interfacial activation” is the most flexible part in the lipase structure. In this work, rational design was applied to explore the relationship between lid rigidity and lipase activity by introducing a disulfide bond in the hinge region of the lid, in the hope of improving the thermostability of R. chinensis lipase through stabilization of the lid domain without interfering with its catalytic performance. A disulfide bridge between F95C and F214C was introduced into the lipase from R. chinensis in the hinge region of the lid according to the prediction of the “Disulfide by Design” algorithm. The disulfide variant showed substantially improved thermostability with an eleven-fold increase in the t1/2 value at 60°C and a 7°C increase of Tm compared with the parent enzyme, probably contributed by the stabilization of the geometric structure of the lid region. The additional disulfide bond did not interfere with the catalytic rate (kcat) and the catalytic efficiency towards the short-chain fatty acid substrate, however, the catalytic efficiency of the disulfide variant towards pNPP decreased by 1.5-fold probably due to the block of the hydrophobic substrate channel by the disulfide bond. Furthermore, in the synthesis of fatty acid methyl esters, the maximum conversion rate by RCLCYS reached 95% which was 9% higher than that by RCL. This is the first report on improving the thermostability of the lipase from R. chinensis by introduction of a disulfide bond in the lid hinge region without compromising the catalytic rate. PMID:23056295

  11. Characterization of infectious laryngotracheitis virus isolates from the US by polymerase chain reaction and restriction fragment length polymorphism of multiple genome regions.

    PubMed

    Oldoni, Ivomar; García, Maricarmen

    2007-04-01

    Infectious laryngotracheitis (ILT) is an acute viral respiratory disease, primarily of chickens. Economic losses attributable to ILT affect many poultry-producing areas throughout the United States (US) and the world. Despite efforts to control the disease by vaccination, prolonged epidemics of ILT remain a threat to the poultry industry. Earlier epidemiological and molecular evidence indicated that outbreaks in the US are caused by vaccine-related strains. In this study, polymerase chain reaction and restriction fragment polymorphism (PCR-RFLP) of four genome regions was utilized to characterize 25 isolates from commercial poultry and backyard flocks from the US. Combinations of PCR-RFLP patterns classified the ILT virus isolates into nine groups. Backyard flock isolates were categorized in three separate groups. The ILT virus US Department of Agriculture (USDA) reference strain and the tissue culture origin (TCO) vaccine strain were categorized into two separate groups. Twenty-two isolates from commercial poultry were categorized into four groups: one group, of six isolates, showed patterns identical to the chicken embryo origin (CEO) vaccines; a second group, of nine isolates, differed in only one pattern from the CEO vaccines; a third group, of two isolates, differed in only one pattern from the TCO vaccine; a fourth group, of five isolates, differed in six and nine patterns from the CEO and TCO vaccines, respectively. Results obtained from this study clearly demonstrated that most of the commercial poultry isolates (17 of 22 isolates) were closely related to the vaccine strains. However, isolates different to the vaccine strains were also identified in commercial poultry. PMID:17479379

  12. Molecular Analysis of Fungal Populations in Patients with Oral Candidiasis Using Internal Transcribed Spacer Region

    PubMed Central

    Ieda, Shinsuke; Moriyama, Masafumi; Takashita, Toru; Maehara, Takashi; Imabayashi, Yumi; Shinozaki, Shoichi; Tanaka, Akihiko; Hayashida, Jun-Nosuke; Furukawa, Sachiko; Ohta, Miho; Yamashita, Yoshihisa; Nakamura, Seiji

    2014-01-01

    Oral candidiasis is closely associated with changes in the oral fungal flora and is caused primarily by Candida albicans. Conventional methods of fungal culture are time-consuming and not always conclusive. However, molecular genetic analysis of internal transcribed spacer (ITS) regions of fungal rRNA is rapid, reproducible and simple to perform. In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions. Fifty-two patients with pseudomembranous oral candidiasis (POC) and 30 healthy controls were included in the study. Fungal DNA from oral rinse was examined for fungal species diversity by LH-PCR. Fungal populations were quantified by real-time PCR and previously-unidentified signals were confirmed by nucleotide sequencing. Relationships between the oral fungal flora and treatment-resistant factors were also examined. POC patients showed significantly more fungal species and a greater density of fungi than control individuals. Sixteen fungi were newly identified. The fungal populations from both groups were composed predominantly of C. albicans, though the ratio of C. dubliniensis was significantly higher in POC patients than in controls. The diversity and density of fungi were significantly reduced after treatment. Furthermore, fungal diversity and the proportion of C. dubliniensis were positively correlated with treatment duration. These results suggest that C. dubliniensis and high fungal flora diversity might be involved in the pathogenesis of oral candidiasis. We therefore conclude that LH-PCR is a useful technique for diagnosing and assessing the severity of oral candidal infection. PMID:24979710

  13. Genetic polymorphism of toll-like receptors 4 gene by polymerase chain reaction-restriction fragment length polymorphisms, polymerase chain reaction-single-strand conformational polymorphism to correlate with mastitic cows

    PubMed Central

    Gupta, Pooja H.; Patel, Nirmal A.; Rank, D. N.; Joshi, C. G.

    2015-01-01

    Aim: An attempt has been made to study the toll-like receptors 4 (TLR4) gene polymorphism from cattle DNA to correlate with mastitis cows. Materials and Methods: In present investigation, two fragments of TLR4 gene named T4CRBR1 and T4CRBR2 of a 316 bp and 382 bp were amplified by polymerase chain reaction (PCR), respectively from Kankrej (22) and Triple cross (24) cattle. The genetic polymorphisms in the two populations were detected by a single-strand conformational polymorphism in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one. Results: Results showed that both alleles (A and B) of two loci were found in all the two populations and the value of polymorphism information content indicated that these were highly polymorphic. Statistical results of χ2 test indicated that two polymorphism sites in the two populations fit with Hardy–Weinberg equilibrium (p<0.05). Meanwhile, the effect of polymorphism of TLR4 gene on the somatic cell score (SCS) indicated the cattle with allele a in T4CRBR1 showed lower SCS than that of allele B (p<0.05). Thus, the allele A might play an important role in mastitis resistance in cows. Conclusion: The relationship between the bovine mastitis trait and the polymorphism of TLR4 gene indicated that the bovine TLR4 gene may play an important role in mastitis resistance. PMID:27047144

  14. Isolation of Coxiella burnetii by a centrifugation shell-vial assay from ticks collected in Cyprus: detection by nested polymerase chain reaction (PCR) and by PCR-restriction fragment length polymorphism analyses.

    PubMed

    Spyridaki, Ioanna; Psaroulaki, Anna; Loukaides, Fidias; Antoniou, Maria; Hadjichristodolou, Christos; Tselentis, Yannis

    2002-01-01

    Ticks are the principal vectors and reservoirs of Coxiella burnetii. The identification of isolates is necessary for understanding the clinical diversity of Q fever in different geographic areas. This is the first report of isolation of C. burnetii from ticks by the shell-vial assay and by nested polymerase chain reaction (PCR) assay for the detection of this pathogen in ticks. Of 141 ticks collected in Cyprus (Rhipicephalus sanguineus and Hyalloma spp.), 10% were found to be infected with C. burnetii. Three ticks were positive by hemolymph test, and 11 triturated ticks were positive by nested PCR. Three isolates were obtained by the centrifugation shell-vial technique. Analysis by PCR, then restriction fragment length polymorphism showed that the 3 Cyprus isolates had identical restriction profiles to reference strains Nine Mile and Q212. The methods described are useful in studying the epidemiology and ecology of C. burnetii. PMID:12135275

  15. Diversity and Inheritance of Intergenic Spacer Sequences of 45S Ribosomal DNA among Accessions of Brassica oleracea L. var. capitata

    PubMed Central

    Yang, Kiwoung; Robin, Arif Hasan Khan; Yi, Go-Eun; Lee, Jonghoon; Chung, Mi-Young; Yang, Tae-Jin; Nou, Ill-Sup

    2015-01-01

    Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were quite similar in length. The 45S IGSs were found to follow Mendelian inheritance in a population of 15 F1s and their 30 inbred parental lines, which suggests that these sequences could be useful for development of new breeding tools. In addition, this study represents the first report of intra-specific (within subspecies) variation of the 45S IGS in B. oleracea. PMID:26633391

  16. NEUTRONIC REACTOR SHIELD AND SPACER CONSTRUCTION

    DOEpatents

    Wigner, E.P.; Ohlinger, L.A.

    1958-11-18

    Reactors of the heterogeneous, graphite moderated, fluid cooled type and shielding and spacing plugs for the coolant channels thereof are reported. In this design, the coolant passages extend horizontally through the moderator structure, accommodating the fuel elements in abutting end-to-end relationship, and have access openings through the outer shield at one face of the reactor to facilitate loading of the fuel elements. In the outer ends of the channels which extend through the shields are provided spacers and shielding plugs designed to offer minimal reslstance to coolant fluid flow while preventing emanation of harmful radiation through the access openings when closed between loadings.

  17. Structure and NIR-luminescence of ytterbium(III) beta-diketonate complexes with 5-nitro-1,10-phenanthroline ancillary ligand: assessment of chain length and fluorination impact.

    PubMed

    Martín-Ramos, Pablo; Pereira da Silva, Pedro S; Lavín, Victor; Martín, Inocencio R; Lahoz, Fernando; Chamorro-Posada, Pedro; Silva, Manuela Ramos; Martín-Gil, Jesús

    2013-10-01

    Seven new tris(β-diketonear-nate)ytterbium(III) complexes with the general formula [Yb(β-diketonate)3(5NO2phen)] (where the β-diketone is either 4,4,4-trifluoro-1-(2-naphthyl)-1,3-butanedione, 4,4,4-trifluoro-1-(2-furyl)-1,3-butanedione, 1,1,1-trifluoro-2,4-pentanedione, 1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedione, 1,1,1,5,5,6,6,7,7,7-decafluoro-2,4-heptanedione, 2,4-hexanedione or 2,6-dimethyl-3,5-heptanedione, and 5NO2phen = 5-nitro-1,10-phenanthroline) were synthesized and characterized by elemental analysis, attenuated total reflectance Fourier transform infrared spectroscopy and photoluminescence spectroscopy. Single crystal X-ray structures have been determined for three fluorinated complexes and ground state geometries of the other four complexes have been predicted using the Sparkle/PM6 model. These experimental structures and those designed by semi-empirical models reveal octacoordination around the Yb(3+) ion. Photoluminescence studies and lifetime measurements show that the increase in the fluorinated β-diketonate chain length is associated with a decrease in Yb(3+) luminescence intensity of the (2)F5/2→(2)F7/2 transition at around 980 nm and the (2)F5/2 excited state lifetime, while the ligand lifetime value remains almost unaffected. Finally, fluorination of the ligands is only advised when the complexes are to be used for co-doping with isostructural Er(3+) complexes for optical amplifiers, since it leads to a slight decrease in luminescence intensity for the same β-diketonate chain length. PMID:23900403

  18. Effect of alkyl chain length on the interfacial strength of surgical sealants composed of hydrophobically-modified Alaska-pollock-derived gelatins and poly(ethylene)glycol-based four-armed crosslinker.

    PubMed

    Mizuta, Ryo; Ito, Temmei; Taguchi, Tetsushi

    2016-10-01

    Surgical sealants are widely used clinically. Fibrin sealant is a commonly used sealant, but is ineffective under wet conditions during surgery. In this study, we developed surgical sealants composed of hydrophobically modified Alaska-pollock-derived gelatins (hm-ApGltns) with different alkyl chain lengths from C3 to C18 and a poly(ethylene)glycol-based 4-armed crosslinker (4S-PEG). The burst strength of the hm-ApGltns-based sealant was evaluated using a fresh porcine blood vessel and was found to increase with increasing alkyl chain length from 167±22 to 299±43mmHg when the substitution ratio of amino groups of ApGltn was around 10mol%. The maximum burst strength was observed when stearoyl-group modified ApGltn (Ste-ApGltn)/4S-PEG-based sealant was used, displaying 3-fold higher burst strength than the original ApGltn (Org-ApGltn)/4S-PEG sealant, and 10-fold higher than the commercial fibrin sealant. Ste-ApGltn/4S-PEG-based sealant was biodegraded in rat subcutaneous tissue within 8 weeks without severe inflammation. By molecular interaction analysis using surface plasmon resonance, the binding constant of Ste-ApGltn to fibronectin was found to be 9-fold higher than that of Org-ApGltn. Therefore, the developed sealant, in particular the Ste-ApGltn/4S-PEG-based sealant, has potential applications in the field of cardiovascular surgery as well as thoracic surgery. PMID:27341135

  19. Exploring the effect of chain length of bridging ligands in cobalt(II) coordination polymers based on flexible bis(5,6-dimethylbenzimidazole) ligands: Synthesis, crystal structures, fluorescence and catalytic properties

    NASA Astrophysics Data System (ADS)

    Qin, Li; Li, Yue-Hua; Ma, Pei-Juan; Cui, Guang-Hua

    2013-11-01

    Two Co(II) coordination polymers derived from a dicarboxylate and two flexible bis(5,6-dimethylbenzimidazole) ligands with varying chain lengths equipped, namely [Co(bdmbmm)(nip)]n (1) and [Co2(bdmbmb)2(nip)2ṡH2O]n (2) (bdmbmm = 1,1'-bis(5,6-dimethylbenzimidazole)methane, H2nip = 5-nitroisophthalic acid, bdmbmb = 1,4-bis(5,6-dimethylbenzimidazole)butane), have been synthesized by hydrothermal methods and characterized by elemental analyses, IR spectra, thermogravimetric analysis (TGA), X-ray powder diffraction (XRPD) and single-crystal X-ray diffraction. Complex 1 forms a 1D looped-like chain consisting of two kinds of macrocycles, which is further arranged into a 2D supramolecular layer through face-to-face π-π stacking interactions; whereas complex 2 exhibits a 3D framework with a twofold interpenetrating diamondoid topology. The fluorescence and catalytic properties of the complexes for the degradation of methyl orange by sodium persulfate have been investigated.

  20. Chain formation and chain dynamics in a dilute magnetorheological fluid.

    PubMed

    Hagenbüchle, M; Liu, J

    1997-10-20

    Magnetorheological fluids are suspensions of magnetizable particles that reversibly change from liquid to solid when subjected to a magnetic field. A field-induced structure of dipolar chains is responsible for these changes. Our work aimed at understanding chain dynamics and the kinetics of chain formation by using dynamic light scattering. Chain length is determined by measurement of the diffusion coefficient. Chain-length growth shows a Smoluchowski behavior. PMID:18264283

  1. Current-perpendicular-to-the-plane giant magnetoresistance in spin-valves with AgSn alloy spacers

    SciTech Connect

    Read, J. C.; Nakatani, T. M.; Smith, Neil; Choi, Y.-S.; York, B. R.; Brinkman, E.; Childress, J. R.

    2015-07-28

    We investigate the use of AgSn alloys as the spacer layer in current-perpendicular-to-the-plane magnetoresistance devices. Alloying with Sn increases resistivity but results in a reasonably long (>10 nm) spin-diffusion length, so large magnetoresistance can be achieved with thin AgSn spacers. Compared to Ag thin films, AgSn forms smaller grain sizes, reduced roughness, and exhibits less interdiffusion upon annealing, resulting in decreased interlayer magnetic coupling in exchange biased spin-valves. AgSn also shows improved corrosion resistance compared to Ag, which is advantageous for nanofabrication, including magnetic recording head sensors. Combining a AgSn spacer with Co-based Heusler alloy ferromagnet in an exchange biased, polycrystalline trilayer thinner than 12 nm results in magnetoresistance values up to 15% at room temperature.

  2. Current-perpendicular-to-the-plane giant magnetoresistance in spin-valves with AgSn alloy spacers

    NASA Astrophysics Data System (ADS)

    Read, J. C.; Nakatani, T. M.; Smith, Neil; Choi, Y.-S.; York, B. R.; Brinkman, E.; Childress, J. R.

    2015-07-01

    We investigate the use of AgSn alloys as the spacer layer in current-perpendicular-to-the-plane magnetoresistance devices. Alloying with Sn increases resistivity but results in a reasonably long (>10 nm) spin-diffusion length, so large magnetoresistance can be achieved with thin AgSn spacers. Compared to Ag thin films, AgSn forms smaller grain sizes, reduced roughness, and exhibits less interdiffusion upon annealing, resulting in decreased interlayer magnetic coupling in exchange biased spin-valves. AgSn also shows improved corrosion resistance compared to Ag, which is advantageous for nanofabrication, including magnetic recording head sensors. Combining a AgSn spacer with Co-based Heusler alloy ferromagnet in an exchange biased, polycrystalline trilayer thinner than 12 nm results in magnetoresistance values up to 15% at room temperature.

  3. An embedded nonvolatile memory cell with spacer floating gate for power management integrated circuit applications

    NASA Astrophysics Data System (ADS)

    Na, Kee-Yeol; Baek, Ki-Ju; Lee, Gun-Woong; Kim, Yeong-Seuk

    2013-08-01

    This paper describes a simple nonvolatile memory cell with a poly-Si spacer floating gate for power management integrated circuit applications. The proposed memory cell is fabricated using a 0.35 μm double-poly high-voltage CMOS process which includes PIP capacitor, LV (5 V), and HV (20 V) CMOS devices. The floating gates of the proposed cell are buried under a LDD spacer oxide; thus the unit cell can be scaled easily in the channel length direction. In addition, any extra photo masking step is not required for the proposed cell in the applied fabrication process. The proposed cell shows an acceptable threshold voltage window of up to 104 cycles and less than 2% threshold voltage shifts in an 85 °C retention test.

  4. Exchange of Spacer Regions between Rrna Operons in Escherichia Coli

    PubMed Central

    Harvey, S.; Hill, C. W.

    1990-01-01

    The Escherichia coli rRNA operons each have one of two types of spacer separating the 16S and 23S coding regions. The spacers of four operons encode tRNA(Glu2) and the other three encode both tRNA(Ile) and tRNA(Ala 1 B). We have prepared a series of mutants in which the spacer region of a particular rrn operon has been replaced by the opposite type. Included among these were a mutant retaining only a single copy of the tRNA(Glu2) spacer (at rrnG) and another retaining only a single copy of the tRNA(Ile)-tRNA(Ala 1 B) spacer (at rrnA). While both mutants grew more slowly than controls, the mutant deficient in tRNA(Glu2) spacers was more severely affected. At a frequency of 6 X 10(-5), these mutants phenotypically reverted to faster growing types by increasing the copy number of the deficient spacer. In most of these phenotypic revertants, the deficient spacer type appeared in a rrn operon which previously contained the surplus type, bringing the ratio of spacer types closer to normal. In a few cases, these spacer changes were accompanied by an inversion of the chromosomal material between the donor and recipient rrn operons. Two examples of inversion of one-half of the E. coli chromosome between rrnG and rrnH were observed. The correlation of spacer change with inversion indicated that, in these particular cases, the change was due to an intrachromatid gene conversion event accompanied by a reciprocal crossover rather than reciprocal exchange between sister chromatids. PMID:2168847

  5. The Relationship of Pretilt Angle and Chemical Structure of Rubbed Organo-Soluble Side-Chain Polyimides

    NASA Astrophysics Data System (ADS)

    Mann, Ian K.; Bai, F.; Bai, Z.; Ge, J.; Sun, L.; Wang, H.; Zhang, Z.; Harris, Frank W.; Cheng, Stephen Z. D.

    2000-03-01

    This work is concerned with the relationship between the properties of the pretilt angles and chemical structure of the alignment layer for a series of novel organo-soluble side-chain polyimides developed at The University of Akron. The polyimides were spin cast on ITO glass substrates and mechanically rubbed with a velvet cloth. Liquid crystal display cells were constructed with an anti-parallel geometry using 10μm glass spacers and filled with the nematic liquid crystal mixture E7. The pretilt angle, which is defined as the angle between the liquid crystal director and the substrate, was measured using the magnetic null method. Various side-chain polyimide films were prepared and pretilt angles were determined employing identical processing conditions. In general, polyimides containing long flexible aliphatic side-chains (no. carbons >12) resulted in high pretilt angles (>20^o) however over time the pretilt shifted to a homeotropic alignment (i.e. 90^o to the substrate). The stability of the pretilt angles was improved when polyimide copolymers were used. Further enhancement of the stability was achieved by crosslinking the system prior to rubbing. Liquid crystal like side-chains (cyanobiphenol and biphenol based) resulted in stable pretilt angles ranging from 20 to 40^o for a spacer length of six carbons. Several surface techniques were used to study the effect of rubbing, including; atomic force microscopy, surfaced enhanced Raman scattering, and contact angle.

  6. Improvement of inhaler efficacy by home-made spacer.

    PubMed

    Sritara, P; Janvitayanuchit, S

    1993-12-01

    The delivery of aerosol from a metered dose inhaler (MDI) was reported to be more efficient with a spacer. Hence, a home-made spacer modified from a 950 ml low cost plastic bottle, was compared with a MDI and with a 750 ml imported spacer (Nebuhaler). On three consecutive days, at the same time of day, 20 adult patients with chronic asthma inhaled two puffs of terbutaline sulphate (0.5 mg), delivered from MDI alone, MDI with a 750 ml Nebuhlaer and MDI with a home-made spacer. The following measurements were made: forced expiratory volume in one second (FEV1), forced vital capacity (FVC) and pulse rate. These measurements were carried out immediately before and at 5, 20, 60 min after inhalation of terbutaline. FEV1 was significantly increased (P < 0.05) at 5, 20 and 60 min after administration of terbutaline with MDI via either spacers than with MDI alone but no significant difference was observed between Nebuhaler and the home-made spacer. FVC and pulse rate showed no significant change with each method of administration. In conclusion, terbutaline delivered by MDI and home-made spacer was more effective in bronchodilatation than by MDI alone and was just as effective as MDI and Nebuhaler. The home-made spacer therefore offers a simple, inexpensive and more effective method for delivering aerosol drug. PMID:7798822

  7. Orthognathic model surgery with LEGO key-spacer.

    PubMed

    Tsang, Alfred Chee-Ching; Lee, Alfred Siu Hong; Li, Wai Keung

    2013-12-01

    A new technique of model surgery using LEGO plates as key-spacers is described. This technique requires less time to set up compared with the conventional plaster model method. It also retains the preoperative setup with the same set of models. Movement of the segments can be measured and examined in detail with LEGO key-spacers. PMID:24045189

  8. Molecular recordings by directed CRISPR spacer acquisition.

    PubMed

    Shipman, Seth L; Nivala, Jeff; Macklis, Jeffrey D; Church, George M

    2016-07-29

    The ability to write a stable record of identified molecular events into a specific genomic locus would enable the examination of long cellular histories and have many applications, ranging from developmental biology to synthetic devices. We show that the type I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas system of Escherichia coli can mediate acquisition of defined pieces of synthetic DNA. We harnessed this feature to generate records of specific DNA sequences into a population of bacterial genomes. We then applied directed evolution so as to alter the recognition of a protospacer adjacent motif by the Cas1-Cas2 complex, which enabled recording in two modes simultaneously. We used this system to reveal aspects of spacer acquisition, fundamental to the CRISPR-Cas adaptation process. These results lay the foundations of a multimodal intracellular recording device. PMID:27284167

  9. Novel extracellular medium-chain-length polyhydroxyalkanoate depolymerase from Streptomyces exfoliatus K10 DSMZ 41693: a promising biocatalyst for the efficient degradation of natural and functionalized mcl-PHAs.

    PubMed

    Martínez, Virginia; de Santos, Patricia Gómez; García-Hidalgo, Javier; Hormigo, Daniel; Prieto, M Auxiliadora; Arroyo, Miguel; de la Mata, Isabel

    2015-11-01

    Cloning and biochemical characterization of a novel extracellular medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase from Streptomyces exfoliatus K10 DSMZ 41693 are described. The primary structure of the depolymerase (PhaZSex2) includes the lipase consensus sequence (serine-histidine-aspartic acid) which is known for serine hydrolases. Secondary structure analysis shows 7.9 % α-helix, 43.9 % β-sheet, 19.4 % β-turns, and 31.2 % random coil, suggesting that this enzyme belongs to the α/β hydrolase fold family, in agreement with other PHA depolymerases and lipases. The enzyme was efficiently produced as an extracellular active form in Rhodococcus and purified by two consecutive hydrophobic chromatographic steps. Matrix-assisted laser desorption-time-of-flight (MALDI-TOF) analysis of the purified enzyme revealed a monomer of 27.6 kDa with a midpoint transition temperature of 44.2 °C. Remarkably, the activity is significantly enhanced by low concentrations of nonionic and anionic detergents and thermal stability is improved by the presence of 10 % glycerol. PhaZSex2 is an endo-exohydrolase that cleaves both large and small PHA molecules, producing (R)-3-hydroxyoctanoic acid monomers as the main reaction product. Markedly, PhaZSex2 is able to degrade functionalized polymers containing thioester groups in the side chain (PHACOS), releasing functional thioester-based monomers and oligomers demonstrating the potentiality of this novel biocatalyst for the industrial production of enantiopure (R)-3-hydroxyalkanoic acids. PMID:26156240

  10. Detection and quantification of schistosome DNA in freshwater snails using either fluorescent probes in real-time PCR or oligochromatographic dipstick assays targeting the ribosomal intergenic spacer.

    PubMed

    Kane, Richard A; Stothard, J Russell; Rollinson, David; Leclipteux, Thierry; Evraerts, Jonathan; Standley, Claire J; Allan, Fiona; Betson, Martha; Kaba, Rehana; Mertens, Pascal; Laurent, Thierry

    2013-11-01

    Several DNA probes were designed for use in real-time polymerase chain reaction (PCR) assays to target sequence variation within the ribosomal intergenic spacer (IGS) of schistosomes. A sub-section of the IGS (∼300bp) was amplified, with cross-specific primers, after which group-specific fluorescent, locked nucleic acid probes were assessed for their ability to differentiate and quantify DNA from Schistosoma haematobium and Schistosoma mansoni group parasites. A number of fluorescent probe candidates were screened and validated against genomic DNA from adult schistosome worms and laboratory infected freshwater snails. Two fluorescent, locked nucleic acid probes ShaemLNA5 and SmanLNA2, of 20-26bp in length, were identified and found to be effective in providing evidence of infection in field-collected snails. To adapt these real-time PCR assays for more resource-poor laboratory settings, a PCR-restriction fragment length polymorphism (RFLP) assay was developed and primer/probe combinations were modified for use in oligochromatography, a DNA 'dipstick' technology. An appropriate dipstick was developed, inclusive of internal amplification and amplicon migration controls that could be of particular importance for assessing schistosome transmission dynamics. These assays and tools also have future potential for use in detection of schistosome infections in humans and livestock. PMID:22100540

  11. Preclinical investigations towards the first spacer gel application in prostate cancer treatment during particle therapy at HIT

    PubMed Central

    2013-01-01

    Background The application of spacer gel represents a promising approach to reliably spare the rectal frontal wall during particle therapy (IJROBP 76:1251-1258, 2010). In order to qualify the spacer gel for the clinical use in particle therapy, a variety of measurements were performed in order to ensure the biological compatibility of the gel, its physical stability during and after the irradiation, and a proper definition of the gel in terms of the Hounsfield Unit (HU) values for the treatment planning system. The potential for the use of the spacer gel for particle therapy monitoring with off-line Positron Emission Tomography (PET) was also investigated. Results The spacer gel implanted to the prostate patient in direct neighbourhood to the clinical target volume does not interfere with the particle therapy treatment planning procedure applied at Heidelberg Ion Beam Therapy Centre (HIT). The performed measurements show that Bragg-peak position of the particles can be properly predicted on the basis of computed tomography imaging with the treatment planning system used at HIT (measured water equivalent path length of 1.011 ±0.011 (2σ), measured Hounsfield Unit of 28.9 ±6.1 (2σ)). The spacer gel samples remain physically unchanged after irradiation with a dose exceeding the therapeutic dose level. The independently measured Bragg-Peak position does not change within the time interval of 10 weeks. Conclusions As a result of the presented experiments, the first clinical application of spacer gel implant during prostate cancer treatment with carbon ions and protons was possible at HIT in 2012. The reported pre-clinical investigations demonstrate that use of spacer gel is safe in particle therapy in presence of therapy target motion and patient positioning induced particle range variations. The spacer gel injected between prostate and rectum enlarge the distance between both organs, which is expected to clinically significantly decrease the undesirable exposure of

  12. Differentiation of canine distemper virus isolates in fur animals from various vaccine strains by reverse transcription-polymerase chain reaction-restriction fragment length polymorphism according to phylogenetic relations in china

    PubMed Central

    2011-01-01

    In order to effectively identify the vaccine and field strains of Canine distemper virus (CDV), a new differential diagnostic test has been developed based on reverse transcription-polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP). We selected an 829 bp fragment of the nucleoprotein (N) gene of CDV. By RFLP analysis using BamHI, field isolates were distinguishable from the vaccine strains. Two fragments were obtained from the vaccine strains by RT-PCR-RFLP analysis while three were observed in the field strains. An 829 nucleotide region of the CDV N gene was analyzed in 19 CDV field strains isolated from minks, raccoon dogs and foxes in China between 2005 and 2007. The results suggest this method is precise, accurate and efficient. It was also determined that three different genotypes exist in CDV field strains in fur animal herds of the north of China, most of which belong to Asian type. Mutated field strains, JSY06-R1, JSY06-R2 and JDH07-F1 also exist in Northern China, but are most closely related to the standard virulent strain A75/17, designated in Arctic and America-2 genetype in the present study, respectively. PMID:21352564

  13. Effects of water content and chain length of n-alkane on the interaction enthalpy between the droplets in water/sodium bis(2-ethylhexyl)-sulfosuccinate/n-alkane microemulsions.

    PubMed

    Fan, Dashuang; Zheng, Peizhu; Ma, Yuanming; Yin, Tianxiang; Zhao, Jihua; Shen, Weiguo

    2015-04-14

    The concentration-dependent enthalpies of mixing for water/sodium bis(2-ethylhexyl)-sulfosuccinate (AOT)/n-alkane microemulsions with different water contents ω0 and chain lengths n of n-alkane were determined by isothermal titration microcalorimetry (ITC) and flow-mixing microcalorimetry at 298.15 K and used to calculate the interaction enthalpies (-ΔH(C)) between the droplets. It was found that -ΔH(C) increased with ω0, and changed from negative to positive at about ω0 = 10. The investigation of the dependence of -ΔH(C) on n revealed that the values of -ΔH(C) were negative and had a minimum for ω0 = 5; while they were positive and had a maximum for ω0 = 15. These phenomena were discussed based on the competition of the overlapping contribution of the surfactant tails between two neighbouring droplets and the penetration contribution of the solvent molecules into the surfactant tails. These results indicated the important role of entropy in the stability of the microemulsion systems. PMID:25727484

  14. Pervasive generation of oppositely oriented spacers during CRISPR adaptation

    PubMed Central

    Shmakov, Sergey; Savitskaya, Ekaterina; Semenova, Ekaterina; Logacheva, Maria D.; Datsenko, Kirill A.; Severinov, Konstantin

    2014-01-01

    During the process of prokaryotic CRISPR adaptation, a copy of a segment of foreign deoxyribonucleic acid referred to as protospacer is added to the CRISPR cassette and becomes a spacer. When a protospacer contains a neighboring target interference motif, the specific small CRISPR ribonucleic acid (crRNA) transcribed from expanded CRISPR cassette can protect a prokaryotic cell from virus infection or plasmid transformation and conjugation. We show that in Escherichia coli, a vast majority of plasmid protospacers generate spacers integrated in CRISPR cassette in two opposing orientations, leading to frequent appearance of complementary spacer pairs in a population of cells that underwent CRISPR adaptation. When a protospacer contains a spacer acquisition motif AAG, spacer orientation that generates functional protective crRNA is strongly preferred. All other protospacers give rise to spacers oriented in both ways at comparable frequencies. This phenomenon increases the repertoire of available spacers and should make it more likely that a protective crRNA is formed as a result of CRISPR adaptation. PMID:24728991

  15. Inhalational drug delivery from seven different spacer devices.

    PubMed Central

    Barry, P. W.; O'Callaghan, C.

    1996-01-01

    BACKGROUND: A study was performed to determine in vitro the difference in drug output of seven currently available spacer devices when used with different inhaled medications. METHODS: A glass multistage liquid impinger (MSLI) was used to determine the amount of disodium cromoglycate (DSCG, 5 mg), salbutamol (100 micrograms), or budesonide (200 micrograms) obtained in various particle size ranges from metered dose inhalers (MDIs) actuated directly into the MSLI or via one of seven different spacer devices; the Fisonair, Nebuhaler, Volumatic, Inspirease, Aerochamber, Aerosol Cloud Enhancer, and Dynahaler. RESULTS: In particles smaller than 5 microns in diameter the dose of DSCG recovered from the Fisonair and Nebuhaler was 118% and 124%, respectively, of that recovered using the MDI alone. The dose recovered from the smaller volume spacers was 90% (Inspirease), 36% (Aerochamber), 33% (Aerosol Cloud Enhancer), and 21% (Dynahaler) of that from the MDI alone. The Volumatic increased the amount of salbutamol in particles smaller than 5 microns to 117% of that from the MDI, and the Inspirease and Aerochamber spacers decreased it by nearly 50%. The amount of budesonide in small particles recovered after use of the Nebuhaler, Inspirease, and the Aerochamber was 92%, 101%, and 78%, respectively, of that from the MDI alone. CONCLUSIONS: Under the test conditions used, large volume spacers such as the Fisonair, Nebuhaler, and Volumatic delivered significantly more DSCG and salbutamol than the smaller spacers tested. The differences between spacers were less for budesonide than the other medications studied. This study shows that there are significant differences in the amount of drug available for inhalation when different spacers are used as inhalational aids with different drugs. Spacer devices need to be fully evaluated for each drug prescribed for them. Images PMID:8795674

  16. Hyperbranched polymer stars with Gaussian chain statistics revisited.

    PubMed

    Polińska, P; Gillig, C; Wittmer, J P; Baschnagel, J

    2014-02-01

    Conformational properties of regular dendrimers and more general hyperbranched polymer stars with Gaussian statistics for the spacer chains between branching points are revisited numerically. We investigate the scaling for asymptotically long chains especially for fractal dimensions df = 3 (marginally compact) and df = 2.5 (diffusion limited aggregation). Power-law stars obtained by imposing the number of additional arms per generation are compared to truly self-similar stars. We discuss effects of weak excluded-volume interactions and sketch the regime where the Gaussian approximation should hold in dense solutions and melts for sufficiently large spacer chains. PMID:24574057

  17. Preclinical Evaluation of Bioabsorbable Polyglycolic Acid Spacer for Particle Therapy

    SciTech Connect

    Akasaka, Hiroaki; Sasaki, Ryohei; Miyawaki, Daisuke; Mukumoto, Naritoshi; Sulaiman, Nor Shazrina Binti; Nagata, Masaaki; Yamada, Shigeru; Murakami, Masao; Demizu, Yusuke; Fukumoto, Takumi

    2014-12-01

    Purpose: To evaluate the efficacy and safety of a polyglycolic acid (PGA) spacer through physical and animal experiments. Methods and Materials: The spacer was produced with surgical suture material made of PGA, forming a 3-dimensional nonwoven fabric. For evaluation or physical experiments, 150-MeV proton or 320-MeV carbon-ion beams were used to generate 60-mm width of spread-out Bragg peak. For animal experiments, the abdomens of C57BL/6 mice, with or without the inserted PGA spacers, were irradiated with 20 Gy of carbon-ion beam (290 MeV) using the spread-out Bragg peak. Body weight changes over time were scored, and radiation damage to the intestine was investigated using hematoxylin and eosin stain. Blood samples were also evaluated 24 days after the irradiation. Long-term thickness retention and safety were evaluated using crab-eating macaques. Results: No chemical or structural changes after 100 Gy of proton or carbon-ion irradiation were observed in the PGA spacer. Water equivalency of the PGA spacer was equal to the water thickness under wet condition. During 24 days' observation after 20 Gy of carbon-ion irradiation, the body weights of mice with the PGA spacer were relatively unchanged, whereas significant weight loss was observed in those mice without the PGA spacer (P<.05). In mice with the PGA spacer, villus and crypt structure were preserved after irradiation. No inflammatory reactions or liver or renal dysfunctions due to placement of the PGA spacer were observed. In the abdomen of crab-eating macaques, thickness of the PGA spacer was maintained 8 weeks after placement. Conclusions: The absorbable PGA spacer had water-equivalent, bio-compatible, and thickness-retaining properties. Although further evaluation is warranted in a clinical setting, the PGA spacer may be effective to stop proton or carbon-ion beams and to separate normal tissues from the radiation field.

  18. Molecular phylogenetic studies on filarial parasites based on 5S ribosomal spacer sequences.

    PubMed

    Xie, H; Bain, O; Williams, S A

    1994-06-01

    This paper is the first large-scale molecular phylogenetic study on filarial parasites (family Onchocercidae) which includes 16 species of 6 genera: Brugia beaveri Ash et Little, 1962, B. buckleyi Dissanaike et Paramananthan, 1961; B. malayi (Brug, 1927) Buckley, 1960; B. pahangi (Buckley et Edeson, 1956) Buckley, 1960; B. patei (Buckley, Nelson et Heisch, 1958) Buckley, 1960; B. timori Partono et al, 1977; Wuchereria bancrofti (Cobbold, 1877) Seurat, 1921: W. kalimantani Palmieri. Purnomo, Dennis and Marwoto, 1980: Mansonella perstans (Manson, 1891) Eberhard et Orihel, 1984; loa loc, Stiles, 1905; Onchocerca volvulus (Leuckart, 1983) Railliet er Henry, 1910; O. ochengi Bwangamoi, 1969; O. gutturosa Neumann, 1910; Dirofilaria immitis (Leidy, 1856) Railliet e Henry, 1911; Acanthocheilonema viteae (Krepkogorskaya, 1933) Bain, Baker et Chabaud, 1982 and Litomosoides sigmodontis Chandler, 1931. 5S rRNA gene spacer region sequence data were collected by PCR, cloning and dideoxy sequencing. The 5S rRNA gene spacer region sequences were aligned and analyzed by maximum parsimony algorithms, distance methods and maximum likelihood methods to construct phylogenetic trees. Bootstrap analysis was used to test the robustness of the different phylogenetic reconstructions. The data indicated that 5S spacer region sequences are highly conserved within species yet differ significantly between species. Spliced leader sequences were observed in all of the 5S rDNA spacers with no sequence variation, although flanking region sequence and length heterogeneity was observed even within species. All of the various tree-building methods gave very similar results. This study identified four clades which are strongly supported by bootstrap analysis the Brugia clade; the Wuchereria clade; the Brugia-Wuchereria clade and the Onchocerca clade. The analyses indicated that L. sigmodontis and A. viteae may be the most primitive among the 16 species studied. The data did not show any close

  19. A new class of pseudopeptide antagonists of the kinin B1 receptor containing alkyl spacers.

    PubMed

    Galoppini, C; Meini, S; Tancredi, M; Di Fenza, A; Triolo, A; Quartara, L; Maggi, C A; Formaggio, F; Toniolo, C; Mazzucco, S; Papini, A; Rovero, P

    1999-02-11

    Four previously reported kinin receptor peptide antagonists, including the B1 receptor-selective peptides desArg10-HOE 140 (H-D-Arg-Arg-Pro-Hyp-Gly-Thi-Ser-D-Tic-Oic-OH) and B-9858 (H-Lys-Lys-Arg-Pro-Hyp-Gly-Igl-Ser-D-Igl-Oic-OH), have been modified by replacement of the central tetrapeptide Pro-Hyp-Gly-Xaa with linear alkyl spacers of variable length. The analogue of desArg10-HOE 140 containing the 11-aminoundecanoic acid as spacer, MEN 11575 [H-D-Arg-Arg-NH-(CH2)10-CO-Ser-D-Tic-Oic-OH], was found to be slightly more potent than the unmodified peptide (pA2 = 7.1) as a kinin B1 receptor antagonist in the rat ileum longitudinal smooth muscle assay. Moreover, MEN 11575 is devoid of residual agonist activity at the kinin B1 receptor (rat ileum) and antagonist activity at the kinin B2 receptor (guinea pig ileum longitudinal smooth muscle). Both these activities are displayed by the parent peptide desArg10-HOE 140. Therefore, despite its greatly simplified chemical structure, MEN 11575 shows an improved pharmacological profile in terms of both potency and selectivity, and it represents a good template for the development of new peptidomimetic kinin B1 receptor antagonists. We also report an attempt to investigate the conformational role of the flexible, linear spacer of MEN 11575 and to design more constrained analogues, possibly locked in the bioactive conformation, using semirigid spacers based on Calpha-tetrasubstituted alpha-amino acids of the family of 1-aminocycloalkane-1-carboxylic acids (Acnc). PMID:9986712

  20. Performance Assessment of the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Method for Rapid Detection of Susceptibility to Ethambutol and Molecular Prediction of Extensively Drug-resistant Tuberculosis in Clinical Isolates of Mycobacterium tuberculosis

    PubMed Central

    Arjomandzadegan, M; Nazari, R; Zolfaghari, MR; Taherahmadi, M; Sadrnia, M; Titov, LP; Ahmadi, A; Shojapoor, M

    2015-01-01

    ABSTRACT Introduction: The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was employed for rapid detection of ethambutol (EMB) resistant clinical isolates of Mycobacterium tuberculosis. Materials and Methods: From 182 clinical isolates of M tuberculosis collected from different regions, 103 strains were entered in the investigation. DNA was extracted by Chelex 100 method and PCR was performed using specific primers for embB gene. Polymerase chain reaction products were digested with HaeIII and NlaII restriction endonucleases and the patterns of restriction fragments were analysed. Some randomly selected samples were sequenced. Results: Out of 103 studied strains, 52 were resistant to EMB. The cases of secondary tuberculosis were 53 (51.50 ± 1.77%), and primary cases 50 (48.50 ± 1.77%; p > 0.05). From 63 extensively drug-resistant (XDR), pre-XDR and multidrug-resistant (MDR) isolates, 27 (87%), 18 (81.8%) and 7 (70%) strains were resistant to EMB, respectively. Results of PCR-RFLP method showed that from 27R EMB XDR isolates, 13 (sensitivity 48% with CI: 0.307, 0.66 and specificity 100%), from 18R EMB pre-XDR strains, 4 (sensitivity 22% with CI: 0.09, 0.45 and specificity 100%) and of 7R EMB MDR, 2 (sensitivity 28% with CI: 0.082, 0.64 and specificity 100%) had mutation in ATG-Met codon 306. Results of sequencing were concordant with RFLP method. Overall, sensitivity of the molecular method was 36.5% (CI: 0.09, 0.45) and specificity 100%. None of the 40 pansusceptible strains was embB306 mutants. Extensively drug-resistant strains had a higher proportion of embB306 mutants (43%) than pre-XDR and MDR isolates (odds ratio 6.78; p < 0.001). Conclusion: Fast detection of susceptibility to EMB drug is possible by PCR-RFLP. The embB306 locus is a candidate marker for rapid prediction of high resistance of MDR and XDR forms to anti-tuberculosis drugs using this method. PMID:26624582

  1. Advantages of the AlGaN spacer in InAlN high-electron-mobility transistors grown using metalorganic vapor phase epitaxy

    NASA Astrophysics Data System (ADS)

    Yamada, Atsushi; Ishiguro, Tetsuro; Kotani, Junji; Tomabechi, Shuichi; Nakamura, Norikazu; Watanabe, Keiji

    2016-05-01

    We demonstrate the advantages of an AlGaN spacer layer in an InAlN high-electron-mobility transistor (HEMT). We investigated the effects of the growth parameters of the spacer layer on electron mobility in InAlN HEMTs grown by metalorganic vapor phase epitaxy, focusing on the surface roughness of the spacer layer and sharpness of the interface with the GaN channel layer. The electron mobility degraded, as evidenced by the formation of a graded AlGaN layer at the top of the GaN channel layer and the surface roughness of the AlN spacer layer. We believe that the short migration length of aluminum atoms is responsible for the observed degradation. An AlGaN spacer layer was employed to suppress the formation of the graded AlGaN layer and improve surface morphology. A high electron mobility of 1550 cm2 V‑1 s‑1 and a low sheet resistance of 211 Ω/sq were achieved for an InAlN HEMT with an AlGaN spacer layer.

  2. 14. TYPICAL WORK DECK SHOWING RING SPACERS, CABLE DRUMS AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    14. TYPICAL WORK DECK SHOWING RING SPACERS, CABLE DRUMS AND OTHER SPECIALIZED HARDWARE; VIEW TO SOUTH. - Cape Canaveral Air Station, Launch Complex 17, Facility 28416, East end of Lighthouse Road, Cape Canaveral, Brevard County, FL

  3. The effect of cardiomyopathy mutation (R97L) in mouse cardiac troponin T on the muscle length-mediated recruitment of crossbridges is modified divergently by α- and β-myosin heavy chain.

    PubMed

    Gollapudi, Sampath K; Chandra, Murali

    2016-07-01

    Hypertrophic cardiomyopathy mutations in cardiac troponin T (TnT) lead to sudden cardiac death. Augmented myofilament Ca(2+) sensitivity is a common feature in TnT mutants, but such observations fail to provide a rational explanation for severe cardiac phenotypes. To better understand the mutation-induced effect on the cardiac phenotype, it is imperative to determine the effects on dynamic contractile features such as the muscle length (ML)-mediated activation against α- and β-myosin heavy chain (MHC) isoforms. α- and β-MHC are not only differentially expressed in rodent and human hearts, but they also modify ML-mediated activation differently. Mouse analog of human TnTR94L (TnTR97L) or wild-type TnT was reconstituted into de-membranated muscle fibers from normal (α-MHC) and transgenic (β-MHC) mouse hearts. TnTR97L augmented myofilament Ca(2+) sensitivity by a similar amount in α- and β-MHC fibers. However, TnTR97L augmented the negative impact of strained crossbridges on other crossbridges (γ) by 22% in α-MHC fibers, but attenuated γ by 21% in β-MHC fibers. TnTR97L decreased the magnitude of ML-mediated recruitment of crossbridges (ER) by 37% in α-MHC fibers, but increased ER by 35% in β-MHC fibers. We provide a mechanistic basis for the TnTR97L-induced effects in α- and β-MHC fibers and discuss the relevance to human hearts. PMID:26792537

  4. Spacer process and alignment assessment for SADP process

    NASA Astrophysics Data System (ADS)

    Lattard, L.; McCallum, M.; Morton, R.; Fujiwara, T.; Makino, K.; Tokui, A.; Takahashi, N.; Sasamoto, S.

    2012-03-01

    Self Aligned Double Patterning (SADP) is now widely accepted as a viable technology for the further extension of 193nm immersion lithography towards the 22nm /18nm technology nodes. SADP was primary introduced for the manufacturing of flash memory due to its 1D design geometry. However, SADP is now becoming a main stream technology for advanced technology nodes for logic product. SADP results in alignment marks with reduced image contrast after completion of spacer patterning. Consequently there is an elevated risk that the alignment performance of the cut lithography layer on the spacer [1] may be negatively impacted. Initial studies indicate that it may be necessary to consider new mark designs. In this paper, we will evaluate different types of SADP processes with the alignment system of the Nikon S620D and S621D immersion scanner. We will discuss the performances and the differences observed due to the SADP materials. Included in this study is an intensive characterization of the morphology of the spacer after SADP process. We will use for this a 3D-AFM from Insight, and characterize the spacer profile of the spacer. Using a standard AFM microscope, we can characterize the surface roughness in the inner and the outer part of the wafer. The self aligned spacer process results in asymmetric spacers. Two types of surface (inside and outside) of the spacer are formed. The impact of this asymmetry is also assessed. The roughness difference, between the two parts, will play an important roll in the alignment contrast.

  5. Ligand-to-ligand charge-transfer transitions of platinum(II) complexes with arylacetylide ligands with different chain lengths: spectroscopic characterization, effect of molecular conformations, and density functional theory calculations.

    PubMed

    Tong, Glenna So Ming; Law, Yuen-Chi; Kui, Steven C F; Zhu, Nianyong; Leung, King Hong; Phillips, David Lee; Che, Chi-Ming

    2010-06-11

    The complexes [Pt(tBu(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)R}](+) (n = 1: R = alkyl and aryl (Ar); n = 1-3: R = phenyl (Ph) or Ph-N(CH(3))(2)-4; n = 1 and 2, R = Ph-NH(2)-4; tBu(3)tpy = 4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine) and [Pt(Cl(3)tpy)(C[triple bond]CR)](+) (R = tert-butyl (tBu), Ph, 9,9'-dibutylfluorene, 9,9'-dibutyl-7-dimethyl-amine-fluorene; Cl(3)tpy = 4,4',4''-trichloro-2,2':6',2''-terpyridine) were prepared. The effects of substituent(s) on the terpyridine (tpy) and acetylide ligands and chain length of arylacetylide ligands on the absorption and emission spectra were examined. Resonance Raman (RR) spectra of [Pt(tBu(3)tpy)(C[triple bond]CR)](+) (R = n-butyl, Ph, and C(6)H(4)-OCH(3)-4) obtained in acetonitrile at 298 K reveal that the structural distortion of the C[triple bond]C bond in the electronic excited state obtained by 502.9 nm excitation is substantially larger than that obtained by 416 nm excitation. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations on [Pt(H(3)tpy)(C[triple bond]CR)](+) (R = n-propyl (nPr), 2-pyridyl (Py)), [Pt(H(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)Ph}](+) (n = 1-3), and [Pt(H(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)C(6)H(4)-N(CH(3))(2)-4}](+)/+H(+) (n = 1-3; H(3)tpy = nonsubstituted terpyridine) at two different conformations were performed, namely, with the phenyl rings of the arylacetylide ligands coplanar ("cop") with and perpendicular ("per") to the H(3)tpy ligand. Combining the experimental data and calculated results, the two lowest energy absorption peak maxima, lambda(1) and lambda(2), of [Pt(Y(3)tpy)(C[triple bond]CR)](+) (Y = tBu or Cl, R = aryl) are attributed to (1)[pi(C[triple bond]CR)-->pi*(Y(3)tpy)] in the "cop" conformation and mixed (1)[d(pi)(Pt)-->pi*(Y(3)tpy)]/(1)[pi(C[triple bond]CR)-->pi*(Y(3)tpy)] transitions in the "per" conformation. The lowest energy absorption peak lambda(1) for [Pt(tBu(3)tpy){C[triple bond]C(C(6)H(4)C

  6. Sidewall spacer optimization for steep switching junctionless transistors

    NASA Astrophysics Data System (ADS)

    Gupta, Manish; Kranti, Abhinav

    2016-06-01

    In this work, we analyze the impact of a high permittivity (high-κ) sidewall spacer and gate dielectric on the occurrence of sub-60 mV/decade subthreshold swing (S-swing) in symmetrical junctionless (JL) double gate (DG) transistors. It is shown that steep S-swing values (≤10 mV/decade) can be achieved in JL devices with a combination of a high permittivity (high-κ) gate dielectric and a narrow low permittivity (low-κ) sidewall spacer. Implementation of a wider high-κ spacer will diminish the degree of impact ionization by the influence of the fringing component of the gate electric field, and will not be useful for steep off-to-on current transition. A wider spacer with low-κ and a narrow spacer with high-κ permittivity will be useful to limit the latching effect that can occur at lower temperatures (250 K). For high temperature operation, the decrease in the impact ionization rate can be compensated by designing a JL transistor with a thicker silicon film. The work demonstrates opportunities to enhance impact ionization at sub bandgap voltages, and proposes optimal guidelines for selecting a sidewall spacer to facilitate steep switching in JL transistors.

  7. Autoclaved metal-on-cement spacer versus static spacer in two-stage revision in periprosthetic knee infection

    PubMed Central

    Chen, Yu-Pin; Wu, Cheng-Chun; Ho, Wei-Pin

    2016-01-01

    Background: Periprosthetic knee infection is troublesome for Orthopedic surgeons and a catastrophy for patients. Reported rates of periprosthetic joint infection following primary total knee arthroplasty (TKA) are 0.39–2%. Two stage revision arthroplasty, which has success rates exceeding 90%, has been the gold standard for treating subacute and chronic periprosthetic infection following TKA. Antibiotic spacers, a well established means of delivering local antibiotic therapy, maintain soft tissue tension during two stage revision arthroplasty. However, controversy remains around whether static or mobile antibiotic impregnated spacers are superior for treating infection following TKA. Various mobile spacers are available, including cement-on-cement, cement-on-polyethylene and metal-on-polyethylene. In this study, the efficacy of the modified metal-on-cement spacer, consisting of reinsertion of the autoclaved femoral component and implantation of antibiotic-loaded cement in the proximal tibia, is assessed. Materials and Methods: Records of 19 patients diagnosed as periprosthetic knee infection were reviewed in this retrospective study. Among these patients, 10 patients received first stage debridement with the autoclaved metal-on-cement spacer and 8 patients with the static spacer, who eventually underwent two-stage re-implantation, were listed in the final comparison. Patient demographics, infection eradication rates, average range of motion (ROM), surgical time and blood loss during the second-stage of the surgery, and Knee Society (KS) knee scores at last followup after revision total knee replacement were clinically evaluated. Results: At a minimum of 2-year followup after re-implantation, infection eradication rates, surgical times, blood loss during the second-stage of the surgery, and KS knee score after re-implantation were similar for the two groups. Patients receiving autoclaved metal-on-cement spacers had superior ROM after re-implantation compared to

  8. Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune.

    PubMed Central

    James, T Y; Moncalvo, J M; Li, S; Vilgalys, R

    2001-01-01

    The common split-gilled mushroom Schizophyllum commune is found throughout the world on woody substrates. This study addresses the dispersal and population structure of this fungal species by studying the phylogeny and evolutionary dynamics of ribosomal DNA (rDNA) spacer regions. Extensive sampling (n = 195) of sequences of the intergenic spacer region (IGS1) revealed a large number of unique haplotypes (n = 143). The phylogeny of these IGS1 sequences revealed strong geographic patterns and supported three evolutionarily distinct lineages within the global population. The same three geographic lineages were found in phylogenetic analysis of both other rDNA spacer regions (IGS2 and ITS). However, nested clade analysis of the IGS1 phylogeny suggested the population structure of S. commune has undergone recent changes, such as a long distance colonization of western North America from Europe as well as a recent range expansion in the Caribbean. Among all spacer regions, variation in length and nucleotide sequence was observed between but not within the tandem rDNA repeats (arrays). This pattern is consistent with strong within-array and weak among-array homogenizing forces. We present evidence for the suppression of recombination between rDNA arrays on homologous chromosomes that may account for this pattern of concerted evolution. PMID:11139499

  9. Effect of polyethylene glycol, alkyl, and oligonucleotide spacers on the binding, secondary structure, and self-assembly of fractalkine binding FKN-S2 aptamer-amphiphiles.

    PubMed

    Waybrant, Brett; Pearce, Timothy R; Kokkoli, Efrosini

    2014-07-01

    Previously we identified an aptamer, named FKN-S2, which binds the cell surface protein fractalkine with high affinity and specificity. In this paper a hydrophobic dialkyl C16 tail was added to the aptamer to create an aptamer-amphiphile. We investigated how the tail and a spacer molecule of varying length and hydrophobicity, inserted between the tail and the aptamer headgroup, affect the binding, structure, and self-assembly properties of the aptamer-amphiphile. We synthesized aptamer-amphiphiles with no spacer (NoSPR), polyethylene glycol (PEG4, PEG8, PEG24), alkyl (C12 and C24), or oligonucleotide (T10 and T5: 10 and 5 thymine, and A10: 10 adenine) spacers. The addition of the tail reduced the binding affinity of the aptamer-amphiphile over 7.5-fold compared to the free aptamer. The hydrophobic alkyl spacers resulted in the greatest loss of affinity, and the hydrophilic PEG spacers improved amphiphile affinity but did not restore it to that of the free aptamer. Interestingly, oligonucleotide spacers produced the highest affinity amphiphiles. Nucleotide composition did not affect affinity, however, as the T10 and A10 spacers had equal affinity. The oligonucleotide spacer amphiphiles had the highest affinity because the oligonucleotide spacer increased the affinity of free aptamer; the FKN-S2 aptamer plus the oligonucleotide spacer had a higher affinity than the free FKN-S2 aptamer. Circular dichroism (CD) spectroscopy and thermal melting studies indicated the aptamer forms a stem-loop and intramolecular G-quadruplex, and the tail strongly stabilized the formation of the G-quadruplex in a buffer. Cryogenic transmission electron microscopy (cryo-TEM) imaging showed the aptamer-amphiphiles, independent of the spacer used, self-assembled into micelles and nanotapes, flat bilayer structures that were often twisted. Finally, liposomes functionalized with the FKN-S2 amphiphile were incubated with fractalkine expressing cells, and the amount of binding was dependent on

  10. Molecular Identification of Closely Related Candida Species Using Two Ribosomal Intergenic Spacer Fingerprinting Methods

    PubMed Central

    Cornet, Muriel; Sendid, Boualem; Fradin, Chantal; Gaillardin, Claude; Poulain, Daniel; Nguyen, Huu-Vang

    2011-01-01

    Recent changes in the epidemiology of candidiasis highlighted an increase in non- Candida albicans species emphasizing the need for reliable identification methods. Molecular diagnostics in fungal infections may improve species characterization, particularly in cases of the closely related species in the Candida complexes. We developed two PCR/restriction fragment length polymorphism assays, targeting either a part of the intergenic spacer 2 or the entire intergenic spacer (IGS) of ribosomal DNA using a panel of 270 isolates. A part of the intergenic spacer was used for discrimination between C. albicans and C. dubliniensis and between species of the C. glabrata complex (C. glabrata/C. bracarensis/C. nivariensis). The whole IGS was applied to C. parapsilosis, C. metapsilosis, and C. orthopsilosis, and to separate C. famata (Debaryomyces hansenii) from C. guilliermondii (Pichia guilliermondii) and from the other species within this complex (ie, C. carpophila, C. fermentati and C. xestobii). Sharing similar biochemical patterns, Pichia norvegensis and C. inconspicua exhibited specific IGS profiles. Our study confirmed that isolates of C. guilliermondii were frequently mis-identified as C. famata. As much as 67% of the clinical isolates phenotypically determined as C. famata were recognized mostly as true P. guilliermondii. Conversely, 44% of the isolates initially identified as C. guilliermondii were corrected by the IGS fingerprints as C. parapsilosis, C. fermentati, or C. zeylanoides. These two PCR/restriction fragment length polymorphism methods may be used as reference tools [either alternatively or adjunctively to the existing ribosomal DNA (26S or ITS) sequence comparisons] for unambiguous determination of the Candida species for which phenotypic characterization remains problematic. PMID:21227390

  11. DNA polymorphism in morels: complete sequences of the internal transcribed spacer of genes coding for rRNA in Morchella esculenta (yellow morel) and Morchella conica (black morel).

    PubMed Central

    Wipf, D; Munch, J C; Botton, B; Buscot, F

    1996-01-01

    The internal transcribed spacer (ITS) of the gene coding for rRNA was sequenced in both directions with the gene walking technique in a black morel (Morchella conica) and a yellow morel (M. esculenta) to elucidate the ITS length discrepancy between the two species groups (750-bp ITS in black morels and 1,150-bp ITS in yellow morels. PMID:8795250

  12. Gel electrophoretic restriction fragment length polymorphism analysis of DNA derived from individual nematodes, using the PhastSystem.

    PubMed

    Triga, D; Pamjav, H; Vellai, T; Fodor, A; Buzás, Z

    1999-06-01

    The DNA sequences constituting the internal transcribed spacer region, located between 18S and 26S rDNA genes within the rRNA operon, derived from single nematodes of two genera (Steinernema and Heterorhabditis) were amplified by polymerase chain reaction (PCR) and subjected to digestion by four restriction enzymes. The digests were analyzed by restriction fragment length polymorphism (RFLP) gel electrophoresis on the PhastSystem, using 7.5%T, 5%C(Bis) polyacrylamide. The downscaling from conventional agarose to PhastSystem gels permitted the analysis to be done on individual nematodes, rather than on mixed samples with average properties. The analysis time was reduced so as to allow for the electrophoretic separation on 200 samples/workday. The resulting patterns of DNA fragments differed from those obtained by agarose gel electrophoresis under conventional conditions by an increased number of detected fragments. The PhastSystem gel analysis provides the basis for taxonomical revisions. PMID:10380768

  13. Magnetic Coupling of Dissimilar ZnO-Co Granular Films Through a ZnO Spacer

    NASA Astrophysics Data System (ADS)

    Li, Xiaoli; Jia, Juan; Gao, Yan; Gehring, G. A.; Xu, Xiaohong

    2015-12-01

    An all-oxide granular film (GF) with a sandwich structure containing cobalt metal nanoparticles embedded in ZnO is fabricated by magnetron sputtering. Large and small Co particles can be obtained simultaneously in a sample by depositing nanostructured ZnO-Co layers at high and low temperatures, respectively. The two ZnO-Co layers couple with each other through a ZnO spacer layer, whose thickness tunes the strength of the coupling. Both the magnetic properties and the magnetoresistance (MR) of the samples depend on the sandwich structure. Magnetic interactions can be transferred through the polycrystalline pure ZnO spacer layer even when the layer is as thick as 40nm due to the long spin coherence length. An analysis of the data found that the spin coherence length was greater than ˜17nm at room temperature (RT) in a polycrystalline film with very small grains. Tuning the resistance of the ZnO-Co layer deposited at a low temperature by adding aluminum so that it more nearly matches the resistance of the ZnO-Co layer deposited at a high temperature, dramatically enhances the MR of the sandwich sample. This study illustrates the power of combining films containing different sizes of nanoparticles in order to optimize the MR and so make the ZnO-based films more suitable for applications in spintronics.

  14. Thiophene-Diketopyrrolopyrrole-Based Quinoidal Small Molecules as Solution-Processable and Air-Stable Organic Semiconductors: Tuning of the Length and Branching Position of the Alkyl Side Chain toward a High-Performance n-Channel Organic Field-Effect Transistor.

    PubMed

    Wang, Chao; Qin, Yunke; Sun, Yuanhui; Guan, Ying-Shi; Xu, Wei; Zhu, Daoben

    2015-07-29

    A series of thiophene-diketopyrrolopyrrole-based quinoidal small molecules (TDPPQ-2-TDPPQ-5) bearing branched alkyl chains with different side-chain lengths and varied branching positions are synthesized. Field-effect transistor (FET) measurement combined with thin-film characterization is utilized to systematically probe the influence of the side-chain length and branching position on the film microstructure, molecular packing, and, hence, charge-transport property. All of these TDPPQ derivatives show air-stable n-channel transporting behavior in spin-coated FET devices, which exhibit no significant decrease in mobility even after being stored in air for 2 months. Most notably, TDPPQ-3 exhibits an outstanding n-channel semiconducting property with electron mobilities up to 0.72 cm(2) V(-1) s(-1), which is an unprecedented value for spin-coated DPP-based n-type semiconducting small molecules. A balance of high crystallinity, satisfactory thickness uniformity and continuity, and strong intermolecular interaction accounts for the superior charge-transport characteristics of TDPPQ-3 films. Our study demonstrates that tuning the length and branching position of alkyl side chains of semiconducting molecules is a powerful strategy for achieving high FET performance. PMID:26134920

  15. Space Station Long Spacer Element begins processing at KSC

    NASA Technical Reports Server (NTRS)

    1998-01-01

    The Long Spacer, a component of the International Space Station, arrives and is moved to its test stand in the northeast corner of the high bay in KSC's Space Station Processing Facility. The Long Spacer provides structural support for the outboard Photovoltaic Modules that supply power to the station. Now just a structure, the Long Spacer will have attached to it as part of processing a heat dissipation radiator and two Pump and Flow Control subassemblies that circulate ammonia to cool the solar array electronics. Also to be mounted are ammonia fluid lines as part of the cooling system and the cabling necessary for power and control of the station. The Long Spacer becomes an integral part of a station truss segment when it is mated with the Integrated Equipment Assembly, which stores the electrical power generated by the solar arrays for use by the station modules. The Long Spacer is being processed in preparation for STS-97, currently planned for launch aboard Discovery in April 1999.

  16. Gas-insulated substation spacer surface degradation analysis

    SciTech Connect

    Chu, F.Y.; Braun, J.M. )

    1990-06-01

    The objective of the project was to develop surface analysis techniques which can correlate the performance of spacers in SF{sub 6} insulated switchgear with changes in their dielectric and chemical characteristics after exposure to SF{sub 6} arcing byproducts and low energy flashovers. Critical material parameters responsible for spacer performance were investigated by optical and scanning electron microscopy, electron spectroscopy for chemical analysis, thermogravimetric analysis and electrical surface resistance measurements. Results related to arc byproduct resistance and tracking resistance of seven types of filled epoxy spacer materials are presented. Degradation mechanisms have been proposed to explain the differing material behaviour. The study shows that the interaction of certain types of filler and resin systems with the SF{sub 6} spark and the decomposed gas is responsible for the degradation in impulse withstand performance. A practical technique using surface electrical resistance to detect degraded spacer after exposure to large quantities of arc byproducts has been developed and the construction of a probe for spacer surface assessment was described. 15 refs., 28 figs., 8 tabs.

  17. Impact of spacer thickness on biofouling in forward osmosis.

    PubMed

    Valladares Linares, R; Bucs, Sz S; Li, Z; AbuGhdeeb, M; Amy, G; Vrouwenvelder, J S

    2014-06-15

    Forward osmosis (FO) indirect desalination systems integrate wastewater recovery with seawater desalination. Niche applications for FO systems have been reported recently, due to the demonstrated advantages compared to conventional high-pressure membrane processes such as nanofiltration (NF) and reverse osmosis (RO). Among them, wastewater recovery has been identified to be particularly suitable for practical applications. However, biofouling in FO membranes has rarely been studied in applications involving wastewater effluents. Feed spacers separating the membrane sheets in cross-flow systems play an important role in biofilm formation. The objective of this study was to determine the influence of feed spacer thickness (28, 31 and 46 mil) on biofouling development and membrane performance in a FO system, using identical cross-flow cells in parallel studies. Flux development, biomass accumulation, fouling localization and composition were determined and analyzed. For all spacer thicknesses, operated at the same feed flow and the same run time, the same amount of biomass was found, while the flux reduction decreased with thicker spacers. These observations are in good agreement with biofouling studies for RO systems, considering the key differences between FO and RO. Our findings contradict previous cross-flow studies on particulate/colloidal fouling, where higher cross-flow velocities improved system performance. Thicker spacers reduced the impact of biofouling on FO membrane flux. PMID:24726992

  18. [Prostate-rectum spacers: optimization of prostate cancer irradiation].

    PubMed

    Zilli, T; Benz, E; Miralbell, R

    2014-06-01

    In the curative radiotherapy of localized prostate cancer, improvements in biochemical control observed with dose escalation have been counterbalanced by an increase in radiation-induced toxicity. The injection of biodegradable spacers between prostate and rectum represents a new frontier in the optimization of radiotherapy treatments for patients with localized disease. Transperineal injection of different types of spacers under transrectal ultrasound guidance allows creating a 7-to-20 mm additional space between the prostate and the anterior rectal wall lasting 3 to 12 months. Dosimetrically, a relative reduction in the rectal volume receiving at least 70 Gy (V70) in the order of 43% to 84% is observed with all types of spacers, regardless of the radiotherapy technique used. Preliminary clinical results show for all spacers a good tolerance and a possible reduction in the acute side effects rate. The aim of the present systematic review of the literature is to report on indications as well as dosimetric and clinical advantages of the different types of prostate-rectum spacers commercially available (hydrogel, hyaluronic acid, collagen, biodegradable balloon). PMID:24746454

  19. Experimental and numerical characterization of the water flow in spacer-filled channels of spiral-wound membranes.

    PubMed

    Bucs, Szilard S; Linares, Rodrigo Valladares; Marston, Jeremy O; Radu, Andrea I; Vrouwenvelder, Johannes S; Picioreanu, Cristian

    2015-12-15

    Micro-scale flow distribution in spacer-filled flow channels of spiral-wound membrane modules was determined with a particle image velocimetry system (PIV), aiming to elucidate the flow behaviour in spacer-filled flow channels. Two-dimensional water velocity fields were measured in a flow cell (representing the feed spacer-filled flow channel of a spiral wound reverse osmosis membrane module without permeate production) at several planes throughout the channel height. At linear flow velocities (volumetric flow rate per cross-section of the flow channel considering the channel porosity, also described as crossflow velocities) used in practice (0.074 and 0.163 m·s(-1)) the recorded flow was laminar with only slight unsteadiness in the upper velocity limit. At higher linear flow velocity (0.3 m·s(-1)) the flow was observed to be unsteady and with recirculation zones. Measurements made at different locations in the flow cell exhibited very similar flow patterns within all feed spacer mesh elements, thus revealing the same hydrodynamic conditions along the length of the flow channel. Three-dimensional (3-D) computational fluid dynamics simulations were performed using the same geometries and flow parameters as the experiments, based on steady laminar flow assumption. The numerical results were in good agreement (0.85-0.95 Bray-Curtis similarity) with the measured flow fields at linear velocities of 0.074 and 0.163 m·s(-1), thus supporting the use of model-based studies in the optimization of feed spacer geometries and operational conditions of spiral wound membrane systems. PMID:26433778

  20. Wheeze in childhood: is the spacer good enough?

    PubMed Central

    Rajkumar, Veena; Rajendra, Barathi; How, Choon How; Ang, Seng Bin

    2014-01-01

    Max was treated with SABA using an MDI and spacer with facemask and responded well to the initial treatment. You explained to the parents that nebulisers are neither required nor recommended in the treatment of wheezing in their child’s situation. You advised the parents on the proper technique of MDI use with spacer and facemask, as well as care of the equipment. You also gave them a clearly written action plan regarding the efficient management of the next episode of wheeze with MDI and spacer. You further explained the side effects of oral bronchodilators and nebulisers, and why you refrained from using them. Max was given a follow-up appointment to assess his progress, and his parents were advised on the situations when they should go to a doctor or the emergency department. PMID:25631964

  1. Spacer effect on nanostructures and self-assembly in organogels via some bolaform cholesteryl imide derivatives with different spacers

    PubMed Central

    2013-01-01

    In this paper, new bolaform cholesteryl imide derivatives with different spacers were designed and synthesized. Their gelation behaviors in 23 solvents were investigated, and some of them were found to be low molecular mass organic gelators. The experimental results indicated that these as-formed organogels can be regulated by changing the flexible/rigid segments in spacers and organic solvents. Suitable combination of flexible/rigid segments in molecular spacers in the present cholesteryl gelators is favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle and belt to fiber with the change of spacers and solvents. Spectral studies indicated that there existed different H-bond formations between imide groups and assembly modes, depending on the substituent spacers in molecular skeletons. The present work may give some insight into the design and character of new organogelators and soft materials with special molecular structures. PMID:24083361

  2. Effects of dual-spacer dielectrics on low-power and high-speed performance of sub-10 nm tunneling field-effect transistors

    NASA Astrophysics Data System (ADS)

    Yoon, Young Jun; Seo, Jae Hwa; Cho, Seongjae; Kwon, Hyuck-In; Lee, Jung-Hee; Kang, In Man

    2016-06-01

    In this paper, we propose and investigate a dual-spacer dielectric structure for realizing a sub-10 nm tunneling field-effect transistors (TFET) with excellent low-power (LP) and switching performance. The effects of the dual-spacer dielectric were assessed by analyzing the direct current (DC) and radio frequency (RF) performance of the GaAs0.5Sb0.5/In0.53Ga0.47As heterojunction-based short channel TFETs. The dual-spacer dielectric that consists of hafnium oxide (HfO2) and silicon dioxide (SiO2) raises an energy-band on drain-side because of the fringe field induced by the high-k spacer dielectric HfO2. The raised energy-band suppresses direct band-to-band tunneling (BBT) through the channel region and drain-induced barrier thinning (DIBT) phenomenon with improvement in the off-state current (I off) and subthreshold swing (S). The dual-spacer dielectric also influences total gate capacitance (C gg) because the HfO2 in the dual-spacer dielectric increases out-fringe capacitance (C of) in gate-to-drain capacitance (C gd). Although the proposed TFET has a high C gd, the optimized TFET with the HfO2 length (L dual-spacer) of 30 nm achieves a lower intrinsic delay time (τ), a higher cut-off frequency (f T), and a higher maximum oscillation frequency (f max) owing to higher current performance and smaller gate-to-source capacitance (C gs).

  3. Impact of the spacer dielectric constant on parasitic RC and design guidelines to optimize DC/AC performance in 10-nm-node Si-nanowire FETs

    NASA Astrophysics Data System (ADS)

    Hong, Jae-Ho; Lee, Sang-Hyun; Kim, Ye-Ram; Jeong, Eui-Young; Yoon, Jun-Sik; Lee, Jeong-Soo; Baek, Rock-Hyun; Jeong, Yoon-Ha

    2015-04-01

    In this paper, we propose an optimized design for Si-nanowire FETs in terms of spacer dielectric constant (κsp), extension length (LEXT), nanowire diameter (Dnw), and operation voltage (VDD) for the sub-10 nm technology node. Using well-calibrated TCAD simulations and analytic RC models, we have quantitatively evaluated geometry-dependent parasitic series resistances (RSD) and capacitances (Cpara). Compared with low-κ spacers, high-κ spacers exhibit a higher on/off-current ratio with a lower RSD, but show severe degradation in their AC performance owing to a higher Cpara. Considering the trade-off between RSD and Cpara, optimal geometry-dependent κsp values at various supply voltages (VDD) are determined using gate delay (CV/I) and current-gain cutoff frequency (fT). We found that as LEXT and VDD decrease and Dnw increases, the optimal κsp value shifts from the high-κ to low-κ regime.

  4. Molecular authentication of Radix Puerariae Lobatae and Radix Puerariae Thomsonii by ITS and 5S rRNA spacer sequencing.

    PubMed

    Sun, Ye; Shaw, Pang-Chui; Fung, Kwok-Pui

    2007-01-01

    In the present study, we examined nuclear DNA sequences in an attempt to reveal the relationships between Pueraria lobata (Willd). Ohwi, P. thomsonii Benth., and P. montana (Lour.) Merr. We found that internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA are highly divergent in P. lobata and P. thomsonii, and four types of ITS with different length are found in the two species. On the other hand, DNA sequences of 5S rRNA gene spacer are highly conserved across multiple copies in P. lobata and P. thomsonii, they could be used to identify P. lobata, P. thomsonii, and P. montana of this complex, and may serve as a useful tool in medical authentication of Radix Puerariae Lobatae and Radix Puerariae Thomsonii. PMID:17202681

  5. Ilizarov bone transport combined with antibiotic cement spacer for infected tibial nonunion

    PubMed Central

    Peng, Jing; Min, Li; Xiang, Zhou; Huang, Fuguo; Tu, Chongqi; Zhang, Hui

    2015-01-01

    Purpose: To evaluate the curative effect of Ilizarov bone transport combined with antibiotic cement spacer for infected tibial nonunion with bone defect. Methods: We retrospectively reviewed the outcomes of 58 patients with infected tibial nonunion from January 2008 to March 2011 at our institution. Patients were treated with complete debridement, radical sequestrectomy, antibiotic cement spacer implantation, bone transport using the Ilizarov external fixator, and soft tissue reconstruction. Clinical efficacy was assessed using Paley’s grading system and patient satisfaction at the last follow-up. Results: Follow-up ranged from 24 to 63 months (average, 31.6 months). Mean size of the tibial defect was 9.2 cm (range, 6-15 cm). The soft tissue defect was closed successfully in all cases. Patients eventually achieved union with a mean bone union index of 1.2 months/cm at an average of 10.6 months (range, 8-31 months). In terms of Paley grade, 30 patients had excellent results, 23 good, and 5 fair. Functional results were excellent in 28 patients, good in 18, and fair in 12. Thirty-five patients felt extremely satisfied, 18 satisfied, and 5 acceptable with the functional outcome. Complications included pin site infection in 18 cases, limb length discrepancy less than 1.5 cm in 10, knee stiffness in 5, equinus deformity in 4, infectious recurrence in 1 and pin breakage in 1. There was no refracture at the reconstruction site. Conclusion: Ilizarov bone transport combined with antibiotic cement spacer is a versatile and effective method for treatment of infected tibial nonunion. PMID:26309700

  6. Cationic gemini surfactants with cleavable spacer: chemical hydrolysis, biodegradation, and toxicity.

    PubMed

    Tehrani-Bagha, A R; Holmberg, K; van Ginkel, C G; Kean, M

    2015-07-01

    The paper describes synthesis and characterization of a new type of cationic gemini surfactant, which has dodecyl tails and a spacer that contains an ester bond. The nomenclature used to describe the structure is 12Q2OCO1Q12, with Q being a quaternary ammonium group and the numbers indicating the number of methylene or methyl groups. Due to the close proximity to the two quaternary ammonium groups, the ester bond is very stable on the acid side and very labile already at slightly alkaline conditions. The hydrolysis products are two single chain surfactants (i.e. 12Q2OH and 12Q1COOH) which are less surface active than the intact gemini surfactant. 12Q2OCO1Q12 was found to be readily biodegradable, i.e. it gave more than 60% biodegradation after 28 days. This is interesting because similar gemini surfactants but with ester bonds in the tails instead of the spacer, have previously been found not to be readily biodegradable. The gemini surfactant was found to be toxic to aquatic organisms (ErC50 value of 0.27 mg/l), although less toxic than the two hydrolysis products. PMID:25446957

  7. Spacer oligonucleotide typing of Mycobacterium bovis strains from cattle and other animals: a tool for studying epidemiology of tuberculosis.

    PubMed Central

    Aranaz, A; Liébana, E; Mateos, A; Dominguez, L; Vidal, D; Domingo, M; Gonzolez, O; Rodriguez-Ferri, E F; Bunschoten, A E; Van Embden, J D; Cousins, D

    1996-01-01

    The spacer oligonucleotide typing (spoligotyping) method was evaluated for its ability to differentiate Mycobacterium bovis strains. This method detects the presence or absence of spacers of the direct repeat locus of the M. bovis genome. The spacers in the direct repeat locus are amplified by PCR and are detected by hybridization of the biotin-labelled PCR product with a membrane containing oligonucleotides derived from spacer sequences that have previously been bound to a membrane. One hundred eighty-two M. bovis isolates from domestic animals (cattle, goat, sheep, and cats) and wild animals (deer and wild boar) were spoligotyped, and the results were compared with those obtained by IS6110 restriction fragment length polymorphism analysis. Two rather homogeneous clusters of isolates containing 20 and 4 types, respectively, were identified by spoligotyping. The first cluster included isolates from cattle, cats, and feral animals. By spoligotyping, isolates from the Spanish wild boar and deer had the same pattern as some bovine isolates, suggesting transmission between these animals and cattle and highlighting the importance of the study of these reservoirs. The second cluster included all the caprine and ovine isolates. Within each cluster, the patterns of the different strains differed only slightly, suggesting that the spoligotypes may be characteristic of strains from particular animal species. Spoligotyping proved to be useful for studying the epidemiology of bovine M. bovis isolates, especially of those isolates containing only a single copy of IS6110. In view of our results, we suggest fingerprinting all M. bovis strains by the spoligotyping method initially and then by IS6110 restriction fragment length polymorphism typing of the strains belonging to the most common spoligotypes. PMID:8897175

  8. Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences.

    PubMed

    Moller, M; Cronk, Q

    1997-07-01

    Phylogenetic relationships of eight species of Saintpaulia H. Wendl., 19 species of Streptocarpus Lindl. (representing all major growth forms within the genus), and two outgroups (Haberlea rhodopensis Friv., Chirita spadiciformis W. T. Wang) were examined using comparative nucleotide sequences from the two internal transcribed spacers (ITS) of nuclear ribosomal DNA. The length of the ITS 1 region ranged from 228 to 249 base pairs (bp) and the ITS 2 region from 196 to 245 bp. Pairwise sequence divergence across both spacers for ingroup and outgroup species ranged from 0 to 29%. Streptocarpus is not monophyletic, and Saintpaulia is nested within Streptocarpus subgenus Streptocarpella. Streptocarpus subgenus Streptocarpus is monophyletic. The ITS sequence data demonstrate that the unifoliate Streptocarpus species form a clade, and are also characterized by a unique 47-bp deletion in ITS 2. The results strongly support the monophyly of (1) Saintpaulia, and (2) Saintpaulia plus the African members of the subgenus Streptocarpella of Streptocarpus. The data suggest the evolution of Saintpaulia from Streptocarpus subgenus Streptocarpella. The differences in flower and vegetative characters are probably due to ecological adaptation leading to a relatively rapid radiation of Saintpaulia. PMID:21708650

  9. CRISPR interference and priming varies with individual spacer sequences

    PubMed Central

    Xue, Chaoyou; Seetharam, Arun S.; Musharova, Olga; Severinov, Konstantin; J. Brouns, Stan J.; Severin, Andrew J.; Sashital, Dipali G.

    2015-01-01

    CRISPR–Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring ‘spacer’ sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid ‘primed’ adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR–Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed ‘naïve’ adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection. PMID:26586800

  10. Filter holder assembly having extended collar spacer ring

    DOEpatents

    Alvin, Mary Anne; Bruck, Gerald J.

    2002-01-01

    A filter holder assembly is provided that utilizes a fail-safe regenerator unit with an annular spacer ring having an extended metal collar for containment and positioning of a compliant ceramic gasket used in the assembly. The filter holder assembly is disclosed for use with advanced composite, filament wound, and metal candle filters.

  11. Imidacloprid and Thiamethoxam