Sample records for reaction assay coupled

  1. Response reactions: equilibrium coupling.

    Hoffmann, Eufrozina A; Nagypal, Istvan


    It is pointed out and illustrated in the present paper that if a homogeneous multiple equilibrium system containing k components and q species is composed of the reactants actually taken and their reactions contain only k + 1 species, then we have a unique representation with (q - k) stoichiometrically independent reactions (SIRs). We define these as coupling reactions. All the other possible combinations with k + 1 species are the coupled reactions that are in equilibrium when the (q - k) SIRs are in equilibrium. The response of the equilibrium state for perturbation is determined by the coupling and coupled equilibria. Depending on the circumstances and the actual thermodynamic data, the effect of coupled equilibria may overtake the effect of the coupling ones, leading to phenomena that are in apparent contradiction with Le Chatelier's principle.

  2. Palladium-catalyzed coupling reactions

    Molnár, Árpád


    This handbook and ready reference brings together all significant issues of practical importance for interested readers in one single volume. While covering homogeneous and heterogeneous catalysis, the text is unique in focusing on such important aspects as using different reaction media, microwave techniques or catalyst recycling. It also provides a comprehensive treatment of modern-day coupling reactions and emphasizes those topics that show potential for future development, such as continuous flow systems, water as a reaction medium, and catalyst immobilization, among others. With i

  3. Palladium-Catalysed Coupling Reactions

    de Vries, Johannes G.; Beller, M; Blaser, HU


    Palladium-catalysed coupling reactions have gained importance as a tool for the production of pharmaceutical intermediates and to a lesser extent also for the production of agrochemicals, flavours and fragrances, and monomers for polymers. In this review only these cases are discussed where it seems

  4. Polymerase chain reaction assay for avian polyomavirus.

    Phalen, D.N.; Wilson, V G; Graham, D L


    A polymerase chain reaction assay was developed for detection of budgerigar fledgling disease virus (BFDV). The assay used a single set of primers complementary to sequences located in the putative coding region for the BFDV VP1 gene. The observed amplification product had the expected size of 550 bp and was confirmed to derive from BFDV DNA by its restriction digestion pattern. This assay was specific for BFDV and highly sensitive, being able to detect as few as 20 copies of the virus. By us...

  5. Polymerase chain reaction assay for avian polyomavirus.

    Phalen, D N; Wilson, V G; Graham, D L


    A polymerase chain reaction assay was developed for detection of budgerigar fledgling disease virus (BFDV). The assay used a single set of primers complementary to sequences located in the putative coding region for the BFDV VP1 gene. The observed amplification product had the expected size of 550 bp and was confirmed to derive from BFDV DNA by its restriction digestion pattern. This assay was specific for BFDV and highly sensitive, being able to detect as few as 20 copies of the virus. By using the polymerase chain reaction, BFDV was detected in adult, nestling, and embryo budgerigar (Melopsitticus undulatus) tissue DNAs and in sera from adult and nestling budgerigars. These results suggest the possibility of persistent infections in adult birds and lend further support to previously described evidence of possible in ovo transmission. BFDV was also detected in chicken embryo fibroblast cell cultures and chicken eggs inoculated with the virus. A 550-bp product with identical restriction enzyme sites was amplified from a suspected polyomavirus isolated from a peach-faced lovebird (Agapornis pesonata) and from tissue DNA from a Hahn's macaw (Ara nobilis) and a sun conure (Aratinga solstitialis) with histological lesions suggestive of polyomavirus infection. These fragments also hybridized with a BFDV-derived probe, proving that they were derived from a polyomavirus very similar, if not identical, to BFDV.

  6. Pinacol Coupling Reactions Catalyzed by Active Zinc

    Hui ZHAO; Wei DENG; Qing Xiang GUO


    Pinacol coupling reactions catalyzed by active zinc revealed high activity and extensive suitability. The efficiency of the reaction was improved apparently owing to decreasing reductive potential of zinc. In addition, the results indicated that the zinc activity has a direct relation to the coupling reactivity compared to untreated zinc or other general active zinc.

  7. Nanocatalysts for Suzuki cross-coupling reactions

    Fihri, Aziz


    This critical review deals with the applications of nanocatalysts in Suzuki coupling reactions, a field that has attracted immense interest in the chemical, materials and industrial communities. We intend to present a broad overview of nanocatalysts for Suzuki coupling reactions with an emphasis on their performance, stability and reusability. We begin the review with a discussion on the importance of Suzuki cross-coupling reactions, and we then discuss fundamental aspects of nanocatalysis, such as the effects of catalyst size and shape. Next, we turn to the core focus of this review: the synthesis, advantages and disadvantages of nanocatalysts for Suzuki coupling reactions. We begin with various nanocatalysts that are based on conventional supports, such as high surface silica, carbon nanotubes, polymers, metal oxides and double hydroxides. Thereafter, we reviewed nanocatalysts based on non-conventional supports, such as dendrimers, cyclodextrin and magnetic nanomaterials. Finally, we discuss nanocatalyst systems that are based on non-conventional media, i.e., fluorous media and ionic liquids, for use in Suzuki reactions. At the end of this review, we summarise the significance of nanocatalysts, their impacts on conventional catalysis and perspectives for further developments of Suzuki cross-coupling reactions (131 references). © 2011 The Royal Society of Chemistry.

  8. Golgi-resident PAP-specific 3'-phosphatase-coupled sulfotransferase assays.

    Prather, Brittany; Ethen, Cheryl M; Machacek, Miranda; Wu, Zhengliang L


    Sulfotransferases are a large group of enzymes that transfer a sulfonate group from the donor substrate, 3'-phosphoadenosine-5'-phosphosulfate (PAPS)(1), to various acceptor substrates, generating 3'-phosphoadenosine-5'-phosphate (PAP) as a by-product. A universal phosphatase-coupled sulfotransferase assay is described here. In this method, Golgi-resident PAP-specific 3'-phosphatase (gPAPP) is used to couple to a sulfotransferase reaction by releasing the 3'-phosphate from PAP. The released phosphate is then detected using malachite green reagents. The enzyme kinetics of gPAPP have been determined, which allows calculation of the coupling rate, the ratio of product-to-signal conversion, of the coupled reaction. This assay is convenient, as it eliminates the need for radioisotope labeling and substrate-product separation, and is more accurate through removal of product inhibition and correction of the results with the coupling rate. This assay is also highly reproducible, as a linear correlation factor above 0.98 is routinely achievable. Using this method, we measured the Michaelis-Menten constants for recombinant human CHST10 and SULT1C4 with the substrates phenolphthalein glucuronic acid and α-naphthol, respectively. The activities obtained with the method were also validated by performing simultaneous radioisotope assays. Finally, the removal of PAP product inhibition by gPAPP was clearly demonstrated in radioisotope assays.

  9. Semiconductor Photocatalysis for Chemoselective Radical Coupling Reactions.

    Kisch, Horst


    Photocatalysis at semiconductor surfaces is a growing field of general photocatalysis because of its importance for the chemical utilization of solar energy. By analogy with photoelectrochemistry the basic mechanism of semiconductor photocatalysis can be broken down into three steps: photogenerated formation of surface redox centers (electron-hole pairs), interfacial electron transfer from and to substrates (often coupled with proton-transfer), and conversion of primary redox intermediates into the products. Sun driven water cleavage and carbon dioxide fixation are still in the state of basic research whereas aerial degradation reactions of pollutants have reached practical application for the cleaning of air. In addition, a great variety of organic transformations (not syntheses) have been reported. They include cis-trans isomerizations, valence isomerizations, cycloaddition reactions, intramolecular or intermolecular C-N and C-C couplings, partial oxidations, and reductions. In all cases, well-known products were formed but very rarely also isolated. As compared to conventional homogeneous organic synthesis, the photocatalytic reaction mode is of no advantage, although the opposite is quite often claimed in the literature. It is also noted that a high quantum yield does not implicate a high product yield, since it is measured at very low substrate conversion in order to minimize secondary photoreactions. That is especially important in semiconductor photocatalysis since photocorrosion of the photocatalyst often prevents long-time irradiation, as is the case for colloidal metal sulfide semiconductors, which in general are photochemically too unstable to be used in synthesis. In this Account, we first classify the numerous organic photoreactions catalyzed by semiconductor powders. The classification is based on easily obtainable experimental facts, namely the nature of the light absorbing reaction component and the reaction stoichiometry. Next we discuss the

  10. Rapid electrochemiluminescence assays of polymerase chain reaction products.

    Kenten, J H; Casadei, J; Link, J; Lupold, S; Willey, J; Powell, M; Rees, A; Massey, R


    We demonstrate the first use of an electrochemiluminescent (ECL) label, [4-(N-succimidyloxycarbonylpropyl)-4'-methyl-2,2'- bipyridine]ruthenium(II) dihexafluorophosphate (Origen label; IGEN Inc.), in DNA probe assays. This label allows rapid (less than 25 min) quantification and detection of polymerase chain reaction (PCR)-amplified products from oncogenes, viruses, and cloned genes. For the PCR, we used labeled oligonucleotide primers complementary to human papiloma virus and the Ha-ras oncogene. These samples were followed by ECL analysis or hybridization with specific, Origen-labeled oligonucleotide probes. These studies demonstrate the speed, specificity, and effectiveness of the new ECL labels, compared with 32P, for nucleic acid probe applications. We describe formats involving conventional methodologies and a new format that requires no wash step, allowing simple and rapid sample analysis. These rapid assays also reduce PCR contamination, by requiring less sample handling. Improvements in ECL detectability are currently under investigation for use in DNA probe assays without amplification.

  11. β-Glucuronidase-coupled assays of glucuronoyl esterases.

    Fraňová, Lucia; Puchart, Vladimír; Biely, Peter


    Glucuronoyl esterases (GEs) are microbial enzymes with potential to cleave the ester bonds between lignin alcohols and xylan-bound 4-O-methyl-d-glucuronic acid in plant cell walls. This activity renders GEs attractive research targets for biotechnological applications. One of the factors impeding the progress in GE research is the lack of suitable substrates. In this work, we report a facile preparation of methyl esters of chromogenic 4-nitrophenyl and 5-bromo-4-chloro-3-indolyl β-D-glucuronides for qualitative and quantitative GE assay coupled with β-glucuronidase as the auxiliary enzyme. The indolyl derivative affording a blue indigo-type product is suitable for rapid and sensitive assay of GE in commercial preparations as well as for high throughput screening of microorganisms and genomic and metagenomic libraries.

  12. A novel assay for monitoring internalization of nanocarrier coupled antibodies

    Pickering Edward M


    Full Text Available Abstract Background Discovery of tumor-selective antibodies or antibody fragments is a promising approach for delivering therapeutic agents to antigen over-expressing cancers. Therefore it is important to develop methods for the identification of target- and function specific antibodies for effective drug delivery. Here we describe a highly selective and sensitive method for characterizing the internalizing potential of multivalently displayed antibodies or ligands conjugated to liposomes into tumor cells. The assay requires minute amounts of histidine-tagged ligand and relies on the non-covalent coupling of these antibodies to fluorescent liposomes containing a metal ion-chelating lipid. Following incubation of cells with antibody-conjugated liposomes, surface bound liposomes are gently removed and the remaining internalized liposomes are quantitated based on fluorescence in a high throughput manner. We have termed this methodology "Chelated Ligand Internalization Assay", or CLIA. Results The specificity of the assay was demonstrated with different antibodies to the ErbB-2 and EGF receptors. Antibody-uptake correlated with receptor expression levels in tumor cell lines with a range of receptor expression. Furthermore, Ni-NTA liposomes containing doxorubicin were used to screen for the ability of antibodies to confer target-specific cytotoxicity. Using an anti-ErbB2 single chain Fv (scFv (F5 antibody, cytotoxicity could be conferred to ErbB2-overexpressing cells; however, a poly(ethylene glycol-linked lipid (DSPE-PEG-NTA-Ni was necessary to allow for efficient loading of the drug and to reduce nonspecific drug leakage during the course of the assay. Conclusion The CLIA method we describe here represents a rapid, sensitive and robust assay for the identification and characterization of tumor-specific antibodies capable of high drug-delivery efficiency when conjugated to liposomal nanocarriers.

  13. Multifold and sequential cross-coupling reactions with indium organometallics.

    Pena, Miguel A; Pérez, Ignacio; Pérez Sestelo, José; Sarandeses, Luis A


    Multifold and sequential palladium-catalyzed cross-coupling reactions can be performed between triorganoindium compounds and oligohaloarenes using only a small excess of the organometallic reagent, low catalyst charge loading and short reaction times.

  14. An enzyme-coupled continuous fluorescence assay for farnesyl diphosphate synthases.

    Dozier, Jonathan K; Distefano, Mark D


    Farnesyl diphosphate synthase (FDPS) catalyzes the conversion of isopentenyl diphosphate and dimethylallyl diphosphate to farnesyl diphosphate, a crucial metabolic intermediate in the synthesis of cholesterol, ubiquinone, and prenylated proteins; consequently, much effort has gone into developing inhibitors that target FDPS. Currently most FDPS assays either use radiolabeled substrates and are discontinuous or monitor pyrophosphate release and not farnesyl diphosphate (FPP) creation. Here we report the development of a continuous coupled enzyme assay for FDPS activity that involves the subsequent incorporation of the FPP product of that reaction into a peptide via the action of protein farnesyltransferase (PFTase). By using a dansylated peptide whose fluorescence quantum yield increases upon farnesylation, the rate of FDPS-catalyzed FPP production can be measured. We show that this assay is more sensitive than existing coupled assays, that it can be used to conveniently monitor FDPS activity in a 96-well plate format, and that it can reproduce IC(50) values for several previously reported FDPS inhibitors. This new method offers a simple, safe, and continuous method to assay FDPS activity that should greatly facilitate the screening of inhibitors of this important target.

  15. Multiplex DNA assay based on nanoparticle probes by single particle inductively coupled plasma mass spectrometry.

    Zhang, Shixi; Han, Guojun; Xing, Zhi; Zhang, Sichun; Zhang, Xinrong


    A multiplex DNA assay based on nanoparticle (NP) tags detection utilizing single particle mode inductively coupled plasma mass spectrometry (SP-ICP-MS) as ultrasensitive readout has been demonstrated in the article. Three DNA targets associated with clinical diseases (HIV, HAV, and HBV) down to 1 pM were detected by DNA probes labeled with AuNPs, AgNPs, and PtNPs via DNA sandwich assay. Single nucleotide polymorphisms in genes can also be effectively discriminated. Since our method is unaffected by the sample matrix, it is well-suited for diagnostic applications. Moreover, with the high sensitivity of SP-ICP-MS and the variety of NPs detectable by SP-ICP-MS, high-throughput DNA assay could be achieved without signal amplification or chain reaction amplification.

  16. Catalytic imine-imine cross-coupling reactions.

    Matsumoto, Masatoshi; Harada, Masashi; Yamashita, Yasuhiro; Kobayashi, Shū


    We report here efficient catalytic imine-imine cross-coupling reactions based on an umpolung strategy; an imine bearing a 9-fluorenyl moiety on its nitrogen atom, which acted as a nucleophile, reacted with another imine to afford an imine-imine cross-coupling adduct in high yield. Furthermore, a chiral guanidine acted as a chiral catalyst for these coupling reactions, and optically active 1,2-diamines were obtained in high yields with high enantioselectivities.

  17. A Database of Reaction Monitoring Mass Spectrometry Assays for Elucidating Therapeutic Response in Cancer

    Remily-Wood, Elizabeth R.; Liu, Richard Z.; Xiang, Yun; Chen, Yi; Thomas, C. Eric; Rajyaguru, Neal; Kaufman, Laura M.; Ochoa, Joana E.; Hazlehurst, Lori; Pinilla-Ibarz, Javier; Lancet, Jeffrey; Zhang, Guolin; Haura, Eric; Shibata, David; Yeatman, Timothy; Smalley, Keiran S.M.; Dalton, William S.; Huang, Emina; Scott, Ed; Bloom, Gregory C.; Eschrich, Steven A.; Koomen, John M.


    Purpose The Quantitative Assay Database (QuAD),, facilitates widespread implementation of quantitative mass spectrometry in cancer biology and clinical research through sharing of methods and reagents for monitoring protein expression and modification. Experimental Design Liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM) assays are developed using SDS-PAGE fractionated lysates from cancer cell lines. Pathway maps created using GeneGO Metacore provide the biological relationships between proteins and illustrate concepts for multiplexed analysis; each protein can be selected to examine assay development at the protein and peptide level. Results The coupling of SDS-PAGE and LC-MRM screening has been used to detect 876 peptides from 218 cancer-related proteins in model systems including colon, lung, melanoma, leukemias, and myeloma, which has led to the development of 95 quantitative assays including stable-isotope labeled peptide standards. Methods are published online and peptide standards are made available to the research community. Protein expression measurements for heat shock proteins, including a comparison with ELISA and monitoring response to the HSP90 inhibitor, 17-DMAG, are used to illustrate the components of the QuAD and its potential utility. Conclusions and Clinical Relevance This resource enables quantitative assessment of protein components of signaling pathways and biological processes and holds promise for systematic investigation of treatment responses in cancer. PMID:21656910

  18. Recent advances in copper-catalyzed asymmetric coupling reactions

    Fengtao Zhou


    Full Text Available Copper-catalyzed (or -mediated asymmetric coupling reactions have received significant attention over the past few years. Especially the coupling reactions of aryl or alkyl halides with nucleophiles became a very powerful tool for the formation of C–C, C–N, C–O and other carbon–heteroatom bonds as well as for the construction of heteroatom-containing ring systems. This review summarizes the recent progress in copper-catalyzed asymmetric coupling reactions for the formation of C–C and carbon–heteroatom bonds.

  19. A diagnostic polymerase chain reaction assay for Zika virus.

    Balm, Michelle N D; Lee, Chun Kiat; Lee, Hong Kai; Chiu, Lily; Koay, Evelyn S C; Tang, Julian W


    Zika virus (ZIKV) is a mosquito-borne flavivirus. Infection results in a dengue-like illness with fever, headache, malaise, and a maculopapular rash. Nearly all cases are mild and self-limiting but in 2007, a large outbreak of ZIKV was reported from the island of Yap (in Micronesia, northwest of Indonesia). Singapore is already endemic for dengue, and its impact on public health and economic burden is significant. Other dengue-like infections (e.g., Chikungunya virus) are present. Yet only 10% of reported dengue cases have laboratory confirmation. The identification and control of other dengue-like, mosquito-transmitted infections is thus important for the health of Singapore's population, as well as its economy. Given that ZIKV shares the same Aedes mosquito vector with both dengue and Chikungunya, it is possible that this virus is present in Singapore and causing some of the mild dengue-like illness. A specific and sensitive one-step, reverse transcription polymerase chain reaction (RT-PCR) with an internal control (IC) was designed and tested on 88 archived samples of dengue-negative, Chikungunya-negative sera from patients presenting to our hospital with a dengue-like illness, to determine the presence of ZIKV in Singapore. The assay was specific for detection of ZIKV and displayed a lower limit of detection (LoD) of 140 copies viral RNA/reaction when tested on synthetic RNA standards prepared using pooled negative patient plasma. Of the 88 samples tested, none were positive for ZIKV RNA, however, the vast majority of these were from patients admitted to hospital and further study may be warranted in community-based environments.

  20. Coupled chemo(enzymatic reactions in continuous flow

    Ruslan Yuryev


    Full Text Available This review highlights the state of the art in the field of coupled chemo(enzymatic reactions in continuous flow. Three different approaches to such reaction systems are presented herein and discussed in view of their advantages and disadvantages as well as trends for their future development.

  1. Minimal coupling schemes in N-body reaction theory

    Picklesimer, A.; Tandy, P. C.; Thaler, R. M.


    A new derivation of the N-body equations of Bencze, Redish, and Sloan is obtained through the use of Watson-type multiple scattering techniques. The derivation establishes an intimate connection between these partition-labeled N-body equations and the particle-labeled Rosenberg equations. This result yields new insight into the implicit role of channel coupling in, and the minimal dimensionality of, the partition-labeled equations. NUCLEAR REACTIONS Scattering theory, multiple scattering, connected kernel reaction theory, minimal coupling, coupling schemes.

  2. Coriolis coupling and nonadiabaticity in chemical reaction dynamics.

    Wu, Emilia L


    The nonadiabatic quantum dynamics and Coriolis coupling effect in chemical reaction have been reviewed, with emphasis on recent progress in using the time-dependent wave packet approach to study the Coriolis coupling and nonadiabatic effects, which was done by K. L. Han and his group. Several typical chemical reactions, for example, H+D(2), F+H(2)/D(2)/HD, D(+)+H(2), O+H(2), and He+H(2)(+), have been discussed. One can find that there is a significant role of Coriolis coupling in reaction dynamics for the ion-molecule collisions of D(+)+H(2), Ne+H(2)(+), and He+H(2)(+) in both adiabatic and nonadiabatic context.

  3. Coriolis Coupling Influence on the H+LiH Reaction

    Zhai, Hongsheng; Liu, Yufang [Henan Normal Univ., Xinxiang (China); Li, Wenliang [Key Laboratory at Universities of Education, Urumqi (China)


    We have reported the reaction probability, integral reaction cross section, and rate constant for the title system calculated with the aid of a time-dependent wave packet approach. The ab initio potential energy surface (PES) of Prudente et al. (Chem. Phys. Lett. 2009, 474, 18) is employed for the purpose. The calculations are carried out over the collision energy range of 0.05-1.4 eV for the two reaction channels of H + LiH → Li + H{sub 2} and H{sub b} + LiH{sub a} → LiH{sub b} + H{sub a}. The Coriolis coupling (CC) effect are taken into account. The importance of including the Coriolis coupling quantum scattering calculations are revealed by the comparison between the Coriolis coupling and the centrifugal sudden (CS) approximation calculations.

  4. Effect of Coriolis coupling in chemical reaction dynamics.

    Chu, Tian-Shu; Han, Ke-Li


    It is essential to evaluate the role of Coriolis coupling effect in molecular reaction dynamics. Here we consider Coriolis coupling effect in quantum reactive scattering calculations in the context of both adiabaticity and nonadiabaticity, with particular emphasis on examining the role of Coriolis coupling effect in reaction dynamics of triatomic molecular systems. We present the results of our own calculations by the time-dependent quantum wave packet approach for H + D2 and F(2P3/2,2P1/2) + H2 as well as for the ion-molecule collisions of He + H2 +, D(-) + H2, H(-) + D2, and D+ + H2, after reviewing in detail other related research efforts on this issue.

  5. Dynamic signaling cascades: reversible covalent reaction-coupled molecular switches.

    Ren, Yulong; You, Lei


    The research of systems chemistry exploring complex mixtures of interacting synthetic molecules has been burgeoning recently. Herein we demonstrate for the first time the coupling of molecular switches with a dynamic covalent reaction (DCR) and the modulation of created chemical cascades with a variety of inputs, thus closely mimicking a biological signaling system. A novel Michael type DCR of 10-methylacridinium perchlorate and monothiols exhibiting excellent regioselectivity and tunable affinity was discovered. A delicate balance between the unique reactivity of the reactant and the stability of the adduct leads to the generation of a strong acid in a thermodynamically controlled system. The dynamic cascade was next created via coupling of the DCR and a protonation-induced configurational switch (E/Z isomerization) through a proton relay. Detailed examination of the interdependence of the equilibrium enabled us to rationally optimize the cascade and also shed light on the possible intermediate of the switching process. Furthermore, relative independence of the coupled reactions was verified by the identification of stimuli that are able to facilitate one reaction but suppress the other. To further enhance systematic complexity, a second DCR of electrophilic aldehydes and thiols was employed for the reversible inhibition of the binary system, thus achieving the interplay of multiple equilibria. Finally, a fluorescence switch was turned on through coupling with the DCR, showcasing the versatility of our strategy. The results described herein should pave the way for the exploitation of multifunctional dynamic covalent cascades.

  6. Polymer-coated palladium nanoparticle catalysts for Suzuki coupling reactions.

    Bortolotto, Tanize; Facchinetto, Sara Elisa; Trindade, Suelen Gauna; Ossig, Andreia; Petzhold, Cesar Liberato; Vargas, Josimar; Rodrigues, Oscar Endrigo Dorneles; Giacomelli, Cristiano; Schmidt, Vanessa


    A set of seven different palladium nanoparticle (PdNP) systems stabilized by small amounts (1.0mg/mL) of structurally related macromolecular capping agents were comparatively tested as catalyst in p-nitrophenol (Nip) reduction and Suzuki cross-coupling reactions. The observed rate constants (kobs) for Nip reduction were in the range of 0.052-3.120×10(-2)s(-1), and the variation reflected the effects of polymer chain conformation, ionic strength and palladium-polymer complex coordination. Macromolecules featuring pendant pyridyl moieties or inverse temperature-dependent solubility were found to be unsuitable capping agents for PdNPs catalysts, despite being active. The catalytic activity in Suzuki cross-coupling reactions followed the same behavior; the most active particles in the Nip reaction also mediated the cross-coupling reaction providing the expected products in quantitative yields under relatively mild conditions after only 4h at 50°C. Experiments involving the successive addition of reactants and catalyst recovery/re-use indicated that the recycling potential was comparable to those of the standards used in this field.

  7. Artificial photosynthetic reaction centers coupled to light-harvesting antennas.

    Ghosh, Pulak Kumar; Smirnov, Anatoly Yu; Nori, Franco


    We analyze a theoretical model for energy and electron transfer in an artificial photosynthetic system. The photosystem consists of a molecular triad (i.e., with a donor, a photosensitive unit, and an acceptor) coupled to four accessory light-harvesting-antenna pigments. The resonant energy transfer from the antennas to the artificial reaction center (the molecular triad) is described here by the Förster mechanism. We consider two different kinds of arrangements of the accessory light-harvesting pigments around the reaction center. The first arrangement allows direct excitation transfer to the reaction center from all the surrounding pigments. The second configuration transmits energy via a cascade mechanism along a chain of light-harvesting chromophores, where only one chromophore is connected to the reaction center. We show that the artificial photosynthetic system using the cascade energy transfer absorbs photons in a broader wavelength range and converts their energy into electricity with a higher efficiency than the system based on direct couplings between all the antenna chromophores and the reaction center.

  8. Technical note: optimization of lactose quantification based on coupled enzymatic reactions.

    Condezo-Hoyos, Luis; Mohanty, Indira P; Noratto, Giuliana D


    A colorimetric microplate-adapted lactose assay was developed to quantify lactose in dairy products. The assay was based on the coupled enzymatic reaction of β-galactosidase-glucose oxidase-horseradish peroxidase using Amplex red as detection probe. The assay showed good linearity in the range of 0.1 to 0.5mmol of lactose/L, with a limit of detection of 0.0433mmol/L and a limit of quantification of 0.1313mmol/L. The lactose assay at optimized conditions (5 U of β-galactosidase/mL, 5 U of glucose oxidase/mL, 1 U of horseradish peroxidase/mL, and 100μmol of Amplex red/L for 1h at 37°C in the dark) showed good correlation with a commercial lactose enzymatic kit with intraassay variation below 10% and interassay variations below 7.6%. The developed lactose microplate assay can be adopted as routine analysis for lactose determination in dairy products due to its relatively low cost compared with a commercial kit, relatively short reaction time, and high sensitivity and reproducibility.

  9. Enzyme catalysis-electrophoresis titration for multiplex enzymatic assay via moving reaction boundary chip.

    Zhong, Ran; Xie, Haiyang; Kong, Fanzhi; Zhang, Qiang; Jahan, Sharmin; Xiao, Hua; Fan, Liuyin; Cao, Chengxi


    In this work, we developed the concept of enzyme catalysis-electrophoresis titration (EC-ET) under ideal conditions, the theory of EC-ET for multiplex enzymatic assay (MEA), and a related method based on a moving reaction boundary (MRB) chip with a collateral channel and cell phone imaging. As a proof of principle, the model enzymes horseradish peroxidase (HRP), laccase and myeloperoxidase (MPO) were chosen for the tests of the EC-ET model. The experiments revealed that the EC-ET model could be achieved via coupling EC with ET within a MRB chip; particularly the MEA analyses of catalysis rate, maximum rate, activity, Km and Kcat could be conducted via a single run of the EC-ET chip, systemically demonstrating the validity of the EC-ET theory. Moreover, the developed method had these merits: (i) two orders of magnitude higher sensitivity than a fluorescence microplate reader, (ii) simplicity and low cost, and (iii) fairly rapid (30 min incubation, 20 s imaging) analysis, fair stability (<5.0% RSD) and accuracy, thus validating the EC-ET method. Finally, the developed EC-ET method was used for the clinical assay of MPO activity in blood samples; the values of MPO activity detected via the EC-ET chip were in agreement with those obtained by a traditional fluorescence microplate reader, indicating the applicability of the EC-ET method. The work opens a window for the development of enzymatic research, enzyme assay, immunoassay, and point-of-care testing as well as titration, one of the oldest methods of analysis, based on a simple chip.

  10. Application of Enzyme Coupling Reactions to Shift Thermodynamically Limited Biocatalytic Reactions

    Abu, Rohana; Woodley, John M.


    shift the equilibrium of otherwise thermodynamically unfavourable reactions to give a higher conversion of the target product. By coupling an energetically unfavourable reaction with a more favourable one, the multi-enzyme cascade mimics the approach taken in nature in metabolic pathways. Nevertheless......, it can be challenging to combine several engineered enzymes in vitro for the conversion of non-natural substrates. In this mini-review we focus on enzyme coupling reactions as a tool to alleviate thermodynamic constraints in synthetically useful biocatalytic reactions. The implications of thermodynamic...... parameters such as the equilibrium constant on the multienzyme cascades and the conventional methods of equilibrium shifting are also discussed in addition to methods used to estimate such values....

  11. Plasmonic harvesting of light energy for Suzuki coupling reactions.

    Wang, Feng; Li, Chuanhao; Chen, Huanjun; Jiang, Ruibin; Sun, Ling-Dong; Li, Quan; Wang, Jianfang; Yu, Jimmy C; Yan, Chun-Hua


    The efficient use of solar energy has received wide interest due to increasing energy and environmental concerns. A potential means in chemistry is sunlight-driven catalytic reactions. We report here on the direct harvesting of visible-to-near-infrared light for chemical reactions by use of plasmonic Au-Pd nanostructures. The intimate integration of plasmonic Au nanorods with catalytic Pd nanoparticles through seeded growth enabled efficient light harvesting for catalytic reactions on the nanostructures. Upon plasmon excitation, catalytic reactions were induced and accelerated through both plasmonic photocatalysis and photothermal conversion. Under the illumination of an 809 nm laser at 1.68 W, the yield of the Suzuki coupling reaction was ~2 times that obtained when the reaction was thermally heated to the same temperature. Moreover, the yield was also ~2 times that obtained from Au-TiOx-Pd nanostructures under the same laser illumination, where a 25-nm-thick TiOx shell was introduced to prevent the photocatalysis process. This is a more direct comparison between the effect of joint plasmonic photocatalysis and photothermal conversion with that of sole photothermal conversion. The contribution of plasmonic photocatalysis became larger when the laser illumination was at the plasmon resonance wavelength. It increased when the power of the incident laser at the plasmon resonance was raised. Differently sized Au-Pd nanostructures were further designed and mixed together to make the mixture light-responsive over the visible to near-infrared region. In the presence of the mixture, the reactions were completed within 2 h under sunlight, while almost no reactions occurred in the dark.

  12. Coupled electrochemical reactions at bipolar microelectrodes and nanoelectrodes.

    Guerrette, Joshua P; Oja, Stephen M; Zhang, Bo


    Here we report the voltammetric study of coupled electrochemical reactions on microelectrodes and nanoelectrodes in a closed bipolar cell. We use steady-state cyclic voltammetry to discuss the overall voltammetric response of closed bipolar electrodes (BPEs) and understand its dependence on the concentration of redox species and electrode size. Much of the previous work in bipolar electroanalytical chemistry has focused on the use of an "open" cell with the BPE located in an open microchannel. A closed BPE, on the other hand, has two poles placed in separate compartments and has remained relatively unexplored in this field. In this work, we demonstrated that carbon-fiber microelectrodes when backfilled with an electrolyte to establish conductivity are closed BPEs. The coupling between the oxidation reaction, e.g., dopamine oxidation, on the carbon disk/cylinder and the reduction of oxygen on the interior fiber is likely to be responsible for the conductivity. We also demonstrated the ability to quantitatively measure voltammetric properties of both the cathodic and anodic poles in a closed bipolar cell from a single cyclic voltammetry (CV) scan. It was found that "secondary" reactions such as oxygen reduction play an important role in this process. We also described the fabrication and use of Pt bipolar nanoelectrodes which may serve as a useful platform for future advances in nanoscale bipolar electrochemistry.

  13. A multiplex real-time polymerase chain reaction assay to diagnose Epiphyas postvittana (Lepidoptera: Tortricidae).

    Barr, N B; Ledezma, L A; Farris, R E; Epstein, M E; Gilligan, T M


    A molecular assay for diagnosis of light brown apple moth, Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae), in North America is reported. The assay multiplexes two TaqMan real-time polymerase chain reaction (RT-PCR) probe systems that are designed to target DNA segments of the internal transcribed spacer region 2 (ITS2) and 18S rRNA gene. The RT-PCR probe designed for the 18S target recognizes a DNA sequence conserved in all of the moths included in the study and functions as a control in the assay. The second probe recognizes a segment of the ITS2 specifically found in E. postvittana and not found in the other moths included in the study, i.e., this segment is not conserved. Inclusion of the two markers in a single multiplex reaction did not affect assay performance. The assay was tested against 637 moths representing > 90 taxa in 15 tribes in all three subfamilies in the Tortricidae. The assay generated no false negatives based on analysis of 355 E. postvittana collected from California, Hawaii, England, New Zealand, and Australia. Analysis of a data set including 282 moths representing 41 genera generated no false positives. Only three inconclusive results were generated from the 637 samples. Spike experiments demonstrated that DNA contamination in the assay can affect samples differently. Contaminated samples analyzed with the ITS2 RT-PCR assay and DNA barcode methodology by using the cytochrome oxidase I gene can generate contradictory diagnoses.

  14. Development of a polymerase chain reaction assay for the detection of pseudorabies virus in clinical samples

    Lester J Pérez; Heidy Díaz de Arce


    Aujeszky's disease, also known as pseudorabies causes severe economic losses in swine industry and affects the pig husbandry all over the world. The conventional diagnostic procedure is time-consuming and false-negative results may occur in submissions from latently infected animals. The development, optimization and evaluation of a polymerase chain reaction (PCR) assay are presented for the diagnosis of pseudorabies infection. This assay was based on the amplification of a highly conserved v...

  15. A reverse transcription-polymerase chain reaction assay for the detection of avian pneumovirus (Colorado strain).

    Ali, A; Reynolds, D L


    A reverse transcription-polymerase chain reaction assay was developed for the detection of avian pneumovirus (Colorado strain) (APV-Col). The specific primers were designed from the published sequence of the matrix protein gene of APV-Col. The primers amplified a product of 631 nucleotides from APV-Col. The assay identified only APV-Col and did not react with Newcastle disease virus and infectious bronchitis virus.

  16. Multiple reaction monitoring and multiple reaction monitoring cubed based assays for the quantitation of apolipoprotein F.

    Kumar, Abhinav; Gangadharan, Bevin; Zitzmann, Nicole


    Apolipoprotein F (APO-F) is a novel low abundance liver fibrosis biomarker and its concentration decreases in human serum and plasma across liver fibrosis stages. Current antibody based assays for APO-F suffer from limitations such as unspecific binding, antibody availability and undetectable target if the protein is degraded; and so an antibody-free assay has the potential to be a valuable diagnostic tool. We report an antibody-free, rapid, sensitive, selective and robust LC-MS/MS (MRM and MRM(3)) method for the detection and quantitation of APO-F in healthy human plasma. With further analysis of clinical samples, this LC-MS based method could be established as the first ever antibody-free biomarker assay for liver fibrosis. We explain the use of Skyline software for peptide selection and the creation of a reference library to aid in true peak identification of endogenous APO-F peptides in digests of human plasma without protein or peptide enrichment. Detection of a glycopeptide using MRM-EPI mode and reduction of interferences using MRM3 are explained. The amount of APO-F in human plasma from a healthy volunteer was determined to be 445.2ng/mL, the coefficient of variation (CV) of precision for 20 injections was <12% and the percentage error of each point along the calibration curve was calculated to be <8%, which is in line with the assay requirements for clinical samples.

  17. Chemiluminescence assay of lipase activity using a synthetic substrate as proenhancer for luminol chemiluminescence reaction.

    Ichibangase, Tomoko; Ohba, Yoshihito; Kishikawa, Naoya; Nakashima, Kenichiro; Kuroda, Naotaka


    A novel chemiluminescence (CL) assay method for lipase (triacylglycerol lipase, E.C. activity was developed by using the lauric acid ester of 2-(4-hydroxyphenyl)-4,5-diphenylimidazole (HDI) as a substrate. The method is based on the enhanced CL reaction of luminol-hydrogen peroxide-horseradish peroxidase (HRP) with HDI that is liberated from the substrate by enzymatic hydrolysis. To simplify the assay procedure, both the hydrolysis of the substrate and the enhanced CL reaction were performed in the same reaction mixture. Lipases from Candida cylindracea and porcine pancreas were successfully determined with the detection limits (blank signal + 3 SD) of 0.05 and 50.0 mU/tube, respectively. The method is simple and rapid, permitting the completion of single assay within 5 min. The reproducibilities obtained with replicate assays were relative standard deviations (RSDs) of 4.7% for within-day and 6.0% for between-day assays.

  18. A polymerase chain reaction assay for ascosporic inoculum of Sclerotinia species

    A PCR assay was developed which amplified a 170-bp fragment of the intergenic spacer region of Sclerotinia sclerotiorum, the cause of white mould. Sensitivity was 10 S. sclerotiorum ascospores per DNA extraction (0.2 ascospores per PCR reaction). The presence of soil did not affect sensitivity a...

  19. Study of the optimal reaction conditions for assay of the mouse alternative complement pathway

    Dijk, H. van; Rademaker, P.M.; Klerx, J.P.A.M.; Willers, J.M.M.


    The optimal reaction conditions for hemolytic assay of alternative complement pathway activity in mouse serum were investigated. A microtiter system was used, in which a number of 7.5×106 rabbit erythrocytes per test well appeared to be optimal. Rabbit erythrocytes were superior as target cells over

  20. Monitoring Acidophilic Microbes with Real-Time Polymerase Chain Reaction (PCR) Assays

    Frank F. Roberto


    Many techniques that are used to characterize and monitor microbial populations associated with sulfide mineral bioleaching require the cultivation of the organisms on solid or liquid media. Chemolithotrophic species, such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, or thermophilic chemolithotrophs, such as Acidianus brierleyi and Sulfolobus solfataricus can grow quite slowly, requiring weeks to complete efforts to identify and quantify these microbes associated with bioleach samples. Real-time PCR (polymerase chain reaction) assays in which DNA targets are amplified in the presence of fluorescent oligonucleotide primers, allowing the monitoring and quantification of the amplification reactions as they progress, provide a means of rapidly detecting the presence of microbial species of interest, and their relative abundance in a sample. This presentation will describe the design and use of such assays to monitor acidophilic microbes in the environment and in bioleaching operations. These assays provide results within 2-3 hours, and can detect less than 100 individual microbial cells.

  1. Tips on the analysis of phosphatidic acid by the fluorometric coupled enzyme assay.

    Hassaninasab, Azam; Han, Gil-Soo; Carman, George M


    The fluorometric coupled enzyme assay to measure phosphatidic acid (PA) involves the solubilization of extracted lipids in Triton X-100, deacylation, and the oxidation of PA-derived glycerol-3-phosphate to produce hydrogen peroxide for conversion of Amplex Red to resorufin. The enzyme assay is sensitive, but plagued by high background fluorescence from the peroxide-containing detergent and incomplete heat inactivation of lipoprotein lipase. These problems affecting the assay reproducibility were obviated by the use of highly pure Triton X-100 and by sufficient heat inactivation of the lipase enzyme. The enzyme assay could accurately measure the PA content from the subcellular fractions of yeast cells. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Theoretical Study on the Mechanism of Sonogashira Coupling Reaction

    CHEN Li-Ping; HONG San-Guo; HOU Hao-Qing


    The mechanism of palladium-catalyzed Sonogashira cross-coupling reaction has been studied theoretically by DFT (density functional theory) calculations. The model system studied consists of Pd(PH3)2 as the starting catalyst complex, phenyl bromide as the substrate and acetylene as the terminal alkyne, without regarding to the co-catalyst and base. Mechanistically and energetically plausible catalytic cycles for the cross-coupling have been identified. The DFT analysis shows that the catalytic cycle occurs in three stages: oxidative addition of phenyl bromide to the palladium center, alkynylation of palladium(II) intermediate, and reductive elimination to phenylacetylene. In the oxidative addition, the neutral and anionic pathways have been investigated, which could both give rise to cis-configured palladium(II) diphosphine intermediate. Starting from the palladium(II) diphosphine intermediate, the only identifiable pathway in alkynylation involves the dissociation of Br group and the formation of square-planar palladium(II) intermediate, in which the phenyl and alkynyl groups are oriented cis to each other. Due to the close proximity of phenyl and alkynyl groups, the reductive elimination of phenylacetylene proceeds smoothly.

  3. Coriolis-coupled wave packet dynamics of H + HLi reaction.

    Padmanaban, R; Mahapatra, S


    We investigated the effect of Coriolis coupling (CC) on the initial state-selected dynamics of H+HLi reaction by a time-dependent wave packet (WP) approach. Exact quantum scattering calculations were obtained by a WP propagation method based on the Chebyshev polynomial scheme and ab initio potential energy surface of the reacting system. Partial wave contributions up to the total angular momentum J=30 were found to be necessary for the scattering of HLi in its vibrational and rotational ground state up to a collision energy approximately 0.75 eV. For each J value, the projection quantum number K was varied from 0 to min (J, K(max)), with K(max)=8 until J=20 and K(max)=4 for further higher J values. This is because further higher values of K do not have much effect on the dynamics and also because one wishes to maintain the large computational overhead for each calculation within the affordable limit. The initial state-selected integral reaction cross sections and thermal rate constants were calculated by summing up the contributions from all partial waves. These were compared with our previous results on the title system, obtained within the centrifugal sudden and J-shifting approximations, to demonstrate the impact of CC on the dynamics of this system.

  4. A novel reverse flow reactor coupling endothermic and exothermic reactions. Part II: sequential reactor configuration for reversible endothermic reactions

    Sint Annaland, van M.; Scholts, H.A.R.; Kuipers, J.A.M.; Swaaij, van W.P.M.


    The new reactor concept for highly endothermic reactions at elevated temperatures with possible rapid catalyst deactivation based on the indirect coupling of endothermic and exothermic reactions in reverse flow, developed for irreversible reactions in Part I, has been extended to reversible endother

  5. A novel reverse flow reactor coupling endothermic and exothermic reactions. Part II: sequential reactor configuration for reversible endothermic reactions

    van Sint Annaland, M.; Scholts, H.A.R.; Kuipers, J.A.M.; van Swaaij, Willibrordus Petrus Maria


    The new reactor concept for highly endothermic reactions at elevated temperatures with possible rapid catalyst deactivation based on the indirect coupling of endothermic and exothermic reactions in reverse flow, developed for irreversible reactions in Part I, has been extended to reversible

  6. Rapid detection of microbial DNA by a novel isothermal genome exponential amplification reaction (GEAR) assay.

    Prithiviraj, Jothikumar; Hill, Vincent; Jothikumar, Narayanan


    In this study we report the development of a simple target-specific isothermal nucleic acid amplification technique, termed genome exponential amplification reaction (GEAR). Escherichia coli was selected as the microbial target to demonstrate the GEAR technique as a proof of concept. The GEAR technique uses a set of four primers; in the present study these primers targeted 5 regions on the 16S rRNA gene of E. coli. The outer forward and reverse Tab primer sequences are complementary to each other at their 5' end, whereas their 3' end sequences are complementary to their respective target nucleic acid sequences. The GEAR assay was performed at a constant temperature 60 °C and monitored continuously in a real-time PCR instrument in the presence of an intercalating dye (SYTO 9). The GEAR assay enabled amplification of as few as one colony forming units of E. coli per reaction within 30 min. We also evaluated the GEAR assay for rapid identification of bacterial colonies cultured on agar media directly in the reaction without DNA extraction. Cells from E. coli colonies were picked and added directly to GEAR assay mastermix without prior DNA extraction. DNA in the cells could be amplified, yielding positive results within 15 min.

  7. Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM).

    Schiffmann, Christian; Hansen, Rasmus; Baumann, Sven; Kublik, Anja; Nielsen, Per Halkjær; Adrian, Lorenz; von Bergen, Martin; Jehmlich, Nico; Seifert, Jana


    Targeted absolute protein quantification yields valuable information about physiological adaptation of organisms and is thereby of high interest. Especially for this purpose, two proteomic mass spectrometry-based techniques namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM) are commonly applied. The objective of this study was to establish an optimal quantification assay for proteins with the focus on those involved in housekeeping functions and putative reductive dehalogenase proteins from the strictly anaerobic bacterium Dehalococcoides mccartyi strain CBDB1. This microbe is small and slow-growing; hence, it provides little biomass for comprehensive proteomic analysis. We therefore compared SRM and PRM techniques. Eleven peptides were successfully quantified by both methods. In addition, six peptides were solely quantified by SRM and four by PRM, respectively. Peptides were spiked into a background of Escherichia coli lysate and the majority of peptides were quantifiable down to 500 amol absolute on column by both methods. Peptide quantification in CBDB1 lysate resulted in the detection of 15 peptides using SRM and 14 peptides with the PRM assay. Resulting quantification of five dehalogenases revealed copy numbers of <10 to 115 protein molecules per cell indicating clear differences in abundance of RdhA proteins during growth on hexachlorobenzene. Our results indicated that both methods show comparable sensitivity and that the combination of the mass spectrometry assays resulted in higher peptide coverage and thus more reliable protein quantification.

  8. Gold(III)-catalyzed three-component coupling reaction (TCC) selective toward furans.

    Li, Jian; Liu, Li; Ding, Dong; Sun, Jiangtao; Ji, Yangxuan; Dong, Jialing


    An efficient three-component coupling reaction toward a variety of furan derivatives has been developed. This cascade transformation proceeds via the gold-catalyzed coupling reaction of phenylglyoxal derivatives, secondary amines, and terminal alkynes, under the reaction conditions, that undergoes cyclization into the furan core.

  9. Application of a coupled enzyme assay to characterize nicotinamide riboside kinases.

    Dölle, Christian; Ziegler, Mathias


    The recently identified nicotinamide riboside kinases (Nrks) constitute a distinct pathway of nicotinamide adenine dinucleotide (NAD) biosynthesis. Here we present the combination of an established optical adenosine triphosphatase (ATPase) test, the pyruvate kinase/lactate dehydrogenase system, with the Nrk-catalyzed reaction to determine kinetic properties of these enzymes, in particular affinities for ATP. The assay allows variation of both nucleoside and phosphate donor substrates, thereby providing major advantages for the characterization of these enzymes. We confirm previously established kinetic parameters and identify differences in substrate selectivity between the two human Nrk isoforms. The proposed assay is inexpensive and may be applied for high-throughput screening.

  10. High content screening for G protein-coupled receptors using cell-based protein translocation assays

    Grånäs, Charlotta; Lundholt, Betina Kerstin; Heydorn, Arne


    G protein-coupled receptors (GPCRs) have been one of the most productive classes of drug targets for several decades, and new technologies for GPCR-based discovery promise to keep this field active for years to come. While molecular screens for GPCR receptor agonist- and antagonist-based drugs...... as valuable discovery tools for several years. The application of high content cell-based screening to GPCR discovery has opened up additional possibilities, such as direct tracking of GPCRs, G proteins and other signaling pathway components using intracellular translocation assays. These assays provide...... the capability to probe GPCR function at the cellular level with better resolution than has previously been possible, and offer practical strategies for more definitive selectivity evaluation and counter-screening in the early stages of drug discovery. The potential of cell-based translocation assays for GPCR...

  11. Suzuki-Miyaura cross-coupling coupling reactions with low catalyst loading: A green and sustainable protocol in pure water

    Fihri, Aziz


    The Suzuki-Miyaura coupling reaction represents one of the most important synthetic transformations developed in the 20th century. However, the use of toxic organic solvents remains a scientific challenge and an aspect of economical and ecological relevance, and benign water as a reaction medium was found to be highly effective to overcome some of these issues. In the present manuscript, we described Suzuki-Miyaura coupling reactions in neat water, without using any phase transfer reagent. Notably, this protocol also works with ultra-low loading of catalyst with high turnover numbers and also able to couple challenging substrates like aryl chlorides. © 2011 The Royal Society of Chemistry.

  12. Acanthamoeba can be differentiated by the polymerase chain reaction and simple plating assays.

    Khan, N A; Jarroll, E L; Paget, T A


    Acanthamoeba are opportunistic pathogens with invasive and noninvasive species. For clinical purposes it is important to differentiate potentially pathogenic from nonpathogenic isolates. For the rapid and sensitive identification of Acanthamoeba at the genus level, we used a polymerase chain reaction (PCR)-based method which detected as few as five cells. Further, we tested nine isolates of Acanthamoeba for their ability to produce cytopathic effects (CPE) on corneal epithelial cells. On the basis of the results, Acanthamoeba were divided into pathogenic or nonpathogenic groups. However, because CPE assays are not available to every diagnostic laboratory, we developed a simple plating assay based on osmotolerance which correlated well with the CPE assays. Pathogenic Acanthamoeba showed growth on higher osmolarity (agar plates containing one molar mannitol), while growth of nonpathogens was inhibited on these plates. In conclusion, we have developed methods for the rapid identification and differentiation of Acanthamoeba.

  13. Impact of phonon coupling on the radiative nuclear reaction characteristics

    Achakovskiy, Oleg; Kamerdzhiev, Sergei


    The pygmy dipole resonance and photon strength functions (PSF) in stable and unstable Ni and Sn isotopes are calculated within the microscopic self-consistent version of the extended theory of finite fermi systems in the quasiparticle time blocking approximation. The approach includes phonon coupling (PC) effects in addition to the standard QRPA approach. The Skyrme force SLy4 is used. A pygmy dipole resonance in 72Ni is predicted at the mean energy of 12.4 MeV exhausting 25.7% of the total energy-weighted sum rule. With our microscopic E1 PSFs in the EMPIRE 3.1 code, the following radiative nuclear reaction characteristics have been calculated for several stable and unstable even-even Sn and Ni isotopes: 1) neutron capture cross sections, 2) corresponding neutron capture gamma-spectra, 3) average radiative widths of neutron resonances. Here, three variants of the microscopic nuclear level density models have been used and a comparison with the phenomenological generalized superfluid model (GSM) has been perf...

  14. Impact of phonon coupling on the radiative nuclear reaction characteristics

    Achakovskiy Oleg


    Full Text Available The pygmy dipole resonance and photon strength functions (PSF in stable and unstable Ni and Sn isotopes are calculated within the microscopic self-consistent version of the extended theory of finite Fermi systems in the quasiparticle time blocking approximation. The approach includes phonon coupling (PC effects in addition to the standard QRPA approach. The Skyrme force SLy4 is used. A pygmy dipole resonance in 72Ni is predicted at the mean energy of 12.4 MeV exhausting 25.7% of the total energy-weighted sum rule. With our microscopic E1 PSFs in the EMPIRE 3.1 code, the following radiative nuclear reaction characteristics have been calculated for several stable and unstable even-even Sn and Ni isotopes: 1 neutron capture cross sections, 2 corresponding neutron capture gamma-spectra, 3 average radiative widths of neutron resonances. Here, three variants of the microscopic nuclear level density models have been used and a comparison with the phenomenological generalized superfluid model has been performed. In all the considered properties, including the recent experimental data for PSF in Sn isotopes, the PC contributions turned out to be significant, as compared with the QRPA one, and necessary to explain the available experimental data.

  15. Palladium-catalyzed Cascade Cyclization-Coupling Reaction of Benzyl Halides with N,N-Diallylbenzoylamide

    Yi Min HU; Yu ZHANG; Jian Lin HAN; Cheng Jian ZHU; Yi PAN


    A novel type of palladium-catalyzed cascade cyclization-coupling reaction has been found. Reaction of N, N-diallylbenzoylamide 1 with benzyl halides 2 afforded the corresponding dihydropyrroles 3 in moderate to excellent yields.

  16. Palladium supported on natural phosphate: Catalyst for Suzuki coupling reactions in water

    Hassine, Ayoub


    The Suzuki-Miyaura coupling reaction is one of the most important synthetic catalytic reactions developed in the 20th century. However, the use of toxic organic solvents for this reaction still poses a scientific challenge and is an aspect of economical and ecological relevance. The use of water as a reaction medium overcomes this issue. In the present work, we described efficient Suzuki coupling reactions in water, without any phase transfer reagents and it is possible to couple challenging substrates like aryl chlorides. Notably, this protocol also works with ultra-low loading of catalyst with high turnover numbers. © 2012 Elsevier B.V.

  17. Diagnosis of herpes simplex virus-1 keratitis using Giemsa stain, immunofluorescence assay, and polymerase chain reaction assay on corneal scrapings

    Farhatullah, S; Kaza, S; Athmanathan, S; Garg, P; Reddy, S B; Sharma, S


    Aims: To evaluate three tests used routinely for the diagnosis of herpes simplex virus (HSV) keratitis. Methods: Corneal scrapings from 28 patients with clinically typical dendritic corneal ulcer suggestive of HSV keratitis, and 30 patients with clinically non-viral corneal ulcers, were tested by (i) Giemsa stain for multinucleated giant cells, (ii) immunofluorescence assay (IFA) for HSV-1 antigen, and (iii) polymerase chain reaction (PCR) for HSV-1 DNA, by investigators masked to clinical diagnosis. The control subjects were also investigated by smears and cultures for bacteria, fungus, and Acanthamoeba. Results: The specificity and positive predictive values of all three tests for the diagnosis of HSV keratitis were between 95–100%. The sensitivity of IFA and PCR was 78.6% and 81.2%, respectively, and the difference was not significant; however, their sensitivity and negative predictive value were significantly higher than Giemsa stain. Conclusions: While a combination of IFA and PCR constitute the choice of tests in clinically suspected cases of HSV keratitis, multinucleated giant cells in Giemsa stain can pre-empt testing by IFA and PCR in otherwise atypical cases of HSV keratitis. PMID:14693792

  18. A novel reverse flow reactor coupling endothermic and exothermic reactions. Part I: comparison of reactor configurations for irreversible endothermic reactions

    van Sint Annaland, M.; Scholts, H.A.R.; Kuipers, J.A.M.; van Swaaij, Willibrordus Petrus Maria


    A new reactor concept is studied for highly endothermic heterogeneously catalysed gas phase reactions at high temperatures with rapid but reversible catalyst deactivation. The reactor concept aims to achieve an indirect coupling of energy necessary for endothermic reactions and energy released by

  19. Synthesis of Diethyl Oxalate by a Coupling-Regeneration Reaction of Carbon Monoxide

    Fandong Meng; Genhui Xu; Baowei Wang; Xinbin Ma


    This article describes a process for the synthesis of diethyl oxalate by a coupling reaction ofcarbon monoxide, catalyzed by palladium in the presence of ethyl nitrite. The kinetics and mechanism ofthe coupling and regeneration reaction are also discussed. This paper presents the results of a scale-uptest of the catalyst and the process based on an a priori computer simulation.

  20. Acute Stress Reactions in Couples after a Burn Event to Their Young Child

    Bakker, A.; Van Loey, N.E.; Van der Heijden, P.G.M.; Van Son, M.J.M.


    Objective This multicenter study examines acute stress reactions in couples following a burn event to their preschool child. Methods Participants were 182 mothers and 154 fathers, including 143 couples, of 193 children (0–4 years) with acute burns. Parents’ self-reported acute stress reactions and e

  1. The Use of Tertiary Alkylmagnesium Nucleophiles in Ni-Catalyzed Cross-Coupling Reactions.

    Joshi-Pangu, Amruta; Biscoe, Mark R


    Nickel-catalyzed cross-coupling reactions of unactivated tertiary alkyl nucleophiles and aryl bromides have been developed using N-heterocyclic carbene ligands. These processes are reviewed alongside earlier attempts to employ unactivated tertiary alkyl nucleophiles in cross-coupling reactions. Potential mechanisms for the transformations, and future challenges in this field are discussed.

  2. Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry.

    Ornatsky, Olga I; Kinach, Robert; Bandura, Dmitry R; Lou, Xudong; Tanner, Scott D; Baranov, Vladimir I; Nitz, Mark; Winnik, Mitchell A


    Advances in the development of highly multiplexed bio-analytical assays with inductively coupled plasma mass spectrometry (ICP-MS) detection are discussed. Use of novel reagents specifically designed for immunological methods utilizing elemental analysis is presented. The major steps of method development, including selection of elements for tags, validation of tagged reagents, and examples of multiplexed assays, are considered in detail. The paper further describes experimental protocols for elemental tagging of antibodies, immunostaining of live and fixed human leukemia cells, and preparation of samples for ICP-MS analysis. Quantitative analysis of surface antigens on model cell lines using a cocktail of seven lanthanide labeled antibodies demonstrated high specificity and concordance with conventional immunophenotyping.

  3. CO2 as Both a Selective Agent and Reaction Media in Palladium-Catalyzed Reductive Ullmann-Type Coupling Reaction

    LI Jin-Heng李金恒; XIE Ye-Xiang谢叶香


    Carbon dioxide as both a selective agent and reaction media in the palladium-catalyzed Ullmann-type coupling has been described. The results showed that aryl chlorides could be easily activated in the presence of carbon dioxide and the chemoselectivity shifted toward the palladium-catalyzed Ullmann-type coupling reaction. In liquid carbon dioxide, homocoupling reactions of aryl halides, including less reactive aryl chlorides, were carried out smoothly in moderate to good yields using Pd/C, zinc, and H2O as the catalytic system at room temperature.

  4. An optimized polymerase chain reaction assay to identify avian virus vaccine contamination with Chicken anemia virus.

    Amer, Haitham M; Elzahed, Hanan M; Elabiare, Elham A; Badawy, Ahmed A; Yousef, Ausama A


    The use of embryonating chicken eggs in preparation of avian virus vaccines is the principle cause for contamination with Chicken anemia virus (CAV). Identification of CAV in contaminated vaccines relies on the expensive, tedious, and time-consuming practice of virus isolation in lymphoblastoid cell lines. The experience of the last 2 decades indicates that polymerase chain reaction is extending to replace most of the classic methods for detection of infectious agents. In the present report, a simple, rapid, and accurate polymerase chain reaction method for detection of CAV in poultry vaccines is described. Oligonucleotide primers homologous to highly conserved sequences of the VP1 gene were used to amplify a fragment of 676 bp. The developed assay was specific for detecting CAV from different sources, with no cross reactivity with many avian viruses. No inter- and intra-assay variations were observed. The analytical sensitivity of the test was high enough to detect 5 TCID(50) (50% tissue culture infective dose) of the virus per reaction; however, different factors related to the vaccine matrix showed considerable effects on the detection limit. In conclusion, this method may represent a suitable alternative to virus isolation for identification of CAV contamination of poultry virus vaccines.

  5. Quantitative methylene blue decolourisation assays as rapid screening tools for assessing the efficiency of catalytic reactions.

    Kruid, Jan; Fogel, Ronen; Limson, Janice Leigh


    Identifying the most efficient oxidation process to achieve maximum removal of a target pollutant compound forms the subject of much research. There exists a need to develop rapid screening tools to support research in this area. In this work we report on the development of a quantitative assay as a means for identifying catalysts capable of decolourising methylene blue through the generation of oxidising species from hydrogen peroxide. Here, a previously described methylene blue test strip method was repurposed as a quantitative, aqueous-based spectrophotometric assay. From amongst a selection of metal salts and metallophthalocyanine complexes, monitoring of the decolourisation of the cationic dye methylene blue (via Fenton-like and non-Fenton oxidation reactions) by the assay identified the following to be suitable oxidation catalysts: CuSO4 (a Fenton-like catalyst), iron(II)phthalocyanine (a non-Fenton oxidation catalyst), as well as manganese(II) phthalocyanine. The applicability of the method was examined for the removal of bisphenol A (BPA), as measured by HPLC, during parallel oxidation experiments. The order of catalytic activity was identified as FePc > MnPc > CuSO4 for both BPA and MB. The quantitative MB decolourisation assay may offer a rapid method for screening a wide range of potential catalysts for oxidation processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Application of quinoxaline based diimidazolium salt in palladium catalyzed cross-coupling reactions

    Mujahuddin M Siddiqui; Mohammed Waheed; Sajad A Bhat; Maravanji S Balakrishna


    The reaction of 2,3-bis(bromomethyl)quinoxaline with imidazole afforded the quinoxaline bridged diimidazolium salt (1) in good yield. Diimidazolium salt (1) in conjunction with Pd(OAc)2 was employed as a catalyst for C–C cross-coupling reactions. The diimidazolium salt was found to be efficient in catalyzing Suzuki-Miyaura cross-coupling reaction in ethanol under ambient conditions. Moderate to good selectivity of the trans product was observed in the Heck cross-coupling reaction. The molecular structure of 1 was confirmed by single crystal X-ray diffraction study.

  7. Colony color assay coupled with 5FOA negative selection greatly improves yeast threehybrid library screening efficiency


    The recently developed yeast three-hybrid system is a powerful tool for analyzing RNA-protein interactions in vivo. However, large numbers of false positives are frequently met due to bait RNA-independent activation of the reporter gene in the library screening using this system. In this report, we coupled the colony color assay with the 5FOA (5-fluoroorotic acid) negative selection in the library screening, and found that this coupled method effectively eliminated bait RNA-independent false positives and hence greatly improved library screening efficiency. We used this method successfully in isolation of cDNA of an RNA-binding protein that might play important roles in certain cellular process. This improvement will facilitate the use of the yeast three-hybrid system in analyzing RNA-protein interaction.

  8. Heterogeneous Palladium Chloride Catalyzed Ligand-free Suzuki-Miyaura Coupling Reactions at Ambient Temperature

    WANG Min; WANG Lei


    A mild and efficient ligand-free Suzuki-Miyaura coupling reaction catalyzed by heterogeneous palladium chloride was developed at room temperature in a short reaction time under air atmosphere.Various phenyl iodides,bromides and activated chlorides were coupled with sodium tetraphenylborate or phenylboronic acids efficiently to afford the corresponding cross-coupled products in good to excellent yields.Furthermore,the catalyst could be recycled up to four times without loss of its activity.

  9. Microwave-Assisted Cross-Coupling Reaction of Sodium Tetraphenylboratewith Carboxylic Anhydrides Catalyzed by Palladium

    ZHANG Yu-Quan; WANG Jin-Xian; WANG Ke-Hu; ZHAO Lian-Biao


    @@ Cross-coupling processes of aryl or alkenyl halides with organometallic compounds of main group elements cat alyzed by palladium complexes have been found extensive use in organic synthesis. These cross-coupling reactions offer a powerful tool for the formation of carbon-carbon bonds. [1] The Suzuki-Miyaura cross-coupling reaction has been employed for the synthesis of ketone as well.

  10. Development and validation of a Myxoma virus real-time polymerase chain reaction assay.

    Albini, Sarah; Sigrist, Brigitte; Güttinger, Regula; Schelling, Claude; Hoop, Richard K; Vögtlin, Andrea


    To aid in the rapid diagnosis of myxomatosis in rabbits, a real-time polymerase chain reaction (PCR) for the specific detection of Myxoma virus is described. Primers and probe were designed to amplify a 147-bp fragment within the Serp2 gene. The assay was able to detect 23 copies of a synthesized oligo indicating a reliable sensitivity. In addition, the real-time PCR did not detect the Rabbit fibroma virus used in myxomatosis vaccines. The novel PCR was shown to be able to detect Myxoma virus in fresh and paraffin-embedded rabbit tissues originating from myxomatosis cases from various regions in Switzerland.

  11. Development and validation of a Myxoma virus real-time polymerase chain reaction assay

    Albini, S; Sigrist, B; Guttinger, R; Schelling, C; Hoop, R K; Vogtlin, A


    To aid in the rapid diagnosis of myxomatosis in rabbits, a real-time polymerase chain reaction (PCR) for the specific detection of Myxoma virus is described. Primers and probe were designed to amplify a 147-bp fragment within the Serp2 gene. The assay was able to detect 23 copies of a synthesized oligo indicating a reliable sensitivity. In addition, the real-time PCR did not detect the Rabbit fibroma virus used in myxomatosis vaccines. The novel PCR was shown to be able to detect Myxoma virus...

  12. An improved coupling reaction for the preparation of pyridylethynyl benzonitrile compounds


    An improved coupling reaction between aro matic ring and acetylene triple bond catalyzed by palladium (0) catalyses for the preparation of pyridylethynyl benzoni trile compounds is described. Efforts were made to improve the reaction by changing different reaction conditions and it was found that the solvent is one important factor in this situation.

  13. Cyanidin-horseradish peroxidase-hydroperoxide reaction system and its application in enzyme linked immunosensing assays

    GONG FuChun; LI DingZhong; YANG Rong; WEI JianKe; CAO Zhong; TAN ShuZhen; TAN YaFei


    A cyanidin-based horseradish peroxidase(HRP)-catalyzed reaction system was established in this work.In B-R buffer solutions(pH 6.8),a UV-visible ebsorbance peak of cyanidin(CAG)at 540 nm(Ap1)appeared.After the oxidation reaction of CAG catalyzed by HRP in the presence of H2O2,a significant absorbance peak at 482 nm(Ap2)occurred.The ratio R(Ap2/Ap1)was proportional to the HRP concentration.The application of CAG in the enzyme-linked immunosensing assays was investigated using food and mouth disease virus antigen(FMDVAg)as e model sandwich immunoreaction,the analyte FMDVAg and food and mouth disease virus antibody(FMDVAb)-modified magnetic nanoparticles bound the supported conconvalina(Con A)bound with HRP-FMDVAb.After de-absorbing and separating,the HRP-FMDVAb-FMDVAg-FMDVAb-magnetic nanoparticles complexes were subject to enzymatic reaction and UV-visible absorbance measurements.The HRP moiety of the immunoreaction complexes can catalyze the oxidation reaction of CAG by H2O2,and the substrate CAG is converted to products.Based on this principle,a sandwich assay model has been employed to determine FMDVAg in rabbit serum samples with the aid of FMDVAb-Fe3O4 magnetic nanoparticles.The linear range of the FMDVAg determination is 1.5×10-8-2.7×10-6 g/mL with the relatively standard deviation of 3.7%(n=11).The detection limit is 3.1×10 g/mL.Additional advantages of the typical substrate such as OPD,OAP and TMB are good water-solubility and stability.

  14. Coupling solid-phase extraction and enzyme-linked immunosorbent assay for ultratrace determination of herbicides in pristine water

    Aga, D.S.; Thurman, E.M.


    Solid-phase extraction (SPE) and enzyme-linked immunosorbent assay (ELISA) were coupled for automated trace analysis of pristine water samples containing 2-chloro-4-ethylamino-6-isopropylamine-s-triazine (atrazine) and 2-chloro-2???,6???-diethyl-N-(methoxymethyl)acetanilide (alachlor). The isolation of the two herbicides on a C18-resin involved the selection of an elution solvent that both removes interfering substances and is compatible with ELISA. Ethyl acetate was selected as the elution solvent followed by a solvent exchange with methanol/water (20/80, % v/v). The SPE-ELISA method has a detection limit of 5.0 ng/L (5 ppt), >90% recovery, and a relative standard deviation of ??10%. The performance of a microtiter plate-based ELISA and a magnetic particle-based ELISA coupled to SPE was also evaluated. Although the sensitivity of the two ELISA methods was comparable, the precision using magnetic particles was improved considerably (??10% versus ??20%) because of the faster reaction kinetics provided by the magnetic particles. Finally, SPE-ELISA and isotope dilution gas chromatography/ mass spectrometry correlated well (correlation coefficient of 0.96) for lake-water samples. The SPE-ELISA method is simple and may have broader applications for the inexpensive automated analysis of other contaminants in water at trace levels.

  15. Multiplex polymerase chain reaction-capillary gel electrophoresis: a promising tool for GMO screening--assay for simultaneous detection of five genetically modified cotton events and species.

    Nadal, Anna; Esteve, Teresa; Pla, Maria


    A multiplex polymerase chain reaction assay coupled to capillary gel electrophoresis for amplicon identification by size and color (multiplex PCR-CGE-SC) was developed for simultaneous detection of cotton species and 5 events of genetically modified (GM) cotton. Validated real-time-PCR reactions targeting Bollgard, Bollgard II, Roundup Ready, 3006-210-23, and 281-24-236 junction sequences, and the cotton reference gene acp1 were adapted to detect more than half of the European Union-approved individual or stacked GM cotton events in one reaction. The assay was fully specific (PCR-CGE-SC assay to allow simultaneous detection of 6 cotton and 5 maize targets (two endogenous genes and 9 GM events) in two multiplex PCRs and a single CGE, making the approach more economic. Besides allowing simultaneous detection of many targets with adequate specificity and sensitivity, the multiplex PCR-CGE-SC approach has high throughput and automation capabilities, while keeping a very simple protocol, e.g., amplification and labeling in one step. Thus, it is an easy and inexpensive tool for initial screening, to be complemented with quantitative assays if necessary.

  16. Detection of Staphylococcus aureus in Dairy Products by Polymerase Chain Reaction Assay

    YANG Yang; SU Xu-dong; YUAN Yao-wu; KANG Chun-yu; LI Ying-jun; ZHANG wei; ZHONG Xiao-ying


    A polymerase chain reaction (PCR) assay was employed for direct detection of Staphylococcus aureus without enrichment in dairy products. A solvent extraction procedure was successfully modified for the extraction of Staphylococcus aureus DNA from artificially contaminated whole milk, skim milk, and cheese. A primer targeting the thermostable nuclease gene (nuc) was used in the PCR. A DNA fragment of 279 bp was amplified. The PCR product was confirmed by DNA sequencing. In this study, the PCR, GB- 4789.10-94, Perifilm RSA.Count Plate, and Baird-Parker + RPF Agar were compared.The sensitivity of the PCR was 10 CFU mL-1 of whole milk, skim milk, and 55 CFU g-1 of cheese. The developed methodology allowed for detection of Staphylococcus aureus in dairy products in less than 6 h. The time taken for the development of this PCR assay was 12-24 h, less than the time taken by the general PCR assay using the enrichment method, and the coincidence rate of this developed PCR was 94.3%, the sensitivity was 100%. It was a rapid, sensitive, and effective method for PCR to detect Staphylococcus aureus in milk and milk products.

  17. Detection of Alternaria fungal contamination in cereal grains by a polymerase chain reaction-based assay.

    Zur, Gideon; Shimoni, Eyal; Hallerman, Eric; Kashi, Yechezkel


    Alternaria sp. are important fungal contaminants of grain products; they secrete four structural classes of compounds that are toxic or carcinogenic to plants and animals and cause considerable economic losses to growers and the food-processing industry. Alternaria toxins have been detected by high-performance liquid chromatography (HPLC), enzyme-linked immunosorbent assay, and other techniques. Here, we report the development of a polymerase chain reaction (PCR)-based method for the detection of Alternaria DNA. PCR primers were designed to anneal to the ITS1 and ITS2 regions of the 5.8S rDNA gene of Alternaria alternata or Alternaria solani but not to other microbial or plant DNA. We compared the sensitivity of PCR in detecting Alternaria DNA, that of the HPLC method in detecting Alternaria alternariol and alternariol methyl ether toxins, and that of the morphological examination of mycelia and conidia in experimentally infested corn samples. The sensitivity of toxin detection for HPLC was above the level of contamination in a set of commercially obtained grain samples, resulting in negative scores for all samples, while the PCR-based method and mold growth plating followed by morphological identification of Alternaria gave parallel, positive results for 8 of 10 samples. The PCR assay required just 8 h, enabling the rapid and simultaneous testing of many samples at a low cost. PCR-based evidence for the presence of Alternaria DNA followed by positive assay results for Alternaria toxins would support the rejection of a shipment of grain.

  18. Palladium(0 Deposited on PAMAM Dendrimers as a Catalyst for C–C Cross Coupling Reactions

    Tomasz Borkowski


    Full Text Available PAMAM dendrimers of generations G2–G3 as well as a partially substituted derivative of generation G4 and a low-molecular-weight tricyclic ligand 4 were used to bind Pd(0 nanoparticles. The obtained adducts were tested as catalysts for C–C cross-coupling reactions, such as the Suzuki-Miyaura, Hiyama, Heck and Sonogashira reaction. The highest yields of the coupling product, diphenylacetylene, were obtained with all the catalysts studied in the Sonogashira coupling performed in ethanol with K2CO3 as base. Very good results, 85–100%, were also found in the Suzuki-Miyaura cross-coupling, while the efficiency of the Hiyama coupling appeared lower, with 38–52% of 2-Methylbiphenyl formed. In all reactions, the G2–Pd(0 catalyst, containing an unmodified dendrimer, afforded the highest yields of the cross-coupling products.

  19. Exact stochastic simulation of coupled chemical reactions with delays

    Cai, Xiaodong


    Gillespie's exact stochastic simulation algorithm (SSA) [J. Phys. Chem. 81, 2350 (1977)] has been widely used to simulate the stochastic dynamics of chemically reacting systems. In this algorithm, it is assumed that all reactions occur instantly. While this is true in many cases, it is also possible that some chemical reactions, such as gene transcription and translation in living cells, take certain time to finish after they are initiated. Thus, the product of such reactions will emerge after certain delays. Apparently, Gillespie's SSA is not an exact algorithm for chemical reaction systems with delays. In this paper, the author develops an exact SSA for chemical reaction systems with delays, based upon the same fundamental premise of stochastic kinetics used by Gillespie in the development of his SSA. He then shows that an algorithm modified from Gillespie's SSA by Barrio et al. [PLOS Comput. Biol. 2, 1017 (2006)] is also an exact SSA for chemical reaction systems with delays, but it needs to generate more random variables than the author's algorithm.

  20. Mycoplasma bovis real-time polymerase chain reaction assay validation and diagnostic performance.

    Clothier, Kristin A; Jordan, Dianna M; Thompson, Curtis J; Kinyon, Joann M; Frana, Timothy S; Strait, Erin L


    Mycoplasma bovis is an important bacterial pathogen in cattle, producing a variety of clinical diseases. The organism, which requires specialized culture conditions and extended incubation times to isolate and identify, is frequently associated with concurrent infection with other pathogens which can potentially be more easily identified. Real-time polymerase chain reaction (real-time PCR) is a valuable diagnostic technique that can rapidly identify infectious agents in clinical specimens. A real-time PCR assay was designed based on the uvrC gene to identify M. bovis in diagnostic samples. Using culture as the gold standard test, the assay performed well in a variety of diagnostic matrices. Initial validation testing was conducted on 122 milk samples (sensitivity: 88.9% [95% confidence interval (CI): 68.4-100%], specificity: 100%); 154 lung tissues (sensitivity: 89.0% [95% CI: 83.1-94.9%], specificity: 97.8% [95% CI: 93.5-100%]); 70 joint tissue/fluid specimens (sensitivity: 92.3% [95% CI: 82.1-100%], specificity: 95.5% [95% CI: 89.3-100%]); and 26 nasal swabs (sensitivity: 75.0% [95% CI: 45.0-100%], specificity: 83.3% [95% CI: 66.1-100%]). Low numbers of other sample matrices showed good agreement between results of culture and PCR. A review of clinical cases from 2009 revealed that, in general, PCR was used much more frequently than culture and provided useful diagnostic information in conjunction with clinical signs, signalment, and gross and histopathologic lesions. Diagnostic performance of the real-time PCR assay developed as a testing method indicates that it is a rapid, accurate assay that is adaptable to a variety of PCR platforms and can provide reliable results on an array of clinical samples.

  1. A novel high-throughput format assay for HIV-1 integrase strand transfer reaction using magnetic beads

    Hong-qiu HE; Xiao-hui MA; Bin LIU; Wei-zu CHEN; Cun-xin WANG; Shao-hui CHENG


    Aim:To develop a novel high-throughput format assay to monitor the integrase (IN) strand transfer (ST) reaction in vitro and apply it to a reaction character study and the identification of antiviral drugs.Methods:The donor DNA duplex,with a sequence identical to the U5 end of HIV-1 long terminal repeats,is labeled at its 5' end with biotin (BIO).The target DNA duplex is labeled at its 3' end with digoxin (DIG).IN mediates the integration of donor DNA into target DNA and results in a 5' BIO and 3' DIG-labeled duplex DNA product.Streptavidin-coated magnetic beads were used to capture the product,and the amount of DIG was measured as the ST reaction product.The assay was optimized in 96-well microplate format for high-throughput screening purpose.Moreover,the assay was applied in a ST reaction character study,and the efficiency of the assay in the identification of antiviral compounds was tested.Results:The end-point values,measured as absorbance at 405 nm was approximately 1.5 for the IN-mediated ST reaction as compared with no more than 0.05 of background readings.The ST reaction char-acter and the half maximal inhibitory concentration (IC50) values of 2 known IN inhibitors obtained in our assay were similar to previously reported results using other assays.The evaluation parameter Z' factor for this assay ranged from 0.6 to 0.9.Conclusion:The assay presented here has been proven to be rapid,sensitive,and specific for the detection of IN ST activity,the reaction character study,as well as for the identification of antiviral drugs targeting IN.

  2. Coupling and Reactions of 5-Hydroxyconiferyl Alcohol in Lignin Formation

    Elder, Thomas; Berstis, Laura; Beckham, Gregg T.; Crowley, Michael F.


    The catechol alcohols, caffeyl and 5-hydroxyconiferyl alcohol, may be incorporated into lignin either naturally or through genetic manipulation. Due to the presence of o-OH groups, these compounds form benzodioxanes, a departure from the interunit connections found in lignins derived from the cinnamyl alcohols. In nature, lignins composed of caffeyl and 5-hydroxyconiferyl alcohol are linear homopolymers and, as such, may have properties that make them amenable for use in value-added products, such as lignin-based carbon fibers. In the current work, results from density functional theory calculations for the reactions of 5-hydroxyconiferyl alcohol, taking stereochemistry into account, are reported. Dehydrogenation and quinone methide formation are found to be thermodynamically favored for 5-hydroxyconiferyl alcohol, over coniferyl alcohol. The comparative energetics of the rearomatization reactions suggest that the formation of the benzodioxane linkage is under kinetic control. Ring-opening reactions of the benzodioxane groups show that the bond dissociation enthalpy of the ..alpha..-O cleavage reaction is lower than that of the ..beta..-O reaction. The catechol lignins represent a novel form of the polymer that may offer new opportunities for bioproducts and genetic targets.

  3. Chemical Reactions and Kinetics of the Carbon Monoxide Coupling in the Presence of Hydrogen

    Fandong Meng; Genhui Xu; Zhenhua Li; Pa Du


    The chemical reactions and kinetics of the catalytic coupling reaction of carbon monoxide to diethyl oxalate were studied in the presence of hydrogen over a supported palladium catalyst in the gaseous phase at the typical coupling reaction conditions. The experiments were performed in a continuous flow fixed-bed reactor. The results indicated that hydrogen only reacts with ethyl nitrite to form ethanol, and kinetic studies revealed that the rate-determining step is the surface reaction of adsorbed hydrogen and the ethoxy radical (EtO-). A kinetic model is proposed and a comparison of the observed and calculated conversions showed that the rate expressions are of rather high confidence.

  4. Suzuki-Miyaura cross-coupling reactions of aryl tellurides with potassium aryltrifluoroborate salts.

    Cella, Rodrigo; Cunha, Rodrigo L O R; Reis, Ana E S; Pimenta, Daniel C; Klitzke, Clécio F; Stefani, Hélio A


    [reaction: see text] Palladium(0)-catalyzed cross-coupling between potassium aryltrifluoroborate salts and aryl tellurides proceeds readily to afford the desired biaryls in good to excellent yield. The reaction seems to be unaffected by the presence of electron-withdrawing or electron-donating substituents in both the potassium aryltrifluoroborate salts and aryl tellurides partners. Biaryls containing a variety of functional groups can be prepared. A chemoselectivity study was also carried out using aryl tellurides bearing halogen atoms in the same compound. In addition, this new version of the Suzuki-Miyaura cross-coupling reaction was monitored by electrospray ionization mass spectrometry where some reaction intermediates were detected and analyzed.

  5. Dynamical coupled-channels study of meson production reactions from EBAC@Jlab

    Hiroyuki Kamano


    We present the current status of a combined and simultaneous analysis of meson production reactions based on a dynamical coupled-channels (DCC) model, which is conducted at Excited Baryon Analysis Center (EBAC) of Jefferson Lab.

  6. Regioselective Palladium-Catalyzed Cross-Coupling Reactions of 2,4,7-Trichloroquinazoline.

    Wipf, Peter; George, Kara M


    The regioselective palladium-catalyzed cross-coupling reactions of 2,4,7-trichloroquinazoline with various aryl- and heteroarylboronic acids are reported. An efficient, sequential strategy was developed that provides access to novel, functionalized heterocycles.

  7. Direct activation of allylic alcohols in palladium catalyzed coupling reactions

    Gümrükçü, Y.


    The direct use of allylic alcohols in substitution reactions without pre-activation of the hydroxyl-group into a better leaving group or the use of additional stoichiometric in situ activators remains challenging due to the poor leaving group ability of the hydroxyl-group. Hence, it is important to

  8. How does roasting affect the antioxidants of a coffee brew? Exploring the antioxidant capacity of coffee via on-line antioxidant assays coupled with size exclusion chromatography.

    Smrke, Samo; Opitz, Sebastian E W; Vovk, Irena; Yeretzian, Chahan


    During coffee roasting major changes occur in coffee bean composition. Among others dark coloured melanoidins are formed, which are high molecular weight Maillard reaction products. A new approach is presented here to monitor the influence of roasting conditions on the antioxidant capacity of melanoidins and chlorogenic acids (CGAs) in a coffee brew. Validated Folin-Ciocalteu (FC) and ABTS assays were used as on-line antioxidant assays coupled (post-column) with high performance size-exclusion chromatography (HPSEC). HPSEC enabled the separation of melanoidins from CGAs and the determination of the antioxidant capacity of each fraction, within a total elution time of 25 min. Besides the on-line assay measurements, both assays were also applied off-line with flow injection analysis (FIA). The maximum antioxidant capacity was determined to be at a light-to-medium roast degree, measured with both ABTS-FIA and FC-FIA assays as well as on-line ABTS assay. With FC on-line assay the maximum was found to be at a very light roast degree. Based on the peak areas obtained with the new coupled technique the roasting effects on the variability of melanoidin and CGA contents in coffee brews were studied. The majority of melanoidins are already formed in the early stage of the roasting process and the relative contribution of melanoidins to the total antioxidant capacity increases towards darker roasts, mainly because CGAs degrade during roasting. A new parameter, the ratio of melanoidin to CGA peak area, was introduced as a possible predictor of the roast degree.

  9. Advances in Metal-Catalyzed Cross-Coupling Reactions of Halogenated Quinazolinones and Their Quinazoline Derivatives

    Malose Jack Mphahlele


    Full Text Available Halogenated quinazolinones and quinazolines are versatile synthetic intermediates for the metal-catalyzed carbon–carbon bond formation reactions such as the Kumada, Stille, Negishi, Sonogashira, Suzuki-Miyaura and Heck cross-coupling reactions or carbon-heteroatom bond formation via the Buchwald-Hartwig cross-coupling to yield novel polysubstituted derivatives. This review presents an overview of the application of these methods on halogenated quinazolin-4-ones and their quinazolines to generate novel polysubstituted derivatives.

  10. Synthesis of 3,4-disubstituted maleimides by selective cross-coupling reactions using indium organometallics.

    Bouissane, Latifa; Pérez Sestelo, José; Sarandeses, Luis A


    Unsymmetrical 3,4-disubstituted maleimides have been synthesized by palladium-catalyzed cross-coupling reactions of indium organometallics with 3,4-dihalomaleimides. The synthesis was performed by stepwise or sequential one-pot palladium-catalyzed cross-coupling reactions with various triorganoindium reagents. This method was used to prepare a wide variety of alkyl, aryl, heteroaryl, and alkynyl 3,4-disubstituted maleimides in good yields and with high selectivity and atom economy.

  11. Pd(II/HPMoV-Catalyzed Direct Oxidative Coupling Reaction of Benzenes with Olefins

    Yasutaka Ishii


    Full Text Available The direct aerobic coupling reaction of arenes with olefins was successfully achieved by the use of Pd(OAc2/molybdovanadophosphoric acid (HPMoV as a key catalyst under 1 atm of dioxygen. This catalytic system could be extended to the coupling reaction of various substituted benzenes with olefins such as acrylates, aclrolein, and ethylene through the direct aromatic C-H bond activation.

  12. Pinning Control Strategies for Synchronization of Linearly Coupled Neural Networks With Reaction-Diffusion Terms.

    Wang, Jin-Liang; Wu, Huai-Ning; Huang, Tingwen; Ren, Shun-Yan


    Two types of coupled neural networks with reaction-diffusion terms are considered in this paper. In the first one, the nodes are coupled through their states. In the second one, the nodes are coupled through the spatial diffusion terms. For the former, utilizing Lyapunov functional method and pinning control technique, we obtain some sufficient conditions to guarantee that network can realize synchronization. In addition, considering that the theoretical coupling strength required for synchronization may be much larger than the needed value, we propose an adaptive strategy to adjust the coupling strength for achieving a suitable value. For the latter, we establish a criterion for synchronization using the designed pinning controllers. It is found that the coupled reaction-diffusion neural networks with state coupling under the given linear feedback pinning controllers can realize synchronization when the coupling strength is very large, which is contrary to the coupled reaction-diffusion neural networks with spatial diffusion coupling. Moreover, a general criterion for ensuring network synchronization is derived by pinning a small fraction of nodes with adaptive feedback controllers. Finally, two examples with numerical simulations are provided to demonstrate the effectiveness of the theoretical results.

  13. Polymerase chain reaction-based assays for the diagnosis of human brucellosis.

    Wang, Ying; Wang, Zhanli; Zhang, Yaxian; Bai, Liyun; Zhao, Yue; Liu, Chunfang; Ma, An; Yu, Hui


    Polymerase chain reaction (PCR) is an in vitro technique for the nucleic acid amplification, which is commonly used to diagnose infectious diseases. The use of PCR for pathogens detection, genotyping and quantification has some advantages, such as high sensitivity, high specificity, reproducibility and technical ease. Brucellosis is a common zoonosis caused by Brucella spp., which still remains as a major health problem in many developing countries around the world. The direct culture and immunohistochemistry can be used for detecting infection with Brucella spp. However, PCR has the potential to address limitations of these methods. PCR are now one of the most useful assays for the diagnosis in human brucellosis. The aim of this review was to summarize the main PCR techniques and their applications for diagnosis and follow-up of patients with brucellosis. Moreover, advantages or limitation of the different PCR methods as well as the evaluation of PCR results for treatment and follow-up of human brucellosis were also discussed.

  14. Concept and progress in coupling of dehydrogenation and hydrogenation reactions through catalysts

    C V Pramod; C Raghavendra; K Hari Prasad Reddy; G V Ramesh Babu; K S Rama Rao; B David Raju


    This review focuses on the importance of coupling of catalytic reactions which involves dehydrogenation and hydrogenation simultaneously and the study of catalytic materials that are designed, adopted and/or modified for these reactions. The special features of these reactions are minimization of H2 utilization and reduction in production cost. Structural and textural properties also play a decisive role in this kind of coupled reactions. This particular review although not comprehensive discusses the significant progress made in the area of coupled reactions and also helps future researchers or engineers to find out the improvements required in areas such as advancements in catalytic material preparation, design of the new reactors and the application of new technologies.

  15. Minimal coupling schemes in N-body reaction theory

    Picklesimer, A.; Tandy, P.C.; Thaler, R.M.


    A new derivation of the N-body equations of Bencze, Redish, and Sloan is obtained through the use of Watson-type multiple scattering techniques. The derivation establishes an intimate connection between these partition-labeled N-body equations and the particle-labeled Rosenberg equations. This result yields new insight into the implicit role of channel coupling in, and the minimal dimensionality of, the partition-labeled equations.

  16. Investigation of polymerase chain reaction assays to improve detection of bacterial involvement in bovine respiratory disease.

    Bell, Colin J; Blackburn, Paul; Elliott, Mark; Patterson, Tony I A P; Ellison, Sean; Lahuerta-Marin, Angela; Ball, Hywel J


    Bovine respiratory disease (BRD) causes severe economic losses to the cattle farming industry worldwide. The major bacterial organisms contributing to the BRD complex are Mannheimia haemolytica, Histophilus somni, Mycoplasma bovis, Pasteurella multocida, and Trueperella pyogenes. The postmortem detection of these organisms in pneumonic lung tissue is generally conducted using standard culture-based techniques where the presence of therapeutic antibiotics in the tissue can inhibit bacterial isolation. In the current study, conventional and real-time polymerase chain reaction (PCR) assays were used to assess the prevalence of these 5 organisms in grossly pneumonic lung samples from 150 animals submitted for postmortem examination, and the results were compared with those obtained using culture techniques. Mannheimia haemolytica was detected in 51 cases (34%) by PCR and in 33 cases (22%) by culture, H. somni was detected in 35 cases (23.3%) by PCR and in 6 cases (4%) by culture, Myc. bovis was detected in 53 cases (35.3%) by PCR and in 29 cases (19.3%) by culture, P. multocida was detected in 50 cases (33.3%) by PCR and in 31 cases (20.7%) by culture, and T. pyogenes was detected in 42 cases (28%) by PCR and in 31 cases (20.7%) by culture, with all differences being statistically significant. The PCR assays indicated positive results for 111 cases (74%) whereas 82 cases (54.6%) were culture positive. The PCR assays have demonstrated a significantly higher rate of detection of all 5 organisms in cases of pneumonia in cattle in Northern Ireland than was detected by current standard procedures.

  17. A computational glance at organometallic cyclizations and coupling reactions

    Fiser, Béla


    210 p. Organometallic chemistry is one of the main research topics in chemical science.Nowadays, organometallic reactions are the subject of intensive theoretical investigations.However, in many cases, only joint experimental and theoretical effortscould reveal the answers what we are looking for.The fruits of such experimental and theoretical co-operations will be presentedhere. In this work, we are going to deal with homogeneous organometallic catalysisusing computational chemical tools....

  18. Palladium-Catalyzed Cross-Coupling Reactions of Perfluoro Organic Compounds

    Masato Ohashi


    Full Text Available In this review, we summarize our recent development of palladium(0-catalyzed cross-coupling reactions of perfluoro organic compounds with organometallic reagents. The oxidative addition of a C–F bond of tetrafluoroethylene (TFE to palladium(0 was promoted by the addition of lithium iodide, affording a trifluorovinyl palladium(II iodide. Based on this finding, the first palladium-catalyzed cross-coupling reaction of TFE with diarylzinc was developed in the presence of lithium iodide, affording α,β,β-trifluorostyrene derivatives in excellent yield. This coupling reaction was expanded to the novel Pd(0/PR3-catalyzed cross-coupling reaction of TFE with arylboronates. In this reaction, the trifluorovinyl palladium(II fluoride was a key reaction intermediate that required neither an extraneous base to enhance the reactivity of organoboronates nor a Lewis acid additive to promote the oxidative addition of a C–F bond. In addition, our strategy utilizing the synergetic effect of Pd(0 and lithium iodide could be applied to the C–F bond cleavage of unreactive hexafluorobenzene (C6F6, leading to the first Pd(0-catalyzed cross-coupling reaction of C6F6 with diarylzinc compounds.

  19. Sonogashira Coupling Reaction with Palladium Powder and Potassium Fluoride in Methanol

    王磊; 李品华


    A Sonogashira coupling reaction of aromatic halides with terminal alkynes in the presence of palladium powder,potassium fluoride,cuprous iodide and triphenylphosphine in methanol,giving the corresponding coupling products aryl alkynes in good to excellent yiekls,was investigated.

  20. Silver-catalyzed cross-coupling reactions of alkyl bromides with alkyl or aryl Grignard reagents

    Someya, Hidenori; Yorimitsu, Hideki; Oshima, Koichiro


    reatment of secondary or tertiary alkyl bromides with alkyl Grignard reagents in the presence of catalytic amounts of silver bromide and potassium fluoride in CH2Cl2 afforded the corresponding cross-coupling products in reasonable yields. Moreover, silver showed catalytic activity for the cross-coupling reactions of alkyl bromides with aryl Grignard reagents.

  1. Reductive coupling reaction of benzyl, allyl and alkyl halides in aqueous medium promoted by zinc

    Sá Ana C. P. F. de


    Full Text Available Organic halides undergo reductive dimerization (Wurtz-type coupling promoted by zinc at room temperature in aqueous medium. The reaction yields are strongly enhanced by copper catalysis. This coupling procedure provides an efficient and simple method for the homocoupling of benzylic and allylic bromides and primary alkyl iodides.

  2. Coupled-channels description of the 40Ca+58,64Ni transfer and fusion reactions

    Scamps, G; Hagino, K; Haas, F; Courtin, S


    Preliminary experimental data for nucleon transfer reactions of the 40Ca+58Ni and 40Ca+64Ni systems are analyzed with the coupled- channels approach. It is shown that a simple treatment for the transfer in the coupled-channels method cannot reproduce simultaneously the transfer probabilities and the sub-barrier enhancement of fusion cross sections.

  3. A rapid and sensitive assay of intercellular coupling by voltage imaging of gap junction networks.

    Ceriani, Federico; Mammano, Fabio


    A variety of mechanisms that govern connexin channel gating and permeability regulate coupling in gap junction networks. Mutations in connexin genes have been linked to several pathologies, including cardiovascular anomalies, peripheral neuropathy, skin disorders, cataracts and deafness. Gap junction coupling and its patho-physiological alterations are commonly assayed by microinjection experiments with fluorescent tracers, which typically require several minutes to allow dye transfer to a limited number of cells. Comparable or longer time intervals are required by fluorescence recovery after photobleaching experiments. Paired electrophysiological recordings have excellent time resolution but provide extremely limited spatial information regarding network connectivity. Here, we developed a rapid and sensitive method to assay gap junction communication using a combination of single cell electrophysiology, large-scale optical recordings and a digital phase-sensitive detector to extract signals with a known frequency from Vf2.1.Cl, a novel fluorescent sensor of plasma membrane potential. Tests performed in HeLa cell cultures confirmed that suitably encoded Vf2.1.Cl signals remained confined within the network of cells visibly interconnected by fluorescently tagged gap junction channels. We used this method to visualize instantly intercellular connectivity over the whole field of view (hundreds of cells) in cochlear organotypic cultures from postnatal mice. A simple resistive network model reproduced accurately the spatial dependence of the electrical signals throughout the cellular network. Our data suggest that each pair of cochlear non-sensory cells of the lesser epithelial ridge is coupled by ~1500 gap junction channels, on average. Junctional conductance was reduced by 14% in cochlear cultures harboring the T5M mutation of connexin30, which induces a moderate hearing loss in connexin30T5M/T5M knock-in mice, and by 91% in cultures from connexin30-/- mice, which are

  4. Microwave-Assisted Synthesis of 5-Phenyl-2-Hydroxyacetophenone Derivatives by a Green Suzuki Coupling Reaction

    Soares, Pedro; Fernandes, Carlos; Chavarria, Daniel; Borges, Fernanda


    In recent years, the use of boron-containing reagents in palladium-assisted C-C coupling reactions (the Suzuki reaction) has gained prominence due to the vast array of reagents commercially available. Consequently, the generation of carbon-carbon bonds, namely of functionalized biphenyl systems, is at present considered the backbone of organic…

  5. Palladium-catalyzed cross-coupling reactions of allylic halides and acetates with indium organometallics.

    Rodríguez, David; Pérez Sestelo, José; Sarandeses, Luis A


    The palladium(0)-catalyzed cross-coupling reaction of allylic halides and acetates with indium organometallics is reported. In this synthetic transformation, triorganoindium compounds and tetraorganoindates (aryl, alkenyl, and methyl) react with cinnamyl and geranyl halides and acetates to afford the S(N)2 product regioselectively and in good yield. The reaction proceeds with net inversion of the stereochemical configuration.

  6. Course of traumatic stress reactions in couples after a burn event to their young child

    Bakker, A.; Van der Heijden, P.G.M.; Van Son, M.J.M.; Van Loey, N.E.E.


    OBJECTIVE: This study examines traumatic stress reactions in couples that were followed prospectively for 18 months after a burn event to their child. METHOD: The participants included 186 mothers and 159 fathers of 198 preschool children. Parents' self-reported traumatic stress reactions were measu

  7. Palladium Catalyzed Suzuki Cross-coupling Reaction in Molten Tetra-n-butylammonium Bromide

    ZOU, Yue(邹岳); WANG, Quan-Rui(王全瑞); TAO, Feng-Gang(陶凤岗); DING, Zong-Biao(丁宗彪)


    A practical procedure for palladium catalyzed Suzuki cross-coupling reaction of arylboronic acids with aryl halides, including aryl chlorides in molten tetra-n-butylammonium bromide (TBAB) was developed. The reaction exhibits high efficiency and functional group tolerance. The recovery of the catalyst and molten n-Bu4NBr was also investigated.

  8. Microwave-Assisted Synthesis of 5-Phenyl-2-Hydroxyacetophenone Derivatives by a Green Suzuki Coupling Reaction

    Soares, Pedro; Fernandes, Carlos; Chavarria, Daniel; Borges, Fernanda


    In recent years, the use of boron-containing reagents in palladium-assisted C-C coupling reactions (the Suzuki reaction) has gained prominence due to the vast array of reagents commercially available. Consequently, the generation of carbon-carbon bonds, namely of functionalized biphenyl systems, is at present considered the backbone of organic…

  9. Efficient Sonogashira and Suzuki-Miyaura coupling reaction catalyzed by Pd-Nanoparticles

    Kishor E Balsane; Suresh S Shendage; Jayashree M Nagarkar


    The Pd nano particles were electrochemically deposited on nafion-graphene. They showed excellent catalytic activity towards Sonogashira and Suzuki-Miyaura cross-coupling reaction. Benzenediazonium salts were used as alternative to aromatic halide. The developed protocol offers recyclability, easy workups with short reaction time and good-to-excellent product yield.

  10. New Oxime Ligand with Potential for Proton-Coupled Electron-Transfer Reactions

    Deville, Claire; Sundberg, Jonas; McKenzie, Christine Joy

    Proton-coupled electron-transfer (PCET) is found in a range of oxidation-reduction reactions in biology.1 This mechanism is of interest for applications in energy conversion processes. The PCET reaction has been shown to be facilitated when the proton is transferred to an intramolecular basic sit...

  11. A novel reverse flow reactor coupling endothermic and exothermic reactions: an experimental study

    van Sint Annaland, M.; Nijssen, R.C.


    A new reactor concept is studied for highly endothermic heterogeneously catalysed gas phase reactions at high temperatures with rapid but reversible catalyst deactivation. The reactor concept aims to achieve an indirect coupling of energy necessary for endothermic reactions and energy released by

  12. Direct activation of allylic alcohols in palladium catalyzed coupling reactions

    Gümrükçü, Y.


    The direct use of allylic alcohols in substitution reactions without pre-activation of the hydroxyl-group into a better leaving group or the use of additional stoichiometric in situ activators remains challenging due to the poor leaving group ability of the hydroxyl-group. Hence, it is important to develop new methods to activate (bio-mass derived) allyl-alcohols, which allow ‘green’ chemical processes for a broad substrate range. This may have a considerable impact on the methodology for fin...

  13. Coupling liquid chromatography/mass spectrometry detection with microfluidic droplet array for label-free enzyme inhibition assay.

    Wang, Xiu-Li; Zhu, Ying; Fang, Qun


    In this work, the combination of droplet-based microfluidics with liquid chromatography/mass spectrometry (LC/MS) was achieved, for providing a fast separation and high-information-content detection method for the analysis of nanoliter-scale droplets with complex compositions. A novel interface method was developed using an oil-covered droplet array chip to couple with an LC/MS system via a capillary sampling probe and a 4 nL injection valve without the need of a droplet extraction device. The present system can perform multistep operations including parallel enzyme inhibition reactions in nanoliter droplets, 4 nL sample injection, fast separation with capillary LC, and label-free detection with ESI-MS, and has significant flexibility in the accurate addressing and sampling of droplets of interest on demand. The system performance was evaluated using angiotensin I and angiotensin II as model samples, and the repeatabilities of peak area for angiotensin I and angiotensin II were 2.7% and 7.5% (RSD, n = 4), respectively. The present system was further applied to the screening for inhibitors of cytochrome P450 (CYP1A2) and measurement of the IC50 value of the inhibitor. The sample consumption for each droplet assay was 100 nL, which is reduced 10-100 times compared with conventional 384-multi-well plate systems usually used in high-throughput drug screening.

  14. Cross-coupling reactions of indium organometallics with 2,5-dihalopyrimidines: synthesis of hyrtinadine A.

    Mosquera, Angeles; Riveiros, Ricardo; Pérez Sestelo, José; Sarandeses, Luis A


    The palladium-catalyzed cross-coupling reaction of triorganoindium reagents (R3In) with 5-bromo-2-chloropyrimidine proceeds chemoselectively, in good yields, to give 5-substituted-2-chloropyrimidines or 2,5-disubstituted pyrimidines using 40 or 100 mol % of R3In, respectively. Sequential cross-couplings are also performed, in one pot, using two different R3In. This method was used to achieve the first synthesis of the alkaloid hyrtinadine A. The key step was a two-fold cross-coupling reaction between a tri(3-indolyl)indium reagent and 5-bromo-2-chloropyrimidine.

  15. Suzuki-Miyaura cross-coupling reactions in aqueous media: Green and sustainable syntheses of biaryls

    Polshettiwar, Vivek


    Carbon-carbon cross-coupling reactions are among the most important processes in organic chemistry, and Suzuki-Miyaura reactions are among the most widely used protocols for the formation of carbon-carbon bonds. These reactions are generally catalyzed by soluble palladium complexes with various ligands. However, the use of toxic organic solvents remains a scientific challenge and an aspect of economical and ecological relevance. This Review will summarize various recently developed significant methods by which the Suzuki-Miyaura coupling was conducted in aqueous media, and analyzes if they are "real green" protocols. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Multiplex bio-assay with inductively coupled plasma mass spectrometry: Towards a massively multivariate single-cell technology

    Tanner, Scott D. [Institute of Biomaterials and Biomedical Engineering, University of Toronto, Room 407, 164 College Street, Toronto, Ontario, M5S 3G9 (Canada)], E-mail:; Ornatsky, Olga; Bandura, Dmitry R.; Baranov, Vladimir I. [Institute of Biomaterials and Biomedical Engineering, University of Toronto, Room 407, 164 College Street, Toronto, Ontario, M5S 3G9 (Canada)


    Recent progress in the development of massively multiplexed bioanalytical assays using element tags with inductively coupled plasma mass spectrometry detection is reviewed. Feasibility results using commercially available secondary immunolabeling reagents for leukemic cell lines are presented. Multiplex analysis of higher order is shown with first generation tag reagents based on functionalized carriers that bind lanthanide ions. DNA quantification using metallointercalation allows for cell enumeration or mitotic state differentiation. In situ hybridization permits the determination of cellular RNA. The results provide a feasibility basis for the development of a multivariate assay tool for individual cell analysis based on inductively coupled plasma mass spectrometry in a cytometer configuration.

  17. A hydrodynamics-reaction kinetics coupled model for evaluating bioreactors derived from CFD simulation.

    Wang, Xu; Ding, Jie; Guo, Wan-Qian; Ren, Nan-Qi


    Investigating how a bioreactor functions is a necessary precursor for successful reactor design and operation. Traditional methods used to investigate flow-field cannot meet this challenge accurately and economically. Hydrodynamics model can solve this problem, but to understand a bioreactor in sufficient depth, it is often insufficient. In this paper, a coupled hydrodynamics-reaction kinetics model was formulated from computational fluid dynamics (CFD) code to simulate a gas-liquid-solid three-phase biotreatment system for the first time. The hydrodynamics model is used to formulate prediction of the flow field and the reaction kinetics model then portrays the reaction conversion process. The coupled model is verified and used to simulate the behavior of an expanded granular sludge bed (EGSB) reactor for biohydrogen production. The flow patterns were visualized and analyzed. The coupled model also demonstrates a qualitative relationship between hydrodynamics and biohydrogen production. The advantages and limitations of applying this coupled model are discussed.

  18. A simple model for lamellar peritectic coupled growth with peritectic reaction


    The lamellar peritectic coupled growth in Fe-Ni peritectic system was investigated using the equilibrium Boettinger-Jackson-Hunt model.It was found that the slope of the undercooling vs.lamellar spacing is very near zero around the minimum overheating,and the coupled growth can exist under this condition even if the slope of the undercooling vs.lamellar spacing curve is slightly smaller than zero.In addition,the peritectic reaction can never reach completion during the peritectic coupled growth.So the equilibrium peritectic coupled growth was modified by considering the incompletion of the peritectic reaction.It was shown that when the fractions of the peritectic reaction reach 60%-80% completion,the calculated undercooling vs.lamellar spacing curves agree well with the experimental obser-vations in the directionally solidified Fe-Ni alloys.

  19. Prevention of a systematic underestimation of antioxidant activity in competition assays. The impact of unspecific reactions of the reactive species.

    Beljaars, Christiaan P; Balk, Jiska M; Bast, Aalt; Haenen, Guido R M M


    In antioxidant competition assays, an antioxidant (A) and a detector compound (D) compete for a reactive species (R). In the evaluation of these assays, it is tacitly assumed that all of R is captured by either D or A. Due to the - by definition - high reactivity of R, unspecific reactions of R are likely to occur and neglecting these reactions will result in a systematic underestimation of antioxidant activity. It was shown that in the standard hydroxyl radical scavenging assay this was indeed the case; the inaccurate mathematical evaluation resulted in an underestimation of antioxidant activity of 25% in this competition assay. The systematic underestimation of antioxidant activity can be prevented by using an adjusted Stern-Volmer equation that takes into account that only part of R is captured by D or A.

  20. Alkali metal mediated C-C bond coupling reaction.

    Tachikawa, Hiroto


    Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2](-) was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

  1. A new polymerase chain reaction (PCR) assay for the trinucleotide repeat that is unstable and expanded on Huntington's disease chromosomes.

    Warner, J P; Barron, L H; Brock, D J


    The Huntington's Disease (HD) Collaborative Research Group has recently published the sequence of a new cDNA, IT15, containing a polymorphic trinucleotide (CAG)n repeat that is expanded and unstable on HD chromosomes. There is a correlation between the repeat size and the age of onset of symptoms. The suggested polymerase chain reaction (PCR) assay of the (CAG)n repeat requires unusual reaction components and primer concentrations and the use of 5% polyacrylamide sequencing gels to resolve the amplification products. We present a simple PCR assay that produces a smaller product using standard reaction conditions. This gives better resolution of the (CAG)n expansion observed on HD chromosomes by acrylamide gel electrophoresis and allows sufficient product to be obtained to perform assays using agarose gels. This will allow diagnostic labs to do rapid and accurate presymptomatic testing of HD in high risk families.

  2. Evaluation of a new multiplex polymerase chain reaction assay STDFinder for the simultaneous detection of 7 sexually transmitted disease pathogens.

    Muvunyi, Claude Mambo; Dhont, Nathalie; Verhelst, Rita; Crucitti, Tania; Reijans, Martin; Mulders, Brit; Simons, Guus; Temmerman, Marleen; Claeys, Geert; Padalko, Elizaveta


    We evaluated a new multiplex polymerase chain reaction (mPCR), "STDFinder assay", a novel multiplex ligation-dependent probe amplification (MLPA) assay for the simultaneous detection of 7 clinically relevant pathogens of STDs, i.e., Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis, Mycoplasma genitalium, Treponema pallidum, and herpes simplex virus type 1 and 2 (HSV-1 and HSV-2). An internal amplification control was included in the mPCR reaction. The limits of detection for the STDFinder assay varied among the 7 target organisms from 1 to 20 copies per MLPA assay. There were no cross-reactions among any of the probes. Two hundred and forty-two vaginal swabs and an additional 80 specimens with known results for N. gonorrhoeae and C. trachomatis, obtained from infertile women seen at an infertility research clinic at the Kigali Teaching Hospital in Rwanda, were tested by STDFinder assay and the results were confirmed by single real-time PCR using different species-specific targets. Compared to the reference standard, the STDFinder assay showed specificities and sensitivities of 100% and 100%, respectively, for N. gonorrhoeae, C. trachomatis, and M. genitalium; 90.2% and 100%, respectively, for Trichomonas vaginalis; and 96.1% and 100%, respectively, for HSV-2. No specimen was found to be positive for HSV-1 by either the STDFinder assay or the comparator method. Similarly, the sensitivity for Treponema pallidum could not be calculated due to the absence of any Treponema pallidum-positive samples. In conclusion, the STDFinder assays have comparable clinical sensitivity to the conventional mono and duplex real-time PCR assay and are suitable for the routine detection of a broad spectrum of these STDs at relatively low cost due to multiplexing.

  3. Catalytic Systems Containing p-Toluenesulfonic Acid for the Coupling Reaction of Formaldehyde and Methyl Formate

    Kebing Wang; Jie Yao; Yue Wang; Gongying Wang


    The coupling reaction of formaldehyde (FA) and methyl formate (MF) to form methyl glycolate (MG) and methyl methoxy acetate(MMAc),catalyzed by p-toluenesulfonic acid(p-TsOH) as well as assisted by different kinds of solvents or Ni-containing compounds.had been investigated.The results showed that when the reaction was carried out at 140℃ with a molar ratio of FA to MF of 0.65:1,molar fraction of p-TsOH to total feedstock of 11.0%,and reaction time of 3 h,the yield of MG and MMAc Was 31.1% and 17.1%.respectively.p-TsOH catalyzed the coupling reaction by means of the synergistic catalysis of protonic acidity and soft basicity.Adding extra solvents to the reaction system Was unfavorable for the reaction.The composite catalytic system consisting of p-TsOH and NiX2(X=Cl,Br,I)exhibited a high catalytic performance for the coupling reaction,and NiX2 acted as a promoter in the reaction,whose promotion for the catalysis increased in the following order:NiCl2<NiBr2<NiI2.The present system is less corrosive when compared with the previous system,in which strong inorganic liquid acids were used as catalysts.

  4. Potential Applications of Zeolite Membranes in Reaction Coupling Separation Processes

    Tunde V. Ojumu


    Full Text Available Future production of chemicals (e.g., fine and specialty chemicals in industry is faced with the challenge of limited material and energy resources. However, process intensification might play a significant role in alleviating this problem. A vision of process intensification through multifunctional reactors has stimulated research on membrane-based reactive separation processes, in which membrane separation and catalytic reaction occur simultaneously in one unit. These processes are rather attractive applications because they are potentially compact, less capital intensive, and have lower processing costs than traditional processes. Therefore this review discusses the progress and potential applications that have occurred in the field of zeolite membrane reactors during the last few years. The aim of this article is to update researchers in the field of process intensification and also provoke their thoughts on further research efforts to explore and exploit the potential applications of zeolite membrane reactors in industry. Further evaluation of this technology for industrial acceptability is essential in this regard. Therefore, studies such as techno-economical feasibility, optimization and scale-up are of the utmost importance.

  5. Hydrotalcite-quinolinate composites as catalysts in a coupling reaction.

    Ríos, Eloisa; Hernández, Magali; Ibarra, Ilich A; Guzmán, Ariel; Lima, Enrique


    Samples of layered double hydroxides were prepared by a sol-gel procedure. Quinolinate Al(C9H6NO)3 units were added during the synthesis, leading to composite quinolinate hydrotalcite-like compounds. The amount of quinolinate was varied, showing that the number of organic building blocks determines the physicochemical properties of materials, which differ significantly from those commonly reported for hydrotalcites without any quinolinate. The order of layers, specific surface area and coordination of aluminium were the parameters most significantly influenced by the presence of the quinolinate as a part of the brucite-like layers. The composite quinolinate-hydrotalcite materials were tested to catalyse the Kabachnik-Fields reaction.Graphical abstractAdding of quinolinate Al(C9H6NO)3 to hydrotalcite-like compounds creates disorder in the stack of brucite-like layers, leading to a significant modification of structural, textural and catalytic properties. The presence of quinolinate inhibits the enchainment of octahedral blocks in hydrotalcite but develop specific surface areas as high as 600 m(2)g(-1).

  6. Potential Applications of Zeolite Membranes in Reaction Coupling Separation Processes

    Daramola, Michael O.; Aransiola, Elizabeth F.; Ojumu, Tunde V.


    Future production of chemicals (e.g., fine and specialty chemicals) in industry is faced with the challenge of limited material and energy resources. However, process intensification might play a significant role in alleviating this problem. A vision of process intensification through multifunctional reactors has stimulated research on membrane-based reactive separation processes, in which membrane separation and catalytic reaction occur simultaneously in one unit. These processes are rather attractive applications because they are potentially compact, less capital intensive, and have lower processing costs than traditional processes. Therefore this review discusses the progress and potential applications that have occurred in the field of zeolite membrane reactors during the last few years. The aim of this article is to update researchers in the field of process intensification and also provoke their thoughts on further research efforts to explore and exploit the potential applications of zeolite membrane reactors in industry. Further evaluation of this technology for industrial acceptability is essential in this regard. Therefore, studies such as techno-economical feasibility, optimization and scale-up are of the utmost importance.

  7. An allele-specific polymerase chain reaction assay for the differentiation of members of the Anopheles culicifacies complex

    O P Singh; Geeta Goswami; N Nanda; K Raghavendra; D Chandra; S K Subbarao


    Anopheles culicifacies, the principal vector of malaria in India, is a complex of five cryptic species which are morphologically indistinguishable at any stage of life. In view of the practical difficulties associated with classical cytotaxonomic method for the identification of members of the complex, an allele-specific polymerase chain reaction (ASPCR) assay targeted to the D3 domain of 28S ribosomal DNA was developed. The assay discriminates An. culicifacies species A and D from species B, C and E. The assay was validated using chromosomally-identified specimens of An. culicifacies from different geographical regions of India representing different sympatric associations. The assay correctly differentiates species A and D from species B, C and E. The possible use of this diagnostic assay in disease vector control programmes is discussed.

  8. Atom-efficient metal-catalyzed cross-coupling reaction of indium organometallics with organic electrophiles.

    Pérez, I; Sestelo, J P; Sarandeses, L A


    The novel metal-catalyzed cross-coupling reaction of indium organometallics with organic electrophiles is described. Triorganoindium compounds (R(3)In) containing alkyl, vinyl, aryl, and alkynyl groups are efficiently prepared from the corresponding lithium or magnesium organometallics by reaction with indium trichloride. The cross-coupling reaction of R(3)In with aryl halides and pseudohalides (iodide 2, bromide 5, and triflate 4), vinyl triflates, benzyl bromides, and acid chlorides proceeds under palladium catalysis in excellent yields and with high chemoselectivity. Indium organometallics also react with aryl chlorides as under nickel catalysis. In the cross-coupling reaction the triorganoindium compounds transfer, in a clear example of atom economy, all three of the organic groups attached to the metal, as shown by the necessity of using only 34 mol % of indium. The feasibility of using R(3)In in reactions with different electrophiles, along with the high yields and chemoselectivities obtained, reveals indium organometallics to be useful alternatives to other organometallics in cross-coupling reactions.

  9. Generalized monotone method and numerical approach for coupled reaction diffusion systems

    Sowmya, M.; Vatsala, Aghalaya S.


    Study of coupled reaction diffusion systems are very useful in various branches of science and engineering. In this paper, we provide a methodology to construct the solution for the coupled reaction diffusion systems, with initial and boundary conditions, where the forcing function is the sum of an increasing and decreasing function. It is known that the generalized monotone method coupled with coupled lower and upper solutions yield monotone sequences which converges uniformly and monotonically to coupled minimal and maximal solutions. In addition, the interval of existence is guaranteed by the lower and upper solutions, which are relatively easy to compute. Using the lower and upper solutions as the initial approximation, we develop a method to compute the sequence of coupled lower and upper solutions on the interval or on the desired interval of existence. Further, if the uniqueness conditions are satisfied, the coupled minimal and maximal solutions converge to the unique solution of the reaction diffusion systems. We will provide some numerical results as an application of our numerical methodology.

  10. Reactions of nitroxides 15. Cinnamates bearing a nitroxyl moiety synthesized using a Mizoroki–Heck cross-coupling reaction

    Jerzy Zakrzewski


    Full Text Available Cinnamic acid derivatives bearing a nitroxyl moiety (2,2,6,6-tetramethyl-1-oxyl-4-piperidyl 3-E-aryl acrylates were synthesized in 30–100% yield using a Mizoroki–Heck cross-coupling reaction between 4-acryloyloxy-2,2,6,6-tetramethylpiperidine-1-oxyl and iodobenzene derivatives in the presence of palladium(II acetate coordinated with a tri(o-tolylphosphine ligand immobilized in a polyurea matrix.

  11. Predicting adverse drug reactions using publicly available PubChem BioAssay data.

    Pouliot, Y; Chiang, A P; Butte, A J


    Adverse drug reactions (ADRs) can have severe consequences, and therefore the ability to predict ADRs prior to market introduction of a drug is desirable. Computational approaches applied to preclinical data could be one way to inform drug labeling and marketing with respect to potential ADRs. Based on the premise that some of the molecular actors of ADRs involve interactions that are detectable in large, and increasingly public, compound screening campaigns, we generated logistic regression models that correlate postmarketing ADRs with screening data from the PubChem BioAssay database. These models analyze ADRs at the level of organ systems, using the system organ classes (SOCs). Of the 19 SOCs under consideration, nine were found to be significantly correlated with preclinical screening data. With regard to six of the eight established drugs for which we could retropredict SOC-specific ADRs, prior knowledge was found that supports these predictions. We conclude this paper by predicting that SOC-specific ADRs will be associated with three unapproved or recently introduced drugs.

  12. Detection of Listeria monocytogenes in cheese with the magnetic immuno-polymerase chain reaction assay.

    Fluit, A C; Torensma, R; Visser, M J; Aarsman, C J; Poppelier, M J; Keller, B H; Klapwijk, P; Verhoef, J


    A new detection system, the magnetic immuno-polymerase chain reaction (PCR) assay (MIPA) has been developed to detect Listeria monocytogenes in food. This method separates Listeria cells from PCR-inhibitory factors present in enrichment broths containing food samples by using magnetic beads coated with specific monoclonal antibodies (MAbs). The separated bacteria were lysed, and the supernatant containing the bacterial DNA was subjected to the PCR. Detection of L. monocytogenes in three naturally contaminated cheese samples with two different MAbs and PCR primers specific for the gene encoding the delayed-hypersensitivity factor showed that with MAb 55 all three samples were positive whereas with MAb A two samples were positive. A further improvement of the method was obtained by using a PCR step based on the listeriolysin O gene. A MIPA employing MAb 55 and the listeriolysin O gene primer set detected L. monocytogenes after 24 h of culture in Listeria Enrichment Broth samples from Port Salut artificially contaminated with 40 CFU/25 g. We could detect 1 CFU of L. monocytogenes per g of cheese after a second enrichment for 24 h in Fraser broth. The analysis time including both enrichments is approximately 55 h.

  13. Modeling of coupled differential equations for cellular chemical signaling pathways: Implications for assay protocols utilized in cellular engineering.

    O'Clock, George D


    Cellular engineering involves modification and control of cell properties, and requires an understanding of fundamentals and mechanisms of action for cellular derived product development. One of the keys to success in cellular engineering involves the quality and validity of results obtained from cell chemical signaling pathway assays. The accuracy of the assay data cannot be verified or assured if the effect of positive feedback, nonlinearities, and interrelationships between cell chemical signaling pathway elements are not understood, modeled, and simulated. Nonlinearities and positive feedback in the cell chemical signaling pathway can produce significant aberrations in assay data collection. Simulating the pathway can reveal potential instability problems that will affect assay results. A simulation, using an electrical analog for the coupled differential equations representing each segment of the pathway, provides an excellent tool for assay validation purposes. With this approach, voltages represent pathway enzyme concentrations and operational amplifier feedback resistance and input resistance values determine pathway gain and rate constants. The understanding provided by pathway modeling and simulation is strategically important in order to establish experimental controls for assay protocol structure, time frames specified between assays, and assay concentration variation limits; to ensure accuracy and reproducibility of results.

  14. A High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening.

    Wigle, Tim J; Swinger, Kerren K; Campbell, John E; Scholle, Michael D; Sherrill, John; Admirand, Elizabeth A; Boriack-Sjodin, P Ann; Kuntz, Kevin W; Chesworth, Richard; Moyer, Mikel P; Scott, Margaret Porter; Copeland, Robert A


    Demethylation of histones by lysine demethylases (KDMs) plays a critical role in controlling gene transcription. Aberrant demethylation may play a causal role in diseases such as cancer. Despite the biological significance of these enzymes, there are limited assay technologies for study of KDMs and few quality chemical probes available to interrogate their biology. In this report, we demonstrate the utility of self-assembled monolayer desorption/ionization (SAMDI) mass spectrometry for the investigation of quantitative KDM enzyme kinetics and for high-throughput screening for KDM inhibitors. SAMDI can be performed in 384-well format and rapidly allows reaction components to be purified prior to injection into a mass spectrometer, without a throughput-limiting liquid chromatography step. We developed sensitive and robust assays for KDM1A (LSD1, AOF2) and KDM4C (JMJD2C, GASC1) and screened 13,824 compounds against each enzyme. Hits were rapidly triaged using a redox assay to identify compounds that interfered with the catalytic oxidation chemistry used by the KDMs for the demethylation reaction. We find that overall this high-throughput mass spectrometry platform coupled with the elimination of redox active compounds leads to a hit rate that is manageable for follow-up work.

  15. High-throughput real-time assay based on molecular beacons for HIV-1 integrase 3'-processing reaction

    Hong-qiu HE; Xiao-hui MA; Bin LIU; Xiao-yi ZHANG; Wei-zu CHEN; Cun-xin WANG; Shao-hui CHENG


    Aim: To develop a high-throughput real-time assay based on molecular beacons to monitor the integrase 3'-processing reaction in vitro and apply it to inhibitor screening.Methods: The recombinant human immunodeficiency virus (HIV)-1 integrase (IN) is incubated with a 38 mer oligonucleotide substrate, a sequence identical to the U5 end of HIV-1 long terminal repeats (LTR). Based on the fluores-cence properties of molecular beacons, the substrate is designed to form a stem-loop structure labeled with a fluorophore at the 5' end and a quencher at the 3'end.IN cleaves the terminal 3'-dinucleotide containing the quencher, resulting in an increase in fluorescence which can be monitored on a spectrofluorometer. To optimize this assay, tests were performed to investigate the effects of substrates, enzyme and the metal ion concentrations on the IN activity and optimal param-eters were obtained. Moreover, 2 IN inhibitors were employed to test the perfor-mance of this assay in antiviral compound screening.Results: The fluorescent intensity of the reaction mixture varies linearly with time and is proportional to the velocity of the 3'-processing reaction. Tests were performed and the results showed that the optimal rate was obtained for a reaction mixture containing 50 mg/L recom-binant HIV-1 IN, 400 nmol/L substrate, and 10 mmol/L Mn2+. The IN 3'-processing reaction under the optimal conditions showed a more than 18-fold increase in the fluorescence intensity compared to the enzyme-free control. The IC50 values of the IN inhibitors obtained in our assay were similar to the values obtained from a radiolabeled substrate assay.Conclusion: Our results demonstrated that this is a fast, reliable, and sensitive method to monitor HIV IN 3'-processing reaction and that it can be used for inhibitor screening.

  16. A coupled chemical burster: The chlorine dioxide-iodide reaction in two flow reactors

    Dolnik, Milos; Epstein, Irving R.


    The dynamical behavior of the chlorine dioxide-iodide reaction has been studied in a system consisting of two continuous flow stirred tank reactors (CSTRs). The reactors are coupled by computer monitoring of the electrochemical potential in each reactor, which is then used to control the input into the other reactor. Two forms of coupling are employed: reciprocally triggered, exponentially decreasing stimulation, and alternating mass exchange. The reaction, which exhibits oscillatory and excitable behavior in a single CSTR, displays neuronlike bursting behavior with both forms of coupling. Reciprocal stimulation yields bursting in both reactors, while with alternating mass exchange, bursting is observed in one reactor and complex oscillation in the other. A simple model of the reaction gives good agreement between the experimental observations and numerical simulations.

  17. A boron-boron coupling reaction between two ethyl cation analogues.

    Litters, Sebastian; Kaifer, Elisabeth; Enders, Markus; Himmel, Hans-Jörg


    The design of larger architectures from smaller molecular building blocks by element-element coupling reactions is one of the key concerns of synthetic chemistry, so a number of strategies were developed for this bottom-up approach. A general scheme is the coupling of two elements with opposing polarity or that of two radicals. Here, we show that a B-B coupling reaction is possible between two boron analogues of the ethyl cation, resulting in the formation of an unprecedented dicationic tetraborane. The bonding properties in the rhomboid B₄ core of the product can be described as two B-B units connected by three-centre, two-electron bonds, sharing the short diagonal. Our discovery might lead the way to the long sought-after boron chain polymers with a structure similar to the silicon chains in β-SiB₃. Moreover, the reaction is a prime textbook example of the influence of multiple-centre bonding on reactivity.

  18. A multiplex reverse transcription-polymerase chain reaction assay for Newcastle disease virus and avian pneumovirus (Colorado strain).

    Ali, A; Reynolds, D L


    Newcastle disease virus (NDV) and avian pneumovirus (APV) cause Newcastle disease and rhinotracheitis respectively, in turkeys. Both of these viruses infect the respiratory system. A one-tube, multiplex, reverse transcription-polymerase chain reaction (RT-PCR) assay for the detection of both NDV and Colorado strain of APV (APV-Col) was developed and evaluated. The primers, specific for each virus, were designed from the matrix protein gene of APV-Col and the fusion protein gene of NDV to amplify products of 631 and 309 nucleotides, respectively. The multiplex RT-PCR assay, for detecting both viruses simultaneously, was compared with the single-virus RT-PCR assays for its sensitivity and specificity. The specific primers amplified products of predicted size from each virus in the multiplex as well as the single-virus RT-PCR assays. The multiplex RT-PCR assay was determined to be equivalent to the single-virus RT-PCR assays for detecting both NDV and APV-Col. This multiplex RT-PCR assay proved to be a sensitive method for the simultaneous and rapid detection of NDV and APV-Col. This assay has the potential for clinical diagnostic applications.

  19. Aqueous microwave-assisted cross-coupling reactions applied to unprotected nucleosides

    Hervé, Gwénaëlle; Len, Christophe


    Metal catalyzed cross-coupling reactions have been the preferred tools to access to modified nucleosides (on the C5-position of pyrimidines and on the C7- or C8-positions of purines). Our objective is to focus this mini-review on the Suzuki-Miyaura and on the Heck cross-couplings of nucleosides using microwave irradiations which is an alternative technology compatible with green chemistry and sustainable development PMID:25741506

  20. Numerical aspects of modelling of coupled chemical reactions and fluid flow in sedimentary basins

    Holstad, Astrid


    Simulation of coupled chemical reactions and fluid flow in porous sedimentary basins, through long time periods, is a numerical challenge. In most models available today the equations representing such a physical problem are solved as PDEs (Partial Differential Equation) where efficient time-stepping with controlled error is very difficult. The DAE (Differential Algebraic Equation) system approach is used where robust adaptive time-stepping algorithms are available in solvers. In this report mathematical and numerical models are derived for coupled chemical reactions and fluid flow. The models have several interesting properties which are discussed. The performance of code is tested. 20 refs., 6 figs., 2 tabs.

  1. Cathodic Aromatic C,C Cross-Coupling Reaction via Single Electron Transfer Pathway.

    Qu, Yang; Tateno, Hiroyuki; Matsumura, Yoshimasa; Kashiwagi, Tsuneo; Atobe, Mahito


    We have successfully developed a novel cathodic cross-coupling reaction of aryl halides with arenes. Utilization of the cathodic single electron transfer (SET) mechanism for activation of aryl halides enables the cross-coupling reaction to proceed without the need for any transition metal catalysts or single electron donors in a mild condition. The SET from a cathode to an aryl halide initiates a radical chain by giving an anion radical of the aryl halide. The following propagation cycle also consists entirely of anion radical intermediates.

  2. Cathodic Aromatic C,C Cross-Coupling Reaction via Single Electron Transfer Pathway

    Yang Qu


    Full Text Available We have successfully developed a novel cathodic cross-coupling reaction of aryl halides with arenes. Utilization of the cathodic single electron transfer (SET mechanism for activation of aryl halides enables the cross-coupling reaction to proceed without the need for any transition metal catalysts or single electron donors in a mild condition. The SET from a cathode to an aryl halide initiates a radical chain by giving an anion radical of the aryl halide. The following propagation cycle also consists entirely of anion radical intermediates.

  3. A fluorescence turn on assay for alkaline phosphatase based on the Cu(2+) catalyzed Fenton-like reaction.

    Zhang, Qingfeng; Zhang, Cuiyun; Shahzad, Sohail Anjum; Yu, Cong


    A fluorescence turn-on assay was established for ALP (alkaline phosphatase) based on Cu(2+) catalyzed Fenton-like reaction and Graphene Oxide (GO). GO was utilized to quench the fluorescence of fluorescein (FAM) labeled single strand DNA (F-DNA). ALP can remove the phosphate group in sodium ascorbyl phosphate (SAP), and convert it into reducing ascorbate. Highly reactive hydroxyl radicals (·OH) were generated in the presence of ascorbate and Cu(2+) through the Fenton-like reaction. The reactive radicals generated in situ caused the cleavage of F-DNA into small fragments. When GO was added, the fluorescence emission of the sample without ALP was quenched and fluorescence emission recovered in the presence of ALP. The intensity of the recovered fluorescence was directly related to the concentration of ALP in the assay solution, and a sensitive and selective facile ALP assay is therefore established.

  4. Experimental and numerical investigation of coupled microvibration dynamics for satellite reaction wheels

    Addari, D.; Aglietti, G. S.; Remedia, M.


    Microvibrations of a satellite reaction wheel assembly are commonly analysed in either hard-mounted or coupled boundary conditions, though coupled wheel-to-structure disturbance models are more representative of the real environment in which the wheel operates. This article investigates the coupled microvibration dynamics of a cantilever configured reaction wheel assembly mounted on either a stiff or flexible platform. Here a method is presented to cope with modern project necessities: (i) need of a model which gives accurate estimates covering a wide frequency range; (ii) reduce the personnel and time costs derived from the test campaign, (iii) reduce the computational effort without affecting the quality of the results. The method involves measurements of the disturbances induced by the reaction wheel assembly in a hard-mounted configuration and of the frequency and speed dependent dynamic mass of the reaction wheel. In addition, it corrects the approximation due to missing speed dependent dynamic mass in conventional reaction wheel assembly microvibration analysis. The former was evaluated experimentally using a previously designed and validated platform. The latter, on the other hand, was estimated analytically using a finite element model of the wheel assembly. Finally, the validation of the coupled wheel-structure disturbance model is presented, giving indication of the level of accuracy that can be achieved with this type of analyses.

  5. Recyclable Polystyrene-Supported Siloxane-Transfer Agent for Palladium-Catalyzed Cross-Coupling Reactions


    The rational design, synthesis, and validation of a significantly improved insoluble polymer-supported siloxane-transfer agent has been achieved that permits efficient palladium-catalyzed cross-coupling reactions. The cross-linked polystyrene support facilitates product purification with excellent siloxane recycling. Drawbacks of a previous polymer-supported siloxane-transfer agent, relating to reaction efficiency and polymer stability after repeated cycles, have been addressed. PMID:24661113

  6. Dynamical Coupled-Channel Model of Meson Production Reactions in the Nucleon Resonance Region

    T.-S. H. Lee; A. Matsuyama; T. Sato


    A dynamical coupled-channel model is presented for investigating the nucleon resonances (N*) in the meson production reactions induced by pions and photons. Our objective is to extract the N* parameters and to investigate the meson production reaction mechanisms for mapping out the quark-gluon substructure of N* from the data. The model is based on an energy-independent Hamiltonian which is derived from a set of Lagrangians by using a unitary transformation method.

  7. Silver(I) and copper(II)-imidazolium carboxylates: Efficient catalysts in Ullmann coupling reactions



    The silver(I) and copper(II)-imidazolium carboxylate coordination assemblies were derived from the reaction between corresponding carboxylic acid ligands and metal salts. These new metal derivatives depict a novel structural motif with variable chemical and thermal properties. These metal complexes act as potentialcatalysts in Ullmann coupling reactions. The imidazolium linker present in these complexes plays a role as both ligand and counter ion to balance the metal charge.

  8. An efficient synthesis of 8-substituted Odoratine derivatives by the Suzuki coupling reaction

    Ravi Kumar P; Balakrishna C; Murali B; Ramakrishna Gudipati; Prasanta K Hota; Avinash B Chaudhary; Jaya Shree A; Satyanarayana Yennam; Manoranjan Behera


    An efficient method for the preparation of 8-substituted odoratine [(3-(3', 4' -methylenedioxyphenyl)-5,6,7-trimethoxyisoflavone] derivatives, structurally similar to glaziovianin A, a known cytotoxic substance, has been described. The key steps in the synthesis are site selective bromination reaction followed by Suzuki coupling reaction in very good yield. The structural assignment of the bromo derivative was determined utilizing 2D-HMBC and NOEs NMR techniques.

  9. Coupling Reaction of Carbonyl Compounds Mediated by Gallium Metal in Aqueous Media

    汪志勇; 袁仕祯; 查正根; 张祖德


    A simple and effective pinacol coupling of various aromatic aldehydes mediated by gallium in good yields has been carried out. The reaction is highly effective in water in the prurience of KOH or HCl and was strongly affected by the steric environ-ment surrounding the carbonyl group. Aliphaflc aldehydes, ke-tones and aromatic ketones appear inert under the same reac-tion conditions.

  10. Palladium-Catalyzed Suzuki-Miyaura Type Coupling Reaction of Aryl Halides with Triphenylborane-Pyridine

    杨明华; 顾勇冰; 王艳; 赵玺玉; 严国兵


    The Suzuki-Miyaura type coupling reaction of aryl halides with triphenylborane-pyridine was described. The reaction can be catalyzed by Pd(OAc)2 (5 mol%) in presence of Cs2CO3 at 50 ℃ or 80 ℃, and functionalized biaryls were obtained in good to excellent yields. This protocol is general and can tolerate a wide range of func- tional groups.

  11. Identification of inhibitors of Plasmodium falciparum phosphoethanolamine methyltransferase using an enzyme-coupled transmethylation assay

    Voelker Dennis R


    Full Text Available Abstract Background The phosphoethanolamine methyltransferase, PfPMT, of the human malaria parasite Plasmodium falciparum, a member of a newly identified family of phosphoethanolamine methyltransferases (PMT found solely in some protozoa, nematodes, frogs, and plants, is involved in the synthesis of the major membrane phospholipid, phosphatidylcholine. PMT enzymes catalyze a three-step S-adenosylmethionine-dependent methylation of the nitrogen atom of phosphoethanolamine to form phosphocholine. In P. falciparum, this activity is a limiting step in the pathway of synthesis of phosphatidylcholine from serine and plays an important role in the development, replication and survival of the parasite within human red blood cells. Results We have employed an enzyme-coupled methylation assay to screen for potential inhibitors of PfPMT. In addition to hexadecyltrimethylammonium, previously known to inhibit PfPMT, two compounds dodecyltrimethylammonium and amodiaquine were also found to inhibit PfPMT activity in vitro. Interestingly, PfPMT activity was not inhibited by the amodiaquine analog, chloroquine, or other aminoquinolines, amino alcohols, or histamine methyltransferase inhibitors. Using yeast as a surrogate system we found that unlike wild-type cells, yeast mutants that rely on PfPMT for survival were sensitive to amodiaquine, and their phosphatidylcholine biosynthesis was inhibited by this compound. Furthermore NMR titration studies to characterize the interaction between amoidaquine and PfPMT demonstrated a specific and concentration dependent binding of the compound to the enzyme. Conclusion The identification of amodiaquine as an inhibitor of PfPMT in vitro and in yeast, and the biophysical evidence for the specific interaction of the compound with the enzyme will set the stage for the development of analogs of this drug that specifically inhibit this enzyme and possibly other PMTs.

  12. Determination of the upper and lower limits of the mechanistic stoichiometry of incompletely coupled fluxes. Stoichiometry of incompletely coupled reactions.

    Beavis, A D; Lehninger, A L


    A rationale is formulated for the design of experiments to determine the upper and lower limits of the mechanistic stoichiometry of any two incompletely coupled fluxes J1 and J2. Incomplete coupling results when there is a branch at some point in the sequence of reactions or processes coupling the two fluxes. The upper limit of the mechanistic stoichiometry is given by the minimum value of dJ2/dJ1 obtained when the fluxes are systematically varied by changes in steps after the branch point. The lower limit is given by the maximum value of dJ2/dJ1 obtained when the fluxes are varied by changes in steps prior to the branch point. The rationale for determining these limits is developed from both a simple kinetic model and from a linear nonequilibrium thermodynamic treatment of coupled fluxes, using the mechanistic approach [Westerhoff, H. V. & van Dam, K. (1979) Curr. Top. Bioenerg. 9, 1-62]. The phenomenological stoichiometry, the flux ratio at level flow and the affinity ratio at static head of incompletely coupled fluxes are defined in terms of mechanistic conductances and their relationship to the mechanistic stoichiometry is discussed. From the rationale developed, experimental approaches to determine the mechanistic stoichiometry of mitochondrial oxidative phosphorylation are outlined. The principles employed do not require knowledge of the pathway or the rate of transmembrane leaks or slippage and may also be applied to analysis of the stoichiometry of other incompletely coupled systems, including vectorial H+/O and K+/O translocation coupled to mitochondrial electron transport.

  13. The sensitivity and specificity of a reverse transcription-polymerase chain reaction assay for the avian pneumovirus (Colorado strain).

    Pedersen, J C; Reynolds, D L; Ali, A


    A reverse transcription-polymerase chain reaction (RT-PCR) assay for the detection of avian pneumovirus (APV), Colorado strain (US/CO), was evaluated for sensitivity and specificity. The single-tube RT-PCR assay utilized primers developed from the matrix (M) gene sequence of the US/CO APV. The RT-PCR amplified the US/CO APV but did not amplify other pneumoviruses, including the avian pneumoviruses subgroups A and B. The RT-PCR was capable of detecting between 10(0.25) mean tissue culture infective dose (TCID50) and 10(-0.44) TCID50 of the US/CO APV. These results have demonstrated that the single-tube RT-PCR assay is a specific and sensitive assay for the detection of US/CO APV.

  14. Present status of coupled-channels calculations for heavy-ion subbarrier fusion reactions

    Hagino, K


    The coupled-channels method has been a standard tool in analyzing heavy-ion fusion reactions at energies around the Coulomb barrier. We investigate three simplifications usually adopted in the coupled-channels calculations. These are i) the exclusion of non-collective excitations, ii) the assumption of coordinate independent coupling strengths, and iii) the harmonic oscillator approximation for multi-phonon excitations. In connection to the last point, we propose a novel microscopic method based on the beyond-mean-field approach in order to take into account the anharmonic effects of collective vibrations.

  15. Cyclopentane-nucleobase coupling in the synthesis of carbocyclic L-nucleosides: is a SN2-reaction an alternative to the Mitsunobu-reaction?

    Jessel, S; Hense, E; Meier, C


    Several carbocyclic L-nucleosides have been synthesized by coupling a cyclopentane-system with heterocycles according to a modified Mitsunobu-protocol. This reaction gave two regioisomers, the N1-alkylated product and an unwanted O(2)-product. A simple S(N)2-reaction has been investigated as an alternative for such couplings.

  16. A fluorescence anisotropy assay for the muscarinic M1 G-protein-coupled receptor.

    Huwiler, Kristin G; De Rosier, Therese; Hanson, Bonnie; Vogel, Kurt W


    In the search for new chemical entities that interact with G-proteincoupled receptors (GPCRs), assays that quantify efficacy and affinity are employed. Traditional methods for measuring affinity involve radiolabeled ligands. To address the need for homogeneous biochemical fluorescent assays to characterize orthosteric ligand affinity and dissociation rates, we have developed a fluorescence anisotropy (FA) assay for the muscarinic M1 receptor that can be conducted in a 384-well plate. We used membranes from a muscarinic M1 cell line optimized for high-throughput functional assays and the previously characterized fluorescent antagonist BODIPY FL pirenzepine. The affinities of reference compounds were determined in the competitive FA assay and compared with those obtained with a competitive filter-based radioligand-binding assay using [(3)H] N-methylscopolamine. The IC(50) values produced from the FA assay were well-correlated with the radioligand-binding K(i) values (R(2) = 0.98). The dissociation of the BODIPY FL pirenzepine was readily monitored in real time using the FA assay and was sensitive to the presence of the allosteric modulator gallamine. This M1 FA assay offers advantages over traditional radioligandbinding assays as it eliminates radioactivity while allowing investigation of orthosteric or allosteric muscarinic M1 ligands in a homogeneous format.

  17. Non-Covalent Fluorescent Labeling of Hairpin DNA Probe Coupled with Hybridization Chain Reaction for Sensitive DNA Detection.

    Song, Luna; Zhang, Yonghua; Li, Junling; Gao, Qiang; Qi, Honglan; Zhang, Chengxiao


    An enzyme-free signal amplification-based assay for DNA detection was developed using fluorescent hairpin DNA probes coupled with hybridization chain reaction (HCR). The hairpin DNAs were designed to contain abasic sites in the stem moiety. Non-covalent labeling of the hairpin DNAs was achieved when a fluorescent ligand was bound to the abasic sites through hydrogen bonding with the orphan cytosine present on the complementary strand, accompanied by quench of ligand fluorescence. As a result, the resultant probes, the complex formed between the hairpin DNA and ligand, showed almost no fluorescence. Upon hybridization with target DNA, the probe underwent a dehybridization of the stem moiety containing an abasic site. The release of ligand from the abasic site to the solution resulted in an effective fluorescent enhancement, which can be used as a signal. Compared with a sensing system without HCR, a 20-fold increase in the sensitivity was achieved using the sensing system with HCR. The fluorescent intensity of the sensing system increased with the increase in target DNA concentration from 0.5 nM to 100 nM. A single mismatched target ss-DNA could be effectively discriminated from complementary target DNA. Genotyping of a G/C single-nucleotide polymorphism of polymerase chain reaction (PCR) products was successfully demonstrated with the sensing system. Therefore, integrating HCR strategy with non-covalent labeling of fluorescent hairpin DNA probes provides a sensitive and cost-effective DNA assay.

  18. Novel assay of competitively differentiated polymerase chain reaction for screening point mutation of hepatitis B virus

    Xiao-Mou Peng; Xue-Juan Chen; Jian-Guo Li; Lin Gu; Yang-Su Huang; Zhi-Liang Gao


    AIM: Point mutation, one of the commonest gene mutations,is the most important molecular pathogenesis of cancer and chronic infection. The commonest methods for detection of point mutation are based on polymerase chain reaction (PCR). These techniques, however, cannot be used in large scale screening since they are neither accurate nor simple.For this reason, this study established a novel method of competitively differentiated PCR (CD-PCR) for screening point mutation in clinical practice.METHODS: Two competitively differentiated primers for mutant-type and wild-type templates respectively with an identically complemented region in 3′ end except for last 2base pairs and a different non-complemented region in 5′end were designed. Thus, competitive amplification might be carried out at a lower annealing temperature at first, and then differentiated amplification at a higher annealing temperature when primers could not combine with initial templates. The amplification was performed in one-tube.The products of CD-PCR were detected using microplate hybridization assay. CD-PCR was evaluated by detecting G1896A variant of hepatitis B virus (HBV) in form of recombinant plasmids and in sera from patients with hepatitis B, and compared with allele-specific PCR (AS-PCR) and competitive AS-PCR.RESULTS: CD-PCR was successfully established. It could clearly distinguish wild-type and mutant-type plasmid DNA of G1896A variant when the amount of plasmid DNA was between 102-108copies/reaction, while for AS-PCR and competitive AS-PCR, the DNA amount was between 102-104copies/reaction. CD-PCR could detect one copy of G1896A variant among 10-100 copies of wild-type plasmid DNA. The specificity of CD-PCR was higher than those of AS-PCR and competitive AS-PCR in the detection of HBV G1896A variant in sera from patients with hepatitis B. CD-PCR was independent of the amount of HBV DNA in serum. HBV G1896A variant was more often found in HBeAg (-) patients with a lower level of

  19. Petasis Three-Component Coupling Reactions of Hydrazides for the Synthesis of Oxadiazolones and Oxazolidinones

    Le Quement, Sebastian Thordal; Flagstad, Thomas; Mikkelsen, Remi Jacob Thomsen;


    An application of readily available hydrazides in the Petasis 3-component coupling reaction is presented. An investigation of the substrate scope was performed to establish a general, synthetically useful protocol for the formation of hydrazido alcohols, which were selectively converted to oxazol...

  20. Microwave-Enhanced Cross-Coupling Reactions Involving Alkynyltrifluoroborates with Aryl Bromides

    George W. Kabalka


    Full Text Available Palladium-catalyzed alkynylation has emerged as one of the most reliable methods for the synthesis of alkynes which are often used in natural product syntheses and material science. An efficient method for coupling alkynyltrifluoroborates with various aryl bromides in the presence of a palladium catalyst has been developed using microwave irradiation. The microwave reactions are rapid and efficient.

  1. Microwave-enhanced cross-coupling reactions involving alkynyltrifluoroborates with aryl bromides.

    Coltuclu, Vitali; Dadush, Eric; Naravane, Abhijit; Kabalka, George W


    Palladium-catalyzed alkynylation has emerged as one of the most reliable methods for the synthesis of alkynes which are often used in natural product syntheses and material science. An efficient method for coupling alkynyltrifluoroborates with various aryl bromides in the presence of a palladium catalyst has been developed using microwave irradiation. The microwave reactions are rapid and efficient.

  2. Efficient palladium-catalyzed coupling reactions of aryl bromides and chlorides with phenols.

    Hu, Tongjie; Schulz, Thomas; Torborg, Christian; Chen, Xiaorong; Wang, Jun; Beller, Matthias; Huang, Jun


    A convenient and general palladium-catalyzed coupling reaction of aryl bromides and chlorides with phenols was developed. Various functional groups such as nitriles, aldehydes, ketones and esters are well tolerated and the corresponding products are obtained in good to excellent yield.

  3. Copper and amine free Sonogashira cross-coupling reaction catalyzed by efficient diphosphane-palladium catalyst

    Ting He; Lei Lei Wu; Xing Li Fu; Hai Yan Fu; Hua Chen; Rui Xiang Li


    The commercially available diphosphane ligand MeO-BIPHEP was first investigated in the palladium-catalyzed Sonogashira reaction in the absence of copper and amine. The coupling of various aryl bromides and aryl chlorides with phenylacetylene gave moderate to excellent yields.

  4. Modular, Catalytic Enantioselective Construction of Quaternary Carbon Stereocenters by Sequential Cross-Coupling Reactions.

    Potter, Bowman; Edelstein, Emma K; Morken, James P


    The catalytic Suzuki-Miyaura cross-coupling with chiral γ,γ-disubstituted allylboronates in the presence of RuPhos ligand occurs with high regioselectivity and enantiospecificity, furnishing nonracemic compounds with quaternary centers. Mechanistic experiments suggest that the reaction occurs by transmetalation with allyl migration, followed by rapid reductive elimination.

  5. DFT Investigation on the Mechanism of Pd(0) Catalyzed Sonogashira Coupling Reaction

    CHEN Li-Ping; CHEN Hui-Ping


    Based on DFT calculations, the catalytic mechanism of palladium(0) atom, commonly considered as the catalytic center for Sonogashira cross-coupling reactions, has been analyzed in this study. In the cross-coupling reaction of iodobenzene with phenylacetylene without co-catalysts and bases involved, mechanistically plausible catalytic cycles have been computationally identified. These catalytic cycles typically occur in three stages: 1) oxidative addition of an iodobenzene to the Pd(0) atom, 2) reaction of the product of oxidative addition with phenylacetylene to generate an intermediate with the Csp bound to palladium, and 3) reductive elimination to couple the phenyl group with the phenylethynyl group and to regenerate the Pd(0) atom. The calculations show that the first stage gives rise to a two-coordinate palladium (Ⅱ) intermediate (ArPdI). Starting from this intermediate, the second oxidative stage, in which the C–H bond of acetylene adds to Pd(Ⅱ) without co-catalyst involved, is called alkynylation instead of transmetalation and proceeds in two steps. Stage 3 of reductive elimination of diphenylacetylene is energetically favorable. The results demonstrate that stage 2 requires the highest activation energy in the whole catalysis cycle and is the most difficult to happen, where co-catalysts help to carry out Sonogashira coupling reaction smoothly.

  6. Phthalimides as exceptionally efficient single electron transfer acceptors in reductive coupling reactions promoted by samarium diiodide.

    Vacas, Tatiana; Alvarez, Eleuterio; Chiara, Jose Luis


    Experimental and theoretical evidence shows that phthalimides are highly efficient single electron transfer acceptors in reactions promoted by samarium diiodide, affording ketyl radical anion intermediates, which participate in high-yielding inter- and intramolecular reductive coupling processes with different radicophiles including imides, oxime ethers, nitrones, and Michael acceptors.

  7. The Manganese-Catalyzed Cross-Coupling Reaction and the Influence of Trace Metals

    Santilli, Carola; Beigbaghlou, Somayyeh Sarvi; Ahlburg, Andreas


    The substrate scope of the MnCl2-catalyzed cross-coupling between aryl halides and Grignard reagents has been extended to several methyl-substituted aryl iodides by performing the reaction at elevated temperature in a microwave oven. A radical clock experiment revealed the presence of an aryl rad...

  8. A general A{sup 3}: coupling reaction based on functionalized alkynes

    Wendler, Edison P.; Santos, Alcindo A. dos, E-mail: [Universidade de Sao Paulo (IQ/USP), SP (Brazil). Inst. de Quimica


    A range of hydroxypropargylpiperidones were efficiently obtained by a one-pot three-component coupling reaction of aldehydes, alkynols, and a primary amine equivalent (4-piperidone hydrochloride hydrate) in ethyl acetate using copper(I) chloride as a catalyst. The developed protocol proved to be equally efficient using a range of aliphatic aldehydes, including paraformaldehyde, and using protected and unprotected alkynols. (author)


    Polyethylene glycol (PEG) is found to be an inexpensive and nontoxic reaction medium for the microwave-assisted Suzuki cross-coupling of arylboronic acids with aryl halides. This environmentally friendly microwave protocol offers the ease of operation and enables the recyclabilit...

  10. Exact solutions of some coupled nonlinear diffusion-reaction equations using auxiliary equation method

    Ranjit Kumar


    Travelling and solitary wave solutions of certain coupled nonlinear diffusion-reaction equations have been constructed using the auxiliary equation method. These equations arise in a variety of contexts not only in biological, chemical and physical sciences but also in ecological and social sciences.

  11. Synthesis of Unsymmetrical Heterobiaryls Using palladium-catalyzed cross-coupling reactions of lithium organozincates

    Seggio, Anne; Jutand, Anny; Priem, Ghislaine; Mongin, Florence


    International audience; Several unsymmetrical heterobiaryls have been synthesized through palladium-catalyzed cross-coupling reactions of lithium triorganozincates. The latter have been prepared by deprotonative lithiation followed by transmetalation using non hygroscopic ZnCl2*TMEDA (1/3 equiv).

  12. Palladium nanoclusters supported on propylurea-modified siliceous mesocellular foam for coupling and hydrogenation reactions.

    Erathodiyil, Nandanan; Ooi, Samuel; Seayad, Abdul M; Han, Yu; Lee, Su Seong; Ying, Jackie Y


    This paper describes the synthesis, characterization and applications of palladium (Pd) nanoparticles supported on siliceous mesocellular foam (MCF). Pd nanoparticles of 2-3 nm and 4-6 nm were used in reactions involving molecular hydrogen (such as hydrogenation of double bonds and reductive amination), transfer hydrogenation of ketones and epoxides, and coupling reactions (such as Heck and Suzuki reactions). They successfully catalyzed all these reactions with excellent yield and selectivity. This heterogeneous catalyst was easily recovered by filtration, and recycled several times without any significant loss in activity and selectivity. The palladium leaching in the reactions was determined to be much less than the FDA-approved limit of 5 ppm. Furthermore, the catalyst can be stored and handled under normal atmospheric conditions. This immobilized catalyst allows for ease of recovery/reuse and minimization of waste generation, which are of great interest in the development of green chemical processes.

  13. Phosphoric Acid-Mediated Synthesis of Vinyl Sulfones through Decarboxylative Coupling Reactions of Sodium Sulfinates with Phenylpropiolic Acids.

    Rong, Guangwei; Mao, Jincheng; Yan, Hong; Zheng, Yang; Zhang, Guoqi


    A novel phosphoric acid -mediated synthesis of vinyl sulfones through decarboxylative coupling reactions of sodium sulfinates with phenylpropiolic acids is described. This transformation is efficient and environmentally friendly.

  14. Slow slip generated by dehydration reaction coupled with slip-induced dilatancy and thermal pressurization

    Yamashita, Teruo; Schubnel, Alexandre


    Sustained slow slip, which is a distinctive feature of slow slip events (SSEs), is investigated theoretically, assuming a fault embedded within a fluid-saturated 1D thermo-poro-elastic medium. The object of study is specifically SSEs occurring at the down-dip edge of seismogenic zone in hot subduction zones, where mineral dehydrations (antigorite, lawsonite, chlorite, and glaucophane) are expected to occur near locations where deep slow slip events are observed. In the modeling, we introduce dehydration reactions, coupled with slip-induced dilatancy and thermal pressurization, and slip evolution is assumed to interact with fluid pressure change through Coulomb's frictional stress. Our calculations show that sustained slow slip events occur when the dehydration reaction is coupled with slip-induced dilatancy. Specifically, slow slip is favored by a low initial stress drop, an initial temperature of the medium close to that of the dehydration reaction equilibrium temperature, a low permeability, and overall negative volume change associated with the reaction (i.e., void space created by the reaction larger than the space occupied by the fluid released). Importantly, if we do not assume slip-induced dilatancy, slip is accelerated with time soon after the slip onset even if the dehydration reaction is assumed. This suggests that slow slip is sustained for a long time at hot subduction zones because dehydration reaction is coupled with slip-induced dilatancy. Such slip-induced dilatancy may occur at the down-dip edge of seismogenic zone at hot subduction zones because of repetitive occurrence of dehydration reaction there.

  15. Multi-reaction-channel fitting calculations in a coupled-channel model: Photoinduced strangeness production

    O Scholten; A Usov


    To describe photo- and meson-induced reactions on the nucleon, one is faced with a rather extensive coupled-channel problem. Ignoring the effects of channel coupling, as one would do in describing a certain reaction at the tree level, invariably creates a large inconsistency between the different reactions that are described. In addition, the imaginary parts of the amplitude, which are related through the optical theorem, to total cross-sections, are directly reflected in certain polarization observables. Performing a full coupled-channel calculation thus offers the possibility to implement the maximum number of constraints. The drawback one is faced with is to arrive at a simultaneous fit of a large number of reaction channels. While some of the parameters are common to many reactions, one is still faced with the challenge to optimize a large number of parameters in a highly non-linear calculation. Here we show that such an approach is possible and present some results for photoinduced strangeness production.

  16. Coriolis coupling effects in the dynamics of deep well reactions: application to the H(+) + D2 reaction.

    Hankel, M


    We present exact and estimated quantum differential and integral cross sections as well as product state distributions for the title reaction. We employ a time-dependent wavepacket method including all Coriolis couplings and also an adapted code where the helicity quantum number and with this the Coriolis couplings have been truncated. Results from helicity truncated as well as helicity conserving (HC) calculation are presented. The HC calculations fail to reproduce the exact results due to the influence of the centrifugal barrier. While the truncated calculation overestimate the exact integral cross sections they reproduce the features of the integral cross section very well. We also find that the product rotational state distributions are well reproduced if the maximum helicity state is chosen carefully. The helicity truncated calculations fail to give a good approximation of differential cross sections.

  17. Real-time reverse transcription-polymerase chain reaction assays for identification of wild poliovirus 1 & 3

    Sharma, Deepa K.; Nalavade, Uma P.; Deshpande, Jagadish M.


    Background & objectives: The poliovirus serotype identification and intratypic differentiation by real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay is suitable for serotype mixtures but not for intratypic mixtures of wild and vaccine poliovirus strains. This study was undertaken to develop wild poliovirus 1 and 3 (WPV1 and WPV3) specific rRT-PCR assays for use. Methods: Specific primers and probes for rRT-PCR were designed based on VP1 sequences of WPV1 and WPV3 isolat...

  18. Use of Existing Diagnostic Reverse-Transcription Polymerase Chain Reaction Assays for Detection of Ebola Virus RNA in Semen.

    Pettitt, James; Higgs, Elizabeth S; Adams, Rick D; Jahrling, Peter B; Hensley, Lisa E


    Sexual transmission of Ebola virus in Liberia has now been documented and associated with new clusters in regions previously declared Ebola free. Assays that have Emergency Use Authorization (EUA) and are routinely used to detect Ebola virus RNA in whole blood and plasma specimens at the Liberian Institute for Biomedical Research were tested for their suitability in detecting the presence of Ebola virus RNA in semen. Qiagen AVL extraction protocols, as well as the Ebola Zaire Target 1 and major groove binder quantitative reverse-transcription polymerase chain reaction assays, were demonstrably suitable for this purpose and should facilitate epidemiologic investigations, including those involving long-term survivors of Ebola.

  19. The Application of Suzuki Coupling Reaction on the Preparation of Carbosilane Dendrimers with 4-(Naphthalen-1-yl)phenyl Core


    Carbosilane dendrimers with p-bromophenyl core were synthesized by alternating Grignard and hydrosilylation reaction. And the α-naphthalenyl was connected to the core by the Suzuki coupling reaction. A new carbosilane dendrimer with big π-conjugated structure[4-(naphthalen-1-yl)phenyl core] was given. It shows Suzuki coupling reaction is an effective and powerful core-functionalization method and the satisfactory result can be obtained through prolonging the reaction time with the increase of the generation of dendrimer.

  20. Transition-metal-free coupling reaction of vinylcyclopropanes with aldehydes catalyzed by tin hydride.

    Ieki, Ryosuke; Kani, Yuria; Tsunoi, Shinji; Shibata, Ikuya


    Donor-acceptor cyclopropanes are useful building blocks for catalytic cycloaddition reactions with a range of electrophiles to give various cyclic products. In contrast, relatively few methods are available for the synthesis of homoallylic alcohols through coupling of vinylcyclopropanes (VCPs) with aldehydes, even with transition-metal catalysts. Here, we report that the hydrostannation of vinylcyclopropanes (VCPs) was effectively promoted by dibutyliodotin hydride (Bu2 SnIH). The resultant allylic tin compounds reacted easily with aldehydes. Furthermore, the use of Bu2 SnIH was effectively catalytic in the presence of hydrosilane as a hydride source, which established a coupling reaction of VCPs with aldehydes for the synthesis of homoallylic alcohols without the use of transition-metal catalysts. In contrast to conventional catalytic reactions of VCPs, the presented method allowed the use of several VCPs in addition to conventional donor-acceptor cyclopropanes.

  1. Mechanistic insights on platinum- and palladium-pincer catalyzed coupling and cyclopropanation reactions between olefins.

    Rajeev, Ramanan; Sunoj, Raghavan B


    The mechanism of M(II)-PNP-pincer catalyzed reaction between (i) ethene, (ii) trans-butene with 2-methylbut-2-ene, 2,3-dimethylbut-2-ene and tert-butylbutene is examined by using density functional theory methods (where M = Pt or Pd). All key intermediates and transition states involved in the reaction are precisely located on the respective potential energy surfaces using the popular DFT functionals such as mPW1K, M06-2X, and B3LYP in conjunction with the 6-31+G** basis set. The reaction between these olefins can lead to a linear coupling product or a substituted cyclopropane. The energetic comparison between coupling as well as cyclopropanation pathways involving four pairs of olefins for both platinum (1-4) and palladium (5-8) catalyzed reactions is performed. The key events in the lower energy pathway in the mechanistic course involves (i) a C-C bond formation between the metal bound olefin (ethene or trans-butene) and a free olefin, and (ii) two successive [1,2] hydrogen migrations in the ensuing carbocationic intermediates (1c-4c, and 1d-4d), toward the formation of the coupling product. The computed barriers for these steps in the reaction of metal bound ethene to free tert-butylbutene (or other butenes) are found to be much lower than the corresponding steps when trans-butene is bound to the metal pincer. The Gibbs free energy differences between the transition states leading to the coupling product (TS(d-e)) and that responsible for cyclopropanated product (TS(d-g)) are found to be diminishingly closer in the case of the platinum pincer as compared to that in the palladium system. The computed energetics indicate that the coupled product prefers to remain as a metal olefin complex, consistent with the earlier experimental reports.

  2. Development of a Polymerase Chain Reaction Assay for Detection of Burkholderia mallei, a Potent Biological Warfare Agent

    Vijai Pal


    Full Text Available Burkholderia mallei is the etiological agent of glanders, primarily a disease of equines. B. mallei is closely related to B. pseudomallei, the causative agent of melioidosis. Therefore, detection of B. mallei and its differentiation from B. pseudomallei, has always been troublesome. In present investigation, a B. mallei specific DNA sequence was identified by performing BLASTn search using ~3000 ORFs of B. mallei NCTC 10229. A polymerase chain reaction (PCR assay with internal amplification control (IAC was developed for detection of B. mallei and its differentiation from B. pseudomallei. The PCR assay could amplify a specific 224-bp fragment from all the six B. mallei strains used in the study, whereas other closely related organisms were tested negative. The detection limit of the assay was found to be 10 pg of purified DNA of B. mallei. Incorporation of IAC in the assay makes the results reliable as false negative results which may arise due to presence of PCR inhibitors, can be avoided. For validation, the assay was tested on tap water, Bengal gram and grass artificially spiked with B. mallei. The developed assay can be used as a simple and rapid tool for detection of B. mallei.

  3. Dinuclear Tetrapyrazolyl Palladium Complexes Exhibiting Facile Tandem Transfer Hydrogenation/Suzuki Coupling Reaction of Fluoroarylketone

    Dehury, Niranjan


    Herein, we report an unprecedented example of dinuclear pyrazolyl-based Pd complexes exhibiting facile tandem catalysis for fluoroarylketone: Tetrapyrazolyl di-palladium complexes with varying Pd-Pd distances efficiently catalyze the tandem reaction involving transfer hydrogenation of fluoroarylketone to the corresponding alcohol and Suzuki-Miyaura cross coupling reaction of the resulting fluoroarylalcohol under moderate reaction conditions, to biaryl alcohol. The complex with the shortest Pd-Pd distance exhibits the highest tandem activity among its di-metallic analogues, and exceeds in terms of activity and selectivity the analogous mononuclear compound. The kinetics of the reaction indicates clearly that reductive transformation of haloarylketone into haloaryalcohol is the rate determining step in the tandem reaction. Interestingly while fluoroarylketone undergoes the multistep tandem catalysis, the chloro- and bromo-arylketones undergo only a single step C-C coupling reaction resulting in biarylketone as the final product. Unlike the pyrazole based Pd compounds, the precursor PdCl2 and the phosphine based relevant complexes (PPh3)2PdCl2 and (PPh3)4Pd are found to be unable to exhibit the tandem catalysis.

  4. Enzyme-free and isothermal detection of microRNA based on click-chemical ligation-assisted hybridization coupled with hybridization chain reaction signal amplification.

    Oishi, Motoi


    An enzyme-free and isothermal microRNA (miRNA) detection method has been developed based on click-chemical ligation-assisted hybridization coupled with hybridization chain reaction (HCR) on magnetic beads (MBs). The click-chemical ligation between an azide-modified probe DNA and a dibenzocyclooctyne-modified probe DNA occurred through the hybridization of target miRNA (miR-141). HCR on MBs was performed by the addition of DNA hairpin monomers (H1 and H2). After magnetic separation and denaturation/rehybridization of HCR products ([H1/H2] n ), the resulting HCR products were analyzed by the fluorescence emitted from an intercalative dye, allowing amplification of the fluorescent signal. The proposed assay had a limit of detection of 0.55 fmol, which was 230-fold more sensitive than that of the HCR on the MBs coupled with a conventional sandwich hybridization assay (without click-chemical ligation) (limit of detection 127 fmol). Additionally, the proposed assay could discriminate between miR-141 and other miR-200 family members. In contrast to quantitative reverse transcription polymerase chain reaction techniques using enzymes and thermal cycling, this is an enzyme-free assay that can be conducted under isothermal conditions and can specifically detect miR-141 in fetal bovine serum.

  5. Generic HPLC platform for automated enzyme reaction monitoring: Advancing the assay toolbox for transaminases and other PLP-dependent enzymes.

    Börner, Tim; Grey, Carl; Adlercreutz, Patrick


    Methods for rapid and direct quantification of enzyme kinetics independent of the substrate stand in high demand for both fundamental research and bioprocess development. This study addresses the need for a generic method by developing an automated, standardizable HPLC platform monitoring reaction progress in near real-time. The method was applied to amine transaminase (ATA) catalyzed reactions intensifying process development for chiral amine synthesis. Autosampler-assisted pipetting facilitates integrated mixing and sampling under controlled temperature. Crude enzyme formulations in high and low substrate concentrations can be employed. Sequential, small (1 µL) sample injections and immediate detection after separation permits fast reaction monitoring with excellent sensitivity, accuracy and reproducibility. Due to its modular design, different chromatographic techniques, e.g. reverse phase and size exclusion chromatography (SEC) can be employed. A novel assay for pyridoxal 5'-phosphate-dependent enzymes is presented using SEC for direct monitoring of enzyme-bound and free reaction intermediates. Time-resolved changes of the different cofactor states, e.g. pyridoxal 5'-phosphate, pyridoxamine 5'-phosphate and the internal aldimine were traced in both half reactions. The combination of the automated HPLC platform with SEC offers a method for substrate-independent screening, which renders a missing piece in the assay and screening toolbox for ATAs and other PLP-dependent enzymes.

  6. A clinical comparative study of polymerase chain reaction assay for diagnosis of pneumocystis pneumonia in non-AIDS patients

    MU Xiang-dong; WANG Guang-fa; SU Li


    Background Pneurnocystis jirovecii pneumonia (PCP) is one of the most common and fatal infections in non-AIDS immunocompromised patients,which is difficult to diagnose by traditional morphologic methods.This study evaluated polymerase chain reaction (PCR) assays of Pneumocystis jirovecii mitochondrial large subunits ribosomal RNA in sputum and bronchioalveolar lavage fluid (BALF) for diagnosing PCP.Methods Sputum and BALF specimens from two groups were collected:one group (PCP group) included 20 patients definitely diagnosed of PCP by Gomori methenamine silver (GMS) stains of BALF;the other group (non-PCP group) included 40 patients.Each specimen was examined by GMS stains and PCR assays.Results GMS stains of BALF in PCP group were 100% positive (20/20),GMS stains of sputum in PCP group were 35% positive (7/20);GMS stains of BALF in non-PCP group were 100% negative (40/40),GMS stains of sputum in non-PCP group were 100% negative (40/40).PCR assays of BALF in PCP group were 100% positive (20/20),PCR assays of sputum in PCP group were 100% positive (20/20);PCR assays of BALF in non-PCP group were 100% negative (40/40),PCR assays of sputum in non-PCP group were 100% negative (40/40).Sensitivity and specificity of PCR assays of sputum and BALF were both 100%;positive and negative predictive values were also both 100%.Conclusion The diagnostic value of PCR assays of Pneumocystisjirovecii mitochondrial large subunits ribosomal RNA on sputum and BALF for pneumocystis pneumonia are both high and equivalent.

  7. Windsor and Perry: reactions of siblings in same-sex and heterosexual couples.

    Clark, Jennifer B; Riggle, Ellen D B; Rostosky, Sharon S; Rothblum, Esther D; Balsam, Kimberly F


    The U.S. Supreme Court decisions in U.S. v. Windsor (570 U.S. 307) and Hollingsworth v. Perry (570 U.S. 399) created a focal point for public discussion of marriage equality for same-sex couples. This article reports the results of an exploratory study of the reactions of individuals currently or previously in same-sex couple relationships and a heterosexual sibling who is currently or previously married (N = 371) to the Supreme Court decisions. Thematic content analysis was used to explore participants' responses to an open-ended question on a survey. Reactions of individuals from same-sex couples revealed the following themes: (1) longitudinal perspectives on the advancement of rights for same-sex couples; (2) emotional responses celebrating the decisions or expressing relief; (3) affirmation of their relationship or rights; (4) practical consequences of the extension of rights; and (5) minority stress related to anticipation of future prejudice or discrimination. Themes in the heterosexual siblings' responses were (1) ally support; (2) flat support without emotion or elaboration; (3) indifference to or ignorance about the decisions; and (4) disapproval of the decisions. These themes are compared and discussed in light of prior research on reactions to marriage restriction debates and marriage (in)equality and family relationships.

  8. Multiplex polymerase chain reaction assay for the detection of minute virus of mice and mouse parvovirus infections in laboratory mice.

    Wang, K W; Chueh, L L; Wang, M H; Huang, Y T; Fang, B H; Chang, C Y; Fang, M C; Chou, J Y; Hsieh, S C; Wan, C H


    Mouse parvoviruses are among the most prevalent infectious pathogens in contemporary mouse colonies. To improve the efficiency of routine screening for mouse parvovirus infections, a multiplex polymerase chain reaction (PCR) assay targeting the VP gene was developed. The assay detected minute virus of mice (MVM), mouse parvovirus (MPV) and a mouse housekeeping gene (α-actin) and was able to specifically detect MVM and MPV at levels as low as 50 copies. Co-infection with the two viruses with up to 200-fold differences in viral concentrations can easily be detected. The multiplex PCR assay developed here could be a useful tool for monitoring mouse health and the viral contamination of biological materials.

  9. Rapid Detection/pathotyping of Newcastle disease virus isolates in clinical samples using real time polymerase chain reaction assay



    Authors: Abdul Wajid, Muhammad Wasim, Tahir Yaqub, Shafqat F Rehmani, Tasra Bibi, Nadia Mukhtar, Javed Muhammad, Umar Bacha, Suliman Qadir Afridi, Muhammad Nauman Zahid, Zia u ddin, Muhammad Zubair Shabbir, Kamran Abbas & Muneer Ahmad ### Abstract In the present protocol we describe the real time reverse transcription polymerase chain reaction (rRT-PCR) assay for the rapid detection/pathotyping of Newcastle disease virus (NDV) isoaltes in clinical samples. Fusion gene and matrix ...

  10. Development of a Polymerase Chain Reaction Assay for Detection of Burkholderia mallei, a Potent Biological Warfare Agent


    Burkholderia mallei is the etiological agent of glanders, primarily a disease of equines. B. mallei is closely related to B. pseudomallei, the causative agent of melioidosis. Therefore, detection of B. mallei and its differentiation from B. pseudomallei, has always been troublesome. In present investigation, a B. mallei specific DNA sequence was identified by performing BLASTn search using ~3000 ORFs of B. mallei NCTC 10229. A polymerase chain reaction (PCR) assay with internal amplification ...

  11. Reactions of 1-methyl-2-phenylindole with malondialdehyde and 4-hydroxyalkenals. Analytical applications to a colorimetric assay of lipid peroxidation.

    Gérard-Monnier, D; Erdelmeier, I; Régnard, K; Moze-Henry, N; Yadan, J C; Chaudière, J


    Under acidic and mild-temperature conditions, 1-methyl-2-phenylindole was found to react with malondialdehyde (MDA) and 4-hydroxyalkenals to yield a stable chromophore with intense maximal absorbance at 586 nm. The use of methanesulfonic acid results in optimal yields of chromophore produced from MDA as well as from 4-hydroxynonenal. By contrast, the use of hydrochloric acid results in an optimal yield of chromophore produced from MDA and a negligible reaction of 4-hydroxynonenal. Taking advantage of such chromogenic reactions, we developed a new colorimetric assay of lipid peroxidation. Using a methanesulfonic acid-based medium, MDA and 4-hydroxyalkenals can be measured at the 586 nm wavelength. However, the presence of endogenous inhibitors of the reaction with 4-hydroxyalkenals is common, and this means that the latter may be underestimated in some biological samples. The assay performed in a hydrochloric acid-based medium enables the specific measurement of MDA in the presence of 4-hydroxyalkenals. Upon hydrolysis of Schiff bases in hydrochloric acid (pH 1.5), either assay can be used to specifically measure the amount of total MDA in biological samples because 4-hydroxyalkenals undergo an irreversible cyclization reaction under the hydrochloric acid-based conditions of hydrolysis. The two assays were applied to the determination of the amount of MDA alone and of MDA and 4-hydroxyalkenals in an in vitro model of lipid peroxidation. This methodology was also used to clarify complex patterns of tissue-specific MDA production in vivo, following hydrolysis of Schiff bases, in rodents treated with doxorubicin.

  12. Cross-Coupling Reactions as Valuable Tool for the Preparation of PET Radiotracers

    Marc Pretze


    Full Text Available The increasing application of positron emission tomography (PET in nuclear medicine has stimulated the extensive development of a multitude of new radiotracers and novel radiolabeling procedures with the most prominent short-lived positron emitters carbon-11 and fluorine-18. Radiolabeling with these radionuclides represents a remarkable challenge. Special attention has to be paid to synthesis time and specific labeling techniques due to the short physical half life of the respective radionuclides 11C (t1/2 = 20.4 min and 18F (t1/2 = 109.8 min. In the past, numerous transition metal-catalyzed reactions were employed in organic chemistry, even though only a handful of these coupling reactions were adopted in radiochemical practice. Thus, the implementation of modern synthesis methods like cross-coupling reactions offers the possibility to develop a wide variety of novel radiotracers. The introduction of catalysts based on transition metal complexes bears a high potential for rapid, efficient, highly selective and functional group-tolerating incorporation of carbon-11 and fluorine-18 into target molecules. This review deals with design, application and improvement of transition metal-mediated carbon-carbon as well as carbon-heteroatom cross-coupling reactions as a labeling feature with the focus on the preparation of radiolabeled compounds for molecular imaging.

  13. Single cell kinase signaling assay using pinched flow coupled droplet microfluidics

    Ramji, Ramesh; WANG, MING; Bhagat, Ali Asgar S.; Tan Shao Weng, Daniel; Thakor, Nitish V.; Teck Lim, Chwee; Chen, Chia-Hung


    Droplet-based microfluidics has shown potential in high throughput single cell assays by encapsulating individual cells in water-in-oil emulsions. Ordering cells in a micro-channel is necessary to encapsulate individual cells into droplets further enhancing the assay efficiency. This is typically limited due to the difficulty of preparing high-density cell solutions and maintaining them without cell aggregation in long channels (>5 cm). In this study, we developed a short pinched flow channel...

  14. A Color-Reaction-Based Biochip Detection Assay for RIF and INH Resistance of Clinical Mycobacterial Specimens.

    Xue, Wenfei; Peng, Jingfu; Yu, Xiaoli; Zhang, Shulin; Zhou, Boping; Jiang, Danqing; Chen, Jianbo; Ding, Bingbing; Zhu, Bin; Li, Yao


    The widespread occurrence of drug-resistant Mycobacterium tuberculosis places importance on the detection of TB (tuberculosis) drug susceptibility. Conventional drug susceptibility testing (DST) is a lengthy process. We developed a rapid enzymatic color-reaction-based biochip assay. The process included asymmetric multiplex PCR/templex PCR, biochip hybridization, and an enzymatic color reaction, with specific software for data operating. Templex PCR (tem- PCR) was applied to avoid interference between different primers in conventional multiplex- PCR. We applied this assay to 276 clinical specimens (including 27 sputum, 4 alveolar lavage fluid, 2 pleural effusion, and 243 culture isolate specimens; 40 of the 276 were non-tuberculosis mycobacteria specimens and 236 were M. tuberculosis specimens). The testing process took 4.5 h. A sensitivity of 50 copies per PCR was achieved, while the sensitivity was 500 copies per PCR when tem-PCR was used. Allele sequences could be detected in mixed samples at a proportion of 10%. Detection results showed a concordance rate of 97.46% (230/236) in rifampicin resistance detection (sensitivity 95.40%, specificity 98.66%) and 96.19% (227/236) in isoniazid (sensitivity 93.59%, specificity 97.47%) detection with those of DST assay. Concordance rates of testing results for sputum, alveolar lavage fluid, and pleural effusion specimens were 100%. The assay provides a potential choice for TB diagnosis and treatment.

  15. Coupled reactions of immobilized enzymes and immobilized substrates: clinical application as exemplified by amylase assay.

    Barabino, R C; Gray, D N; Keyes, M H


    We described a partitioned enzyme-sensor system, which incorporates an immoblized substrate and three or more discrete immobilized enzymes. This instrument measures alpha-amylase activity by passing the solution containing alpha-amylase over a column packed with immobilized starch. The resulting oligosaccharides are successively exposed to a column or columns containing immobolized glucose oxidase, catalase, glucoamylase or maltase, and glucose oxidase. The resulting hydrogen peroxide is detected by a three-electrode amperometric cell. All immobilized reagents were immobilized on a particulate, porous alumina to allow rapid and constant flow rate. With use of less than optimum immobilized reagents, alpha-amylase activity has been measured from about 5 to 200 kU/liter with a 50 microliter sample size. Lack of sensitivity is predominantly attributable to the low activity and low stability of immobilized maltase and glucoamylase. We believe that a clinical test using this system is feasible and desirable because the immobilized reagent system should allow for testing of alpha-amylase with excellent precision, convenience to the operator, and low cost.

  16. Windsor and Perry: Reactions of Siblings in Same-Sex and Heterosexual Couples


    The U.S. Supreme Court decisions in U.S. v. Windsor (570 U.S. 307) and Hollingsworth v. Perry (570 U.S. 399) created a focal point for public discussion of marriage equality for same-sex couples. This article reports the results of an exploratory study of the reactions of individuals currently or previously in same-sex couple relationships and a heterosexual sibling who is currently or previously married (N = 371) to the Supreme Court decisions. Thematic content analysis was used to explore p...

  17. Chemical Reaction Between Polyvinyl Alcohol and Titanate Coupling Agent with X-Ray Photoelectron Spectroscopy

    LI Bei-xing; ZHANG Wen-sheng


    The chemical reaction between polyvinyl alcohol (PVA) and tri(dioctylpyrophosphoryloxy) isopropyl titanate (NDZ-201) was studied using X-ray photoelectron spectroscopy (XPS).The results show that some C-OH functional groups of PVA react with the titanate coupling agent to form CPVA-O-Ti-O-CPVA bond.The cross-linking of the PVA chains occurs through the formation of CPVA-O-Ti-O-CPVA bonds and produces a three dimensional hydrophobic polymer network.Accordingly,the mechanism is proposed that the titanate coupling agent improves the moisture sensitivity of high alumina cement/polyvinyl alcohol (HAC/PVA) based macro defect free (MDF) composite material.

  18. Palladium-catalyzed cross coupling reactions of 4-bromo-6H-1,2-oxazines

    Reinhold Zimmer


    Full Text Available A number of 4-aryl- and 4-alkynyl-substituted 6H-1,2-oxazines 8 and 9 have been prepared in good yields via cross coupling reactions of halogenated precursors 2, which in turn are easily accessible by bromination of 6H-1,2-oxazines 1. Lewis-acid promoted reaction of 1,2-oxazine 9c with 1-hexyne provided alkynyl-substituted pyridine derivative 12 thus demonstrating the potential of this approach for the synthesis of pyridines.

  19. Development of a SYBR Green quantitative polymerase chain reaction assay for rapid detection and quantification of infectious laryngotracheitis virus.

    Mahmoudian, Alireza; Kirkpatrick, Naomi C; Coppo, Mauricio; Lee, Sang-Won; Devlin, Joanne M; Markham, Philip F; Browning, Glenn F; Noormohammadi, Amir H


    Infectious laryngotracheitis is an acute viral respiratory disease of chickens with a worldwide distribution. Sensitive detection of the causative herpesvirus is particularly important because it can persist in the host at a very low copy number and be transmitted to other birds. Quantification of viral genome copy number is also useful for clinical investigations and experimental studies. In the study presented here, a quantitative polymerase chain reaction (qPCR) assay was developed using SYBR Green chemistry and the viral gene UL15a to detect and quantify infectious laryngotracheitis virus (ILTV) in ILTV-inoculated chicken embryos or naturally infected birds. The specificity of the assay was confirmed using a panel of viral and bacterial pathogens of poultry. The sensitivity of the assay was compared with two conventional PCR assays, virus titration and an antigen-detecting enzyme-linked immunosorbent assay. The qPCR developed in this study was highly sensitive and specific, and has potential for quantification of ILTV in tissues from naturally and experimentally infected birds and embryos.

  20. Strand-Specific Quantitative Reverse Transcription-Polymerase Chain Reaction Assay for Measurement of Arenavirus Genomic and Antigenomic RNAs.

    Kelsey Haist

    Full Text Available Arenaviruses are bi-segmented, single-stranded RNA viruses that cause significant human disease. The manner in which they regulate the replication of their genome is not well-understood. This is partly due to the absence of a highly sensitive assay to measure individual species of arenavirus replicative RNAs. To overcome this obstacle, we designed a quantitative reverse transcription (RT-PCR assay for selective quantitation of each of the lymphocytic choriomeningitis virus (LCMV genomic or antigenomic RNAs. During the course of assay design, we identified a nonspecific priming phenomenon whereby, in the absence of an RT primer, cDNAs complementary to each of the LCMV replicative RNA species are generated during RT. We successfully circumvented this nonspecific priming event through the use of biotinylated primers in the RT reaction, which permitted affinity purification of primer-specific cDNAs using streptavidin-coated magnetic beads. As proof of principle, we used the assay to map the dynamics of LCMV replication at acute and persistent time points and to determine the quantities of genomic and antigenomic RNAs that are incorporated into LCMV particles. This assay can be adapted to measure total S or L segment-derived viral RNAs and therefore represents a highly sensitive diagnostic platform to screen for LCMV infection in rodent and human tissue samples and can also be used to quantify virus-cell attachment.

  1. Preparation of Pd-Diimine@SBA-15 and Its Catalytic Performance for the Suzuki Coupling Reaction

    Jiahuan Yu


    Full Text Available A highly efficient and stable Pd-diimine@SBA-15 catalyst was successfully prepared by immobilizing Pd onto diimine-functionalized mesoporous silica SBA-15. With the help of diimine functional groups grafted onto the SBA-15, Pd could be anchored on a support with high dispersion. Pd-diimine@SBA-15 catalyst exhibited excellent catalytic performance for the Suzuki coupling reaction of electronically diverse aryl halides and phenylboronic acid under mild conditions with an ultralow amount of Pd (0.05 mol % Pd. When the catalyst amount was increased, it could catalyze the coupling reaction of chlorinated aromatics with phenylboronic acid. Compared with the catalytic performances of Pd/SBA-15 and Pd-diimine@SiO2 catalysts, the Pd-diimine@SBA-15 catalyst exhibited higher hydrothermal stability and could be repeatedly used four times without a significant decrease of its catalytic activity.

  2. Highly Efficient Synthesis of 2-Aryl-3-methoxyacrylates via Suzuki-Miyaura Coupling Reaction

    Kim, Hyung Ho; Lee, Chun Ho; Song, Young Seob; Park, No Kyun; Kim, Bum Tae; Heo, Jung Nyoung [Korea Research Institute of Chemical Technology, Daejeon (Korea, Republic of)


    We have developed a highly efficient and convergent synthesis of 2-aryl-3-methoxyacrylates via the Suzuki-Miyaura coupling reaction of α-iodo-β-methoxy-acrylate with arylboronic acids. The biological activities of 2-aryl-3-methoxyacrylate derivatives will be reported in due course. The Suzuki-Miyaura coupling reaction provides a convenient access to the carbon-carbon bond formation with high efficiency. Recently, a number of 2-aryl-3-methoxy-acrylates served as a key scaffold for the development of biologically active pharmaceuticals and agrochemicals. Especially, the discovery of the naturally-occurring fungicides, such as strobilurin A and oudemansin A, possessing a β-methoxyacrylate moiety was immediately seized great attention by industrial research groups to open a new era of the strobilurin family including azoxy-strobin and picoxystrobin.

  3. A General Palladium-Catalyzed Hiyama Cross-Coupling Reaction of Aryl and Heteroaryl Chlorides.

    Yuen, On Ying; So, Chau Ming; Man, Ho Wing; Kwong, Fuk Yee


    A general palladium-catalyzed Hiyama cross-coupling reaction of aryl and heteroaryl chlorides with aryl and heteroaryl trialkoxysilanes by a Pd(OAc)2 /L2 catalytic system is presented. A newly developed water addition protocol can dramatically improve the product yields. The conjugation of the Pd/L2 system and the water addition protocol can efficiently catalyze a broad range of electron-rich, -neutral, -deficient, and sterically hindered aryl chlorides and heteroaryl chlorides with excellent yields within three hours and the catalyst loading can be down to 0.05 mol % Pd for the first time. Hiyama coupling of heteroaryl chlorides with heteroaryl silanes is also reported for the first time. The reaction can be easily scaled up 200 times (100 mmol) without any degasification and purification of reactants; this facilitates the practical application in routine synthesis.

  4. Numerical simulation and analysis of complex patterns in a two-layer coupled reaction diffusion system

    李新政; 白占国; 李燕; 贺亚峰; 赵昆


    The resonance interaction between two modes is investigated using a two-layer coupled Brusselator model. When two different wavelength modes satisfy resonance conditions, new modes will appear, and a variety of superlattice patterns can be obtained in a short wavelength mode subsystem. We find that even though the wavenumbers of two Turing modes are fixed, the parameter changes have infl uences on wave intensity and pattern selection. When a hexagon pattern occurs in the short wavelength mode layer and a stripe pattern appears in the long wavelength mode layer, the Hopf instability may happen in a nonlinearly coupled model, and twinkling-eye hexagon and travelling hexagon patterns will be obtained. The symmetries of patterns resulting from the coupled modes may be different from those of their parents, such as the cluster hexagon pattern and square pattern. With the increase of perturbation and coupling intensity, the nonlinear system will con-vert between a static pattern and a dynamic pattern when the Turing instability and Hopf instability happen in the nonlinear system. Besides the wavenumber ratio and intensity ratio of the two different wavelength Turing modes, perturbation and coupling intensity play an important role in the pattern formation and selection. According to the simulation results, we find that two modes with different symmetries can also be in the spatial resonance under certain conditions, and complex patterns appear in the two-layer coupled reaction diffusion systems.

  5. Reaction monitoring using hyperpolarized NMR with scaling of heteronuclear couplings by optimal tracking

    Zhang, Guannan; Schilling, Franz; Glaser, Steffen J.; Hilty, Christian


    Off-resonance decoupling using the method of Scaling of Heteronuclear Couplings by Optimal Tracking (SHOT) enables determination of heteronuclear correlations of chemical shifts in single scan NMR spectra. Through modulation of J-coupling evolution by shaped radio frequency pulses, off resonance decoupling using SHOT pulses causes a user-defined dependence of the observed J-splitting, such as the splitting of 13C peaks, on the chemical shift offset of coupled nuclei, such as 1H. Because a decoupling experiment requires only a single scan, this method is suitable for characterizing on-going chemical reactions using hyperpolarization by dissolution dynamic nuclear polarization (D-DNP). We demonstrate the calculation of [13C, 1H] chemical shift correlations of the carbanionic active sites from hyperpolarized styrene polymerized using sodium naphthalene as an initiator. While off resonance decoupling by SHOT pulses does not enhance the resolution in the same way as a 2D NMR spectrum would, the ability to obtain the correlations in single scans makes this method ideal for determination of chemical shifts in on-going reactions on the second time scale. In addition, we present a novel SHOT pulse that allows to scale J-splittings 50% larger than the respective J-coupling constant. This feature can be used to enhance the resolution of the indirectly detected chemical shift and reduce peak overlap, as demonstrated in a model reaction between p-anisaldehyde and isobutylamine. For both pulses, the accuracy is evaluated under changing signal-to-noise ratios (SNR) of the peaks from reactants and reaction products, with an overall standard deviation of chemical shift differences compared to reference spectra of 0.02 ppm when measured on a 400 MHz NMR spectrometer. Notably, the appearance of decoupling side-bands, which scale with peak intensity, appears to be of secondary importance.

  6. [Bmim]PF6-promoted ligandless Suzuki-Miyaura coupling reaction of potassium aryltrifluoroborates in water.

    Liu, Leifang; Dong, Yan; Pang, Bo; Ma, Jiahai


    The Suzuki-Miyaura coupling reactions of potassium aryltrifluoroborates with aryl bromides in water are promoted by the addition of [bmim]PF6 using Pd(OAc)2 as a catalyst and Na2CO3 as a base under air. The quantity of [bmim]PF6 used is crucial to the efficiency of the catalytic system. A wide range of biaryls and polyaryls can be easily prepared in good to excellent yields.

  7. Coupling reaction on gold nanoparticle to yield polythiophene/gold nanoparticle alternate network film.

    Tanaka, Manabu; Fujita, Remi; Nishide, Hiroyuki


    The novel gold nanoparticle, which was stabilized with pi-conjugated molecules bearing functional groups at the terminals, was prepared via conventional procedure by using 5-bromo-2,2'-bithiophene-5'-thiol as a stabilizer. The gold nanoparticle (ca. 3 nm-diameter) showed good dispersion stability in various organic solvents, and its electrochemical and spectroscopic study revealed peculiar properties originated in the pi-conjugated molecular stabilizer, bithiophene derivative. The Pd-catalyzed coupling reaction on the gold nanoparticle was first achieved by using the gold nanoparticle bearing bromo groups at the particle surface and the model boronic acid molecule, 5-formyl-2-thiopheneboronic acid, to yield the terthiophene derivatives on the gold nanoparticle. The 1H-NMR, UV, and TGA analysis supported the progress of the coupling reaction on the gold nanoparticle. This Pd-catalyzed coupling reaction was applied with the borate-terminated polythiophene to form polythiophene/gold nanoparticle alternate network film. The electron microscopic images supported the formation of the network structure. The high electric conductivity on the network film suggested that the conductive characteristic of the film originated from that of the pi-conjugated polythiophene backbone connected with the gold nanoparticle.

  8. Nonadiabatic quantum wave packet dynamics of the H + H2 reaction including the coriolis coupling

    B Jayachander Rao; S Mahapatra


    The effect of coriolis coupling on the dynamics of H + H2 reaction is examined by calculating the initial state-selected and energy resolved reaction probabilities on the coupled manifold of its degenerate 2 (') ground electronic state. H3 in this state is prone to the Jahn-Teller (JT) instability and consequently the degeneracy is split upon distortion from its 3ℎ equilibrium geometry. The orbital degeneracy is, however, restored along the 3ℎ symmetry configuration and it results into conical intersections of the two JT split component states. The energetically lower adiabatic component of latter is repulsive, and mainly (`rather solely’) drive the H + H2 reaction dynamics. On the otherhand, the upper adiabatic component is of bound type and can only impart non-adiabaticity on the dynamics of lower state. Comparison calculations are therefore also carried out on the uncoupled lower adiabatic sheet to assess the nonadiabatic effect. Exact quantum scattering calculations are performed by a chebyshev polynomial propagator and employing the double many body expansion potential energy surface of the electronic ground state of H3. Reaction probabilities are reported up to a total energy of ∼ 3.0 eV, slightly above the energetic minimum of the seam of conical intersections at ∼ 2.74 eV. Reaction probabilities are calculated up to the total angular momentum, = 20 and for each value of , the projection quantum number is varied from 0 to min (, max), with max = 4. Probability results are compared and discussed with those obtained without the coriolis coupling.

  9. Coupled Pervaporation-Reaction Distillation Process for the Production of n-Bromopropane

    毛澄宇; 余立新; 郭庆丰; 席春光


    The reaction of n-C3H7OH+HBr=n-C3H7Br+H2O was used to experimentally study a coupled pervaporation (PV)-reaction distillation (RD) process. The results show that polyvinyl alcohol (PVA) is a suitable membrane material for water removal. The typical separation properties of PVA polyacrylonitrile (PAN) composite membranes are a highest flux of 780 g/(m2*h) and a separation factor of 840 for the C3H7OH concentration in the original feed of 95% at 90℃ and below 3300 Pa(abs). Reaction distillation produced the n-bromopropane from the distillation column as a ternary azeotropic liquid mixture of C3H7OH, H2O and C3H7Br, with a product concentration of about 92%. The coupled PV-RD membrane reactor experiment shows that the BrPr yield can reach 92%, much higher than that for reaction-distillation without pervaporation.

  10. Catalytic Activity of Dual Metal Cyanide Complex in Multi-component Coupling Reactions

    Anaswara RAVINDRAN; Rajendra SRIVASTAVA


    Several dual metal cyanide catalysts were prepared from potassium ferrocyanide,metal chloride (where metal =Zn2+,Mn2+,Ni2+,Co2+ and Fe2+),t-butanol (complexing agent) and PEG-4000 (co-complexing agent).The catalysts were characterized by elemental analysis (CHN and X-ray fluorescence),X-ray diffraction,N2 adsorption-desorption,scanning electron microscopy,Fourier-transform infiared spectroscopy,and UV-Visible spectroscopy.The dual metal cyanide catalysts were used in several acid catalyzed multi-component coupling reactions for the synthesis of pharmaceutically important organic derivatives.In all these reactions,the Fe-Fe containing dual metal cyanide catalyst was the best catalyst.The catalysts can be recycled without loss in catalytic activity.The advantage of this method is the use of mild,efficient and reusable catalysts for various reactions,which makes them candidates for commercial use.

  11. Coupling of a scanning flow cell with online electrochemical mass spectrometry for screening of reaction selectivity

    Grote, Jan-Philipp; Zeradjanin, Aleksandar R.; Cherevko, Serhiy; Mayrhofer, Karl J. J.


    In this work the online coupling of a miniaturized electrochemical scanning flow cell (SFC) to a mass spectrometer is introduced. The system is designed for the determination of reaction products in dependence of the applied potential and/or current regime as well as fast and automated change of the sample. The reaction products evaporate through a hydrophobic PTFE membrane into a small vacuum probe, which is positioned only 50-100 μm away from the electrode surface. The probe is implemented into the SFC and directly connected to the mass spectrometer. This unique configuration enables fast parameter screening for complex electrochemical reactions, including investigation of operation conditions, composition of electrolyte, and material composition. The technical developments of the system are validated by initial measurements of hydrogen evolution during water electrolysis and electrochemical reduction of CO2 to various products, showcasing the high potential for systematic combinatorial screening by this approach.

  12. Development and use of a real-time polymerase chain reaction assay for the detection of Ophidiomyces ophiodiicola in snakes.

    Allender, Matthew C; Bunick, David; Dzhaman, Elena; Burrus, Lucienne; Maddox, Carol


    Fungal pathogens threatening the conservation of wildlife are becoming increasingly common. Since 2008, free-ranging snakes across North America have been experiencing a marked increase in the prevalence of snake fungal disease associated with Ophidiomyces ophiodiicola. Diagnosis has historically relied on histology, microbiology, and conventional polymerase chain reaction (PCR). More sensitive methods are needed to adequately characterize the epidemiology. The current study describes the development of a real-time PCR (qPCR) assay for detecting a segment of the internal transcribed spacer 1 region between the 18S and 5.8S ribosomal RNA gene. The assay was able to detect as few as 1.05 × 10(1) gene copies per reaction. An additional 4 positive cases were detected when comparing a conventional PCR (n = 3) and the qPCR (n = 7) when used on swab samples from 47 eastern massasauga rattlesnakes. The newly developed assay is a sensitive and specific tool for surveillance and monitoring in the conservation of free-ranging snakes.

  13. Simultaneous quantitation of nicotinamide riboside, nicotinamide mononucleotide and nicotinamide adenine dinucleotide in milk by a novel enzyme-coupled assay.

    Ummarino, Simone; Mozzon, Massimo; Zamporlini, Federica; Amici, Adolfo; Mazzola, Francesca; Orsomando, Giuseppe; Ruggieri, Silverio; Raffaelli, Nadia


    Nicotinamide riboside, the most recently discovered form of vitamin B3, and its phosphorylated form nicotinamide mononucleotide, have been shown to be potent supplements boosting intracellular nicotinamide adenine dinucleotide (NAD) levels, thus preventing or ameliorating metabolic and mitochondrial diseases in mouse models. Here we report for the first time on the simultaneous quantitation of nicotinamide riboside, nicotinamide mononucleotide and NAD in milk by means of a fluorometric, enzyme-coupled assay. Application of this assay to milk from different species revealed that the three vitamers were present in human and donkey milk, while being selectively distributed in the other milks. Human milk was the richest source of nicotinamide mononucleotide. Overall, the three vitamers accounted for a significant fraction of total vitamin B3 content. Pasteurization did not affect the bovine milk content of nicotinamide riboside, whereas UHT processing fully destroyed the vitamin. In human milk, NAD levels were significantly affected by the lactation time.

  14. High throughput microwell spectrophotometric assay for olmesartan medoxomil in tablets based on its charge-transfer reaction with DDQ

    Darwish Ibrahim A.


    Full Text Available The study describes the development and validation of a new microwell-based spectrophotometric assay for determination of olmesartan medoxomil (OLM in tablets. The formation of a colored charge-transfer (CT complex between OLM as an n-electron donor and 2,3-dichloro- -5,6-dicyano-1,4-benzoquinone (DDQ as a p-electron acceptor was investigated, and employed as the basis for the development of the new assay. The proposed assay was conducted in 96-microwell plates. The absorbance of the colored-CT complex was measured at 460 nm with a microplate reader. Optimum conditions of the reaction and the analytical procedures of the assay were established. Under the optimum conditions, a linear relationship with a good correlation coefficient was found between the absorbance and the concentration of OLM in the range of 2-200 μg per well. The limits of detection and quantitation were 0.53 and 1.61 μg per well, respectively. No interference was observed from the excipients present in OLM tablets or from hydrochlorothiazide and amlodipine besylate that were co-formulated with OLM in some of its formulations. The assay was successfully applied to the analysis of OLM in tablets with good accuracy and precision. The assay described herein has a great practical value in the routine analysis of OLM in quality control laboratories, since it has a high throughput property and consumes low volumes of organic solvent. It thus offers a reduction in the exposure of analysts to the toxic effects of organic solvents, as well as a reduction in the cost of analysis.

  15. Application of new semisynthetic aequorins with long half-decay time of luminescence to G-protein-coupled receptor assay.

    Inouye, Satoshi; Iimori, Rie; Sahara, Yuiko; Hisada, Sunao; Hosoya, Takamitsu


    Aequorin is a Ca(2+)-binding photoprotein and consists of an apoprotein (apoaequorin) and a 2-peroxide of coelenterazine. Eight new coelenterazine analogues modified at the C2-position were synthesized and incorporated into recombinant apoaequorin with O(2) to yield different semisynthetic aequorins. The luminescence properties and the sensitivity to Ca(2+) of these semisynthetic aequorins were characterized. Two semisynthetic aequorins, namely me- and cf3-aequorin, showed a slow decay of the luminescence pattern with less sensitivity to Ca(2+) and were useful for the cell-based G-protein-coupled receptor (GPCR) reporter assays. Copyright © 2010 Elsevier Inc. All rights reserved.

  16. A New Methodology for Assessing Macromolecular Click Reactions and Its Application to Amine--Tertiary Isocyanate Coupling for Polymer Ligation.

    Gody, Guillaume; Roberts, Derrick A; Maschmeyer, Thomas; Perrier, Sébastien


    Click reactions have provided access to an array of remarkably complex polymer architectures. However, the term "click" is often applied inaccurately to polymer ligation reactions that fail to respect the criteria that typify a true "click" reaction. With the purpose of providing a universal way to benchmark polymer-polymer coupling efficiency at equimolarity and thus evaluate the fulfilment of click criteria, we report a simple one-pot methodology involving the homodicoupling of α-end-functionalized polymers using a small-molecule bifunctional linker. A combination of SEC analysis and chromatogram deconvolution enables straightforward quantification of the coupling efficiency. We subsequently employ this methodology to evaluate an overlooked candidate for the click reaction family: the addition of primary amines to α-tertiary isocyanates (α-(t)NCO). Using our bifunctional linker coupling strategy, we show that the amine-(t)NCO reaction fulfills the criteria for a polymer-polymer click reaction, achieving rapid, chemoselective, and quantitative coupling at room temperature without generating any byproducts. We demonstrate that amine-(t)NCO coupling is faster and more efficient than the more common amine-tertiary active ester coupling under equivalent conditions. Additionally, we show that the α-(t)NCO end group is unprecedentedly stable in aqueous media. Thus, we propose that the amine-(t)NCO ligation is a powerful new click reaction for efficient macromolecular coupling.

  17. Single cell kinase signaling assay using pinched flow coupled droplet microfluidics.

    Ramji, Ramesh; Wang, Ming; Bhagat, Ali Asgar S; Tan Shao Weng, Daniel; Thakor, Nitish V; Teck Lim, Chwee; Chen, Chia-Hung


    Droplet-based microfluidics has shown potential in high throughput single cell assays by encapsulating individual cells in water-in-oil emulsions. Ordering cells in a micro-channel is necessary to encapsulate individual cells into droplets further enhancing the assay efficiency. This is typically limited due to the difficulty of preparing high-density cell solutions and maintaining them without cell aggregation in long channels (>5 cm). In this study, we developed a short pinched flow channel (5 mm) to separate cell aggregates and to form a uniform cell distribution in a droplet-generating platform that encapsulated single cells with >55% encapsulation efficiency beating Poisson encapsulation statistics. Using this platform and commercially available Sox substrates (8-hydroxy-5-(N,N-dimethylsulfonamido)-2-methylquinoline), we have demonstrated a high throughput dynamic single cell signaling assay to measure the activity of receptor tyrosine kinases (RTKs) in lung cancer cells triggered by cell surface ligand binding. The phosphorylation of the substrates resulted in fluorescent emission, showing a sigmoidal increase over a 12 h period. The result exhibited a heterogeneous signaling rate in individual cells and showed various levels of drug resistance when treated with the tyrosine kinase inhibitor, gefitinib.

  18. Coupling the Torpedo microplate-receptor binding assay with mass spectrometry to detect cyclic imine neurotoxins.

    Aráoz, Rómulo; Ramos, Suzanne; Pelissier, Franck; Guérineau, Vincent; Benoit, Evelyne; Vilariño, Natalia; Botana, Luis M; Zakarian, Armen; Molgó, Jordi


    Cyclic imine neurotoxins constitute an emergent family of neurotoxins of dinoflagellate origin that are potent antagonists of nicotinic acetylcholine receptors. We developed a target-directed functional method based on the mechanism of action of competitive agonists/antagonists of nicotinic acetylcholine receptors for the detection of marine cyclic imine neurotoxins. The key step for method development was the immobilization of Torpedo electrocyte membranes rich in nicotinic acetylcholine receptors on the surface of microplate wells and the use of biotinylated-α-bungarotoxin as tracer. Cyclic imine neurotoxins competitively inhibit biotinylated-α-bungarotoxin binding to Torpedo-nicotinic acetylcholine receptors in a concentration-dependent manner. The microplate-receptor binding assay allowed rapid detection of nanomolar concentrations of cyclic imine neurotoxins directly in shellfish samples. Although highly sensitive and specific for the detection of neurotoxins targeting nicotinic acetylcholine receptors as a class, the receptor binding assay cannot identify a given analyte. To address the low selectivity of the microplate-receptor binding assay, the cyclic imine neurotoxins tightly bound to the coated Torpedo nicotinic receptor were eluted with methanol, and the chemical nature of the eluted ligands was identified by mass spectrometry. The immobilization of Torpedo electrocyte membranes on the surface of microplate wells proved to be a high-throughput format for the survey of neurotoxins targeting nicotinic acetylcholine receptors directly in shellfish matrixes with high sensitivity and reproducibility.

  19. Rapid Detection of Filoviruses by Real-time TaqMan Polymerase Chain Reaction Assays

    Yi Huang; Hongping Wei; Yunpeng Wang; Zhengli Shi; Herve Raoul; Zhiming Yuan


    Ebola virus (EBOV) and Marburg virus (MARV) are causative agents of severe hemorrhagic fever with high mortality rates in humans and non-human primates and there is currently no licensed vaccine or therapeutics.To date,there is no specific laboratory diagnostic test in China,while there is a national need to provide differential diagnosis during outbreaks and for instituting acceptable quarantine procedures.In this study,the TaqMan RT-PCR assays targeting the nucleoprotein genes of the Zaire Ebolavirus (ZEBOV) and MARV were developed and their sensitivities and specificities were investigated.Our results indicated that the assays were able to make reliable diagnosis over a wide range of virus copies from 103 to 109,corresponding to the threshold of a standard RNA transcript.The results showed that there were about 1010 RNA copies per milliliter of virus culture supernatant,equivalent to 10,000 RNA molecules per infectious virion,suggesting the presence of many non-infectious particles.These data indicated that the TaqMan RT-PCR assays developed in this study will be suitable for future surveillance and specific diagnosis of ZEBOV and MARV in China.

  20. Detection of mutations by fill-in ligation reaction with enzyme-linked immunosorbent assay for rapid medical diagnosis.

    Tang, Yi-Tong; Xiao, Na; Li, Zhi-Shan; Zou, Jiu-Ming; Cao, Rui; Zhao, Xue-Hong; Shao, Jin-Hui


    Several approaches for parallel genotyping have been developed with increasingly available information on DNA variation. However, these methods require either complex laboratory procedures or expensive instrumentation. None of these procedures is readily performed in local clinical laboratories. In this study, we developed a flexible genotyping method involving fill-in ligation reaction with enzyme-linked immunosorbent assay successfully applied to detect important single-nucleotide polymorphisms (SNPs) for EGFR c.2573T > G (L858R), EGFR c.2582T > A (L861Q), and EGFR c.2155G > T (G719C). This assay exhibited excellent specificity, with a sensitivity as low as 0.5%. Eight out of 62 clinical samples were identified as heterozygotes for the SNP site of L858R, whereas only two samples were identified as heterozygotes by direct sequencing. The developed method enabled accurate identification of SNP in a simple and cost-effective manner adapted to routine analysis.

  1. Evaluation of a commercial real-time polymerase chain reaction assay for detection of environmental contamination with Clostridium difficile.

    Deshpande, A; Kundrapu, S; Sunkesula, V C K; Cadnum, J L; Fertelli, D; Donskey, C J


    Contaminated environmental surfaces are an important source for transmission of Clostridium difficile. However, there are no efficient and easy methods to assess contamination. The performance of a commercial real-time polymerase chain reaction (PCR) assay was evaluated for detection of environmental toxigenic C. difficile in comparison with anaerobic culture followed by toxin testing of isolates. For 66 sites sampled, PCR had a sensitivity of 17.39%, specificity 100%, positive predictive value 100% and negative predictive value 69.35%. Increasing the PCR cycle threshold (CT) value to 45 increased sensitivity to 52% without decreasing specificity. The commercial PCR assay is not sufficiently sensitive for environmental monitoring, but improved sensitivity might be possible through CT value modification.

  2. A homogeneous quenching resonance energy transfer assay for the kinetic analysis of the GTPase nucleotide exchange reaction.

    Kopra, Kari; Ligabue, Alessio; Wang, Qi; Syrjänpää, Markku; Blaževitš, Olga; Veltel, Stefan; van Adrichem, Arjan J; Hänninen, Pekka; Abankwa, Daniel; Härmä, Harri


    A quenching resonance energy transfer (QRET) assay for small GTPase nucleotide exchange kinetic monitoring is demonstrated using nanomolar protein concentrations. Small GTPases are central signaling proteins in all eukaryotic cells acting as a "molecular switches" that are active in the GTP-state and inactive in the GDP-state. GTP-loading is highly regulated by guanine nucleotide exchange factors (GEFs). In several diseases, most prominently cancer, this process in misregulated. The kinetics of the nucleotide exchange reaction reports on the enzymatic activity of the GEF reaction system and is, therefore, of special interest. We determined the nucleotide exchange kinetics using europium-labeled GTP (Eu-GTP) in the QRET assay for small GTPases. After GEF catalyzed GTP-loading of a GTPase, a high time-resolved luminescence signal was found to be associated with GTPase bound Eu-GTP, whereas the non-bound Eu-GTP fraction was quenched by soluble quencher. The association kinetics of the Eu-GTP was measured after GEF addition, whereas the dissociation kinetics could be determined after addition of unlabeled GTP. The resulting association and dissociation rates were in agreement with previously published values for H-Ras(Wt), H-Ras(Q61G), and K-Ras(Wt), respectively. The broader applicability of the QRET assay for small GTPases was demonstrated by determining the kinetics of the Ect2 catalyzed RhoA(Wt) GTP-loading. The QRET assay allows the use of nanomolar protein concentrations, as more than 3-fold signal-to-background ratio was achieved with 50 nM GTPase and GEF proteins. Thus, small GTPase exchange kinetics can be efficiently determined in a HTS compatible 384-well plate format.

  3. Intermolecular coulomb couplings from ab initio electrostatic potentials: application to optical transitions of strongly coupled pigments in photosynthetic antennae and reaction centers.

    Madjet, M E; Abdurahman, A; Renger, T


    An accurate and numerically efficient method for the calculation of intermolecular Coulomb couplings between charge densities of electronic states and between transition densities of electronic excitations is presented. The coupling of transition densities yields the Förster type excitation energy transfer coupling, and from the charge density coupling, a shift in molecular excitation energies results. Starting from an ab initio calculation of the charge and transition densities, atomic partial charges are determined such as to fit the resulting electrostatic potentials of the different states and the transition. The different intermolecular couplings are then obtained from the Coulomb couplings between the respective atomic partial charges. The excitation energy transfer couplings obtained in the present TrEsp (transition charge from electrostatic potential) method are compared with couplings obtained from the simple point-dipole and extended dipole approximations and with those from the ab initio transition density cube method of Krüger, Scholes, and Fleming. The present method is of the same accuracy as the latter but computationally more efficient. The method is applied to study strongly coupled pigments in the light-harvesting complexes of green sulfur bacteria (FMO), purple bacteria (LH2), and higher plants (LHC-II) and the "special pairs" of bacterial reaction centers and reaction centers of photosystems I and II. For the pigment dimers in the antennae, it is found that the mutual orientation of the pigments is optimized for maximum excitonic coupling. A driving force for this orientation is the Coulomb coupling between ground-state charge densities. In the case of excitonic couplings in the "special pairs", a breakdown of the point-dipole approximation is found for all three reaction centers, but the extended dipole approximation works surprisingly well, if the extent of the transition dipole is chosen larger than assumed previously. For the "special

  4. A Highly Sensitive Spectrophotometric Assay of Bleomycins Based on the Fading Reaction of Some Halofluorescein Dyes

    LIU,Jiang-Tao; LIU,Zhong-Fang; HU,Xiao-Li; Kong,Ling; LIU,Shao-Pu


    In weak acidic medium, anticancer antibiotics bleomycin A5 (BLMA5) and bleomycin A2 (BLMA2) can react with halofluorescein dyes such as erythrosin (Ery), eosin Y (EY), eosin B (EB) and rose bengal (RB) by virtue of electrostatic attraction and hydrophobic force to form the ion-association complexes, which can result in the fading reactions of four halofluorescein dyes. The maximum fading wavelengths of these four dyes were located at 527 nm for Ery, 515 nm for EY, 517 nm for EB and 546 nm for RB, respectively. The decrements of absorbance (△A) were directly proportional to the concentrations of bleomycin in a certain range. A new method for the determination of bleomycins anticancer drugs based on fading reactions of halofluorescein dyes has been developed. The method was not only highly sensitive but also simple and rapid. The molar absorptivities (ε) ranged from 1.5 × 105 to 7.5 ×105 L·mol-1·cm-1. It was applied to determination of the bleomycins in human serum, urine and rabbit serum samples. In this work, the spectral properties and the optimum reaction conditions were investigated. The structure of ion-association complexes and the reaction mechanism were discussed.

  5. Exploring Regioselective Bond Cleavage and Cross-Coupling Reactions using a Low-Valent Nickel Complex.

    Desnoyer, Addison N; Friese, Florian W; Chiu, Weiling; Drover, Marcus W; Patrick, Brian O; Love, Jennifer A


    Recently, esters have received much attention as transmetalation partners for cross-coupling reactions. Herein, we report a systematic study of the reactivity of a series of esters and thioesters with [{(dtbpe)Ni}2(μ-η(2):η(2)-C6H6)] (dtbpe=1,2-bis(di-tert-butyl)phosphinoethane), which is a source of (dtbpe)nickel(0). Trifluoromethylthioesters were found to form η(2)-carbonyl complexes. In contrast, acetylthioesters underwent rapid Cacyl-S bond cleavage followed by decarbonylation to generate methylnickel complexes. This decarbonylation could be pushed backwards by the addition of CO, allowing for regeneration of the thioester. Most of the thioester complexes were found to undergo stoichiometric cross-coupling with phenylboronic acid to yield sulfides. While ethyl trifluoroacetate was also found to form an η(2)-carbonyl complex, phenyl esters were found to predominantly undergo Caryl-O bond cleavage to yield arylnickel complexes. These could also undergo transmetalation to yield biaryls. Attempts to render the reactions catalytic were hindered by ligand scrambling to yield nickel bis(acetate) complexes, the formation of which was supported by independent syntheses. Finally, 2-naphthyl acetate was also found to undergo clean Caryl-O bond cleavage, and although stoichiometric cross-coupling with phenylboronic acid proceeded with good yield, catalytic turnover has so far proven elusive.

  6. Dynamical coupled-channel model of meson production reactions in the nucleon resonance region

    Matsuyama, A; Sato, T


    A dynamical coupled-channel model is presented for investigating the nucleon resonances in the meson production reactions induced by pions and photons. The model is based on an energy-independent Hamiltonian which is derived from a set of Lagrangians by using a unitary transformation method. By applying the projection operator techniques,we derive a set of coupled-channel equations which satisfy the unitarity conditions within the channel space spanned by the considered two-particle meson-baryon states and the three-particle $\\pi\\pi N$ state. We present and explain in detail a numerical method based on a spline-function expansion for solving the resulting coupled-channel equations which contain logarithmically divergent one-particle-exchange driving terms resulted from the $\\pi\\pi N$ unitarity cut. We show that this driving term can generate rapidly varying structure in the reaction amplitudes associated with the unstable particle channels. It also has large effects in determining the two-pion production cros...

  7. Dynamical coupled-channels study of pi N --> pi pi N reactions

    Kamano, H; Lee, T -S H; Matsuyama, A; Sato, T


    As a step toward performing a complete coupled-channels analysis of the world data of pi N, gamma^* N --> pi N, eta N, pi pi N reactions, the pi N --> pi pi N reactions are investigated starting with the dynamical coupled-channels model developed in Phys. Rev. C76, 065201 (2007). The channels included are pi N, eta N, and pi pi N which has pi Delta, rho N, and sigma N resonant components. The non-resonant amplitudes are generated from solving a set of coupled-channels equations with the meson-baryon potentials defined by effective Lagrangians. The resonant amplitudes are generated from 16 bare excited nucleon (N^*) states which are dressed by the non-resonant interactions as constrained by the unitarity condition. The available total cross section data of pi^+ p --> pi^+ pi^+ n, pi^+ pi^0p and pi^- p --> pi^+ pi^- n, pi^- pi^0 n, pi^0 pi^0 n can be reproduced to a very large extent both in magnitudes and energy-dependence. Possible improvements of the model are investigated, in particular on the role of the n...

  8. A general strategy for nanohybrids synthesis via coupled competitive reactions controlled in a hybrid process.

    Wang, Rongming; Yang, Wantai; Song, Yuanjun; Shen, Xiaomiao; Wang, Junmei; Zhong, Xiaodi; Li, Shuai; Song, Yujun


    A new methodology based on core alloying and shell gradient-doping are developed for the synthesis of nanohybrids, realized by coupled competitive reactions, or sequenced reducing-nucleation and co-precipitation reaction of mixed metal salts in a microfluidic and batch-cooling process. The latent time of nucleation and the growth of nanohybrids can be well controlled due to the formation of controllable intermediates in the coupled competitive reactions. Thus, spatiotemporal-resolved synthesis can be realized by the hybrid process, which enables us to investigate nanohybrid formation at each stage through their solution color changes and TEM images. By adjusting the bi-channel solvents and kinetic parameters of each stage, the primary components of alloyed cores and the second components of transition metal doping ZnO or Al2O3 as surface coatings can be successively formed. The core alloying and shell gradient-doping strategy can efficiently eliminate the crystal lattice mismatch in different components. Consequently, varieties of gradient core-shell nanohybrids can be synthesized using CoM, FeM, AuM, AgM (M = Zn or Al) alloys as cores and transition metal gradient-doping ZnO or Al2O3 as shells, endowing these nanohybrids with unique magnetic and optical properties (e.g., high temperature ferromagnetic property and enhanced blue emission).

  9. Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation.

    Andrea Ciliberto


    Full Text Available In metabolic networks, metabolites are usually present in great excess over the enzymes that catalyze their interconversion, and describing the rates of these reactions by using the Michaelis-Menten rate law is perfectly valid. This rate law assumes that the concentration of enzyme-substrate complex (C is much less than the free substrate concentration (S0. However, in protein interaction networks, the enzymes and substrates are all proteins in comparable concentrations, and neglecting C with respect to S0 is not valid. Borghans, DeBoer, and Segel developed an alternative description of enzyme kinetics that is valid when C is comparable to S0. We extend this description, which Borghans et al. call the total quasi-steady state approximation, to networks of coupled enzymatic reactions. First, we analyze an isolated Goldbeter-Koshland switch when enzymes and substrates are present in comparable concentrations. Then, on the basis of a real example of the molecular network governing cell cycle progression, we couple two and three Goldbeter-Koshland switches together to study the effects of feedback in networks of protein kinases and phosphatases. Our analysis shows that the total quasi-steady state approximation provides an excellent kinetic formalism for protein interaction networks, because (1 it unveils the modular structure of the enzymatic reactions, (2 it suggests a simple algorithm to formulate correct kinetic equations, and (3 contrary to classical Michaelis-Menten kinetics, it succeeds in faithfully reproducing the dynamics of the network both qualitatively and quantitatively.

  10. Pd complexes based on phosphine-linked cyclophosphazenes: synthesis, characterization and application in Suzuki coupling reactions

    Paula, Vanderlei I. de; Sato, Cintia A.; Buffon, Regina, E-mail: [Instituto de Quimica, Universidade Estadual de Campinas (IQ/UNICAMP), SP (Brazil)


    Palladium complexes were obtained by reaction of phosphine-linked cyclophosphazenes, (P{sub 3}N{sub 3})(O-C{sub 6}H{sub 4}-PR{sub 2}){sub 6}, where R = phenyl, i-propyl or cyclohexyl, with using a Pd/ligand molar ratio of 3/1. The (P{sub 3}N{sub 3})(O-C{sub 6}H{sub 4}-PR{sub 2}){sub 6} Pd{sub 3}(dba)x complexes were characterized by elemental analyses, mass spectrometry, {sup 31}P NMR and FT-IR where a characteristic {nu}{sub C}={sub C} band of dba coordinated to palladium was always observed. All complexes were tested in Suzuki coupling reactions between phenylboronic acid and aryl halides. Turnover numbers as high as ca. 17,500 for the coupling of 2-bromotoluene with chloro phenylboronic acid could be obtained for R = cyclohexyl. The complex based on -PPh{sub 2} was also immobilized in silica matrixes by the sol-gel method. Preliminary experiments showed that the immobilized catalyst could be used in at least three consecutive Suzuki reactions with the same catalytic activity. (author)

  11. Avian haemosporidian parasites (Haemosporida): A comparative analysis of different polymerase chain reaction assays in detection of mixed infections.

    Bernotienė, Rasa; Palinauskas, Vaidas; Iezhova, Tatjana; Murauskaitė, Dovilė; Valkiūnas, Gediminas


    Mixed infections of different species and genetic lineages of haemosporidian parasites (Haemosporida) predominate in wildlife, and such infections are particularly virulent. However, currently used polymerase chain reaction (PCR)-based detection methods often do not read mixed infections. Sensitivity of different PCR assays in detection of mixed infections has been insufficiently tested, but this knowledge is essential in studies addressing parasite diversity in wildlife. Here, we applied five different PCR assays, which are broadly used in wildlife avian haemosporidian research, and compared their sensitivity in detection of experimentally designed mixed infections of Haemoproteus and Plasmodium parasites. Three of these PCR assays use primer sets that amplify fragments of cytochrome b gene (cyt b), one of cytochrome oxidase subunit I (COI) gene, and one target apicoplast genome. We collected blood from wild-caught birds and, using microscopic and PCR-based methods applied in parallel, identified single infections of ten haemosporidian species with similar parasitemia. Then, we prepared 15 experimental mixes of different haemosporidian parasites, which often are present simultaneously in wild birds. Similar concentration of total DNA was used in each parasite lineage during preparation of mixes. Positive amplifications were sequenced, and the presence of mixed infections was reported by visualising double-base calling in sequence electropherograms. This study shows that the use of each single PCR assay markedly underestimates biodiversity of haemosporidian parasites. The application of at least 3 PCR assays in parallel detected the majority, but still not all lineages present in mixed infections. We determined preferences of different primers in detection of parasites belonging to different genera of haemosporidians during mixed infections.

  12. Cyanidin-horseradish peroxidase-hydroperoxide reaction system and its application in enzyme-linked immunosensing assays


    A cyanidin-based horseradish peroxidase(HRP)-catalyzed reaction system was established in this work.In B-R buffer solutions(pH 6.8),a UV-visible absorbance peak of cyanidin(CAG) at 540 nm(Ap1) appeared.After the oxidation reaction of CAG catalyzed by HRP in the presence of H2O2,a significant absorbance peak at 482 nm(Ap2) occurred.The ratio R(AP2/AP1)was proportional to the HRP concentration.The application of CAG in the enzyme-linked immunosensing assays was investigated using food and mouth disease virus antigen(FMDVAg) as a model analyte.In sandwich immunoreaction,the analyte FMDVAg and food and mouth disease virus antibody(FMDVAb)-modified magnetic nanoparticles bound the supported conconvalina(Con A) bound with HRP-FMDVAb.After de-absorbing and separating,the HRP-FMDVAb-FMDVAg-FMDVAb-magnetic nanoparticles complexes were subject to enzymatic reaction and UV-visible absorbance measurements.The HRP moiety of the immunoreaction complexes can catalyze the oxidation reaction of CAG by H2O2,and the substrate CAG is converted to products.Based on this principle,a sandwich assay model has been employed to determine FMDVAg in rabbit serum samples with the aid of FMDVAb-Fe3O4 magnetic nanoparticles.The linear range of the FMDVAg determination is 1.5×10-8-2.7×10-6 g/mL with the relatively standard deviation of 3.7%(n = 11).The detection limit is 3.1×10-9 g/mL.Additional advantages of the typical substrate such as OPD,OAP and TMB are good water-solubility and stability.

  13. Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1

    Goyette, Jesse; Salas, Citlali Solis; Coker-Gordon, Nicola; Bridge, Marcus; Isaacson, Samuel A.; Allard, Jun; Dushek, Omer


    Tethered enzymatic reactions are ubiquitous in signaling networks but are poorly understood. A previously unreported mathematical analysis is established for tethered signaling reactions in surface plasmon resonance (SPR). Applying the method to the phosphatase SHP-1 interacting with a phosphorylated tether corresponding to an immune receptor cytoplasmic tail provides five biophysical/biochemical constants from a single SPR experiment: two binding rates, two catalytic rates, and a reach parameter. Tether binding increases the activity of SHP-1 by 900-fold through a binding-induced allosteric activation (20-fold) and a more significant increase in local substrate concentration (45-fold). The reach parameter indicates that this local substrate concentration is exquisitely sensitive to receptor clustering. We further show that truncation of the tether leads not only to a lower reach but also to lower binding and catalysis. This work establishes a new framework for studying tethered signaling processes and highlights the tether as a control parameter in clustered receptor signaling.

  14. Identification of aflatoxigenic fungi using polymerase chain reaction-based assay

    Šošo Vladislava M.


    Full Text Available As the aflatoxins represent a health-risk for humans because of their proven carcinogenicity, food-borne fungi that produce them as secondary metabolites, mainly Aspergillus flavus and Aspergillus parasiticus, have to be isolated and identified. The best argument for identifying problem fungi is that it indicates control points within the food system as part of a hazard analysis critical control point (HACCP approach. This assumes there is a close link between fungus and toxin. Conventional methods for isolation and identification of fungi are time consuming and require admirably dedicated taxonomists. Hence, it is imperative to develop methodologies that are relatively rapid, highly specific and as an alternative to the existing methods. The polymerase chain reaction (PCR facilitates the in vitro amplification of the target sequence. The main advantages of PCR is that organisms need not be cultured, at least not for a long time, prior to their detection, target DNA can be detected even in a complex mixture, no radioactive probes are required, it is rapid, sensitive and highly versatile. The gene afl-2 has been isolated and shown to regulate aflatoxin biosynthesis in A. flavus. Also, the PCR reaction was targeted against aflatoxin synthesis regulatory gene (aflR1 since these genes are nearly identical in A. flavus and A. parasiticus in order to indicate the possibility of detection of both the species with the same PCR system (primers/reaction. [Projekat Ministarstva nauke Republike Srbije, br. III46009

  15. Fluorescence assay for glycan expression on living cancer cells based on competitive strategy coupled with dual-functionalized nanobiocomposites.

    Fu, Ying; Lu, Danqin; Lin, Bin; Sun, Qianqian; Liu, Kai; Xu, Lili; Zhang, Shengping; Hu, Chen; Wang, Chuangui; Xu, Zhiai; Zhang, Wen


    Cell surface glycans are a class of sophisticated biomolecules related to cancer development and progression, and their analysis is of great significance for early cancer diagnosis and treatment. In this paper, we proposed a fluorescence assay to evaluate glycan expression on living cancer cells based on a competitive strategy coupled with dual-functionalized nanobiocomposites. The competitive assay was conducted between living cancer cells and thiomannosyl derivatives using concanavalin A (Con A)-modified electrode as the interaction platform. To impart fluorescence signaling ability to competitive derivatives, quantum dots (QDs) were anchored on BSA-protected Au nanoparticles, and thiomannosyl derivatives were further immobilized on the nanoparticle surface through Au-S binding. Due to the spacing between QDs and Au nanoparticles by BSA, the {QDs-Au-BSA-mannose} nanobiocomposites maintained the fluorescence of QDs and showed binding ability with the Con A-modified electrode. Au nanorods (AuNRs)-modified electrode was used as an effective substrate to immobilize Con A. This assay was successfully applied to the analysis of two cancer cells lines (A549 and QGY-7701). The method is simple and shows promise for the study of glycan expression on living cancer cells.

  16. Development and characterization of a Pseudomonas aeruginosa in vitro coupled transcription-translation assay system for evaluation of translation inhibitors

    Fyfe, Corey; Sutcliffe, Joyce A.; Grossman, Trudy H.


    Bacterial transcription and translation have proven to be effective targets for broad-spectrum antimicrobial therapies owing to the critical role they play in bacterial propagation and the overall conservation of the associated machinery involved. Escherichia coli is the most common source of S30 extract used in bacterial in vitro coupled transcription-translation assays, however, transcription-translation assays in other important pathogens including Staphylococcus aureus and Streptococcus pneumoniae have been described (Murray et al., 2001; Dandliker et al., 2003). Pseudomonas aeruginosa is an important and difficult-to-treat Gram-negative pathogen. In a drug discovery program, to de-risk any potential species specificity of novel inhibitors, we developed and optimized a robust method for the preparation of S30 extract from P. aeruginosa strain PAO1. Further, a P. aeruginosa transcription-translation assay using a firefly luciferase reporter plasmid was validated and compared to an E. coli S30-based system using a wide range of antibiotics encompassing multiple classes of translation inhibitors. Results showed a similar ranking of the activities of known inhibitors, illustrative of the high degree of conservation between the transcription-translation pathways in both organisms. PMID:22677604

  17. A colorimetric assay for measuring iodide using Au@Ag core–shell nanoparticles coupled with Cu{sup 2+}

    Zeng, Jingbin, E-mail: [State Key Laboratory of Heavy Oil Processing & College of Science, China University of Petroleum (East China), Qingdao 266555 (China); Cao, Yingying [State Key Laboratory of Heavy Oil Processing & College of Science, China University of Petroleum (East China), Qingdao 266555 (China); Lu, Chun-Hua [The Key Laboratory of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry, Fuzhou University, Fuzhou 350002 (China); Wang, Xu-dong [Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG-1), Hermann-von-Helmholtz-Platz, 76344 Eggenstein-Leopoldshafen (Germany); Wang, Qianru; Wen, Cong-ying; Qu, Jian-Bo; Yuan, Cunguang [State Key Laboratory of Heavy Oil Processing & College of Science, China University of Petroleum (East China), Qingdao 266555 (China); Yan, Zi-feng, E-mail: [State Key Laboratory of Heavy Oil Processing & College of Science, China University of Petroleum (East China), Qingdao 266555 (China); Chen, Xi [Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China)


    Au@Ag core–shell nanoparticles (NPs) were synthesized and coupled with copper ion (Cu{sup 2+}) for the colorimetric sensing of iodide ion (I{sup −}). This assay relies on the fact that the absorption spectra and the color of metallic core–shell NPs are sensitive to their chemical ingredient and dimensional core-to-shell ratio. When I{sup −} was added to the Au@Ag core–shell NPs-Cu{sup 2+} system/solution, Cu{sup 2+} can oxidize I{sup −} into iodine (I{sub 2}), which can further oxidize silver shells to form silver iodide (AgI). The generated Au@AgI core–shell NPs led to color changes from yellow to purple, which was utilized for the colorimetric sensing of I{sup −}. The assay only took 10 min with a lowest detectable concentration of 0.5 μM, and it exhibited excellent selectivity for I{sup −} over other common anions tested. Furthermore, Au@Ag core–shell NPs-Cu{sup 2+} was embedded into agarose gels as inexpensive and portable “test strips”, which were successfully used for the semi-quantitation of I{sup −} in dried kelps. - Highlights: • Au@Ag core–shell NPs were synthesized and coupled with Cu{sup 2+} for the colorimetric I{sup −} sensing. • This assay is simple, rapid and selective. • Au@Ag core–shell NPs-Cu{sup 2+} were embedded into agarose gels as test strips.

  18. Palladium nanoparticle anchored polyphosphazene nanotubes: preparation and catalytic activity on aryl coupling reactions

    V Devi; A Ashok Kumar; S Sankar; K Dinakaran


    Highly accessible-supported palladium (Pd) nanoparticles anchored polyphosphazene (PPZ) nanotubes (NTs) having average diameter of 120 nm were synthesized rapidly at room temperature and homogeneously decorated with Pd nanoparticles. The resultant PPZ–Pd nanocomposites were morphologically and structurally characterized by means of transmission electron microscope equipped with energy-dispersive X-ray spectroscopy and X-ray diffraction analysis. Characterization results showed that the Pd nanoparticles with good dispersibility could be well anchored onto the surfaces of the PPZ NTs. The PPZ–Pd NTs show enhanced catalytic activity for the Suzuki coupling of aryl bromides with arylboronic acid. In addition, these PPZ–Pd NTs show excellent behaviour as reusable catalysts of the Suzuki and Heck coupling reactions.

  19. Fibrous nano-silica (KCC-1)-supported palladium catalyst: Suzuki coupling reactions under sustainable conditions

    Fihri, Aziz


    Noble amines recycled: Fibrous high-surface-area nano-silica functionalized with aminopropyl groups and loaded with well-dispersed Pd nanoparticles is evaluated for the Suzuki coupling of aromatic halides. It is active for the reaction of a range of aryl bromides and iodides as well as chlorides with aryl boronic acids in good to excellent yields. The catalyst can be recovered and reused for a number of cycles with negligible loss in activity. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Regioselective, Transition Metal-Free C-O Coupling Reactions Involving Aryne Intermediates.

    Dong, Yuyang; Lipschutz, Michael I; Tilley, T Don


    A new transition-metal-free synthetic method for C-O coupling between various aryl halides and alkoxides is described. This type of transformation is typically accomplished using palladium catalysts containing a specialized phosphine ligand. The reactions reported here can be performed under mild, ambient conditions using certain potassium alkoxides and a range of aryl halides, with iodide and bromide derivatives giving the best results. A likely mechanistic pathway involves the in situ generation of an aryne intermediate, and directing groups on the aryl ring inductively control regioselectivity.

  1. A sensitive DNA biosensor based on a facile sulfamide coupling reaction for capture probe immobilization

    Wang, Qingxiang, E-mail: [Department of Chemistry and Environment Science, Zhangzhou Normal University, Zhangzhou 363000 (China); Ding, Yingtao; Gao, Feng [Department of Chemistry and Environment Science, Zhangzhou Normal University, Zhangzhou 363000 (China); Jiang, Shulian [Zhangzhou Product Quality Supervision and Inspection Institute, Zhangzhou 363000 (China); Zhang, Bin; Ni, Jiancong; Gao, Fei [Department of Chemistry and Environment Science, Zhangzhou Normal University, Zhangzhou 363000 (China)


    Graphical abstract: A novel DNA biosensor was fabricated through a facile sulfamide coupling reaction between probe DNA and the sulfonic dye of 1-amino-2-naphthol-4-sulfonic acid that electrodeposited on a glassy carbon electrode. -- Highlights: •A versatile sulfonic dye of ANS was electrodeposited on a GCE. •A DNA biosensor was fabricated based on a facile sulfamide coupling reaction. •High probe DNA density of 3.18 × 10{sup 13} strands cm{sup −2} was determined. •A wide linear range and a low detection limit were obtained. -- Abstract: A novel DNA biosensor was fabricated through a facile sulfamide coupling reaction. First, the versatile sulfonic dye molecule of 1-amino-2-naphthol-4-sulfonate (AN-SO{sub 3}{sup −}) was electrodeposited on the surface of a glassy carbon electrode (GCE) to form a steady and ordered AN-SO{sub 3}{sup −} layer. Then the amino-terminated capture probe was covalently grafted to the surface of SO{sub 3}{sup −}-AN deposited GCE through the sulfamide coupling reaction between the amino groups in the probe DNA and the sulfonic groups in the AN-SO{sub 3}{sup −}. The step-by-step modification process was characterized by electrochemistry and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Using Ru(NH{sub 3}){sub 6}{sup 3+} as probe, the probe density and the hybridization efficiency of the biosensor were determined to be 3.18 × 10{sup 13} strands cm{sup −2} and 86.5%, respectively. The hybridization performance of the biosensor was examined by differential pulse voltammetry using Co(phen){sub 3}{sup 3+/2+} (phen = 1,10-phenanthroline) as the indicator. The selectivity experiments showed that the biosensor presented distinguishable response after hybridization with the three-base mismatched, non-complementary and complementary sequences. Under the optimal conditions, the oxidation peak currents of Co(phen){sub 3}{sup 3+/2+} increased linearly with the logarithm values of the concentration

  2. Partitioned coupling of advection-diffusion-reaction systems and Brinkman flows

    Lenarda, Pietro; Paggi, Marco; Ruiz Baier, Ricardo


    We present a partitioned algorithm aimed at extending the capabilities of existing solvers for the simulation of coupled advection-diffusion-reaction systems and incompressible, viscous flow. The space discretisation of the governing equations is based on mixed finite element methods defined on unstructured meshes, whereas the time integration hinges on an operator splitting strategy that exploits the differences in scales between the reaction, advection, and diffusion processes, considering the global system as a number of sequentially linked sets of partial differential, and algebraic equations. The flow solver presents the advantage that all unknowns in the system (here vorticity, velocity, and pressure) can be fully decoupled and thus turn the overall scheme very attractive from the computational perspective. The robustness of the proposed method is illustrated with a series of numerical tests in 2D and 3D, relevant in the modelling of bacterial bioconvection and Boussinesq systems.

  3. Coupling sample paths to the partial thermodynamic limit in stochastic chemical reaction networks

    Levien, Ethan


    We present a new technique for reducing the variance in Monte Carlo estimators of stochastic chemical reaction networks. Our method makes use of the fact that many stochastic reaction networks converge to piecewise deterministic Markov processes in the large system-size limit. The statistics of the piecewise deterministic process can be obtained much more efficiently than those of the exact process. By coupling sample paths of the exact model to the piecewise deterministic process we are able to reduce the variance, and hence the computational complexity of the Monte Carlo estimator. In addition to rigorous results concerning the asymptotic behavior of our method, numerical simulations are performed on some simple biological models suggesting that significant computational gains are made for even moderate system-sizes.


    Jun Shi; Zhi-wei Jiang; Li Zhang; Shao-kui Cao


    A series of polymers bearing azobenzene and carbazole groups for photorefractive purpose were prepared via post-azo-coupling reaction. The successful reaction was identified by spectroscopic analysis and gel permeation chromatography. This approach is more facile compared with the direct polymerization of corresponding functional monomer. The polymers prepared have weight average molecular weight of higher than 1.5 × 104 and are easily soluble in common organic solvents like chloroform and tetrahydrofuran, polymer films with high optical quality could be easily fabricated through solution casting. Glass transition temperature (Tg) of the polymers ranges from 60℃ to 182℃, depending on the alkylene spacer length between the functional side group and the polymer backbone, and the polymers are relatively stable under 300℃.

  5. A duplex polymerase chain reaction assay for the identification of goat cashmere and sheep wool.

    Geng, Qing-Rong


    In this article attempts were made to establish one-step duplex PCR assay for the identification of goat cashmere and sheep wool. Primers were selected from published papers or designed in the well-conserved region of mitochondrial D-loop genes after alignment of the available sequences in the GenBank database. A fragment of 294 bp from cashmere goat was amplified and three PCR fragments including a bright main band of approximately 404 bp in length were obtained from sheep. The duplex PCR was found to be effective in detecting mixed samples precisely when sheep wool was mixed to goat cashmere with the relative proportion of over 9.09%. The duplex PCR could be considered as a simple and promising method in identification of goat cashmere and sheep wool.

  6. Pinacol Coupling Reaction of Benzaldehyde Mediated by TiCl3-Zn in Basic Media Under Ultrasound Irradiation

    Wang Shu-Xiang


    Full Text Available Pinacol coupling of benzaldehyde mediated by TiCl3-Zn in basic media under ultrasound irradiation can lead to the corresponding pinacol rapidly. The optimum reaction condition is chosen.

  7. Rapid Microwave-promoted Base-free Suzuki Coupling Reaction of Sodium Tetraphenylborate with Hypervalent Iodonium Salts in Water


    The palladium chloride-catalyzed Suzuki coupling reaction of sodium tetraphenylborate with hypervalent iodonium salts was achieved under microwave irradiation in water without base in excellent yield. A convenient and rapidmethod for formation of carbon-carbon bonds was afforded.

  8. Preparation of zwitterionic hydroquinone-fused [1,4]oxazinium derivatives via a photoinduced intramolecular dehydrogenative-coupling reaction.

    Yi, Chenyi; Liu, Shi-Xia; Neels, Antonia; Renaud, Philippe; Decurtins, Silvio


    A simple and efficient photochemical reaction can be performed to construct functionalized [1,4]oxazinium derivatives via a direct dehydrogenative coupling between sp(3)- and sp(2)-hybridized C-atoms, starting from easily accessible stable semiquinone radicals.

  9. Understanding colonization and proliferation potential of endophytes and pathogen in planta via plating, polymerase chain reaction, and ergosterol assay

    Yiing Yng Chow


    Full Text Available This study aimed to establish the colonization behavior and proliferation potential of three endophytes and one pathogen Ganoderma boninense (Gb introduced into oil palm ramets (host model. The endophytes selected were Diaporthe phaseolorum (WAA02, Trichoderma asperellum (T2, and Penicillium citrinum (BTF08. Ramets were first inoculated with 100 mL of fungal cells (106 cfu mL−1 via soil drenching. For the next 7 days, ramets were sampled and subjected to three different assays to detect and identify fungal colonization, and establish their proliferation potential in planta. Plate assay revealed the presence of endophytes in root, stem and leaf tissues within 7 days after inoculation. Polymerase Chain Reaction (PCR detected and identified the isolates from the plant tissues. The ergosterol assay (via high-performance liquid chromatography, HPLC confirmed the presence of endophytes and Gb in planta. The increase in ergosterol levels throughout 49 days was however insignificant, suggesting that proliferation may be absent or may occur very slowly in planta. This study strongly suggests that the selected endophytes could colonize the host upon inoculation, but proliferation occurs at a slower rate, which may subsequently influence the biocontrol expression of endophytes against the pathogen.

  10. Sensitive electrochemical determination of miRNAs based on a sandwich assay onto magnetic microcarriers and hybridization chain reaction amplification.

    Torrente-Rodríguez, R M; Campuzano, S; Montiel, V Ruiz-Valdepeñas; Montoya, J J; Pingarrón, J M


    A novel electrochemical approach for determination of miRNAs involving a sandwich hybridization assay onto streptavidin-magnetic beads (Strep-MBs), hybridization chain reaction (HCR) amplification and amperometric detection at disposable screen-printed carbon electrodes is reported. Using miRNA-21 as the target analyte, a dynamic linear range from 0.2 to 5.0nM with a 60pM (1.5fmol in 25μL) detection limit was obtained. The achieved sensitivity is 24-fold higher than a non-HCR amplification approach involving conventional sandwich type assay onto MBs. Moreover, the whole assay time lasted 1h 45min which is remarkably shorter than other reported methodologies. The methodology exhibited full selectivity against other non-complementary miRNAs as well as an acceptable discrimination between homologous miRNA family members. The applicability of this novel approach was demonstrated by determining mature miRNA-21 in total RNA (RNAt) extracted from tumor cells and human tissues.

  11. Application of a real time Polymerase Chain Reaction (PCR) assay for the early diagnosis of human leptospirosis in Sri Lanka.

    Denipitiya, D T H; Chandrasekharan, N V; Abeyewickreme, W; Hartskeerl, C M; Hartskeerl, R A; Jiffrey, A M; Hapugoda, M D


    Leptospirosis has a major impact on health in Sri Lanka but is probably grossly under-recognized due to difficulties in clinical diagnosis and lack of diagnostic laboratory services. The objective of this study was to establish and evaluate a SYBR Green-based real-time Polymerase Chain Reaction (rt-PCR) assay for early, rapid and definitive laboratory diagnosis of leptospirosis in Sri Lanka. The rt-PCR assay was established and analytical specificity and sensitivity were determined using reference DNA samples. Evaluation of the assay for diagnosis of clinical samples was performed using two panels of serum samples obtained from 111 clinically suspected adult patients. Patients were confirmed as leptospirosis (n = 65) and non-leptospirosis (n = 30) by the Patoc - MAT. Other 16 samples gave ambiguous results. The analytical sensitivity of the rt-PCR was approximately 60 genome copies and no cross-reactivity was observed with saprophytic Leptospira spp. and other pathogenic microorganisms. Based on confirmation with Patoc-MAT on paired samples this corresponds to a diagnostic sensitivity and specificity of 67.7% (44/65) and 90.0% (27/30), respectively. This study showed that rt-PCR has the potential to facilitate rapid and definitive diagnosis of leptospirosis during early phase of infection in Sri Lanka. Copyright © 2016 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

  12. A real time polymerase chain reaction assay for quantification of Edwardsiella ictaluri in catfish pond water and genetic homogeneity of diagnostic case isolates from Mississippi

    A quantitative polymerase chain reaction (qPCR) assay was developed for the detection and quantification of Edwardsiella ictaluri in channel catfish Ictalurus punctatus pond water using modifications to a published E. ictaluri–specific qPCR assay and previously established protocols for the molecula...

  13. Detection of infectious bursal disease virus in various lymphoid tissues of experimentally infected specific pathogen free chickens by different reverse transcription polymerase chain reaction assays

    Kabell, Susanne; Handberg, Kurt; Kusk, Mette;


    transcription polymerase chain reaction (RT-PCR) assays, including two recently developed strain-specific assays, were employed for detection of ribonucleic acid (RNA) from three different IBDV strains in bursa tissue samples from experimentally infected specific pathogen free chickens. The virus strains...

  14. Use of a high resolution melt real-time polymerase chain reaction (PCR) assay for the environmental monitoring of Vibrio cholerae

    Le Rouw, Wouter J


    Full Text Available A real-time polymerase chain reaction (PCR) assay utilizing high resolution melt (HRM) curve analysis was developed and tested for the monitoring of Vibrio cholerae in water samples. The assay utilized previously published primers that are specific...

  15. Palladium-catalyzed heck coupling reaction of aryl bromides in aqueous media using tetrahydropyrimidinium salts as carbene ligands.

    Yaşar, Sedat; Ozcan, Emine Ozge; Gürbüz, Nevin; Cetinkaya, Bekir; Ozdemir, Ismail


    An efficient and stereoselective catalytic system for the Heck cross coupling reaction using novel 1,3-dialkyl-3,4,5,6-tetrahydropyrimidinium salts (1, LHX) and Pd(OAc)2 loading has been reported. The palladium complexes derived from the salts 1a-f prepared in situ exhibit good catalytic activity in the Heck coupling reaction of aryl bromides under mild conditions.

  16. Palladium-Catalyzed Heck Coupling Reaction of Aryl Bromides in Aqueous Media Using Tetrahydropyrimidinium Salts as Carbene Ligands

    İsmail Özdemir


    Full Text Available An efficient and stereoselective catalytic system for the Heck cross coupling reaction using novel 1,3-dialkyl-3,4,5,6-tetrahydropyrimidinium salts (1, LHX and Pd(OAc2 loading has been reported. The palladium complexes derived from the salts 1a-f prepared in situ exhibit good catalytic activity in the Heck coupling reaction of aryl bromides under mild conditions.

  17. Catalytic Upgrading of Biomass-Derived Compounds via C-C Coupling Reactions. Computational and Experimental Studies of Acetaldehyde and Furan Reactions in HZSM-5

    Liu, Cong [Argonne National Lab. (ANL), Argonne, IL (United States); Evans, Tabitha J. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Cheng, Lei [Argonne National Lab. (ANL), Argonne, IL (United States); Nimlos, Mark R. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Mukarakate, Calvin [National Renewable Energy Lab. (NREL), Golden, CO (United States); Robichaud, David J. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Assary, Rajeev S. [Argonne National Lab. (ANL), Argonne, IL (United States); Curtiss, Larry A. [Argonne National Lab. (ANL), Argonne, IL (United States)


    These catalytic C–C coupling and deoxygenation reactions are essential for upgrading of biomass-derived oxygenates to fuel-range hydrocarbons. Detailed understanding of mechanistic and energetic aspects of these reactions is crucial to enabling and improving the catalytic upgrading of small oxygenates to useful chemicals and fuels. Using periodic density functional theory (DFT) calculations, we have investigated the reactions of furan and acetaldehyde in an HZSM-5 zeolite catalyst, a representative system associated with the catalytic upgrading of pyrolysis vapors. Comprehensive energy profiles were computed for self-reactions (i.e., acetaldehyde coupling and furan coupling) and cross-reactions (i.e., acetaldehyde + furan) of this representative mixture. Major products proposed from the computations are further confirmed using temperature controlled mass spectra measurements. Moreover, the computational results show that furan interacts with acetaldehyde in HZSM-5 via an alkylation mechanism, which is more favorable than the self-reactions, indicating that mixing furans with aldehydes could be a promising approach to maximize effective C–C coupling and dehydration while reducing the catalyst deactivation (e.g., coke formation) from aldehyde condensation.

  18. Palladium-catalyzed cross coupling reaction of N-alkoxyimidoyl bromides and its application to one-pot synthesis of N-arylamines.

    Ueda, Masafumi; Sugita, Shoichi; Aoi, Naoki; Sato, Aoi; Ikeda, Yuki; Ito, Yuta; Miyoshi, Tetsuya; Naito, Takeaki; Miyata, Okiko


    The synthetic utility of N-alkoxyimidoyl halides is demonstrated using the palladium-catalyzed cross-coupling reaction. The Sonogashira and Suzuki-Miyaura coupling reactions of N-alkoxyimidoyl bromides produced versatile ketoxime ethers in good to excellent yields. A one-pot reaction of the imidoyl bromides with arylboronic acid and allylmagnesium bromide to produce N-arylamines via Suzuki-Miyaura coupling followed by domino reaction involving sequential addition-eliminative rearrangement-addition reactions was developed.

  19. Multiplex time-reducing quantitative polymerase chain reaction assay for determination of telomere length in blood and tissue DNA.

    Jiao, Jingjing; Kang, Jing X; Tan, Rui; Wang, Jingdong; Zhang, Yu


    In this paper we describe a multiplex time-reducing quantitative polymerase chain reaction (qPCR) method for determination of telomere length. This multiplex qPCR assay enables two pairs of primers to simultaneously amplify telomere and single copy gene (albumin) templates, thus reducing analysis time and labor compared with the previously established singleplex assay. The chemical composition of the master mix and primers for the telomere and albumin were systematically optimized. The thermal cycling program was designed to ensure complete separation of the melting processes of the telomere and albumin. Semi-log standard curves of DNA concentration versus cycle threshold (C (t)) were established, with a linear relationship over an 81-fold DNA concentration range. The well-performed intra-assay (RSD range 2.4-4.7%) and inter-assay (RSD range: 3.1-5.0%) reproducibility were demonstrated to ensure measurement stability. Using wild-type, Lewis lung carcinoma and H22 liver carcinoma C57BL/6 mouse models, significantly different telomere lengths among different DNA samples were not observed in wild-type mice. However, the relative telomere lengths of the tumor DNA in the two strains of tumor-bearing mice were significantly shorter than the lengths in the surrounding non-tumor DNA of tumor-bearing mice and the tissue DNA of wild-type mice. These results suggest that the shortening of telomere lengths may be regarded as an important indicator for cancer control and prevention. Quantification of telomere lengths was further confirmed by the traditional Southern blotting method. This method could be successfully used to reduce the time needed for rapid, precise measurement of telomere lengths in biological samples.

  20. Discovering Green, Aqueous Suzuki Coupling Reactions: Synthesis of Ethyl (4-Phenylphenyl)Acetate, a Biaryl with Anti-Arthritic Potential

    Costa, Nancy E.; Pelotte, Andrea L.; Simard, Joseph M.; Syvinski, Christopher A.; Deveau, Amy M.


    Suzuki couplings are powerful chemical reactions commonly employed in academic and industrial research settings to generate functionalized biaryls. We have developed and implemented a discovery-based, microscale experiment for the undergraduate organic chemistry laboratory that explores green Suzuki coupling using water as the primary solvent.…

  1. Synthesis of functionalized thiophenes and oligothiophenes by selective and iterative cross-coupling reactions using indium organometallics.

    Montserrat Martínez, M; Peña-López, Miguel; Pérez Sestelo, José; Sarandeses, Luis A


    The synthesis of unsymmetrical 2,5-disubstituted thiophenes by selective and sequential palladium-catalyzed cross-coupling reactions of indium organometallics with 2,5-dibromothiophene is reported. Following an iterative coupling sequence, α-oligothiophenes were synthesized in good yields and with high atom economy.

  2. The role of Ile87 of CYP158A2 in oxidative coupling reaction

    Zhao, Bin; Bellamine, Aouatef; Lei, Li; Waterman, Michael R. (Vanderbilt)


    Both CYP158A1 and CYP158A2 are able to catalyze an oxidative C-C coupling reaction producing biflaviolin or triflaviolin in Streptomyces coelicolor A3(2). The substrate-bound crystal structures of CYP158A2 and CYP158A1 reveal that the side chain of Ile87 in CYP158A2 points to the active site contacting the distal flaviolin molecule, however, the bulkier side chain of Lys90 in CYP158A1 (corresponding to Ile87 in CYP158A2) is toward the distal surface of the protein. These results suggest that these residues could be important in determining product regiospecificity. In order to explore the role of the two residues in catalysis, the reciprocal mutants, Ile87Lys and Lys90Ile, of CYP158A2 and CYP158A1, respectively, were generated and characterized. The mutant Ile87Lys enzyme forms two isomers of biflaviolin instead of three isomers of biflaviolin in wild-type CYP158A2. CYP158A1 containing the substitution of lysine with isoleucine has the same catalytic activity compared with the wild-type CYP158A1. The crystal structure of Ile87Lys showed that the BC loop in the mutant is in a very different orientation compared with the BC loop in both CYP158A1/A2 structures. These results shed light on the mechanism of the oxidative coupling reaction catalyzed by cytochrome P450.

  3. Bite angle effects of diphosphines in C-C and C-X bond forming cross coupling reactions

    Birkholz, M.N.; Freixa, Z.; van Leeuwen, P.W.N.M.


    Catalytic reactions of C-C and C-X bond formation are discussed in this critical review with particular emphasis on cross coupling reactions catalyzed by palladium and wide bite angle bidentate diphosphine ligands. Especially those studies have been collected that allow comparison of the ligand bite

  4. Application of bisphosphomide-palladium(II) pincer complex in Suzuki-Miyaura cross-coupling reaction under microwave irradiation

    Maruthai Kumaravel; Pawan Kumar; Maravanji S Balakrishna


    The bisphosphomide-based pincer complex [PdBr{2,6-{Ph2PC(O)}2(C6H3)}] (2) has shown very high catalytic activity in Suzuki-Miyaura cross coupling reaction under microwave irradiation for a variety of aryl bromides and aryl boronic acids. The complex showed the same efficiency for gram scale reactions.

  5. Influence of Ionic Liquids on an Iron(III) Catalyzed Three-Component Coupling/Hydroarylation/Dehydrogenation Tandem Reaction.

    Muntzeck, Maren; Wilhelm, René


    A three-component oxidative dehydrogenation tandem reaction via the coupling and hydroarylation of benzaldehyde, aniline and phenylacetylene to a quinoline derivate was catalyzed by an iron-containing ionic liquid. The reaction was air mediated and could be performed under neat conditions. The iron(III) of the ionic liquid was the oxidizing species.

  6. A novel use of oxidative coupling reactions for determination of some statins (cholesterol-lowering drugs) in pharmaceutical formulations

    Ashour, Safwan; Bahbouh, Mahmoud; Khateeb, Mouhammed


    New, accurate and reliable spectrophotometric methods for the assay of three statin drugs, atorvastatin calcium (AVS), fluvastatin sodium (FVS) and pravastatin sodium (PVS) in pure form and pharmaceutical formulations have been described. All methods involve the oxidative coupling reaction of AVS, FVS and PVS with 3-methyl-2-benzothiazolinone hydrazone hydrochloride monohydrate (MBTH) in the presence of Ce(IV) in an acidic medium to form colored products with λmax at 566, 615 and 664 nm, respectively. Beer's law was obeyed in the ranges of 2.0-20.0, 4.9-35.4 and 7.0-30.0 μg mL -1 for AVS-MBTH, FVS-MBTH and PVS-MBTH, respectively. Molar absorptivities for the above three methods were found to be 3.24 × 10 4, 1.05 × 10 4 and 0.68 × 10 4 L mol -1 cm -1, respectively. Statistical treatment of the experimental results indicates that the methods are precise and accurate. The proposed methods have been applied to the determination of the components in commercial forms with no interference from the excipients. A comparative study between the suggested procedures and the official methods for these compounds in the commercial forms showed no significant difference between the two methods.

  7. Arsenic bioaccessibility in contaminated soils: Coupling in vitro assays with sequential and HNO3 extraction.

    Li, Shi-Wei; Li, Jie; Li, Hong-Bo; Naidu, Ravi; Ma, L Q


    Arsenic bioaccessibility varies with in vitro methods and soils. Four assays including unified BARGE method (UBM), Solubility Bioaccessibility Research Consortium method (SBRC), in vitro gastrointestinal method (IVG), and physiologically based extraction test (PBET), were used to determine As bioaccessibility in 11 contaminated soils (22-4,172 mg kg(-1)). The objective was to understand how bioaccessible As by different methods was related to different As pools based on sequential extraction and 0.43 M HNO3 extraction. Arsenic bioaccessibility was 7.6-25, 2.3-49, 7.3-44, and 1.3-38% in gastric phase (GP), and 5.7-53, 0.46-33, 2.3-42, and 0.86-43% in intestinal phase (IP) for UBM, SBRC, IVG, and PBET, respectively, with HNO3-extractable As being 0.90-60%. Based on sequential extraction, As was primarily associated with amorphous (AF3; 17-79%) and crystallized Fe/Al oxides (CF4; 6.4-73%) while non-specifically sorbed (NS1), specifically sorbed (SS2), and residual fractions (RS5) were 0-10%, 3.4-20% and 3.2-25%. Significant correlation was found between As bioaccessibility by PBET and NS1+SS2 (R(2) = 0.55-0.69), and UBM-GP and NS1 + SS2 + AF3 (R(2) = 0.58), indicating PBET mostly targeted As in NS1+SS2 whereas UBM in NS1 + SS2 + AF3. HNO3-extractable As was correlated to bioaccessible As by four methods (R(2) = 0.42-0.72) with SBRC-GP having the best correlation. The fact that different methods targeted different As fractions in soils suggested the importance of validation by animal test. Our data suggested that HNO3 may have potential to determine bioaccessible As in soils. Published by Elsevier B.V.

  8. Modeling of the Reaction Mechanism of Enzymatic Radical C–C Coupling by Benzylsuccinate Synthase

    Maciej Szaleniec


    Full Text Available Molecular modeling techniques and density functional theory calculations were performed to study the mechanism of enzymatic radical C–C coupling catalyzed by benzylsuccinate synthase (BSS. BSS has been identified as a glycyl radical enzyme that catalyzes the enantiospecific fumarate addition to toluene initiating its anaerobic metabolism in the denitrifying bacterium Thauera aromatica, and this reaction represents the general mechanism of toluene degradation in all known anaerobic degraders. In this work docking calculations, classical molecular dynamics (MD simulations, and DFT+D2 cluster modeling was employed to address the following questions: (i What mechanistic details of the BSS reaction yield the most probable molecular model? (ii What is the molecular basis of enantiospecificity of BSS? (iii Is the proposed mechanism consistent with experimental observations, such as an inversion of the stereochemistry of the benzylic protons, syn addition of toluene to fumarate, exclusive production of (R-benzylsuccinate as a product and a kinetic isotope effect (KIE ranging between 2 and 4? The quantum mechanics (QM modeling confirms that the previously proposed hypothetical mechanism is the most probable among several variants considered, although C–H activation and not C–C coupling turns out to be the rate limiting step. The enantiospecificity of the enzyme seems to be enforced by a thermodynamic preference for binding of fumarate in the pro(R orientation and reverse preference of benzyl radical attack on fumarate in pro(S pathway which results with prohibitively high energy barrier of the radical quenching. Finally, the proposed mechanism agrees with most of the experimental observations, although the calculated intrinsic KIE from the model (6.5 is still higher than the experimentally observed values (4.0 which suggests that both C–H activation and radical quenching may jointly be involved in the kinetic control of the reaction.

  9. HPLC method development for the online-coupling of chromatographic Perilla frutescens extract separation with xanthine oxidase enzymatic assay.

    Kaufmann, Christine M; Grassmann, Johanna; Letzel, Thomas


    Enzyme-regulatory effects of compounds contained in complex mixtures can be unveiled by coupling a continuous-flow enzyme assay to a chromatographic separation. A temperature-elevated separation was developed and the performance was tested using Perilla frutescens plant extracts of various polarity (water, methanol, ethanol/water). Owning to the need of maintaining sufficient enzymatic activity, only low organic solvent concentrations can be added to the mobile phase. Hence, to broaden the spectrum of eluting compounds, two different organic solvents and various contents were tested. The chromatographic performance and elution was further improved by the application of a moderate temperature gradient to the column. By taking the effect of eluent composition as well as calculated logD values and molecular structure of known extract compounds into account, unknown features were tentatively assigned. The method used allowed the successful observation of an enzymatic inhibition caused by P. frutescens extract.

  10. Formation process of liquid in interface of Ti/Cu contact reaction couple

    WU Ming-fang; YU Chun; YU Zhi-shi; LI Rui-feng


    By using the Ti/Cu contact reaction couples,the dissolution behavior of Ti and Cu in the eutectic reaction process was investigated under different conditions.The results show that the formation of eutectic liquid phase has a directional property,I.e.the eutectic liquid phase forms first at the Cu side and then spreads along the depth direction of Cu.The width of the eutectic liquid zone when Ti is placed on Cu is wider than that when Ti is placed under Cu.The shape of the upside liquid zone is wave-like.This phenomenon indicates that the formation process and spreading behavior in the upside are different from those in the underside,and there exists void effect in the Cu side of underside liquid zone,this will result in the delaying phenomenon of the contact reaction between Ti and Cu,and distinctly different shapes of the both liquid zones.The formation process of Ti/Cu eutectic liquid zone is similar to that of the traditional solid-state diffusion layer,and the relationship between the width of liquid zone and holding time obeys a square root law.

  11. The anharmonic effect study of coupled Morse oscillators for the unimolecular reaction

    YAO Li; LIN Sheng-Hsien


    The importance of anharmonic effect in dissociation of molecular systems especially clusters has been noted. In this paper, we shall study the effect of coupled anharmonic oscillator of the standard bilinear form (SBF) Morse oscillator (MO) potential on unimolecular reaction. We shall use the systematic theoretical approach, YL method, proposed by Yao and Lin (YAO L, et. al. J Phys Chem A, 2007, 111(29): 6722-6729), which can evaluate anharmonic effects on the rate constants based on the transition state theory. In treating the anharmonic effect with the Morse oscillator potential on unimolecular reactions under collision-free conditions by using the RRKM (Rice-Ramsperger-Kassel-Marcus) theory, the in-verse Laplace transformation of the partition functions was used to obtain the total amount of state and density of state by using the first-order and the second-order approximations of the saddle-point method. To demonstrate the anharmonic effect of the SBF Morse model, we choose some model sys-tems and a real reaction as examples.

  12. The anharmonic effect study of coupled Morse oscillators for the unimolecular reaction


    The importance of anharmonic effect in dissociation of molecular systems especially clusters has been noted. In this paper, we shall study the effect of coupled anharmonic oscillator of the standard bilinear form (SBF) Morse oscillator (MO) potential on unimolecular reaction. We shall use the systematic theoretical approach, YL method, proposed by Yao and Lin (YAO L, et. al. J Phys Chem A, 2007, 111(29): 6722-6729), which can evaluate anharmonic effects on the rate constants based on the transition state theory. In treating the anharmonic effect with the Morse oscillator potential on unimolecular reactions under collision-free conditions by using the RRKM (Rice-Ramsperger-Kassel-Marcus) theory, the in-verse Laplace transformation of the partition functions was used to obtain the total amount of state and density of state by using the first-order and the second-order approximations of the saddle-point method. To demonstrate the anharmonic effect of the SBF Morse model, we choose some model systems and a real reaction as examples.

  13. Coupling Solar Energy into Reactions: Materials Design for Surface Plasmon-Mediated Catalysis.

    Long, Ran; Li, Yu; Song, Li; Xiong, Yujie


    Enabled by surface plasmons, noble metal nanostructures can interact with and harvest incident light. As such, they may serve as unique media to generate heat, supply energetic electrons, and provide strong local electromagnetic fields for chemical reactions through different mechanisms. This solar-to-chemical pathway provides a new approach to solar energy utilization, alternative to conventional semiconductor-based photocatalysis. To provide readers with a clear picture of this newly recognized process, this review presents coupling solar energy into chemical reactions through plasmonic nanostructures. It starts with a brief introduction of surface plasmons in metallic nanostructures, followed by a demonstration of tuning plasmonic features by tailoring their physical parameters. Owing to their tunable plasmonic properties, metallic materials offer a platform to trigger and drive chemical reactions at the nanoscale, as systematically overviewed in this article. The design rules for plasmonic materials for catalytic applications are further outlined based on existing examples. At the end of this article, the challenges and opportunities for further development of plasmonic-mediated catalysis toward energy and environmental applications are discussed.

  14. Diagnosis of enzootic pneumonia in Danish cattle: reverse transcription-polymerase chain reaction assay for detection of bovine respiratory syncytial virus in naturally and experimentally infected cattle

    Larsen, Lars Erik; Tjørnehøj, Kirsten; Viuff, B.;


    A reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for detection of bovine respiratory syncytial virus (BRSV) in lung tissue of naturally and experimentally infected cattle. Primers were selected from the gene coding the F fusion protein, which is relatively conserved...... among BRSV isolates. The RT-PCR assay was highly specific, it yielded positive reactions only when performed on BRSV-infected cell cultures or tissues. The detection limit of the RT-PCR assay was assessed as 5 TCID50. BRSV was detected in tissues of the respiratory tract and in the tracheobroncheal....... (7%), and Pasteurella haemolytica (7%) were the most common bacterial agents found in the lungs. BRSV was identified using a conventional antigen enzyme-linked immunosorbent assay (ELISA) in 23 (17%) animals. The established BRSV-specific RT-PCR assay yielded positive results for the same 23 animals...

  15. Diagnosis of enzootic pneumonia in Danish cattle: reverse transcription-polymerase chain reaction assay for detection of bovine respiratory syncytial virus in naturally and experimentally infected cattle

    Larsen, Lars Erik; Tjørnehøj, Kirsten; Viuff, B.


    A reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for detection of bovine respiratory syncytial virus (BRSV) in lung tissue of naturally and experimentally infected cattle. Primers were selected from the gene coding the F fusion protein, which is relatively conserved...... among BRSV isolates. The RT-PCR assay was highly specific, it yielded positive reactions only when performed on BRSV-infected cell cultures or tissues. The detection limit of the RT-PCR assay was assessed as 5 TCID50. BRSV was detected in tissues of the respiratory tract and in the tracheobroncheal....... (7%), and Pasteurella haemolytica (7%) were the most common bacterial agents found in the lungs. BRSV was identified using a conventional antigen enzyme-linked immunosorbent assay (ELISA) in 23 (17%) animals. The established BRSV-specific RT-PCR assay yielded positive results for the same 23 animals...

  16. A novel 4-aminoantipyrine-Pd(II complex catalyzes Suzuki–Miyaura cross-coupling reactions of aryl halides

    Claudia A. Contreras-Celedón


    Full Text Available A simple and efficient catalytic system based on a Pd complex of 4-aminoantipyrine, 4-AAP–Pd(II, was found to be highly active for Suzuki–Miyaura cross-coupling of aryl iodides and bromides with phenylboronic acids under mild reaction conditions. Good to excellent product yields from the cross-coupling reaction can be achieved when the reaction is carried out in ethanol, in the open air, using low loading of 4-AAP–Pd(II as a precatalyst, and in the presence of aqueous K2CO3 as the base. A variety of functional groups are tolerated.

  17. NHC Nickel-Catalyzed Suzuki-Miyaura Cross-Coupling Reactions of Aryl Boronate Esters with Perfluorobenzenes.

    Zhou, Jing; Berthel, Johannes H J; Kuntze-Fechner, Maximilian W; Friedrich, Alexandra; Marder, Todd B; Radius, Udo


    An efficient Suzuki-Miyaura cross-coupling reaction of perfluorinated arenes with aryl boronate esters using NHC nickel complexes as catalysts is described. The efficiencies of different boronate esters (p-tolyl-Beg, p-tolyl-Bneop, p-tolyl-Bpin, p-tolyl-Bcat) and the corresponding boronic acid (p-tolyl-B(OH)2) in this type of cross-coupling reaction were evaluated (eg, ethyleneglycolato; neop, neopentylglycolato; pin, pinacolato; cat, catecholato). Aryl-Beg was shown to be the most reactive boronate ester among those studied. The use of CsF as an additive is essential for an efficient reaction of hexafluorobenzene with aryl neopentylglycolboronates.

  18. Cross-coupling reaction of cy- clopropylboronic acids with a- ryl w-halo-oxo-perfluoroalkyl- sulfonates


    The cross-coupling reaction of cyclopropylboronic acids with aryl w-halo-oxo-perfluoroalkylsulfonates is investigated. It was found that the stereodefined cyclopropylboronic acids can readily react with aryl w-halo-oxo- perfluoroalkylsulfonates to give the corresponding cross- coupling products in high yields under the appropriate con-ditions and in the presence of transition metal catalysts. For the reaction of various aryl perfluoroalkylsulfonates bearing the substituents, the use of corresponding bases was essential. During these reactions, the cyclopropyl configurations of cyclopropylboronic acids are retained. Thus, the procedure provides a new convenient route to stereodefined cyclopro-pane derivatives from phenols and commerce-available w-chloro-oxo-perfluoroalkylsulfonyl fluoride.

  19. Electrochemical branched-DNA assay for polymerase chain reaction-free detection and quantification of oncogenes in messenger RNA.

    Lee, Ai-Cheng; Dai, Ziyu; Chen, Baowei; Wu, Hong; Wang, Jun; Zhang, Aiguo; Zhang, Lurong; Lim, Tit-Meng; Lin, Yuehe


    We describe a novel electrochemical branched-DNA (bDNA) assay for polymerase chain reaction (PCR)-free detection and quantification of p185 BCR-ABL leukemia fusion transcripts in the population of messenger ribonucleic acid (mRNA) extracted from cell lines. The bDNA amplifier carrying high loading of alkaline phosphatase (ALP) tracers was used to amplify the target signal. The targets were captured on microplate well surfaces through cooperative sandwich hybridization prior to the labeling of bDNA. The activity of captured ALP was monitored by square-wave voltammetric (SWV) analysis of the electroactive enzymatic product in the presence of 1-naphthyl phosphate. The voltammetric characteristics of substrate and enzymatic product as well as the parameters of SWV analysis were systematically optimized. A detection limit of 1 fM (1 x 10(-19) mol of target transcripts in 100 microL) and a 3-order-wide dynamic range of target concentration were achieved by the electrochemical bDNA assay. Such limit corresponded to approximately 17 fg of the p185 BCR-ABL fusion transcripts. The specificity and sensitivity of assay enabled direct detection of target transcripts in as little as 4.6 ng of mRNA population without PCR amplification. In combination with the use of a well-quantified standard, the electrochemical bDNA assay was capable of direct use for a PCR-free quantitative analysis of target transcripts in mRNA population. A mean transcript copy number of 62,900/ng of mRNA was determined, which was at least 50-fold higher than that of real-time quantitative PCR (qPCR). The finding was consistent with the underestimation of targets by qPCR reported earlier. In addition, the unique design based on bDNA technology increases the assay specificity as only the p185 BCR-ABL fusion transcripts will respond to the detection. The approach thus provides a simple, sensitive, accurate, and quantitative tool alternative to the qPCR for early disease diagnosis.

  20. Density Functional Theory and MP2 Calculations of the Transition States and Reaction Paths on Coupling Reaction of Methane through Plasma

    YANG,En-Cui(杨恩翠); ZHAO,Xiao-Jun(赵小军); TIAN,Peng(田鹏); HAO,Jin-Ku(郝金库)


    The two possible reaction paths of producing ethane on coupling reaction of methane through plasma were theoretically investigated by B3LYP and MP2 methods with 6-311G* respectively and further compared with the previous results calculated from B3LYP/6-31G*.The new investigated results consistently confirmed the previous conclusion.And the influences of the calculation methods and basis sets on the calculated results were also discussed.

  1. A novel multiplex polymerase chain reaction assay for profile analyses of gene expression in peripheral blood

    Jia Xingwang


    Full Text Available Abstract Background Studies have demonstrated that inflammation has a key role in the pathogenesis of atherosclerosis due to the abnormal gene expressions of multiple cytokines. We established an accurate and precise method to observe gene expression in whole blood that might provide specific diagnostic information for coronary artery disease (CAD and other related diseases. Methods The fifteen selected CAD-related genes (IL1B, IL6, IL8, IFNG, MCP-1, VWF, MTHFR, SELL, TNFalpha, ubiquitin, MCSF, ICAM1, ID2, HMOX1 and LDLR and two housekeeping genes (ACTB and GK as internal references have been measured simultaneously with a newly developed multiplex polymerase chain reaction (multi-PCR method. Moreover, the precision was evaluated, and a procedure for distinguishing patients from the normal population has been developed based upon analyses of peripheral blood. A total of 148 subjects were divided into group A (control group without plaques, group B (calcified plaques and group C (non-calcified plaques, and combination group according dual-source CT criteria. Gene expression in blood was analyzed by multi-PCR, and levels of glucose and lipids measured in 50 subjects to explore the relationship among them. Results The precision results of the multi-PCR system revealed within-run and between-run CV values of 3.695–12.537% and 4.405–13.405%, respectively. The profiles of cytokine gene expression in peripheral blood were set: a positive correlation between glucose and MCSF, HMOX1 or TNFalpha were found. We also found that triglyceride levels were negatively correlated with SELL gene expression in 50 subjects. Compared with controls, gene expression levels of IL1B, IL6, IL8 and MCP-1 increased significantly in group C. Conclusions A new multiple gene expression analysis system has been developed. The primary data suggested that gene expression was related to CAD. This system might be used for risk assessment of CVDs and other related diseases.

  2. Conformational gating of the electron transfer reaction QA−⋅QB → QAQB−⋅ in bacterial reaction centers of Rhodobacter sphaeroides determined by a driving force assay

    Graige, M. S.; Feher, G.; Okamura, M. Y.


    The mechanism of the electron transfer reaction, QA−⋅QB → QAQB−⋅, was studied in isolated reaction centers from the photosynthetic bacterium Rhodobacter sphaeroides by replacing the native Q10 in the QA binding site with quinones having different redox potentials. These substitutions are expected to change the intrinsic electron transfer rate by changing the redox free energy (i.e., driving force) for electron transfer without affecting other events that may be associated with the electron transfer (e.g., protein dynamics or protonation). The electron transfer from QA−⋅ to QB was measured by three independent methods: a functional assay involving cytochrome c2 to measure the rate of QA−⋅ oxidation, optical kinetic spectroscopy to measure changes in semiquinone absorption, and kinetic near-IR spectroscopy to measure electrochromic shifts that occur in response to electron transfer. The results show that the rate of the observed electron transfer from QA−⋅ to QB does not change as the redox free energy for electron transfer is varied over a range of 150 meV. The strong temperature dependence of the observed rate rules out the possibility that the reaction is activationless. We conclude, therefore, that the independence of the observed rate on the driving force for electron transfer is due to conformational gating, that is, the rate limiting step is a conformational change required before electron transfer. This change is proposed to be the movement, controlled kinetically either by protein dynamics or intermolecular interactions, of QB by ≈5 Å as observed in the x-ray studies of Stowell et al. [Stowell, M. H. B., McPhillips, T. M., Rees, D. C., Soltis, S. M., Abresch, E. & Feher, G. (1997) Science 276, 812–816]. PMID:9751725

  3. Dynamics of reaction-diffusion patterns controlled by asymmetric nonlocal coupling as a limiting case of differential advection.

    Siebert, Julien; Alonso, Sergio; Bär, Markus; Schöll, Eckehard


    A one-component bistable reaction-diffusion system with asymmetric nonlocal coupling is derived as a limiting case of a two-component activator-inhibitor reaction-diffusion model with differential advection. The effects of asymmetric nonlocal couplings in such a bistable reaction-diffusion system are then compared to the previously studied case of a system with symmetric nonlocal coupling. We carry out a linear stability analysis of the spatially homogeneous steady states of the model and numerical simulations of the model to show how the asymmetric nonlocal coupling controls and alters the steady states and the front dynamics in the system. In a second step, a third fast reaction-diffusion equation is included which induces the formation of more complex patterns. A linear stability analysis predicts traveling waves for asymmetric nonlocal coupling, in contrast to a stationary Turing patterns for a system with symmetric nonlocal coupling. These findings are verified by direct numerical integration of the full equations with nonlocal coupling.

  4. Relative analytical sensitivity of donor nucleic acid amplification technology screening and diagnostic real-time polymerase chain reaction assays for detection of Zika virus RNA.

    Stone, Mars; Lanteri, Marion C; Bakkour, Sonia; Deng, Xutao; Galel, Susan A; Linnen, Jeffrey M; Muñoz-Jordán, Jorge L; Lanciotti, Robert S; Rios, Maria; Gallian, Pierre; Musso, Didier; Levi, José E; Sabino, Ester C; Coffey, Lark L; Busch, Michael P


    Zika virus (ZIKV) has spread rapidly in the Pacific and throughout the Americas and is associated with severe congenital and adult neurologic outcomes. Nucleic acid amplification technology (NAT) assays were developed for diagnostic applications and for blood donor screening on high-throughput NAT systems. We distributed blinded panels to compare the analytical performance of blood screening relative to diagnostic NAT assays. A 25-member, coded panel (11 half-log dilutions of a 2013 French Polynesia ZIKV isolate and 2015 Brazilian donor plasma implicated in transfusion transmission, and 3 negative controls) was sent to 11 laboratories that performed 17 assays with 2 to 12 replicates per panel member. Results were analyzed for the percentage reactivity at each dilution and by probit analysis to estimate the 50% and 95% limits of detection (LOD50 and LOD95 , respectively). Donor-screening NAT assays that process approximately 500 µL of plasma into amplification reactions were comparable in sensitivity (LOD50 and LOD95 , 2.5 and 15-18 copies/mL) and were approximately 10-fold to 100-fold more sensitive than research laboratory-developed and diagnostic reverse transcriptase-polymerase chain reaction tests that process from 10 to 30 µL of plasma per amplification. Increasing sample input volume assayed with the Centers for Disease Control and Prevention reverse transcriptase-polymerase chain reaction assays increased the LODs by 10-fold to 30-fold. Blood donor-screening ZIKV NAT assays demonstrate similar excellent sensitivities to assays currently used for screening for transfusion-transmitted viruses and are substantially more sensitive than most other laboratory-developed and diagnostic ZIKV reverse transcriptase-polymerase chain reaction assays. Enhancing sensitivities of laboratory-developed and diagnostic assays may be achievable by increasing sample input. © 2017 AABB.

  5. Clinical validation of a real-time polymerase chain reaction assay for rapid detection of Acinetobacter baumannii colonization.

    Blanco-Lobo, P; González-Galán, V; García-Quintanilla, M; Valencia, R; Cazalla, A; Martín, C; Alonso, I; Pérez-Romero, P; Cisneros, J M; Aznar, J; McConnell, M J


    Real-time polymerase chain reaction (PCR)-based approaches have not been assessed in terms of their ability to detect patients colonized by Acinetobacter baumannii during active surveillance. This prospective, double-blind study demonstrated that a real-time PCR assay had high sensitivity (100%) and specificity (91.2%) compared with conventional culture for detecting A. baumannii in 397 active surveillance samples, and provided results within 3h. Receiver-operator curve analyses demonstrated that the technique has diagnostic accuracy of 97.7% (95% confidence interval 96.0-99.3%). This method could facilitate the rapid implementation of infection control measures for preventing the transmission of A. baumannii.

  6. Screening of Riboflavin-Producing Lactobacilli by a Polymerase-Chain-Reaction-Based Approach and Microbiological Assay.

    Thakur, Kiran; Tomar, Sudhir Kumar; Brahma, Biswajit; De, Sachinandan


    Riboflavin has an important role in various cellular metabolic activities through its participation in oxidation-reduction reactions. In this study, as many as 60 lactobacilli were screened for the presence or absence of riboflavin biosynthesis genes and riboflavin production. Of these, only 14 strains were able to grow in a commercial riboflavin-free medium. We observed that the presence of riboflavin biosynthesis genes is strain-specific across different species of lactobacilli. The microbiological assay was found to be appreciably reproducible, sensitive, rapid, and inexpensive and, hence, can be employed for screening the riboflavin-producing strains. The study thus represents a convenient and efficient method for selection of novel riboflavin producers. These riboflavin(+) strains thus identified and characterized could be explored as potent candidates for the development of a wide range of dairy- and cereal-based foods for the delivery of in situ riboflavin to consumers.

  7. Nonsymmetrical 3,4-dithienylmaleimides by cross-coupling reactions with indium organometallics: synthesis and photochemical studies.

    Mosquera, Angeles; Férnandez, M Isabel; Canle Lopez, Moisés; Pérez Sestelo, José; Sarandeses, Luis A


    The synthesis and photochemical study of novel nonsymmetrical 1,2-dithienylethenes (DTEs) with a maleimide bridge have been carried out. The synthetic approach to the DTEs was based on successive selective palladium-catalyzed cross-coupling reactions of 5-susbtituted-2-methyl-3-thiophenyl indium reagents with 3,4-dichloromaleimides. The required organoindium reagents were prepared from 2-methyl-3,5-dibromothiophene by a selective (C-5) coupling reaction with triorganoindium compounds (R3 In) and subsequent metal-halogen exchange. The coupling reactions usually gave good yields and have a high atom economy with substoichiometric amounts of R3 In. The results of photochemical studies show that these novel dithienylmaleimides undergo a photocyclization reaction upon irradiation in the UV region and a photocycloreversion after excitation in the visible region, thus they can be used as photochemical switches. ON-OFF operations can be repeated in successive cycles without appreciable loss of effectiveness in the process.

  8. Interfacial Reactions in the Ni/Sn- xZn/Cu Sandwich Couples

    Yen, Yee-Wen; Lin, Chung-Yung; Lai, Mei-Ting; Chen, Wan-Ching


    The interfacial reactions in Ni/Sn- xZn/Cu sandwich couples which were reflowed at 270°C for 1 h and then aged at 160°C for 1-1000 h were investigated. When the 1000- μm-thick Sn-Zn alloy reacted with Ni and Cu in this couple, the results indicated that the (Ni, Cu)3Sn4, (Ni, Cu)5Zn21, and Ni5Zn21 phases were formed at Sn-1Zn/Ni, Sn-5Zn/Ni, and Sn-9Zn/Ni interfaces for 1 h reflowing, respectively. After 1000 h aging, each intermetallic compound (IMC) was converted to (Cu, Ni, Zn)6Sn5, (Ni, Cu, Sn)5Zn21/Ni5Zn21, and Ni5Zn21 (two layers) phases in the related couples. On the Cu side, the Cu6Sn5 phase in the Sn-1Zn/Cu interface and the Cu5Zn8 phase in the Sn-5Zn/Cu and Sn-9Zn/Cu interfaces were observed when the couple was reflowed at 270°C for 1 h. After 100 h aging, the (Cu, Ni, Zn)6Sn5, Cu5Zn8/(Cu, Zn)6Sn5, and Cu5Zn8 phases were formed at the Sn-1Zn/Cu, Sn-5Zn/Cu and Sn-9Zn/Cu interfaces. When the Sn-Zn alloy thickness was decreased to 500 μm, the (Cu, Ni, Zn)6Sn5 phase at the Sn-1Zn/Ni interface and the (Ni, Cu, Sn)5Zn21 phase at the Sn-5Zn/Ni and Sn-9Zn/Ni interfaces were observed after 1 h reflowing. When the couple was aged at 160°C for 1000 h, each IMC was converted to (Cu, Ni, Zn)6Sn5 and Cu5Zn8/(Cu, Ni, Sn)Zn/Ni5Zn21 phases at the Sn-1Zn/Ni and Sn-(5, 9)Zn/Ni interfaces. (Cu, Ni, Zn)6Sn5 and Cu5Zn8 were, respectively, formed at the Sn-1Zn/Cu and Sn-(5, 9)Zn/Cu interfaces for 1 h reflowing. After 100 h aging, the IMCs were converted to (Cu, Ni, Zn)6Sn5 and Cu5Zn8/(Cu, Zn)6Sn5 phases. This current study reveals that the IMC formation in Ni/(Sn- xZn)/Cu sandwich couples are very sensitive to the Zn concentration and thickness in Sn- xZn alloys.

  9. Quantitative analysis of energy metabolic pathways in MCF-7 breast cancer cells by selected reaction monitoring assay.

    Drabovich, Andrei P; Pavlou, Maria P; Dimitromanolakis, Apostolos; Diamandis, Eleftherios P


    To investigate the quantitative response of energy metabolic pathways in human MCF-7 breast cancer cells to hypoxia, glucose deprivation, and estradiol stimulation, we developed a targeted proteomics assay for accurate quantification of protein expression in glycolysis/gluconeogenesis, TCA cycle, and pentose phosphate pathways. Cell growth conditions were selected to roughly mimic the exposure of cells in the cancer tissue to the intermittent hypoxia, glucose deprivation, and hormonal stimulation. Targeted proteomics assay allowed for reproducible quantification of 76 proteins in four different growth conditions after 24 and 48 h of perturbation. Differential expression of a number of control and metabolic pathway proteins in response to the change of growth conditions was found. Elevated expression of the majority of glycolytic enzymes was observed in hypoxia. Cancer cells, as opposed to near-normal MCF-10A cells, exhibited significantly increased expression of key energy metabolic pathway enzymes (FBP1, IDH2, and G6PD) that are known to redirect cellular metabolism and increase carbon flux through the pentose phosphate pathway. Our quantitative proteomic protocol is based on a mass spectrometry-compatible acid-labile detergent and is described in detail. Optimized parameters of a multiplex selected reaction monitoring (SRM) assay for 76 proteins, 134 proteotypic peptides, and 401 transitions are included and can be downloaded and used with any SRM-compatible mass spectrometer. The presented workflow is an integrated tool for hypothesis-driven studies of mammalian cells as well as functional studies of proteins, and can greatly complement experimental methods in systems biology, metabolic engineering, and metabolic transformation of cancer cells.

  10. Development of a new duplex real-time polymerase chain reaction assay for detection of dicer in G. gallus.

    Ji, Xiaolin; Wang, Qi; Gao, Yulong; Wang, Yongqiang; Qin, Liting; Qi, Xiaole; Gao, Honglei; Wang, Xiaomei


    Recently, there has been a growing body of evidence showing that cellular microRNAs (miRNAs) are involved in virus-host interactions. Numerous studies have focused on analyses of the expression profiles of cellular miRNAs, but the expression patterns of Dicer, which is responsible for the generation of miRNAs, have only rarely been explored in Gallus gallus. We developed a duplex realtime reverse transcriptase polymerase chain reaction (RTPCR) assay for the relative quantification of the mRNAs of Dicer and beta-actin in G. gallus. To apply this method, the expression of Dicer in avian cells after infection with avian leukosis virus subgroup J (ALV-J) was detected using our established duplex real-time RT-PCR. The duplex realtime RT-PCR assay is sufficiently sensitive, specific, accurate, reproducible, and cost-effective for the detection of Dicer in G. gallus. Furthermore, this study, for the first time, demonstrated that ALV-J can induce differential expression of Dicer mRNA in the ALV-J-infected cells.

  11. Development of a quantitative polymerase chain reaction assay for detection of Kudoa septempunctata in olive flounder (Paralichthys olivaceus).

    Harada, Tetsuya; Kawai, Takao; Sato, Hiroshi; Yokoyama, Hiroshi; Kumeda, Yuko


    Kudoa septempunctata is a newly identified myxosporean parasite that infects the trunk muscles of olive flounder (Paralichthys olivaceus) and a causative agent of the increasing number of foodborne gastroenteritis outbreaks with unknown etiology which have occurred in Japan over the last few years. Here, we developed a quantitative polymerase chain reaction (QPCR) assay for the detection of K. septempunctata 18S rDNA in olive flounder muscle tissue samples. Additionally, we compared the relative efficacy of four DNA extraction methods, including two commercial kits, and assessed intrafish variability in the distribution of K. septempunctata spores in flounder using this QPCR method in order to establish a more accurate quantitative measurement. Our QPCR assay displayed high sensitivity, specificity, and reproducibility, and had good correlation with a microscopic detection method. Our data also indicated that the DNeasy® Blood & Tissue Kit was more efficient method for the extraction of K. septempunctata DNA than the three other methods (heating, alkaline lysis, and FastDNA® SPIN Kit method). We believe that our method would be useful for investigating foodborne outbreaks caused by K. septempunctata and for the monitoring and quantification of this parasite in retail or aquacultured olive flounders to prevent such outbreaks. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Multiplex quantification of Escherichia coli, Salmonella typhi and Vibrio cholera with three DNA targets in single reaction assay.

    Jangampalli Adi, Pradeepkiran; Naidu, Jagadish R; Matcha, Bhaskar


    Escherichia coli (E. coli), Salmonella typhi and Vibrio cholera harmful pathogens, which causes various diseases in humans. Rapid diagnosis of bacterial infection is an important for patient management and appropriate therapy during the early phase of the bacterial infected diseases. Among the existing techniques for identifying pathogens were less sensitive and time-consuming processes. In the present study total, 48 clinical 31 blood and 17 urine samples of patients suspected with the infections were collected from SVRR Hospital and used to detect the pathogens. Multiplex polymerase chain reaction (PCR) assay was set to design for the identification of Escherichia coli, Salmonella typhi and Vibrio cholera from the different clinical samples. Rapid diagnosis of Escherichia coli (E. coli), Salmonella and Vibrio cholera pathogens can be done with simultaneously in a single multiplex PCR assay by using specific primers with adjusted PCR conditions. Through this approach, the results represented with out of 31 blood samples 1-15 shows the positive with E. coli and remaining 14 only 11 were correlated with multiplex results of Vibrio cholera, remaining the urine samples all are positive with 17 samples correlate with the Salmonella typhi. Through the high specificity benefits of excellent sensitivity, with high resolution and reproducibility. This method of results proved and illustrates the best potential system for diagnosing the infectious disease with modern trendy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Development of real-time quantitative polymerase chain reaction assays to track treatment response in retinoid resistant acute promyelocytic leukemia

    Jelena V Jovanovic


    Full Text Available Molecular detection of minimal residual disease (MRD has become established to assess remission status and guide therapy in patients with PML-RARA+ acute promyelocytic leukemia (APL. However, there are few data on tracking disease response in patients with rarer retinoid resistant subtypes of APL, characterized by PLZF-RARA and STAT5b-RARA. Despite their relative rarity (<1% of APL we identified 6 cases (PLZF-RARA, n=5; STAT5b-RARA, n=1, established the respective breakpoint junction regions and designed real-time quantitative polymerase chain reaction (RQ-PCR assays to detect leukemic transcripts. The relative level of fusion gene expression in diagnostic samples was comparable to that observed in t(15;17-associated APL, affording assay sensitivities of ~1 in 104-105. Serial samples were available from 2 PLZF-RARA APL patients. One showed persistent PCR positivity, predicting subsequent relapse, and remains in CR2, ~11 years post-autograft. The other, achieved molecular remission (CRm with combination chemotherapy, remaining in CR1 at 6 years. The STAT5b-RARA patient failed to achieve CRm following frontline combination chemotherapy and ultimately proceeded to allogeneic transplant on the basis of a steadily rising fusion transcript level. These data highlight the potential of RQ-PCR detection of MRD to facilitate development of more individualized approaches to the management of rarer molecularly-defined subsets of acute leukemia.

  14. Development of field-based real-time reverse transcription-polymerase chain reaction assays for detection of Chikungunya and O'nyong-nyong viruses in mosquitoes.

    Smith, Darci R; Lee, John S; Jahrling, Jordan; Kulesh, David A; Turell, Michael J; Groebner, Jennifer L; O'Guinn, Monica L


    Chikungunya (CHIK) and O'nyong-nyong (ONN) are important emerging arthropod-borne diseases. Molecular diagnosis of these two viruses in mosquitoes has not been evaluated, and the effects of extraneous mosquito tissue on assay performance have not been tested. Additionally, no real-time reverse transcription-polymerase chain reaction (RT-PCR) assay exists for detecting ONN virus (ONNV) RNA. We describe the development of sensitive and specific real-time RT-PCR assays for detecting CHIK and ONN viral RNA in mosquitoes, which have application for field use. In addition, we compared three methods for primer/probe design for assay development by evaluating their sensitivity and specificity. This comparison resulted in development of virus-specific assays that could detect less than one plaque-forming unit equivalent of each of the viruses in mosquitoes. The use of these assays will aid in arthropod-borne disease surveillance and in the control of the associated diseases.

  15. Sensitive electrochemical monitoring of nucleic acids coupling DNA nanostructures with hybridization chain reaction

    Zhuang, Junyang; Fu, Libing; Xu, Mingdi; Yang, Huanghao; Chen, Guonan; Tang, Dianping, E-mail:


    Graphical abstract: -- Highlights: •A new signal-on metallobioassay was developed for detection of nucleic acids. •Target-triggered long-range self-assembled DNA nanostructures are used for amplification of electronic signal. •Hybridization chain reaction is utilized for construction of long-range DNA nanostructures. -- Abstract: Methods based on metal nanotags have been developed for metallobioassay of nucleic acids, but most involve complicated labeling or stripping procedures and are unsuitable for routine use. Herein, we report the proof-of-concept of a novel and label-free metallobioassay for ultrasensitive electronic determination of human immunodeficiency virus (HIV)-related gene fragments at an ultralow concentration based on target-triggered long-range self-assembled DNA nanostructures and DNA-based hybridization chain reaction (HCR). The signal is amplified by silver nanotags on the DNA duplex. The assay mainly consists of capture probe, detection probe, and two different DNA hairpins. In the presence of target DNA, the capture probe immobilized on the sensor sandwiches target DNA with the 3′ end of detection probe. Another exposed part of detection probe at the 5′ end opens two alternating DNA hairpins in turn, and propagates a chain reaction of hybridization events to form a nicked double-helix. Finally, numerous silver nanotags are immobilized onto the long-range DNA nanostructures, each of which produces a strong electronic signal within the applied potentials. Under optimal conditions, the target-triggered long-range DNA nanostructures present good electrochemical behaviors for the detection of HIV DNA at a concentration as low as 0.5 fM. Importantly, the outstanding sensitivity can make this approach a promising scheme for development of next-generation DNA sensors without the need of enzyme labeling or fluorophore labeling.

  16. Kinetic method for assaying the halogenating activity of myeloperoxidase based on reaction of celestine blue B with taurine halogenamines.

    Sokolov, A V; Kostevich, V A; Kozlov, S O; Donskyi, I S; Vlasova, I I; Rudenko, A O; Zakharova, E T; Vasilyev, V B; Panasenko, O M


    Myeloperoxidase (MPO) is a challenging molecular target which, if put under control, may allow regulating the development of inflammatory reactions associated with oxidative/halogenative stress. In this paper, a new kinetic method for assaying the halogenating activity of MPO is described. The method is based on measuring the rate of iodide-catalyzed oxidation of celestine blue B (CB) by oxygen and taurine N-chloramine (bromamine). The latter is produced in a reaction of taurine with HOCl (HOBr). CB is not a substrate for the peroxidase activity of MPO and does not react with hydrogen peroxide and superoxide anion radical. Taurine N-chloramine (bromamine) reacts with CB in molar ratio of 1:2. Using the new method, we studied the dependence of MPO activity on concentration of substrates and inhibitors. The specificity of MPO inhibition by non-proteolyzed ceruloplasmin is characterized. The inhibition of taurine N-chloramine production by neutrophils and HL-60 cells in the presence of MPO-affecting substances is demonstrated. The new method allows determining the kinetic parameters of MPO halogenating activity and studying its inhibition by various substances, as well as screening for potential inhibitors of the enzyme.

  17. Numerical method using cubic B-spline for a strongly coupled reaction-diffusion system.

    Muhammad Abbas

    Full Text Available In this paper, a numerical method for the solution of a strongly coupled reaction-diffusion system, with suitable initial and Neumann boundary conditions, by using cubic B-spline collocation scheme on a uniform grid is presented. The scheme is based on the usual finite difference scheme to discretize the time derivative while cubic B-spline is used as an interpolation function in the space dimension. The scheme is shown to be unconditionally stable using the von Neumann method. The accuracy of the proposed scheme is demonstrated by applying it on a test problem. The performance of this scheme is shown by computing L∞ and L2 error norms for different time levels. The numerical results are found to be in good agreement with known exact solutions.

  18. Numerical method using cubic B-spline for a strongly coupled reaction-diffusion system.

    Abbas, Muhammad; Majid, Ahmad Abd; Md Ismail, Ahmad Izani; Rashid, Abdur


    In this paper, a numerical method for the solution of a strongly coupled reaction-diffusion system, with suitable initial and Neumann boundary conditions, by using cubic B-spline collocation scheme on a uniform grid is presented. The scheme is based on the usual finite difference scheme to discretize the time derivative while cubic B-spline is used as an interpolation function in the space dimension. The scheme is shown to be unconditionally stable using the von Neumann method. The accuracy of the proposed scheme is demonstrated by applying it on a test problem. The performance of this scheme is shown by computing L∞ and L2 error norms for different time levels. The numerical results are found to be in good agreement with known exact solutions.

  19. Click and chemically triggered declick reactions through reversible amine and thiol coupling via a conjugate acceptor

    Diehl, Katharine L.; Kolesnichenko, Igor V.; Robotham, Scott A.; Bachman, J. Logan; Zhong, Ye; Brodbelt, Jennifer S.; Anslyn, Eric V.


    The coupling and decoupling of molecular units is a fundamental undertaking of organic chemistry. Herein we report the use of a very simple conjugate acceptor, derived from Meldrum's acid, for the sequential ‘clicking’ together of an amine and a thiol in aqueous conditions at neutral pH. Subsequently, this linkage can be ‘declicked’ by a chemical trigger to release the original amine and thiol undisturbed. The reactivity differs from that of other crosslinking agents because the selectivity for sequential functionalization derives from an altering of the electrophilicity of the conjugate acceptor on the addition of the amine. We describe the use of the procedure to modify proteins, create multicomponent libraries and synthesize oligomers, all of which can be declicked to their starting components in a controlled fashion when desired. Owing to the mild reaction conditions and ease of use in a variety of applications, the method is predicted to have wide utility.

  20. Implicit coupling of turbulent diffusion with chemical reaction mechanisms for prognostic atmospheric dispersion models

    Berlowitz, D.R.


    In the last few decades the negative impact by humans on the thin atmospheric layer enveloping the earth, the basis for life on this planet, has increased steadily. In order to halt, or at least slow down this development, the knowledge and study of these anthropogenic influence has to be increased and possible remedies have to be suggested. An important tool for these studies are computer models. With their help the atmospheric system can be approximated and the various processes, which have led to the current situation can be quantified. They also serve as an instrument to assess short or medium term strategies to reduce this human impact. However, to assure efficiency as well as accuracy, a careful analysis of the numerous processes involved in the dispersion of pollutants in the atmosphere is called for. This should help to concentrate on the essentials and also prevent excessive usage of sometimes scarce computing resources. The basis of the presented work is the EUMAC Zooming Model (ETM), and particularly the component calculating the dispersion of pollutants in the atmosphere, the model MARS. The model has two main parts: an explicit solver, where the advection and the horizontal diffusion of pollutants are calculated, and an implicit solution mechanism, allowing the joint computation of the change of concentration due to chemical reactions, coupled with the respective influence of the vertical diffusion of the species. The aim of this thesis is to determine particularly the influence of the horizontal components of the turbulent diffusion on the existing implicit solver of the model. Suggestions for a more comprehensive inclusion of the full three dimensional diffusion operator in the implicit solver are made. This is achieved by an appropriate operator splitting. A selection of numerical approaches to tighten the coupling of the diffusion processes with the calculation of the applied chemical reaction mechanisms are examined. (author) figs., tabs., refs.

  1. Mechanism of coupling drug transport reactions located in two different membranes

    Helen I. Zgurskaya


    Full Text Available Gram- negative bacteria utilize a diverse array of multidrug transporters to pump toxic compounds out of cells. Some transporters together with periplasmic membrane fusion proteins (MFPs and outer membrane channels assemble trans-envelope complexes that expel multiple antibiotics across outer membranes of Gram-negative bacteria and into the external medium. Others further potentiate this efflux by pumping drugs across the inner membrane into the periplasm. Together these transporters create a powerful network of efflux that protect bacteria against a broad range of antimicrobial agents. This review is focused on the mechanism of coupling transport reactions located in two different membranes of Gram-negative bacteria. Using a combination of biochemical, genetic and biophysical approaches we have reconstructed the sequence of events leading to the assembly of trans-envelope drug efflux complexes and characterized the roles of periplasmic and outer membrane proteins in this process. Our recent data suggest a critical step in the activation of intermembrane efflux pumps, which is controlled by MFPs. We propose that the reaction cycles of transporters are tightly coupled to the assembly of the trans-envelope complexes. Transporters and MFPs exist in the inner membrane as dormant complexes. The activation of complexes is triggered by MFP binding to the outer membrane channel, which leads to a conformational change in the membrane proximal domain of MFP needed for stimulation of transporters. The activated MFP-transporter complex engages the outer membrane channel to expel substrates across the outer membrane. The recruitment of the channel is likely triggered by binding of effectors (substrates to MFP or MFP-transporter complexes. This model together with recent structural and functional advances in the field of drug efflux provides a fairly detailed understanding of the mechanism of drug efflux across the two membranes.

  2. Coupled effects of dehydration reaction, dilatant strengthening and shear heating on dynamic fault slip

    Yamashita, T.


    It is believed that dynamic fault slip is affected by thermal pressurization. However, dilatant strengthening and dehydration reaction may significantly affect the degree of thermal pressurization. In addition, it is not clear how such effects influence the fault slip as a whole. We theoretically study how dilatant strengthening, frictional heating and dehydration reaction are coupled and how they affect dynamic slip assuming a fault in a thermoporoelastic medium saturated with fluid. After mathematical analysis is carried out for 1D model, the behavior of 2D fault model is studied numerically. The porosity is assumed to increase with increasing fault slip following Suzuki and Yamashita (2008). Our mathematical formulation of dehydration reaction is based on Brantut et al.(2010); the dehydration reaction is assumed to be endothermic. In addition, starting from the temperature Ts, all the frictional energy is assumed to be absorbed by the dehydration reaction rather than converted into heat. Although Brantut et al.(2010) assumed a constant slip velocity, we consider the temporal evolution of slip assuming the Coulomb law of friction on the fault. We first make the analysis assuming adiabatic and undrained conditions for the 1D model. We find that three nondimensional parameters Su, P0 and G0 determine the system behavior if the initial temperature T0 and dehydration starting temperature Ts are given, where Su (>0) is a parameter proportional to the pore creation rate, P0 (>0) is the initial nondimensional frictional stress and G0 (>0) is a parameter proportional to the mass fraction of fluid released per unit of total rock mass divided by the energy change per unit volume of the slip zone. The nondimensional frictional stress P is defined by the Coulomb frictional stress divided by the initial shear stress, which suggests the relation 0Ts, where Te is the temperature. We find for Te>Ts that the evolution of P is described by the equation dP/dT=(1-P)(Su-G0*P), where

  3. Excited-state charge coupled proton transfer reaction in dipole-functionalized salicylideneaniline

    Chen, Kew-Yu, E-mail:; Hu, Jiun-Wei


    Based on design and synthesis of salicylideneaniline derivatives 1–4, we demonstrate an exceedingly useful system to investigate the excited-state intramolecular charge transfer (ESICT) coupled with excited-state intramolecular proton transfer (ESIPT) reaction via the dipolar functionality of Schiff base salicylideneaniline. In solid and aprotic solvents 1–4 exist mainly as E conformers that possess a strong intramolecular six-membered-ring hydrogen bond. Compounds 2–4 exhibit solely a long-wavelength proton-transfer tautomer emission, while dipole-functionalized Schiff base 1 exhibits remarkable dual emission due to the different solvent-polarity environments between ESICT and ESIPT states. Moreover, the geometric structures, frontier molecular orbitals (MOs) and the potential energy curves for 1–4 in the ground and the first singlet excited state were fully rationalized by density functional theory (DFT) and time-dependent DFT calculations. - Highlights: • A dipole-functionalized salicylideneaniline derivative was synthesized. • The Schiff base exhibits remarkable dual emission. • A novel ESICT/ESIPT coupled system was created.

  4. A two-dimensional conjugated aromatic polymer via C-C coupling reaction

    Liu, Wei; Luo, Xin; Bao, Yang; Liu, Yan Peng; Ning, Guo-Hong; Abdelwahab, Ibrahim; Li, Linjun; Nai, Chang Tai; Hu, Zhi Gang; Zhao, Dan; Liu, Bin; Quek, Su Ying; Loh, Kian Ping


    The fabrication of crystalline 2D conjugated polymers with well-defined repeating units and in-built porosity presents a significant challenge to synthetic chemists. Yet they present an appealing target because of their desirable physical and electronic properties. Here we report the preparation of a 2D conjugated aromatic polymer synthesized via C-C coupling reactions between tetrabromopolyaromatic monomers. Pre-arranged monomers in the bulk crystal undergo C-C coupling driven by endogenous solid-state polymerization to produce a crystalline polymer, which can be mechanically exfoliated into micrometre-sized lamellar sheets with a thickness of 1 nm. Isothermal gas-sorption measurements of the bulk material reveal a dominant pore size of ~0.6 nm, which indicates uniform open channels from the eclipsed stacking of the sheets. When employed as an organic anode in an ambient-temperature sodium cell, the material allows a fast charge/discharge of sodium ions, with impressive reversible capacity, rate capability and stability metrics.

  5. Comparison of Parasite Burden Using Real-Time Polymerase Chain Reaction Assay and Limiting Dilution Assay in Leishma-nia major Infected Mouse

    Somayeh GHOTLOO


    Full Text Available Background:Limiting dilution assay is considered as the gold standard method for quantifying the number of parasites in the animal model of Leishmania infection. Nowadays, real-time PCR is being increasingly applied to quantify infectious agents. In the present study, a real-time PCR assay was developed to estimate para­site burdens in lymph nodes of Leishmania major infected BALB/C mice. Enumera­tion of parasites was also performed by limiting dilution assay and compared with the results of real-time PCR based quantification.Methods:The SYBR Green based real- time PCR assay was performed to amplify a 75 bp fragment of superoxide dismutase B1 gene in the lymph nodes of L. major infected BALB/C mice 8 weeks post infection. Mice were infected subcutaneously at the base of their tail with 2 × 105L. major promastigotes in the stationary phase of growth. To compare parasite burdens obtained by real-time PCR assay with those of limiting dilution assay, twelve 8-fold serial dilutions of the lymph node homoge­nates were prepared in the Schneider medium and incubated at 26°C.After 7 days, wells containing motile parasites were identified by direct observation under an inverted light microscope and the total number of parasites was estimated using the ELIDA software.Results:Spearman's correlation coefficient of the parasite burdens between real-time PCR and limiting dilution assay was 0.72 (Pvalue = 0.008.Conclusion:Real-time PCR assay is an appropriate replacement to existing limit­ing dilution assay in quantifying parasite burden in the experimental model of Leishma­nia infection.

  6. Peroxyl Radical Reactions in Water Solution: A Gym for Proton-Coupled Electron-Transfer Theories.

    Amorati, Riccardo; Baschieri, Andrea; Morroni, Gloria; Gambino, Rossana; Valgimigli, Luca


    The reactions of alkylperoxyl radicals with phenols have remained difficult to investigate in water. We describe herein a simple and reliable method based on the inhibited autoxidation of water/THF mixtures, which we calibrated against pulse radiolysis. With this method we measured the rate constants kinh for the reactions of 2-tetrahydrofuranylperoxyl radicals with reference compounds: urate, ascorbate, ferrocenes, 2,2,5,7,8-pentamethyl-6-chromanol, Trolox, 6-hydroxy-2,5,7,8-tetramethylchroman-2-acetic acid, 2,6-di-tert-butyl-4-methoxyphenol, 4-methoxyphenol, catechol and 3,5-di-tert-butylcatechol. The role of pH was investigated: the value of kinh for Trolox and 4-methoxyphenol increased 11- and 50-fold from pH 2.1 to 12, respectively, which indicate the occurrence of a SPLET-like mechanism. H(D) kinetic isotope effects combined with pH and solvent effects suggest that different types of proton-coupled electron transfer (PCET) mechanisms are involved in water: less electron-rich phenols react at low pH by concerted electron-proton transfer (EPT) to the peroxyl radical, whereas more electron-rich phenols and phenoxide anions react by multi-site EPT in which water acts as proton relay.

  7. A peculiar segmented flow microfluidics for isoquercitrin biosynthesis based on coupling of reaction and separation.

    Gong, An; Gu, Shuang-Shuang; Wang, Jun; Sheng, Sheng; Wu, Fu-An


    A segmented flow containing a buffer-ionic liquid/solvent in a micro-channel reactor was applied to synthesize isoquercitrin by the hesperidinase-catalyzed selective hydrolysis of rutin, based on a novel system of reaction coupling with separation. Within the developed microchannel reactor with one T-shaped inlet and outlet, the maximum isoquercitrin yield (101.7 ± 2.6%) was achieved in 20 min at 30 °C and 4 μL/min. Compared with a continuous-flow reactor, reaction rate was increased 4-fold due to a glycine-sodium hydroxide:[Bmim][BF4]/glycerol triacetate (1:1, v/v) system that formed a slug flow in microchannel and significantly increased mass transfer rates. The mass transfer coefficient significantly increased and exhibited a linear relationship with the flow rate. Hesperidinase could be efficiently reused at least 5 times, without losing any activity. The bonding mechanism and secondary structure of hesperidinase indicated that hesperidinase had a greater affinity to rutin at a production rate of 4 μL/min in this segmented flow microreactor.

  8. New Diazo Coupling Reactions for Visible Spectrophotometric Determination of Alfuzosin in Pharmaceutical Preparations

    M. Vamsi Krishna


    Full Text Available Simple, rapid and sensitive spectrophotometric procedures were developed for the analysis of Alfuzosin hydrochloride (AFZ in pure form as well as in pharmaceutical formulations. The methods are based on the reaction of AFZ with nitrite in acid medium to form diazonium ion, which is coupled with ethoxyethylenemaleic ester (Method A or ethylcyanoacetate (Method B or acetyl acetone (method C in basic medium to form azo dyes, showing absorption maxima at 440, 465 and 490 nm respectively. Beer’s law is obeyed in the concentration of 4-20 μg/mL of AFZ for methods A, B and 3-15 μg/mL of AFZ for method C. The molar absorptivity and sandell’s sensitivity of AFZ- ethoxyethylenemaleic ester, AFZ- ethylcyanoacetate and AFZ-acetyl acetone are1.90 × 104, 0.022; 1.93 × 104, 0.021 and 2.67 × 104 L mole-1 cm-1, 0.015 μg cm-2 respectively. The optimum reaction conditions and other analytical parameters were evaluated. The methods were successfully applied to the determination of AFZ in pharmaceutical formulations.

  9. Stereoselective Synthesis of C-Glycosides by Suzuki Cross-coupling Reaction

    LI,Xiao-Liu; XING,Chun-Yong; WANG,Huan-Xin; TAKAHASHI,Hideyo; IKEGAMI,Shiro


    @@ Carbohydrates and their conjugates have been recognized to play a wide variety of metabolic roles in numerous biological processes.[1] Various modified sugars and analogues have been recently synthesized for further investigation of glycosidase reactions and for the development of specific glycosidase inhibitors.[2] As one of the most important carbohydrate mimics, C-glycosides have attracted great attention due to their stability to chemical or enzymatic hydrolysis of the glycosidic linkage. A number of methodologies for the preparation of C-glycosides have been extensively investigated.[3] We have recently reported the syntheses of novel C-glycosyl amino acids and amino-C-disaccharides possessing a ketose form via the stereoselective 1,3-dipolar cycloaddition of exo-methylenesugars (1) and nitrones.[4,5] As a continuation of our research on the synthesis of C-glycosides using exo-methylenesugar as the precursor, we wish to describe here a stereoselective synthesis of C-glycosides by Suzuki cross-coupling reaction.

  10. A novel duplex real-time reverse transcriptase-polymerase chain reaction assay for the detection of hepatitis C viral RNA with armored RNA as internal control

    Meng Shuang


    Full Text Available Abstract Background The hepatitis C virus (HCV genome is extremely heterogeneous. Several HCV infections can not be detected using currently available commercial assays, probably because of mismatches between the template and primers/probes. By aligning the HCV sequences, we developed a duplex real-time reverse transcriptase-polymerase chain reaction (RT-PCR assay using 2 sets of primers/probes and a specific armored RNA as internal control. The 2 detection probes were labelled with the same fluorophore, namely, 6-carboxyfluorescein (FAM, at the 5' end; these probes could mutually combine, improving the power of the test. Results The limit of detection of the duplex primer/probe assay was 38.99 IU/ml. The sensitivity of the assay improved significantly, while the specificity was not affected. All HCV genotypes in the HCV RNA Genotype Panel for Nucleic Acid Amplification Techniques could be detected. In the testing of 109 serum samples, the performance of the duplex real-time RT-PCR assay was identical to that of the COBAS AmpliPrep (CAP/COBAS TaqMan (CTM assay and superior to 2 commercial HCV assay kits. Conclusions The duplex real-time RT-PCR assay is an efficient and effective viral assay. It is comparable with the CAP/CTM assay with regard to the power of the test and is appropriate for blood-donor screening and laboratory diagnosis of HCV infection.

  11. Diffusive coupling can discriminate between similar reaction mechanisms in an allosteric enzyme system

    Nicola Ernesto M


    Full Text Available Abstract Background A central question for the understanding of biological reaction networks is how a particular dynamic behavior, such as bistability or oscillations, is realized at the molecular level. So far this question has been mainly addressed in well-mixed reaction systems which are conveniently described by ordinary differential equations. However, much less is known about how molecular details of a reaction mechanism can affect the dynamics in diffusively coupled systems because the resulting partial differential equations are much more difficult to analyze. Results Motivated by recent experiments we compare two closely related mechanisms for the product activation of allosteric enzymes with respect to their ability to induce different types of reaction-diffusion waves and stationary Turing patterns. The analysis is facilitated by mapping each model to an associated complex Ginzburg-Landau equation. We show that a sequential activation mechanism, as implemented in the model of Monod, Wyman and Changeux (MWC, can generate inward rotating spiral waves which were recently observed as glycolytic activity waves in yeast extracts. In contrast, in the limiting case of a simple Hill activation, the formation of inward propagating waves is suppressed by a Turing instability. The occurrence of this unusual wave dynamics is not related to the magnitude of the enzyme cooperativity (as it is true for the occurrence of oscillations, but to the sensitivity with respect to changes of the activator concentration. Also, the MWC mechanism generates wave patterns that are more stable against long wave length perturbations. Conclusions This analysis demonstrates that amplitude equations, which describe the spatio-temporal dynamics near an instability, represent a valuable tool to investigate the molecular effects of reaction mechanisms on pattern formation in spatially extended systems. Using this approach we have shown that the occurrence of inward

  12. A coupled mechanical and chemical damage model for concrete affected by alkali–silica reaction

    Pignatelli, Rossella, E-mail: [Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano (Italy); Lombardi Ingegneria S.r.l., Via Giotto 36, 20145 Milano (Italy); Comi, Claudia, E-mail: [Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano (Italy); Monteiro, Paulo J.M., E-mail: [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States)


    To model the complex degradation phenomena occurring in concrete affected by alkali–silica reaction (ASR), we formulate a poro-mechanical model with two isotropic internal variables: the chemical and the mechanical damage. The chemical damage, related to the evolution of the reaction, is caused by the pressure generated by the expanding ASR gel on the solid concrete skeleton. The mechanical damage describes the strength and stiffness degradation induced by the external loads. As suggested by experimental results, degradation due to ASR is considered to be localized around reactive sites. The effect of the degree of saturation and of the temperature on the reaction development is also modeled. The chemical damage evolution is calibrated using the value of the gel pressure estimated by applying the electrical diffuse double-layer theory to experimental values of the surface charge density in ASR gel specimens reported in the literature. The chemo-damage model is first validated by simulating expansion tests on reactive specimens and beams; the coupled chemo-mechanical damage model is then employed to simulate compression and flexure tests results also taken from the literature. -- Highlights: •Concrete degradation due to ASR in variable environmental conditions is modeled. •Two isotropic internal variables – chemical and mechanical damage – are introduced. •The value of the swelling pressure is estimated by the diffuse double layer theory. •A simplified scheme is proposed to relate macro- and microscopic properties. •The chemo-mechanical damage model is validated by simulating tests in literature.

  13. Four-body continuum-discretized coupled-channels calculations applied to {sup 6}He reactions

    Rodriguez-Gallardo, M. [Consejo Superior de Investigaciones Cientificas (CSIC), Madrid (Spain). Inst. de Estructura de la Materia; Arias, J.M.; Gomez-Camacho, J.M.; Moro, A.M. [Universidad de Sevilla (Spain). Dept. de Fisica Atomica, Molecular y Nuclear; Thompson, I.J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical Science Directorate; Tostevin, J.A. [University of Surrey, Guildford (United Kingdom). Dept. of Physics


    Full text. The scattering of a weakly bound three-body system by a target is discussed. The continuum-discretized coupled-channels (CDCC) framework, recently extended to four-body reactions (three-body projectile plus target), is used for the scattering calculations. Two different methods are used to discretized the three-body continuum of the projectile. In the first case, we make use of a Pseudo-State (PS) method in which the states of the projectile are represented by the eigenstates of its internal Hamiltonian in a truncated basis of square-integrable functions. In particular, we use the transformed harmonic oscillator (THO) method, in which the PS basis is obtained by applying a local scale transformation to the Harmonic Oscillator basis. In the second case, we applied the binning procedure that has just been extended to three-body projectiles. This discretization method requires to calculate first the true continuum of the projectile and then this continuum is discretized making bins or packages of energy. This has been the method used for many years in standard three-body (two-body projectile plus target) CDCC calculations. Its extension to three-body projectiles uses the eigenchannel expansion of the three-body S-matrix. We applied this formalism to several reactions induced by the Borromean nucleus {sup 6}He at different energies, namely {sup 6}He+{sup 9}Be at 16.2 MeV, {sup 6}He+{sup 64}Zn at 13.6 MeV, {sup 6}He+{sup 120}Sn at 17.4 MeV, and {sup 6}He+{sup 208}Pb at 22 MeV. Four-body CDCC calculations for elastic and breakup observables are presented for these reactions comparing both discretization methods, THO and binning. The effect of the mass of the target, which is clearly related to the influence of Coulomb couplings, is investigated. The elastic cross sections are also compared to existing experimental data. (author)

  14. Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions

    Ribeiro, Andre S.


    Genetic toggle switches (TSs) are one of the best studied small gene regulatory networks (GRNs), due to their simplicity and relevant role. They have been interpreted as decision circuits in cell differentiation, a process long hypothesized to be bistable [1], or as cellular memory units [2]. In these contexts, they must be reliable. Once a “decision” is made, the system must remain stable. One way to gain stability is by duplicating the genes of a TS and coupling the two TSs. Using a recent modeling strategy of GRNs, driven by a delayed stochastic simulation algorithm (delayed SSA) that allows modeling transcription and translation as multidelayed reactions, we analyze the stability of systems of coupled TSs. For this, we introduce the coupling strength (C) , a parameter to characterize the GRN structure, against which we compare the GRN stability (S) . We first show that time delays in transcription, associated to the promoter region release, ensure bistability of a TS, given no cooperative binding or self-activation reactions. Next, we couple two TSs and measure their toggling frequencies as C varies. Three dynamical regimes are observed: (i) for weak coupling, high frequency synchronized oscillations, (ii) for average coupling, low frequency synchronized oscillations, and (iii) for strong coupling the system becomes stable after a transient, in one of two steady states. The system stability, S , goes through a first order phase transition as C increases, in the average coupling regime. After, we study the effects of spatial separation in two compartments on the dynamics of two coupled TSs, where spatial separation is modeled as normally distributed random time delayed reactions. The phase transition of S , as C increases, occurs for lower values of C than when the two TSs are in the same compartment. Finally, we couple weakly and homogeneously several TSs within a single compartment and observe that as the number of coupled TSs increases, the system goes

  15. Evaluation of a novel real-time fluorescent polymerase chain reaction assay for high-risk human papilloma virus DNA genotypes in cytological cervical screening

    Cheng, Jiaoying; BIAN, MEILU; CONG, XIAO; SUN, AIPING; Li, Min; Ma, Li; Chen, Ying; Liu,Jun


    It has been confirmed that detection of high-risk human papillomavirus (HR HPV) DNA is useful in cervical cancer (CC) screening. Recently, a new real-time fluorescent polymerase chain reaction (PCR) assay was developed to detect HR HPV. This assay can synchronize nucleic acid amplification and testing using specific primers for 13 types of HR HPV genomes, combined with specific TaqMan fluorescent marker probe techniques through the fluorescence automatic PCR instrument. Furthermore, it uses T...

  16. Utility of a single nasal polymerase chain reaction assay in predicting absence of skin and environmental contamination in hospitalized patients with past methicillin-resistant Staphylococcus aureus.

    Guerrero, Dubert M; Wagner, Matthew; Carson, Grace; Hanish, Christine; Thompson, Jody; Orr, Megan; Roth, Felix; Carson, Paul J


    We evaluated hospitalized patients with a history of methicillin-resistant Staphylococcus aureus (MRSA) for persistent colonization and need for contact precautions. Up to 3 daily cultures of nares, skin, and any present wounds were compared with a single nasal polymerase chain reaction (PCR) assay. Most patients (76.2%) were no longer colonized with MRSA. A single PCR assay was sufficient to exclude persistent colonization and environmental contamination and remove the contact precautions.

  17. Quantitative polymerase chain reaction (PCR) assays for a bacterial thiaminase I gene and the thiaminase-producing bacterium Paenibacillus thiaminolyticus.

    Richter, C.A.; Wright-Osment, Maureen K.; Zajicek, J.L.; Honeyfield, D.C.; Tillitt, D.E.


    The thiaminase I enzyme produced by the gram-positive bacterium Paenibacillus thiaminolyticus isolated from the viscera of Lake Michigan alewives Alosa pseudoharengus is currently the only defined source of the thiaminase activity linked to thiamine (vitamin B1) deficiency in early mortality syndrome (EMS) in the larvae of Great Lakes salmonines. Diets of alewife or isolated strains of P. thiaminolyticus mixed in a semipurified diet and fed to lake trout Salvelinus namaycush have been shown to produce EMS in fry. We utilized quantitative polymerase chain reaction (Q-PCR) to aid in studies of the sources of P. thiaminolyticus and thiaminase I. Quantitative PCR assays were established to detect the thiaminase I gene of P. thiaminolyticus, the 16S rRNA gene from most species of bacteria, and the 16S rRNA gene specifically from P. thiaminolyticus and a few closely related taxa. The Q-PCR assays are linear over at least six orders of magnitude and can detect the thiaminase I gene of P. thiaminolyticus from as few as 1,000 P. thiaminolyticus cells/g of sample or the Paenibacillus 16S rRNA gene from as few as 100 P. thiaminolyticus cells/g of sample. The initial results from alewife viscera samples with high thiaminase activity yielded unexpectedly low densities of P. thiaminolyticus cells; Paenibacillus thiaminolyticus was detectable in 2 of 6 alewife viscera tested at densities on the order of 100 cells/g out of 100,000,000 total bacterial cells/g. The low numbers of P. thiaminolyticus detected suggest that alewives contain additional non-P. thiaminolyticus sources of thiaminase activity.

  18. Inhibition of Homo-coupling of Arylboronic Acids in Ligand Free Pd(Ⅱ)-Catalyzed Suzuki Reaction

    TAO,Xiao-Chun; ZHANG,Yue-Ping; HE,Tian-Xiong; SHEN,Dong


    A series of solvents were examined for the ligand free Pd(Ⅱ)-catalyzed Suzuki reaction of 4-bromotoluene with phenylboronic acid. It was found that the PdCl2/i-PrOH system could efficiently inhibit the homo-coupling of phenylboronic acid and give a cross-coupling product in high yields. The substrates with a wide variety of functional groups were tolerated in the system. A possible mechanism for this system was proposed.

  19. Sonogashira coupling reaction of homopropargyl ether with aryl bromides and synthesis of 2,5-disubstituted 3-bromofurans


    This paper presents Sonogashira coupling reaction of aryl bromides with protected homopropargyl alcohols such as tert-butyldimethyl(1-phenylbut-3-ynyloxy)silane and tert-butyldimethyl(1-(2,4-dichlorophenyl)but-3-ynyloxy)silane in piperidine catalyzed by PdCl2/PPh3 without copper(Ⅰ). The coupling products, disubstituted acetylene, are obtained in good or excellent yields. These products can be further used for the synthesis of 2,5-disubstituted 3-bromofurans.

  20. A General,Highly Efficient Ullmann C-O Coupling Reaction under Microwave Irradiation and the Effects of Water

    ZHU,Xin-Hai; CHEN,Gong; MA,Yan; SONG,Hua-Can; XU,Zun-Le; WAN,Yi-Qian


    A general,rapid and highly efficient method for the synthesis of diaryl ethers under the assistance of microwave irradiation was described.A series of diaryl ethers were prepared by direct coupling of phenols and aryl halides in good to excellent yields in anhydrous DMF or NMP at 150℃ within 20 min.The presence of water was found to have a significant impact on the Ullmann C-O coupling reaction between aryl halides and phenols under microwave irradiation.

  1. Spontaneous meningitis due to Streptococcus salivarius subsp. salivarius: cross-reaction in an assay with a rapid diagnostic kit that detected Streptococcus pneumoniae antigens.

    Shirokawa, Taijiro; Nakajima, Jun; Hirose, Kazuhito; Suzuki, Hiromichi; Nagaoka, Shoko; Suzuki, Masatsune


    Streptococcus salivarius subsp. salivarius occasionally causes meningitis associated with iatrogenic or traumatic events. We herein describe a case of meningitis caused by this organism in a patient without any apparent risk factors. In an assay of the patient's cerebrospinal fluid, cross-reaction occurred with Streptococcus pneumoniae antigen-coated latex particles in the Pastorex Meningitis Kit. In the in vitro assays, three of the five clinically isolated S. salivarius strains showed cross-reactions with the kit, indicating that these strains expressed pneumococcal antigen-like antigens. This case shows that meningitis caused by S. salivarius can occur spontaneously and it may sometimes be misdiagnosed as S. pneumoniae infection.

  2. Optimal control of a Cope rearrangement by coupling the reaction path to a dissipative bath or a second active mode

    Chenel, A. [Laboratoire de Chimie Physique, UMR 8000 and CNRS, Université Paris-Sud, F-91405 Orsay (France); Meier, C. [Laboratoire Collisions, Agrégats, Réactivité, UMR 5589, IRSAMC, Université Paul Sabatier, F-31062 Toulouse (France); Dive, G. [Centre d’Ingéniérie des Protéines, Université de Liège, Sart Tilman, B6, B-4000 Liège (Belgium); Desouter-Lecomte, M. [Laboratoire de Chimie Physique, UMR 8000 and CNRS, Université Paris-Sud, F-91405 Orsay (France); Département de Chimie, Université de Liège, Bât B6c, Sart Tilman, B4000 Liège (Belgium)


    We compare the strategy found by the optimal control theory in a complex molecular system according to the active subspace coupled to the field. The model is the isomerization during a Cope rearrangement of Thiele’s ester that is the most stable dimer obtained by the dimerization of methyl-cyclopentadienenylcarboxylate. The crudest partitioning consists in retaining in the active space only the reaction coordinate, coupled to a dissipative bath of harmonic oscillators which are not coupled to the field. The control then fights against dissipation by accelerating the passage across the transition region which is very wide and flat in a Cope reaction. This mechanism has been observed in our previous simulations [Chenel et al., J. Phys. Chem. A 116, 11273 (2012)]. We compare here, the response of the control field when the reaction path is coupled to a second active mode. Constraints on the integrated intensity and on the maximum amplitude of the fields are imposed limiting the control landscape. Then, optimum field from one-dimensional simulation cannot provide a very high yield. Better guess fields based on the two-dimensional model allow the control to exploit different mechanisms providing a high control yield. By coupling the reaction surface to a bath, we confirm the link between the robustness of the field against dissipation and the time spent in the delocalized states above the transition barrier.

  3. Amide as an efficient ligand in the palladium-catalyzed Suzuki coupling reaction in water/ethanol under aerobic conditions

    Hai Yang Liu; Kun Wang; Hai Yan Fu; Mao Lin Yuan; Hua Chen; Rui Xiang Li


    Amide, which is derived from proline and is inexpensive and air-stable, has been synthesized and characterized by 1H NMR,13C NMR, and MS. It was found to be an efficient ligand in the palladium-catalyzed Suzuki cross-coupling reaction. In the Pd/amide catalytic system, aryl bromides can be coupled with phenylboronic acid in ethanol/water (1:2;v/v) in excellent yields even with a low Pd loading of 0.01 mol%. Moreover, the scope of the reaction is broad, and a wide variety of functional groups are tolerant.

  4. A general Suzuki cross-coupling reaction of heteroaromatics catalyzed by nanopalladium on amino-functionalized siliceous mesocellular foam.

    Bratt, Emma; Verho, Oscar; Johansson, Magnus J; Bäckvall, Jan-Erling


    Suzuki-Miyaura cross-coupling reactions of heteroaromatics catalyzed by palladium supported in the cavities of amino-functionalized siliceous mesocellular foam are presented. The nanopalladium catalyst effectively couples not only heteroaryl halides with boronic acids but also heteroaryl halides with boronate esters, potassium trifluoroborates, MIDA boronates, and triolborates, producing a wide range of heterobiaryls in good to excellent yields. Furthermore, the heterogeneous palladium nanocatalyst can easily be removed from the reaction mixture by filtration and recycled several times with minimal loss in activity. This catalyst provides an alternative, environmentally friendly, low-leaching process for the preparation of heterobiaryls.

  5. DABO Boronates: Stable Heterocyclic Boronic Acid Complexes for Use in Suzuki-Miyaura Cross-Coupling Reactions.

    Reilly, Maureen K; Rychnovsky, Scott D


    Diethanolamine complexed heterocyclic boronic acids (DABO boronates) are air-stable reagents that can be used directly in Suzuki-Miyaura reactions in the presence of water or a protic co-solvent. Interestingly, heterocyclic DABO boronates can be stored for extended periods of time at room temperature with no noticeable degradation, unlike their boronic acid counterparts. Heterocyclic DABO boronates constitute an operationally simple and efficient alternative to other boronic acid derivatives as coupling partners in palladium catalyzed cross-coupling reactions under standard Suzuki-Miyaura conditions.

  6. Highly multiplex and sensitive SNP genotyping method using a three-color fluorescence-labeled ligase detection reaction coupled with conformation-sensitive CE.

    Choi, Woong; Jung, Gyoo Yeol


    For the development of clinically useful genotyping methods for SNPs, accuracy, simplicity, sensitivity, and cost-effectiveness are the most important criteria. Among the methods currently being developed for SNP genotyping technology, the ligation-dependent method is considered the simplest for clinical diagnosis. However, sensitivity is not guaranteed by the ligation reaction alone, and analysis of multiple targets is limited by the detection method. Although CE is an attractive alternative to error-prone hybridization-based detection, the multiplex assay process is complicated because of the size-based DNA separation principle. In this study, we employed the ligase detection reaction coupled with high-resolution CE-SSCP to develop an accurate, sensitive, and simple multiplex genotyping method. Ligase detection reaction could amplify ligated products through recurrence of denaturation and ligation reaction, and SSCP could separate these products according to each different structure conformation without size variation. Thus, simple and sensitive SNP analysis can be performed using this method involving the use of similar-sized probes, without complex probe design steps. We found that this method could not only accurately discriminate base mismatches but also quantitatively detect 37 SNPs of the tp53 gene, which are used as targets in multiplex analysis, using three-color fluorescence-labeled probes.

  7. Clinical validation of 3 commercial real-time reverse transcriptase polymerase chain reaction assays for the detection of Middle East respiratory syndrome coronavirus from upper respiratory tract specimens.

    Mohamed, Deqa H; AlHetheel, AbdulKarim F; Mohamud, Hanat S; Aldosari, Kamel; Alzamil, Fahad A; Somily, Ali M


    Since discovery of Middle East respiratory syndrome coronavirus (MERS-CoV), a novel betacoronavirus first isolated and characterized in 2012, MERS-CoV real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assays represent one of the most rapidly expanding commercial tests. However, in the absence of extensive evaluations of these assays on positive clinical material of different sources, evaluating their diagnostic effectiveness remains challenging. We describe the diagnostic performance evaluation of 3 common commercial MERS-CoV rRT-PCR assays on a large panel (n = 234) of upper respiratory tract specimens collected during an outbreak episode in Saudi Arabia. Assays were compared to the RealStar® MERS-CoV RT-PCR (Alton Diagnostics, Hamburg, Germany) assay as the gold standard. Results showed i) the TIB MolBiol® LightMix UpE and Orf1a assays (TIB MolBiol, Berlin, Germany) to be the most sensitive, followed by ii) the Anyplex™ Seegene MERS-CoV assay (Seegene, Seoul, Korea), and finally iii) the PrimerDesign™ Genesig® HCoV_2012 assay (PrimerDesign, England, United Kingdom). We also evaluate a modified protocol for the PrimerDesign™ Genesig® HCoV_2012 assay.

  8. A one-day, dispense-only IP-One HTRF assay for high-throughput screening of Galphaq protein-coupled receptors: towards cells as reagents.

    Bergsdorf, Christian; Kropp-Goerkis, Carmen; Kaehler, Irene; Ketscher, Lars; Boemer, Ulf; Parczyk, Karsten; Bader, Benjamin


    Abstract: Compared to biochemical high-throughput screening (HTS) assays, cell-based functional assays are generally thought to be more time consuming and complex because of additional efforts for running continuous cell cultures as well as the numerous assay steps when transferring media and compounds. A common strategy to compensate the anticipated reduction in overall throughput is to implement highly automated cell culture and screening systems. However, such systems require substantial investments in sophisticated hardware and highly specialized personnel. In trying to set up alternatives to increasing throughput in functional cell-based screening, we combined several approaches. By using (1) cryopreserved cell aliquots instead of continuous cell culture, (2) cells in suspension instead of adherent cells, and (3) "ready-to-screen" assay plates with nanoliter aliquots of test compounds, an assay procedure was developed that very much resembles a standard biochemical, enzymatic assay comprising only a few dispense steps. Chinese hamster ovary cells stably overexpressing a Galphaq-coupled receptor were used as a model system to measure receptor activation by detection of intracellular D-myo-inositol 1-phosphate with the help of homogeneous time-resolved fluorescence (HTRF, CISbio International, Bagnols-sur-Cèze, France). Initially established in 384-well adherent cell format, the assay was successfully transferred to 1,536-well format. The assay quality was sufficient to run HTS campaigns in both formats with good Z'-factors and excellent reproducibility of antagonists. Subsequently, the assay procedure was optimized for usage of suspension cells. The influences of cell culture media, plate type, cell number, and incubation time were assessed. Finally, the suspension cell assay was applied to pharmacological characterization of a small molecule antagonist by Schild plot analysis. Our data demonstrate not only the application of the IP-One HTRF assay (CISbio

  9. Coupling ex vivo electroporation of mouse retinas and luciferase reporter assays to assess rod-specific promoter activity.

    Boulling, Arnaud; Escher, Pascal


    Ex vivo electroporation of mouse retinas is an established tool to modulate gene expression and to study cell type-specific gene expression. Here we coupled ex vivo electroporation to luciferase reporter assays to facilitate the study of rod-photoreceptor-specific gene promoters. The activity of the rod-specific proximal bovine rhodopsin promoter was significantly increased in C57BL/6J wild-type retinas at postnatal days 1 and 7 by 3.4-fold and 8.7-fold respectively. In C57BL/6J Nr2e3(rd7/rd7) retinas, where the rod photoreceptor-specific nuclear receptor Nr2e3 is not expressed, a significant increase by 2.5-fold was only observed at postnatal day 7. Cone-specific S-opsin promoter activity was not modulated in C57BL/6J wild-type and Nr2e3(rd7/rd7) retinas. Taken together, we describe an easily implementable protocol to assess rod-specific promoter activity in a physiological context resembling that of the developing postnatal mouse retina.

  10. Establishment and Application of a TaqMan Real-Time Quantitative Reverse Transcription-Polymerase Chain Reaction Assay for Rubella Virus RNA

    Li-Hong ZHAO; Yu-Yan MA; Hong WANG; Shu-Ping ZHAO; Wei-Ming ZHAO; Hua LI; Lei-Yi WANG


    The aim of this study was to establish and apply a real-time quantitative reverse transcription polymerase chain reaction (RT-PCR) for rubella virus (RV) RNA. First, the primer and TaqMan probe concentrations, as well as reaction temperatures were optimized to establish an efficient real-time quantitative RT-PCR assay for RV RNA. Next, an RV-specific PCR amplicon was made as an external standard to estimate the linearity, amplification efficiency, analytical sensitivity and reproducibility of the real time quantitative assay. Finally, the assay was applied to quantify RVRNA in clinical samples for rubella diagnosis.The RV-specific PCR amplicon was prepared for evaluation of the assay at 503 bp, and its original concentration was 2.75×109 copies/μl. The real time quantitative assay was shown to have good linearity (R2=0.9920), high amplification efficiency (E=1.91), high sensitivity (275 copies/ml), and high reproducibility (variation coefficient range, from 1.25% to 3.58%). Compared with the gold standard, the specificity and sensitivity of the assay in clinical samples was 96.4% and 86.4%, respectively. Therefore, the established quantitative RT-PCR method is a simple, rapid, less-labored, quantitative, highly specific and sensitive assay for RV RNA.


    CHEN Min; CHEN Xiaonong; YUAN Xinhua; ZHANG Yan; ZHANG Chunyan; LIU Hua; DAI Qixun


    To obtain new functional aromatic polymer material. 3.3'-biacenophthene. which is used as macrotnolecule intermediate of function aromatic polymer material. was synthesized through the coupling reaction of acenaphthene catalyzing by ionic liquid (/bmim/Cl/FeCl3) at mild reaction condition. Pure 3,3' -biacenaphthene was obtained by recrystalling and column chromatography from the reaction mixture, and was determined by GC/MS. 1HNMR and FTIR analysis. The influence of various reaction conditions on the yield of 3,3'-biacenaphthene were studied by GC analysis. The result shows that the optimun synthesis conditions of the coupling reaction are as following: the molar ratio of FeCl3 to [Bmim]Cl being 3. the mole ratio of FeCl3 in [Bmim]Cl/FeCl3 to acenaphthene being 4. the reaction temperature being 20 ℃, the reaction time being 4h and the solvent of the reaction system being PhNO2. Under those conditions, the yield of the 3,3'-biacenaphthene will be 48.71% and selectivity of that will be 78.56 %. Further more.[bmim ]Cl/FeCl3 has no pollution to environments and can be reused.

  12. Translation of a laboratory-validated equine herpesvirus-1 specific real-time PCR assay into an insulated isothermal polymerase chain reaction (iiPCR) assay for point-of-need diagnosis using POCKIT™ nucleic acid analyzer.

    Balasuriya, Udeni B R; Lee, Pei-Yu Alison; Tsai, Yun-Long; Tsai, Chuan-Fu; Shen, Yu-Han; Chang, Hsiao-Fen Grace; Skillman, Ashley; Wang, Hwa-Tang Thomas; Pronost, Stéphane; Zhang, Yan


    Equine herpesvirus myeloencephalopathy (EHM), a major problem for the equine industry in the United States, is caused by equine herpesvirus-1 (EHV-1). In addition, EHV-1 is associated with upper respiratory disease, abortion, and chorioretinal lesions in horses. Here we describe the development and evaluation of an inexpensive, user-friendly insulated isothermal PCR (iiPCR) method targeting open reading 30 (ORF30) to detect both neuropathogenic and non-neuropathogenic strains on the field-deployable POCKIT™ device for point-of-need detection of EHV-1. The analytical sensitivity of the EHV-1 iiPCR assay was 13 genome equivalents per reaction. The assay did not cross react with ten non-target equine viral pathogens. Performance of the EHV-1 iiPCR assay was compared to two previously described real-time PCR (qPCR) assays in two laboratories by using 104 archived clinical samples. All 53 qPCR-positive and 46 of the 51 qPCR-negative samples tested positive and negative, respectively, by the iiPCR. The agreement between the two assays was 95.19% (confidence interval 90.48-99.90%) with a kappa value of 0.90. In conclusion, the newly developed EHV-1 iiPCR assay is robust to provide specificity and sensitivity comparable to qPCR assays for the detection of EHV-1 nucleic acid in clinical specimens.

  13. Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations

    Flegga, Mark B.; Hellander, Stefan; Erban, Radek


    In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a “ghost cell” in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: (i) Δt → 0 and h is fixed; (ii) Δt → 0 and h → 0 such that √Δt/h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model. PMID:26568640

  14. Development of a universal high-throughput calcium assay for G-protein-coupled receptors with promiscuous G-protein Gα15/16

    Ting ZHU; Li-yan FANG; Xin XIE


    Aim:To develop a universal high-throughput screening assay based on Gα15/16-mediated calcium mobilization for the identification of novel modulators of G-protein-coupled receptors (GPCR). Methods:In the present study, CHO-K1 or HEK293 cells were co-transfected with plasmids encoding promiscuous G-protein Cα15/16 and various receptors originally coupled to Gαs, Gαi, or Gαq pathways. Intracellular calcium change was monitored with fluorescent dye Fluo-4. Results:We found out for all the receptors tested, Gα15/16 could shift the receptors' coupling to the calcium mobilization pathway, and the EC50 values of the ligands generated with this method were comparable with reported values that were ob-tained using traditional methods. This assay was validated and optimized with the δ-opioid receptor, which originally coupled to God and was recently found to play important roles in neurodegenerative and autoimmune diseases. A large-scale screening of 48 000 compounds was performed based on this system. Sev-eral new modulators were identified and confirmed with the traditional GTPγS binding assay. Conclusion:This cell-based calcium assay was proved to be robust and easy to automate, and could be used as a universal method in search-ing for GPCR modulators.

  15. Polymerase chain reaction assay of ureaplasma strains isolated from high vaginal swabs of women in Ibadan, Nigeria.

    Agbakoba, N R; Adetosoye, A I; Adesina, O A; Adewole, I F


    Human ureaplasma previously had one species known as Ureaplasma urealyticum but was recently separated into 2 species, U. urealyticum and U. parvum. This study was carried out to separate the ureaplasma strains isolated from women attending a tertiary-care hospital in Nigeria. Thirty (30) Ureaplasma strains isolated from the vaginal tracts of 13 pregnant and 17 non-pregnant women were assayed. The polymerase chain reaction (PCR) technique was employed using two primer pairs: UMS-170/UMA-263 specific for U. urealyticum and UMS-57/UMA-222 specific for U. parvum. The positivity bands of the primer pairs were 476 bp and 326 bp for U. urealyticum and U. parvum respectively. All isolates were found to be U. urealyticumn (100%). Eleven (84.6%) of the 13 U. urealyticum from pregnant women were from asymptomatic women while from the non-pregnant women; 6 (35.3%) were from women with complaint of infertility problems; 5 (29.4%) from those who complained of vaginal discharge, one (5.9%) was asymptomatic while the remaining 5 (29.4%) had various other complaints. U. urealyticum is thus the prevalent species of Ureaplasma among pregnant and non-pregnant women in the study population and this to the best of our knowledge is a pioneer study to speciate human ureaplasmas in this country.

  16. Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis.

    Roca, Maite; De Maria, Leonardo; Wodak, Shoshana J; Moliner, Vicente; Tuñón, Iñaki; Giraldo, Jesús


    To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gchi) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2 '. Similar energetic profiles featuring two minima corresponding to the anti and syn Gchi regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of approximately 4 kcal/mol were obtained for the anti --> syn transition. Structural analysis showed a remarkable sensitivity of the phosphate moiety to the conformation of the Gchi angle, suggesting a possible connection between this conformation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O2 '--P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O2'. The simulations revealed that the O2 ' attack along the syn Gchi was more favorable than that along the anti Gchi: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the O--P bond formation; structurally, a lesser O2 '--P initial distance, and a better suited orientation for an in-line attack was observed in the syn relative to the anti conformation. These results are consistent with the catalytically competent conformation of barnase-ribonucleotide complex, which requires a guanine syn conformation of the substrate to enable abstraction of the ribose H2 ' proton by the general base Glu73, thereby suggesting a coupling between the reactive substrate conformation and enzyme structure

  17. Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

    Jinsong Liu [Royal Institute of Technology, Stockholm (Sweden). Dept. of Chemical Engineering and Technology


    Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10{sup 5} years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10{sup 5} years.

  18. Fusion and neutron transfer reactions with weakly bound nuclei within time-dependent and coupled channel approaches

    Samarin, V. V.


    The time-dependent Schrödinger equation and the coupled channel approach based on the method of perturbed stationary two-center states are used to describe nucleon transfers and fusion in low-energy nuclear reactions. Results of the cross sections calculation for the formation of the 198Au and fusion in the 6He+197Au reaction and for the formation of the 65Zn in 6He+64Zn reaction agree satisfactorily with the experimental data near the barrier. The Feynman's continual integrals calculations for a few-body systems were used for the proposal of the new form of the shell model mean field for helium isotopes.

  19. Synthesis of C-4 Substituted Amido Nicotine Derivatives via Copper(I)- and (II)-Catalyzed Cross-Coupling Reactions.

    Zhu, Jiancheng; Enamorado, Monica F; Comins, Daniel L


    The syntheses of seven novel amido nicotine derivatives 12-18 from (S)-nicotine are presented. (S)-Nicotine and (S)-6-chloronicotine derivatives were cross-coupled with the corresponding amides 6-10 at the C-4 position of the pyridine ring via copper(I)-mediated reactions. Derivatives 16-18 were also obtained via copper(II)-mediated reactions from (S)-nicotine containing a C-4 boronic acid pinacol ester group. The optimization of reaction conditions for both routes provided a useful method for preparing C-4 amide-containing nicotine analogs.

  20. Kinetic Studies of Oxidative Coupling of Methane Reaction on Model Catalysts

    Khan, Abdulaziz M.


    With the increasing production of natural gas as a result of the advancement in the technology, methane conversion to more valuable products has become a must. One of the most attractive processes which allow the utilization of the world’s most abundant hydrocarbon is the oxidative coupling. The main advantage of this process is the ability of converting methane into higher paraffins and olefins (primarily C2) in a direct way using a single reactor. Nevertheless, low C2+ yields have prevented the process to be commercialized despite the fact that great number of attempts to prepare catalysts were conducted so that it can be economically viable. Due to these limitations, understanding the mechanism and kinetics of the reaction can be utilized in improving the catalysts’ performance. The reaction involves the formation of methyl radicals that undergo gas-phase radical reactions. CH4 activation is believed to be done the surface oxygen species. However, recent studies showed that, in addition to the surface oxygen mediated pathway, an OH radical mediated pathway have a large contribution on the CH4 activation. The experiments of Li/MgO, Sr/La2O3 and NaWO4/SiO2 catalysts revealed variation of behavior in activity and selectivity. In addition, water effect analysis showed that Li/MgO deactivate at the presence of water due to sintering phenomena and the loss of active sites. On the other hand, negative effect on the C2 yield and CH4 conversion rate was observed with Sr/La2O3 with increasing the water partial pressure. Na2WO4/SiO2 showed a positive behavior with water in terms of CH4 conversion and C2 yield. In addition, the increment in CH4 conversion rate was found to be proportional with PO2 ¼ PH2O ½ which is consistent with the formation of OH radicals and the OH-mediated pathway. Experiments of using ring-dye laser, which is used to detect OH in combustion experiments, were tried in order to detect OH radicals in the gas-phase of the catalyst. Nevertheless

  1. Conservation laws and path-independent integrals in mechanical-diffusion-electrochemical reaction coupling system

    Yu, Pengfei; Wang, Hailong; Chen, Jianyong; Shen, Shengping


    In this study, the conservation laws οf dissipative mechanical-diffusion-electrochemical reaction system are systematically obtained based on Noether's theorem. According to linear, irreversible thermodynamics, dissipative phenomena can be described by an irreversible force and an irreversible flow. Additionally, the Lagrange function, L and the generalized Hamilton least-action principle are proposed to be used to obtain the conservation integrals. A group of these integrals, including the J-, M-, and L-integrals, can be then obtained using the classical Noether approach for dissipative processes. The relation between the J-integral and the energy release rate is illustrated. The path-independence of the J-integral is then proven. The J-integral, derived based on Noether's theorem, is a line integral, contrary to the propositions of existing published works that describe it both as a line and an area integral. Herein, we prove that the outcomes are identical, and identify the physical meaning of the area integral, a concept that was not explained previously. To show that the J-integral can dominate the distribution of the corresponding field quantities, an example of a partial, stress-diffusion coupling process is disscussed.

  2. Element fingerprinting of marine organisms by dynamic reaction cell inductively coupled plasma mass spectrometry.

    Cubadda, Francesco; Raggi, Andrea; Coni, Ettore


    A method for the determination of sixteen elements (Al, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Se, Sn, V, Zn) in seafood by dynamic reaction cell inductively coupled plasma mass spectrometry (ICP-DRC-MS) is presented. A preliminary study of polyatomic interferences was carried out in relation to the chemical composition of marine organisms belonging to different taxa. Acid effects and other matrix effects in marine organisms submitted to closed-vessel microwave digestion were investigated as well. Ammonia was the reactive gas used in the DRC to remove polyatomic ions interfering with 27Al, 52Cr, 56Fe and 51V. Optimal conditions for the simultaneous determination of analytes were identified in order to develop a fast multielement method. A suite of real samples (mussels and various fish species) were used during method development along with three certified reference materials: BCR CRM 278R (mussel tissue), BCR CRM 422 (cod muscle) and DORM-2 (dogfish muscle). The proposed analytical approach can be used in conjunction with suitable chemometric procedures to address quality and safety issues in aquaculture and fisheries. As an example, a case study is described in which mussels from three farming sites in the Venice Lagoon were distinguished by multivariate analysis of element fingerprints.

  3. Phenylenevinylene oligomers by Mizoroki-Heck cross coupling reaction. Structural and optoelectronic characterization

    Estrada, Sandra E.; Ochoa-Puentes, Cristian; Sierra, Cesar A.


    In order to study the effect of the molecular structure on the optical properties of totally trans-trans phenylenevinylene oligomers (OPVs), sixteen 1,4-distyrylbenzene derivatives (1a-i and 2a-g) functionalized with different electron-donating (ED) and electron-withdrawing (EW) groups were synthesized by the Mizoroki-Heck cross coupling reaction in moderate to good yields (40-95%). The implemented methodology, with a small modification previously reported by our group, allows obtaining the desired vinyl configuration as well as one novel OPV compound (1h). After structural characterization by several techniques (e.g. FTIR, 1H, 13C and Solid-State NMR), particular emphasis was placed upon the investigation of their optical properties by UV-vis and fluorescence spectroscopies. The results showed that, with only one exception, the ED and EW groups at the ends of OPV systems lead to a bathochromic shift. This effect is intensified with the introduction of methoxy groups on the central ring. Consistent with these, the HOMO-LUMO gaps (ΔE) decreases as the strength of ED and EW substituents increases. The ED and EW substituents also lead to a decrease in the Φf values. This contribution in the area of organic electronics can be used as a reference to better select the most appropriate technological application for each OPV and this can be extrapolated to their respective structurally analogous segmented polymer.

  4. Coupled reactions on bioparticles: Stereoselective reduction with cofactor regeneration on PhaC inclusion bodies.

    Spieler, Valerie; Valldorf, Bernhard; Maaß, Franziska; Kleinschek, Alexander; Hüttenhain, Stefan H; Kolmar, Harald


    Chiral alcohols are important building blocks for specialty chemicals and pharmaceuticals. The production of chiral alcohols from ketones can be carried out stereo selectively with alcohol dehydrogenases (ADHs). To establish a process for cost-effective enzyme immobilization on solid phase for application in ketone reduction, we used an established enzyme pair consisting of ADH from Rhodococcus erythropolis and formate dehydrogenase (FDH) from Candida boidinii for NADH cofactor regeneration and co-immobilized them on modified poly-p-hydroxybutyrate synthase (PhaC)-inclusion bodies that were recombinantly produced in Escherichia coli cells. After separate production of genetically engineered and recombinantly produced enzymes and particles, cell lysates were combined and enzymes endowed with a Kcoil were captured on the surface of the Ecoil presenting particles due to coiled-coil interaction. Enzyme-loaded particles could be easily purified by centrifugation. Total conversion of 4'-chloroacetophenone to (S)-4-chloro-α-methylbenzyl alcohol could be accomplished using enzyme-loaded particles, catalytic amounts of NAD(+) and formate as substrates for FDH. Chiral GC-MS analysis revealed that immobilized ADH retained enantioselectivity with 99 % enantiomeric excess. In conclusion, this strategy may become a cost-effective alternative to coupled reactions using purified enzymes.

  5. An analysis of model proton-coupled electron transfer reactions via the mixed quantum-classical Liouville approach.

    Shakib, Farnaz A; Hanna, Gabriel


    The nonadiabatic dynamics of model proton-coupled electron transfer (PCET) reactions is investigated for the first time using a surface-hopping algorithm based on the solution of the mixed quantum-classical Liouville equation (QCLE). This method provides a rigorous treatment of quantum coherence/decoherence effects in the dynamics of mixed quantum-classical systems, which is lacking in the molecular dynamics with quantum transitions surface-hopping approach commonly used for simulating PCET reactions. Within this approach, the protonic and electronic coordinates are treated quantum mechanically and the solvent coordinate evolves classically on both single adiabatic surfaces and on coherently coupled pairs of adiabatic surfaces. Both concerted and sequential PCET reactions are studied in detail under various subsystem-bath coupling conditions and insights into the dynamical principles underlying PCET reactions are gained. Notably, an examination of the trajectories reveals that the system spends the majority of its time on the average of two coherently coupled adiabatic surfaces, during which a phase enters into the calculation of an observable. In general, the results of this paper demonstrate the applicability of QCLE-based surface-hopping dynamics to the study of PCET and emphasize the importance of mean surface evolution and decoherence effects in the calculation of PCET rate constants.

  6. Nickel-catalyzed cross-coupling reactions of benzylic zinc reagents with aromatic bromides, chlorides and tosylates.

    Schade, Matthias A; Metzger, Albrecht; Hug, Stephan; Knochel, Paul


    Benzylic zinc reagents prepared by direct insertion of zinc to benzylic chlorides in the presence of LiCl undergo smooth cross-coupling reactions with aromatic chlorides, bromides and tosylates using Ni(acac)(2) and PPh(3) as a catalyst system.

  7. Highly efficient coupling of beta-substituted aminoethane sulfonyl azides with thio acids, toward a new chemical ligation reaction.

    Merkx, Remco; Brouwer, Arwin J; Rijkers, Dirk T S; Liskamp, Rob M J


    [reaction: see text] A highly efficient coupling of protected beta-substituted aminoethane sulfonyl azides with thio acids is reported. In the case of peptide thio acids, this method encompasses a new chemoselective ligation method. Furthermore, the resulting alpha-amino acyl sulfonamides can be alkylated with suitable electrophiles to obtain densely functionalized sulfonamide scaffolds.

  8. The coupling effect of gas-phase chemistry and surface reactions on oxygen permeation and fuel conversion in ITM reactors

    Hong, Jongsup


    © 2015 Elsevier B.V. The effect of the coupling between heterogeneous catalytic reactions supported by an ion transport membrane (ITM) and gas-phase chemistry on fuel conversion and oxygen permeation in ITM reactors is examined. In ITM reactors, thermochemical reactions take place in the gas-phase and on the membrane surface, both of which interact with oxygen permeation. However, this coupling between gas-phase and surface chemistry has not been examined in detail. In this study, a parametric analysis using numerical simulations is conducted to investigate this coupling and its impact on fuel conversion and oxygen permeation rates. A thermochemical model that incorporates heterogeneous chemistry on the membrane surface and detailed chemical kinetics in the gas-phase is used. Results show that fuel conversion and oxygen permeation are strongly influenced by the simultaneous action of both chemistries. It is shown that the coupling somewhat suppresses the gas-phase kinetics and reduces fuel conversion, both attributed to extensive thermal energy transfer towards the membrane which conducts it to the air side and radiates to the reactor walls. The reaction pathway and products, in the form of syngas and C2 hydrocarbons, are also affected. In addition, the operating regimes of ITM reactors in which heterogeneous- or/and homogeneous-phase reactions predominantly contribute to fuel conversion and oxygen permeation are elucidated.

  9. Stereoselective Synthesis of 1,3-Enynylstannanes via Palladium Catalyzed Cross-Coupling Reactions of (Z)-α-Bromovinylstannanes

    蔡明中; 章荣立; 赵红


    Based on the different reactivity of stannyl and bromo groups, (Z)-α-bromovinylstannanes can undergo the cross-coupling reaction with alkynyl Grignard reagents in the presence of tetrakis(triphenylphosphine)palladium(0)catalyst in THF at room temperature to afford stereoselectively 1,3-enynylstannanes in good yields.

  10. Charge-transfer reaction of 1,4-benzoquinone with crizotinib: spectrophotometric study, computational molecular modeling and use in development of microwell assay for crizotinib.

    Darwish, Ibrahim A; Alshehri, Jamilah M; Alzoman, Nourah Z; Khalil, Nasr Y; Abdel-Rahman, Hamdy M


    The reaction of 1,4-benzoquinone (BQ) with crizotinib (CZT); a novel drug used for treatment of non-small cell lung cancer) was investigated in different solvents of varying dielectric constants and polarity indexes. The reaction resulted in the formation of a red-colored product. Spectrophotometric investigations confirmed that the reaction proceeded through charge-transfer (CT) complex formation. The molar absorptivity of the complex was found to be linearly correlated with the dielectric constant and polarity index of the solvent; the correlation coefficients were 0.9425 and 0.8340, respectively. The stoichiometric ratio of BQ:CZT was found to be 2:1 and the association constant of the complex was found to be 0.26×10(3)lmol(-1). The kinetics of the reaction was studied; the order of the reaction, rate and rate constant were determined. Computational molecular modeling for the complex between BQ and CZT was conducted, the sites of interaction on CZT molecule were determined, and the mechanism of the reaction was postulated. The reaction was employed as a basis in the development of a novel 96-microwell assay for CZT. The assay limits of detection and quantitation were 5.2 and 15.6μgml(-1), respectively. The assay was validated as per the guidelines of the International Conference on Harmonization (ICH) and successfully applied to the analysis of CZT in its bulk and capsules with good accuracy and precision. The assay has high throughput and consumes minimum volume of organic solvent thus it reduces the exposures of the analysts to the toxic effects of organic solvents, and significantly reduces the analysis cost. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. A multiplex real-time polymerase chain reaction (TaqMan) assay for the simultaneous detection of Meloidogyne chitwoodi and M-fallax

    Zijlstra, C.; Hoof, van R.A.


    This study describes a multiplex real-time polymerase chain reaction (PCR) approach for the simultaneous detection of Meloidogyne chitwoodi and M. fallax in a single assay. The approach uses three fluorogenic minor groove binding (MGB) TaqMan probes: one FAM-labeled to detect M. chitwoodi, one VIC-l

  12. Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

    Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.


    Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs

  13. Detection of Babesia canis vogeli and Hepatozoon canis in canine blood by a single-tube real-time fluorescence resonance energy transfer polymerase chain reaction assay and melting curve analysis.

    Kongklieng, Amornmas; Intapan, Pewpan M; Boonmars, Thidarut; Thanchomnang, Tongjit; Janwan, Penchom; Sanpool, Oranuch; Lulitanond, Viraphong; Taweethavonsawat, Piyanan; Chungpivat, Sudchit; Maleewong, Wanchai


    A real-time fluorescence resonance energy transfer polymerase chain reaction (qFRET PCR) coupled with melting curve analysis was developed for detection of Babesia canis vogeli and Hepatozoon canis infections in canine blood samples in a single tube assay. The target of the assay was a region within the 18S ribosomal RNA gene amplified in either species by a single pair of primers. Following amplification from the DNA of infected dog blood, a fluorescence melting curve analysis was done. The 2 species, B. canis vogeli and H. canis, could be detected and differentiated in infected dog blood samples (n = 37) with high sensitivity (100%). The detection limit for B. canis vogeli was 15 copies of a positive control plasmid, and for H. canis, it was 150 copies of a positive control plasmid. The assay could simultaneously distinguish the DNA of both parasites from the DNA of controls. Blood samples from 5 noninfected dogs were negative, indicating high specificity. Several samples can be run at the same time. The assay can reduce misdiagnosis and the time associated with microscopic examination, and is not prone to the carryover contamination associated with the agarose gel electrophoresis step of conventional PCR. In addition, this qFRET PCR method would be useful to accurately determine the range of endemic areas or to discover those areas where the 2 parasites co-circulate.

  14. An emerging reactor technology for chemical synthesis: surface acoustic wave-assisted closed-vessel Suzuki coupling reactions.

    Kulkarni, Ketav; Friend, James; Yeo, Leslie; Perlmutter, Patrick


    In this paper we demonstrate the use of an energy-efficient surface acoustic wave (SAW) device for driving closed-vessel SAW-assisted (CVSAW), ligand-free Suzuki couplings in aqueous media. The reactions were carried out on a mmolar scale with low to ultra-low catalyst loadings. The reactions were driven by heating resulting from the penetration of acoustic energy derived from RF Raleigh waves generated by a piezoelectric chip via a renewable fluid coupling layer. The yields were uniformly high and the reactions could be executed without added ligand and in water. In terms of energy density this new technology was determined to be roughly as efficient as microwaves and superior to ultrasound.

  15. Development of real-time polymerase chain reaction assay for specific detection of Tsukamurella by targeting the 16S rRNA gene.

    Yassin, Atteyet F; Müller, Jens


    Recently, members of the genus Tsukamurella have been implicated as important etiologic pathogens contributing to bloodstream and pulmonary infections in immunocompromised patients. Tsukamurella species share many features with other mycolic acid-containing genera of the order Actinomycetales and might therefore be misidentified as belonging to one of these genera. We developed a TaqMan-based real-time polymerase chain reaction assay for the rapid and specific detection of infections due to Tsukamurella species. The assay amplifies and detects a 157-bp segment of the 16S rRNA gene of Tsukamurella. The specificity of the assay was confirmed using a panel of DNAs from 12 Tsukamurella strains and 11 strains belonging to 8 phylogenetic closely related genera. The sensitive and specific nature of the assay provides a valuable tool for the early and precise diagnosis of Tsukamurella infections in clinical diagnostic laboratories. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Detection of egg drop syndrome virus antigen or genome by enzyme-linked immunosorbent assay or polymerase chain reaction.

    Dhinakar Raj, G; Sivakumar, S; Matheswaran, K; Chandrasekhar, M; Thiagarajan, V; Nachimuthu, K


    Mouse monoclonal antibodies (mAbs) were produced against an Indian isolate of egg drop syndrome (EDS) virus and characterized. Four hybridoma clones were secreting mAbs that bound to a 100 kDa protein, presumably the hexon protein. These mAbs were found to cross-react with two other Indian isolates of EDS virus and to the reference UK 127 strain. Three of these mAbs were mapped to the same epitope compared with the other mAb (F8), which bound to a different epitope. An antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) was developed using the F8 mAbs as capture antibody and polyclonal chicken serum against EDS virus as detection antibody. A polymerase chain reaction (PCR) was used to detect the EDS viral genome. Following experimental infection of oestrogen-treated chickens with EDS virus, cloacal swabs, oviduct, uterus and spleen were collected at different days post-infection and used in both AC-ELISA and PCR, directly and after a single passage in embryonated duck eggs. The sensitivity and specificity of antigen detection by AC-ELISA or PCR was 95% and 98%, respectively. For diagnosis of EDS viral infections, PCR is recommended due to its ease and the lack of requirement of prepared reagents such as mAbs or conjugates. We recommend that PCR be performed directly on boiled tissue homogenates. Any negative samples may be passaged in embryonated duck eggs and the allantoic fluids tested by PCR before a conclusive negative diagnosis is given.

  17. Nested real-time quantitative polymerase chain reaction assay for detection of hepatitis B virus covalently closed circular DNA

    XU Chun-hai; LI Zhao-shen; DAI Jun-ying; ZHU Hai-yang; YU Jian-wu; L(U) Shu-Ian


    peripheral blood mononuclear cells; marrow mononuclear cells Background Successful treatment of hepatitis B can be achieved only if the template for hepatitis B virus (HBV) DNA replication, the covalently closed circular HBV DNA (cccDNA) can be completely cleared. To date, detecting cccDNA remains clinically challenging. The purpose of this study was to develop a nested real-time quantitative polymerase chain reaction (PCR) assay for detecting HBV cccDNA in peripheral blood mononuclear cells (PBMCs) and bone marrow mononuclear cells (MMNCs).Methods Based on the structural differences between HBV cccDNA and HBV relaxed circular DNA (rcDNA), two pairs of primers were synthesized as well as a downstream TaqMan probe. Blood and bone marrow samples were collected from hepatitis B patients and healthy controls. To remove rcDNA, samples were incubated with mung bean nuclease and the resultant purified HBV cccDNA was then amplified by nested real-time fluorescence quantitative PCR. The cccDNA levels were calculated using a positive standard.Results The nested real-time fluorescence quantitative PCR method for HBV cccDNA was successful, with a linear range of 3.0x102 copies/ml to 3.9x108 copies/ml. Of the 25 PBMC samples and 7 MMNC samples obtained from chronic hepatitis B or liver cirrhosis patients, 3 MMNC samples and 9 PBMC samples were positive for HBV cccDNA, while all of the 21 PBMC samples from healthy controls were negative.Conclusion The nested real-time fluorescence quantitative PCR may be used as an important tool for detecting cccDNA in hepatitis B patients.

  18. A Rapid Field-Deployable Reverse Transcription-Insulated Isothermal Polymerase Chain Reaction Assay for Sensitive and Specific Detection of Bluetongue Virus.

    Ambagala, A; Pahari, S; Fisher, M; Lee, P-Y A; Pasick, J; Ostlund, E N; Johnson, D J; Lung, O


    Bluetongue is a non-contagious, haemorrhagic, Culicoides-borne disease of ruminants. The causative agent, bluetongue virus (BTV), is a member of the Orbivirus genus of the Reoviridae family. So far, 26 BTV serotypes have been identified worldwide. The global distribution of bluetongue has been expanding, and rapid detection of BTV, preferably in the field, is critical for timely implementation of animal movement restrictions and vector control measures. To date, many laboratory-based, molecular assays for detection of BTV have been developed. These methods require the samples to be shipped to a central laboratory with sophisticated instruments and highly skilled technicians to perform the assays, conduct analyses and interpret the results. Here, we report the development and evaluation of a rapid, portable, user-friendly, pan-BTV reverse transcription-insulated isothermal polymerase chain reaction (RT-iiPCR) assay that can potentially be used in low-resource field conditions. The total length of the assay was <60 min, and at the end of the assay, the results were automatically displayed as '+' or '-' without the need for data interpretation. The RT-iiPCR assay detected 36 BTV isolates and two in vitro transcribed RNA samples representing all 26 BTV serotypes. The assay did not cross-react with other animal viruses tested, including two closely related orbiviruses. The analytical sensitivity of the assay was as low as nine copies of in vitro transcribed double-stranded BTV RNA. Analysis of BTV-infected whole blood samples showed that the BTV RT-iiPCR assay was as sensitive as real-time RT-PCR. The assay can potentially be used for rapid screening of animals for BTV in routine diagnostics and for monitoring bluetongue outbreaks both in ruminants and in Culicoides vectors in the field and in the laboratory.

  19. Detection of the Pandemic H1N1/2009 Influenza A Virus by a Highly Sensitive Quantitative Real-time Reverse-transcription Polymerase Chain Reaction Assay

    Zhu Yang; Guoliang Mao; Yujun Liu; Yuan-Chuan Chen; Chengjing Liu; Jun Luo; Xihan Li


    A quantitative real time reverse-transcription polymerase chain reaction (qRT-PCR) assay with specific primers recommended by the World Health Organization (WHO) has been widely used successfully for detection and monitoring of the pandemic H1N 1/2009 influenza A virus.In this study,we report the design and characterization of a novel set of primers to be used in a qRT-PCR assay for detecting the pandemic H1N1/2009 virus.The newly designed primers target three regions that are highly conserved among the hemagglutinin (HA) genes of the pandemic H1N1/2009 viruses and are different from those targeted by the WHO-recommended primers.The qRT-PCR assays with the newly designed primers are highly specific,and as specific as the WHO-recommended primers for detecting pandemic H1N1/2009 viruses and other influenza viruses including influenza B viruses and influenza A viruses of human,swine,and raccoon dog origin.Furthermore,the qRT-PCR assays with the newly designed primers appeared to be at least 10-fold more sensitive than those with the WHO-recommended primers as the detection limits of the assays with our primers and the WHO-recommended primers were 2.5 and 25 copies of target RNA per reaction,respectively.When tested with 83 clinical samples,32 were detected to be positive using the qRT-PCR assays with our designed primers,while only 25 were positive by the assays with the WHO-recommended primers.These results suggest that the qRT-PCR system with the newly designed primers represent a highly sensitive assay for diagnosis of the pandemic H1N1/2009 virus infection.

  20. Understanding the Effects of Roasting on Antioxidant Components of Coffee Brews by Coupling On-line ABTS Assay to High Performance Size Exclusion Chromatography.

    Opitz, Sebastian E W; Goodman, Bernard A; Keller, Marco; Smrke, Samo; Wellinger, Marco; Schenker, Stefan; Yeretzian, Chahan


    Coffee is a widely consumed beverage containing antioxidant active compounds. During roasting the phytochemical composition of the coffee bean changes dramatically and highly polymeric substances are produced. Besides chlorogenic acids that are already present in green coffee beans, melanoidins show antioxidant capacity as well. To employ post-column derivatisation by coupling high performance size exclusion chromatography (HPSEC) to an antioxidant assay to investigate the effect of roasting on the properties of antioxidant active compounds in coffee brews. We have investigated the antioxidant capacity of Coffea arabica (Arabica) and C. canephora (Robusta) beans that were roasted over the full spectrum of roast conditions (four roasting speeds to three roast degrees) by comparing the results from HPSEC coupled on-line to the ABTS assay with those from two batch assays, Folin Ciocalteu (FC) and oxygen radical absorbance capacity (ORAC) assay. The antioxidant capacity showed a general decrease towards slower and darker roasted coffee for all three assays, indicative of heat degradation of active compounds. Hence, low molecular weight (LMW) compounds such as chlorogenic acids (CGAs) decreased progressively already from relatively mild roasting conditions. In contrast, high molecular weight (HMW) compounds (e.g. melanoidins) increased from light to dark roast degrees with lowering magnitude towards slower roasting profiles. By coupling HPSEC on-line to the ABTS assay we were able to separately quantify the contribution of HMW and LMW compounds to the total antioxidant capacity, increasing our understanding of the roast process. © 2016 The Authors. Phytochemical Analysis Published by John Wiley & Sons Ltd. © 2016 The Authors. Phytochemical Analysis Published by John Wiley & Sons Ltd.

  1. Understanding the Effects of Roasting on Antioxidant Components of Coffee Brews by Coupling On‐line ABTS Assay to High Performance Size Exclusion Chromatography

    Opitz, Sebastian E.W.; Goodman, Bernard A.; Keller, Marco; Smrke, Samo; Wellinger, Marco; Schenker, Stefan


    Abstract Introduction Coffee is a widely consumed beverage containing antioxidant active compounds. During roasting the phytochemical composition of the coffee bean changes dramatically and highly polymeric substances are produced. Besides chlorogenic acids that are already present in green coffee beans, melanoidins show antioxidant capacity as well. Objective To employ post‐column derivatisation by coupling high performance size exclusion chromatography (HPSEC) to an antioxidant assay to investigate the effect of roasting on the properties of antioxidant active compounds in coffee brews. Methodology We have investigated the antioxidant capacity of Coffea arabica (Arabica) and C. canephora (Robusta) beans that were roasted over the full spectrum of roast conditions (four roasting speeds to three roast degrees) by comparing the results from HPSEC coupled on‐line to the ABTS assay with those from two batch assays, Folin Ciocalteu (FC) and oxygen radical absorbance capacity (ORAC) assay. Results The antioxidant capacity showed a general decrease towards slower and darker roasted coffee for all three assays, indicative of heat degradation of active compounds. Hence, low molecular weight (LMW) compounds such as chlorogenic acids (CGAs) decreased progressively already from relatively mild roasting conditions. In contrast, high molecular weight (HMW) compounds (e.g. melanoidins) increased from light to dark roast degrees with lowering magnitude towards slower roasting profiles. Conclusion By coupling HPSEC on‐line to the ABTS assay we were able to separately quantify the contribution of HMW and LMW compounds to the total antioxidant capacity, increasing our understanding of the roast process. © 2016 The Authors. Phytochemical Analysis Published by John Wiley & Sons Ltd. PMID:28008674

  2. Development of a multiplex PCR-ligase detection reaction assay for diagnosis of infection by the four parasite species causing malaria in humans.

    McNamara, David T; Thomson, Jodi M; Kasehagen, Laurin J; Zimmerman, Peter A


    The diagnosis of infections caused by Plasmodium species is critical for understanding the nature of malarial disease, treatment efficacy, malaria control, and public health. The demands of field-based epidemiological studies of malaria will require faster and more sensitive diagnostic methods as new antimalarial drugs and vaccines are explored. We have developed a multiplex PCR-ligase detection reaction (LDR) assay that allows the simultaneous diagnosis of infection by all four parasite species causing malaria in humans. This assay exhibits sensitivity and specificity equal to those of other PCR-based assays, identifying all four human malaria parasite species at levels of parasitemias equal to 1 parasitized erythrocyte/microl of blood. The multiplex PCR-LDR assay goes beyond other PCR-based assays by reducing technical procedures and by detecting intraindividual differences in species-specific levels of parasitemia. Application of the multiplex PCR-LDR assay will provide the sensitivity and specificity expected of PCR-based diagnostic assays and will contribute new insight regarding relationships between the human malaria parasite species and the human host in future epidemiological studies.

  3. First half-reaction mechanism of nitric oxide synthase: the role of proton and oxygen coupled electron transfer in the reaction by quantum mechanics/molecular mechanics.

    Cho, Kyung-Bin; Carvajal, Maria Angels; Shaik, Sason


    The first half-reaction of nitric oxide synthase (NOS) is investigated by means of quantum mechanical/molecular mechanical (QM/MM) calculations. An energetically feasible arginine hydroxylation path was found only when the iron-oxy complex accepted one proton from an external source. The so formed species has not been considered in heme chemistry; it is described as Por(+*)Fe(III)-OOH and is characterized by the same molecular constituency as the more known ferric-hydroperoxide species, compound 0, but has a cation-radical porphyrin moiety. The reaction itself is found to involve proton coupled electron transfer (PCET) and oxygen coupled electron transfer (OCET) steps en route to the formation of compound I and the ultimate monooxygenation of arginine. The cofactor H(4)B turns out to be a key player in the mechanism acting alternatively as an electron donor (when neutral) and an electron sink (when in its radical-cation state) and, thereby, providing the electron transfer component in the various coupled proton and oxygen transfer steps (see Scheme 4 ). The various pieces of this mechanism account for many of the experimental observations, such as the following: (a) the origins of the second proton supplied to the heme, (b) the elusiveness of compound I, (c) the inactivity of peroxide-shunt pathways in NOS first half-reaction, (d) the inhibition of the H(4)B analogue 4-amino-H(4)B due to protonation at the N3 position, (e) the roles of Trp188 (iNOS numbering) and the crystal water at the active site (W115), and so on. Alternative mechanistic hypotheses are tested and excluded, and a new mechanism for the NOS second half-reaction is proposed.

  4. The Copper-nicotinamide complex: sustainable applications in coupling and cycloaddition reactions

    Crystalline copper (II)-nicotinamide complex, synthesized via simple mixing of copper chloride and nicotinamide solution at room temperature, catalyzes the C-S, C-N bond forming and cycloaddition reactions under a variety of sustainable reaction conditions.

  5. A CuAAC/Ullmann C-C coupling tandem reaction: copper-catalyzed reactions of organic azides with N-(2-iodoaryl)propiolamides or 2-iodo-N-(prop-2-ynyl)benzenamines.

    Cai, Qian; Yan, Jiajie; Ding, Ke


    A novel copper-catalyzed tandem reaction was developed by utilizing two famous copper-catalyzed reactions, CuAAC and Ullmann coupling. The trapping of the C-Cu intermediate produced in CuAAC led to further formation of an aryl C-C bond through intramolecular Ullmann C-C coupling.

  6. HYDROBIOGEOCHEM: A coupled model of HYDROlogic transport and mixed BIOGEOCHEMical kinetic/equilibrium reactions in saturated-unsaturated media

    Yeh, G.T.; Salvage, K.M. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Civil and Environmental Engineering; Gwo, J.P. [Oak Ridge National Lab., TN (United States); Zachara, J.M.; Szecsody, J.E. [Pacific Northwest National Lab., Richland, WA (United States)


    The computer program HYDROBIOGEOCHEM is a coupled model of HYDROlogic transport and BIOGEOCHEMical kinetic and/or equilibrium reactions in saturated/unsaturated media. HYDROBIOGEOCHEM iteratively solves the two-dimensional transport equations and the ordinary differential and algebraic equations of mixed biogeochemical reactions. The transport equations are solved for all aqueous chemical components and kinetically controlled aqueous species. HYDROBIOGEOCHEM is designed for generic application to reactive transport problems affected by both microbiological and geochemical reactions in subsurface media. Input to the program includes the geometry of the system, the spatial distribution of finite elements and nodes, the properties of the media, the potential chemical and microbial reactions, and the initial and boundary conditions. Output includes the spatial distribution of chemical and microbial concentrations as a function of time and space, and the chemical speciation at user-specified nodes.

  7. Measurement Uncertainty of Chromogenic LAL Assays: Reaction Time and Proportion of Endotoxin and LAL Reagent Affect Release of p-Nitroaniline.

    Ostronoff, Celina Silva; Lourenço, Felipe Rebello


    Limulus Amebocyte Lysate (LAL) assays are widely used for detection and quantification of bacterial endotoxins in pharmaceuticals and medical devices. However, there are only a few studies on the measurement uncertainty of LAL assays. The aim of this work was to identify and quantify the main sources of measurement uncertainty for end point and kinetic-chromogenic LAL assays. Response surface methodology was used to study how the release of p-nitroaniline (pNA) is affected by reaction time and proportion of endotoxin and LAL reagent in end point and kinetic-chromogenic LAL assays, respectively. Increased release of pNA was observed when reaction time was increased. In addition, if different volumes of sample (or endotoxin standard) and LAL reagent are used, the pNA release rate will be affected. These results may be due to the increased interaction between the bacterial endotoxin and LAL-activated enzyme. Final measurement uncertainties (95% confidence interval) were 90-120% and 90-127% of bacterial endotoxin content for end point and kinetic-chromogenic assays, respectively. These values are reasonable for the scope of the method and allow the application of these measurement uncertainties in routine analysis of pharmaceuticals and medical devices.

  8. Separation of reaction product and palladium catalyst after a Heck coupling reaction by means of organic solvent nanofiltration.

    Tsoukala, Anna; Peeva, Ludmila; Livingston, Andrew G; Bjørsvik, Hans-René


    Organic solvent nanofiltration (OSN) is a recently commercialized technology, which we have used to develop a method for the separation of a target product and the Pd catalyst from a Heck coupling postreaction mixture. The experimental setup included commercially available polyimide copolymer membranes with molecular weight cut-off (MWCO) values in the range of 150-300 Da, acetone as the solvent, and a working pressure (N(2)) of 3 MPa. The investigation of the membranes revealed that a membrane with a MWCO of 200 Da provided quantitative retention of the Pd catalyst and quantitative recovery of the target product by means of a cross-flow dia-nanofiltration procedure.

  9. Stereospecific nickel-catalyzed cross-coupling reactions of alkyl ethers: enantioselective synthesis of diarylethanes.

    Taylor, Buck L H; Swift, Elizabeth C; Waetzig, Joshua D; Jarvo, Elizabeth R


    Secondary benzylic ethers undergo stereospecific substitution reactions with Grignard reagents in the presence of nickel catalysts. Reactions proceed with inversion of configuration and high stereochemical fidelity. This reaction allows for facile enantioselective synthesis of biologically active diarylethanes from readily available optically enriched carbinols.

  10. Simultaneous detection of five enteric viruses associated with gastroenteritis by use of a PCR assay: a single real-time multiplex reaction and its clinical application.

    Jiang, Yixiang; Fang, Lin; Shi, Xiaolu; Zhang, Hailong; Li, Yinghui; Lin, Yiman; Qiu, Yaqun; Chen, Qingliang; Li, Hui; Zhou, Li; Hu, Qinghua


    We developed a highly sensitive reverse transcription and multiplex real-time PCR (rtPCR) assay that can identify five viruses, including six genogroups, in a single reaction: norovirus genogroups I and II; sapovirus genogroups I, II, IV, and V; human rotavirus A; adenovirus serotypes 40 and 41; and human astrovirus. In comparison to monoplex rtPCR assays, the sensitivities and specificities of the multiplex rtPCR ranged from 75% to 100% and from 99% to 100%, respectively, evaluated on 812 clinical stool specimens.

  11. Exact and truncated Coriolis coupling calculations for the S(1D)+HD reaction employing the ground adiabatic electronic state.

    Yang, Huan; Han, Keli; Schatz, George C; Smith, Sean C; Hankel, Marlies


    We present exact quantum differential cross sections and exact and estimated integral cross sections and branching ratios for the title reaction. We employ a time-dependent wavepacket method as implemented in the DIFFREALWAVE code including all Coriolis couplings and also an adapted DIFFREALWAVE code where the helicity quantum number and with this the Coriolis couplings have been truncated. Our exact differential cross sections at 0.453 eV total energy, one of the experimental energies, show good agreement with the experimental results for one of the product channels. While the truncated calculation present a significant reduction in the computational effort needed they overestimate the exact integral cross sections.

  12. Cross-coupling reaction of saccharide-based alkenyl boronic acids with aryl halides: the synthesis of bergenin.

    Parkan, Kamil; Pohl, Radek; Kotora, Martin


    A convenient synthetic pathway enabling D-glucal and D-galactal pinacol boronates to be prepared in good isolated yields was achieved. Both pinacol boronates were tested in a series of cross-coupling reactions under Suzuki-Miyaura cross-coupling conditions to obtain the corresponding aryl, heteroaryl, and alkenyl derivatives in high isolated yields. This methodology was applied to the formal synthesis of the glucopyranoside moiety of papulacandin D and the first total synthesis of bergenin. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Synthesis of carbodiimides by I2/CHP-mediated cross-coupling reaction of isocyanides with amines under metal-free conditions.

    Zhu, Tong-Hao; Wang, Shun-Yi; Tao, Yang-Qing; Ji, Shun-Jun


    An I2/CHP-mediated cross-coupling reaction of isocyanides with readily accessible amines via C-N formation is described for carbodiimide synthesis in moderate to excellent yields. This represents a metal-free strategy for a coupling reaction of isocyanides with amines, and it provides an efficient approach for symmetric and unsymmetric functionalized carbodiimide derivative synthesis under mild conditions.

  14. Oxidative photoredox-catalytic activation of aliphatic nucleophiles for C(sp(3))-C(sp(2)) cross-coupling reactions.

    Jahn, Emanuela; Jahn, Ullrich


    In the light you will find the road (Led Zeppelin): Visible-light photoredox catalysis leads the way in overcoming the reactivity limitations of alkyl nucleophiles in cross-coupling reactions. Iridium-triggered oxidative photoredox activation of alkyltrifluoroborate or carboxylic acids affords alkyl radicals, which undergo nickel-catalyzed cross-coupling reactions.

  15. Ligand-Free Suzuki-Miyaura Coupling Reactions Using an Inexpensive Aqueous Palladium Source: A Synthetic and Computational Exercise for the Undergraduate Organic Chemistry Laboratory

    Hill, Nicholas J.; Bowman, Matthew D.; Esselman, Brian J.; Byron, Stephen D.; Kreitinger, Jordan; Leadbeater, Nicholas E.


    An inexpensive procedure for introducing the Suzuki-Miyaura coupling reaction into a high-enrollment undergraduate organic chemistry laboratory course is described. The procedure employs an aqueous palladium solution as the catalyst and a range of para-substituted aryl bromides and arylboronic acids as substrates. The coupling reactions proceed…

  16. Computational tools for mechanistic discrimination in the reductive and metathesis coupling reactions mediated by titanium(IV) isopropoxide

    Akshai Kumar; Ashoka G Samuelson


    A theoretical study has been carried out at the B3LYP/LANL2DZ level to compare the reactivity of phenyl isocyanate and phenyl isothiocyanate towards titanium(IV) alkoxides. Isocyanates are shown to favour both mono insertion and double insertion reactions. Double insertion in a head-to-tail fashion is shown to be more exothermic than double insertion in a head-to-head fashion. The head-to-head double insertion leads to the metathesis product, a carbodiimide, after the extrusion of carbon dioxide. In the case of phenyl isothiocyanate, calculations favour the formation of only mono insertion products. Formation of a double insertion product is highly unfavourable. Further, these studies indicate that the reverse reaction involving the metathesis of N,N'-diphenyl carbodiimide with carbon dioxide is likely to proceed more efficiently than the metathesis reaction with carbon disulphide. This is in excellent agreement with experimental results as metathesis with carbon disulphide fails to occur. In a second study, multilayer MM/QM calculations are carried out on intermediates generated from reduction of titanium(IV) alkoxides to investigate the effect of alkoxy bridging on the reactivity of multinuclear Ti species. Bimolecular coupling of imines initiated by Ti(III) species leads to a mixture of diastereomers and not diastereoselective coupling of the imine. However if the reaction is carried out by a trimeric biradical species, diastereoselective coupling of the imine is predicted. The presence of alkoxy bridges greatly favours the formation of the d,l (±) isomer, whereas the intermediate without alkoxy bridges favours the more stable meso isomer. As a bridged trimeric species, stabilized by bridging alkoxy groups, correctly explains the diastereoselective reaction, it is the most likely intermediate in the reaction.

  17. Multiplexing Fluo-4 NW and a GeneBLAzer transcriptional assay for high-throughput screening of G-protein-coupled receptors.

    Hanson, Bonnie J


    Activation of G-protein-coupled receptors (GPCRs) leads to a cascade of signaling events, including calcium mobilization and downstream transcriptional activation of various proteins. Two commonly used methods of high-throughput screening for GPCRs include calcium-sensitive dyes, such as Fluo-4 NW, and reporter gene assays, such as beta-lactamase. To determine whether the advantages of each assay format could be combined by multiplexing, Jurkat and CHO-K1 cell lines over-expressing the M1 muscarinic receptor and beta-lactamase under control of an NFAT response element were tested in a multiplexed format. The Jurkat cell line was further screened with a subset of the LOPAC(1280) library. The multiplexing assay was compatible with both the CHO-K1 and Jurkat cell lines. For the screen, there was 100% correlation of on-target hits in the multiplexed format, and several false positives with each assay format were identified. Therefore, not only can the assays be multiplexed, but by multiplexing, the false positives associated with each assay format also could be easily identified. In addition to enhanced reliability, this method saves time and money because only half the amount of compounds, cells, and consumables are needed to screen a cell line in a multiplexed mode versus separate screening by both methods.

  18. Evaluation of two real-time polymerase chain reaction assays for Porcine epidemic diarrhea virus (PEDV) to assess PEDV transmission in growing pigs.

    Miller, Laura C; Crawford, Kimberly K; Lager, Kelly M; Kellner, Steven G; Brockmeier, Susan L


    In April 2013, a Porcine epidemic diarrhea virus (PEDV) epidemic began in the United States. As part of the response, real-time reverse transcription polymerase chain reaction (RT-PCR) assays to detect PEDV were developed by several veterinary diagnostic laboratories. Our study evaluated RT-PCR PEDV assays that detect the N gene (gN) and S gene (gS) for their ability to detect PEDV infection and the transmission potential of pigs experimentally exposed to PEDV. Detection limits and quantification cycle (Cq) values of real-time RT-PCR were assayed for PEDV samples and positive controls for both gN and gS. The limit of detection for the gN assay was 10(-6) (mean Cq: 39.82 ± 0.30) and 10(-5) (mean Cq: 39.39 ± 0.72) for the gS assay with PEDV strain USA/Colorado/2013. Following recommended guidelines, rectal swabs (n = 1,064) were tested; 354 samples were positive by gN assay and 349 samples were positive by gS assay (Cq ≤ 34.99), 710 samples were negative by gN assay and 715 were negative by gS assay (Cq > 34.99) of which 355 and 344 were "undetermined" (i.e., undetected within a threshold of 40 RT-PCR cycles, by gN and gS assays, respectively). The coefficient of variation (intra-assay variation) ranged from 0.00% to 2.65% and interassay variation had an average of 2.75%. PEDV could be detected in rectal swabs from all pigs for ~2 weeks postinfection at which time the prevalence began to decrease until all pigs were RT-PCR negative by 5 weeks postinfection. Our study demonstrated that RT-PCR assays functioned well to detect PEDV and that the gN assay was slightly better. © 2015 The Author(s).

  19. Cationic Pd(II)-catalyzed C–H activation/cross-coupling reactions at room temperature: synthetic and mechanistic studies

    Nishikata, Takashi; Abela, Alexander R; Huang, Shenlin


    Summary Cationic palladium(II) complexes have been found to be highly reactive towards aromatic C–H activation of arylureas at room temperature. A commercially available catalyst [Pd(MeCN)4](BF4)2 or a nitrile-free cationic palladium(II) complex generated in situ from the reaction of Pd(OAc)2 and HBF4, effectively catalyzes C–H activation/cross-coupling reactions between aryl iodides, arylboronic acids and acrylates under milder conditions than those previously reported. The nature of the directing group was found to be critical for achieving room temperature conditions, with the urea moiety the most effective in promoting facile coupling reactions at an ortho C–H position. This methodology has been utilized in a streamlined and efficient synthesis of boscalid, an agent produced on the kiloton scale annually and used to control a range of plant pathogens in broadacre and horticultural crops. Mechanistic investigations led to a proposed catalytic cycle involving three steps: (1) C–H activation to generate a cationic palladacycle; (2) reaction of the cationic palladacycle with an aryl iodide, arylboronic acid or acrylate, and (3) regeneration of the active cationic palladium catalyst. The reaction between a cationic palladium(II) complex and arylurea allowed the formation and isolation of the corresponding palladacycle intermediate, characterized by X-ray analysis. Roles of various additives in the stepwise process have also been studied. PMID:27340491

  20. CFD modeling of reaction and mass transfer through a single pellet:Catalytic oxidative coupling of methane

    Siavash Seyednej adian; Nakisa Yaghobi; Ramin Maghrebi; Leila Vafajoo


    In this study a mathematical model of a small scale single pellet for the oxidative coupling of methane (OCM) over titanite pervoskité isdeveloped.The method is based on a computational fluid dynamics (CFD) code which known as Fluent may be adopted to model the reactions that take place inside the porous catalyst pellet.The steady state single pellet model is coupled with a kinetic model and the intra-pellet concentration profiles of species are provided.Subsequent to achieving this goal,a nonlinear reaction network consisting of nine catalytic reactions and one gas phase reaction as an external program is successfully implemented to CFD-code as a reaction term in solving the equations.This study is based on the experimental design which is conducted in a differential reactor with a Sn/BaTiO3 catalyst (7-8 mesh) at atmospheric pressure,GHSV of 12000 h-1,ratio of methane to oxygen of 2,and three different temperatures of 1023,1048 and 1073 K.The modeling results such as selectivity and conversion at the pellet exit are in good agreement with the experimental data.Therefore,it is suggested that to achieve high yield in OCM process the modeling of the single pellet should be considered as the heart of catalytic fixed bed reactor.

  1. Cationic Pd(II-catalyzed C–H activation/cross-coupling reactions at room temperature: synthetic and mechanistic studies

    Takashi Nishikata


    Full Text Available Cationic palladium(II complexes have been found to be highly reactive towards aromatic C–H activation of arylureas at room temperature. A commercially available catalyst [Pd(MeCN4](BF42 or a nitrile-free cationic palladium(II complex generated in situ from the reaction of Pd(OAc2 and HBF4, effectively catalyzes C–H activation/cross-coupling reactions between aryl iodides, arylboronic acids and acrylates under milder conditions than those previously reported. The nature of the directing group was found to be critical for achieving room temperature conditions, with the urea moiety the most effective in promoting facile coupling reactions at an ortho C–H position. This methodology has been utilized in a streamlined and efficient synthesis of boscalid, an agent produced on the kiloton scale annually and used to control a range of plant pathogens in broadacre and horticultural crops. Mechanistic investigations led to a proposed catalytic cycle involving three steps: (1 C–H activation to generate a cationic palladacycle; (2 reaction of the cationic palladacycle with an aryl iodide, arylboronic acid or acrylate, and (3 regeneration of the active cationic palladium catalyst. The reaction between a cationic palladium(II complex and arylurea allowed the formation and isolation of the corresponding palladacycle intermediate, characterized by X-ray analysis. Roles of various additives in the stepwise process have also been studied.

  2. Reaction Chemistry of W-Mn/SiO2 Catalyst for the Oxidative Coupling of Methane

    Shuben Li


    Reaction chemistry of the OCM reaction on W-Mn/SiO2 catalyst has been reviewed in thisaccount. Initial activity and selectivity, stability in a long-term reaction, reaction at elevated pressures anda modelling test in a stainless-steel fluidized-bed reactor show that W-Mn/SiO2 has promising performancefor the development of an OCM process that directly produces ethylene from natural gas. A study onsurface catalytic reaction kinetics and used catalyst structure characterization revealed a possible reasonwhy C2 and COx selectivity changed during the long-term reaction. Further improvement of the catalystcomposition and preparation method should be a future direction of study on OCM reaction over W-Mn/SiO2 catalyst.

  3. Description of Four-Body Breakup Reaction with the Method of Continuum-Discretized Coupled-Channels

    Egami, Tomoaki; Ogata, Kazuyuki; Yahiro, Masanobu


    We present a method for smoothing discrete breakup $S$-matrix elements calculated by the method of continuum-discretized coupled-channels (CDCC). This smoothing method makes it possible to apply CDCC to four-body breakup reactions. The reliability of the smoothing method is confirmed for two cases, $^{58}$Ni($d$, $p n$) at 80 MeV and the $E1$ transition of $^6$He. We apply CDCC with the smoothing method to $^6$He breakup reaction at 22.5 MeV. Multi-step breakup processes are found to be important.

  4. Modular Construction of Fluoroarenes from a New Difluorinated Building Block by Cross-Coupling/Electrocyclisation/Dehydrofluorination Reactions.

    Percy, Jonathan M; Emerson, Helena; Fyfe, James W B; Kennedy, Alan R; Maciuk, Sergej; Orr, David; Rathouská, Lucie; Redmond, Joanna M; Wilson, Peter G


    Palladium-catalysed coupling reactions based on a novel and easy-to-synthesise difluorinated organotrifluoroborate were used to assemble precursors to 6π-electrocyclisations of three different types. Electrocyclisations took place at temperatures between 90 and 240 °C, depending on the central component of the π-system; nonaromatic trienes were most reactive, but even systems that required the temporary dearomatisation of two arenyl subunits underwent electrocyclisation, albeit at elevated temperatures. Photochemical conditions were effective for these more demanding reactions. The package of methods delivered a structurally diverse set of fluorinated arenes, spanning a 20 kcal mol(-1) range of reactivity, by a flexible route.

  5. Simple, Efficient Protocols for the Pd-Catalyzed Cross-Coupling Reaction of Aryl Chlorides and Dimethylamine

    Lee, Brian K.; Biscoe, Mark R.; Buchwald, Stephen L.


    Simple and efficient procedures for the Pd-catalyzed cross-coupling reaction of aryl chlorides and dimethylamine are described. At room temperature with a strong base, t-BuXPhos is employed as the supporting ligand; at 110 °C with a weak base, XPhos is employed as the supporting ligand. In each of these cases, commercially available solutions constitute the source of the dimethylamine, and recently disclosed precatalysts constitute the source of the ligand and Pd. This work further expands the utility of these precatalysts in reactions that benefit from an easily activated source of L1Pd(0). PMID:21818164

  6. Pd-catalyzed Suzuki cross-Coupling reaction of bromostilbene: insights on the nature of the boron Species

    Nunes, Carolina M.; Monteiro, Adriano L. [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil). Inst. de Quimica]. E-mail:


    Arylboronate esters and arylborate salts can be used as partner for the Suzuki reaction of (E)-bromostilbene in the presence of Pd(OAc){sub 2}/PPh{sub 3} as catalyst precursor. While KOH is necessary for the coupling reaction with arylboronic acids and pinacol esters, aryl borate sodium salt can be used in a base-free protocol. The comparison between the three organoboron compounds using competitive experiments and electrospray ionization mass spectrometry analysis supports the proposition that the base initially reacts with the arylboronic acid or ester to form an arylborate species which undergoes the transmetallation process with the palladium catalyst. (author)

  7. Droplet digital polymerase chain reaction assay for screening of ESR1 mutations in 325 breast cancer specimens.

    Takeshita, Takashi; Yamamoto, Yutaka; Yamamoto-Ibusuki, Mutsuko; Inao, Toko; Sueta, Aiko; Fujiwara, Saori; Omoto, Yoko; Iwase, Hirotaka


    Droplet digital polymerase chain reaction (ddPCR), which could perform thousands of PCRs on a nanoliter scale simultaneously, would be an attractive method to massive parallel sequencing for identifying and studying the significance of low-frequency rare mutations. Recent evidence has shown that the key potential mechanisms of the failure of aromatase inhibitors-based therapy involve identifying activating mutations affecting the ligand-binding domain of the ESR1 gene. Therefore, the detection of ESR1 mutations may be useful as a biomarker predicting an effect of the treatment. We aimed to develop a ddPCR-based method for the sensitive detection of ESR1 mutations in 325 breast cancer specimens, in which 270 primary and 55 estrogen receptor-positive (ER+) metastatic breast cancer (MBC) specimens. Our ddPCR assay could detect the ESR1 mutant molecules with low concentration of 0.25 copies/μL. According to the selected cutoff, ESR1 mutations occurred in 7 (2.5%) of 270 primary breast cancer specimens and in 11 (20%) of 55 ER+ MBC specimens. Among the 11 MBC specimens, 5 specimens (45.5%) had the most common ESR1 mutation, Y537S, 4 specimens (36.3%) each had D538G, Y537N, and Y537C. Interestingly, 2 patients had 2 ESR1 mutations, Y537N/D538G and Y537S/Y537C, and 2 patients had 3 ESR1 mutations, Y537S/Y537N/D538G. Biopsy was performed in heterochrony in 8 women twice. In 8 women, 4 women had primary breast cancer and MBC specimens and 4 women had 2 specimens when treatment was failure. Four of these 8 women acquired ESR1 mutation, whereas no ESR1 mutation could be identified at first biopsy. ddPCR technique could be a promising tool for the next-generation sequencing-free precise detection of ESR1 mutations in endocrine therapy resistant cases and may assist in determining the treatment strategy.

  8. Access to a polymerase chain reaction assay method targeting 13 respiratory viruses can reduce antibiotics: a randomised, controlled trial

    Lindh Magnus


    Full Text Available Abstract Background Viral respiratory infections are common worldwide and range from completely benign disease to life-threatening illness. Symptoms can be unspecific, and an etiologic diagnosis is rarely established because of a lack of suitable diagnostic tools. Improper use of antibiotics is common in this setting, which is detrimental in light of the development of bacterial resistance. It has been suggested that the use of diagnostic tests could reduce antibiotic prescription rates. The objective of this study was to evaluate whether access to a multiplex polymerase chain reaction (PCR assay panel for etiologic diagnosis of acute respiratory tract infections (ARTIs would have an impact on antibiotic prescription rate in primary care clinical settings. Methods Adult patients with symptoms of ARTI were prospectively included. Nasopharyngeal and throat swabs were analysed by using a multiplex real-time PCR method targeting thirteen viruses and two bacteria. Patients were recruited at 12 outpatient units from October 2006 through April 2009, and samples were collected on the day of inclusion (initial visit and after 10 days (follow-up visit. Patients were randomised in an open-label treatment protocol to receive a rapid or delayed result (on the following day or after eight to twelve days. The primary outcome measure was the antibiotic prescription rate at the initial visit, and the secondary outcome was the total antibiotic prescription rate during the study period. Results A total sample of 447 patients was randomised. Forty-one were excluded, leaving 406 patients for analysis. In the group of patients randomised for a rapid result, 4.5% (9 of 202 of patients received antibiotics at the initial visit, compared to 12.3% (25 of 204 (P = 0.005 of patients in the delayed result group. At follow-up, there was no significant difference between the groups: 13.9% (28 of 202 in the rapid result group and 17.2% (35 of 204 in the delayed result group (P

  9. An optics-based variable-temperature assay system for characterizing thermodynamics of biomolecular reactions on solid support

    Fei, Yiyan; Landry, James P.; Zhu, X. D., E-mail: [Department of Physics, University of California, One Shields Avenue, Davis, California 95616 (United States); Li, Yanhong; Yu, Hai; Lau, Kam; Huang, Shengshu; Chokhawala, Harshal A.; Chen, Xi [Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616 (United States)


    A biological state is equilibrium of multiple concurrent biomolecular reactions. The relative importance of these reactions depends on physiological temperature typically between 10 °C and 50 °C. Experimentally the temperature dependence of binding reaction constants reveals thermodynamics and thus details of these biomolecular processes. We developed a variable-temperature opto-fluidic system for real-time measurement of multiple (400–10 000) biomolecular binding reactions on solid supports from 10 °C to 60 °C within ±0.1 °C. We illustrate the performance of this system with investigation of binding reactions of plant lectins (carbohydrate-binding proteins) with 24 synthetic glycans (i.e., carbohydrates). We found that the lectin-glycan reactions in general can be enthalpy-driven, entropy-driven, or both, and water molecules play critical roles in the thermodynamics of these reactions.

  10. Sensitive Glycoprotein Sandwich Assays by the Synergistic Effect of In Situ Generation of Raman Probes and Plasmonic Coupling of Ag Core-Au Satellite Nanostructures.

    Bi, Xiaoshuang; Li, Xueyuan; Chen, Dong; Du, Xuezhong


    Sensitive surface-enhanced Raman scattering (SERS) assays of glycoproteins have been proposed using p-aminothiophenol (PATP)-embedded Ag core-Au satellite nanostructures modified with p-mercaptophenylboronic acid (PMBA) and the self-assembled monolayer of PMBA on a smooth gold-coated wafer. The apparent Raman probe PATP on the surfaces of the Ag cores underwent a photodimerization to generate 4,4'-dimercaptoazobenzene (DMAB) in situ upon excitation of laser, and the in situ generated DMAB acted as the actual Raman probe with considerably strong SERS signals, which was further enhanced by the plasmonic coupling of the Ag core-Au satellite nanostructures due to the synergistic effect. The sandwich assays of glycoproteins showed high sensitivity and excellent selectivity against nonglycoproteins. The Ag core-Au satellite SERS nanostructures can be used for highly sensitive SERS assays of other analytes.

  11. Stereoselectivity in Autoionization Reactions of Hydrogenated Molecules by Metastable Noble Gas Atoms: The Role of Electronic Couplings.

    Falcinelli, Stefano; Rosi, Marzio; Cavalli, Simonetta; Pirani, Fernando; Vecchiocattivi, Franco


    Focus in the present paper is on the analysis of total and partial ionization cross sections, measured in absolute value as a function of the collision energy, representative of the probability of ionic product formation in selected electronic states in Ne*-H2 O, H2 S, and NH3 collisions. In order to characterize the imaginary part of the optical potential, related to electronic couplings, we generalize a methodology to obtain direct information on the opacity function of these reactions. Such a methodology has been recently exploited to test the real part of the optical potential (S. Falcinelli et al., Chem. Eur. J., 2016, 22, 764-771). Depending on the balance of noncovalent contributions, the real part controls the approach of neutral reactants, the removal of ionic products, and the structure of the transition state. Strength, range, and stereoselectivity of electronic couplings, triggering these and many other reactions, are directly obtained from the present investigation.

  12. Treatment of ammonia in waste air using packed column coupling with chemical reaction

    Thepchai, R.


    Full Text Available Ammonia is a common chemical used in various industries. Emission of air contaminated with ammonia to the atmosphere without any treatment causes several effects on human health and environment.A high efficiency method for ammonia removal from waste air is then necessary. In this research, an absorption coupling with chemical reaction was investigated for ammonia removal from waste air using a packedcolumn. The packed column of 10 cm diameter and 200 cm height was packed with 1.4x1.4 cm Raschig rings. Three liquids including water, NaOCl and H2SO4 solution were used as an absorbent for the investigation.The objectives of this research were to determine a suitable absorbent and the optimum condition for ammonia removal from waste air. The packed column was operated at room temperature and atmosphericpressure. The tested conditions were as follows: the gas to liquid ratio (G:L ratio was 35-90 m3 gas/m3 liquid, the inlet concentration of ammonia was 150-500 ppm and the air flow rate was 18 m3/h. The results showedthat the ammonia removal efficiency depends on type of the absorbent and the operating condition. The efficiencies increased with decreasing of G:L ratio and with increasing absorbent concentration. They were70%, 80-92%, and 95-100% for pure water, sodium hypochlorite solution and sulphuric acid solution, respectively. The efficiency decreased with time when water was used as an absorbent while it was almostconstant when NaOCl and H2SO4 solution were applied. The ammonia removal efficiency when using H2SO4 as the absorbent was not dependent on G:L ratio and inlet ammonia concentration, in the range used in thisinvestigation. Since H2SO4 solution gave the highest removal efficiency and can reduce ammonia concentration in waste air to levels which meet the TLV-TWA standard, it is recommended as an absorbent solution forammonia removal from waste air.

  13. Adaptive synchronization in an array of linearly coupled neural networks with reaction-diffusion terms and time delays

    Wang, Kai; Teng, Zhidong; Jiang, Haijun


    In this paper, the adaptive synchronization in an array of linearly coupled neural networks with reaction-diffusion terms and time delays is discussed. Based on the LaSalle invariant principle of functional differential equations and the adaptive feedback control technique, some sufficient conditions for adaptive synchronization of such a system are obtained. Finally, a numerical example is given to show the effectiveness of the proposed synchronization method.

  14. Dye conjugation to linseed oil by highly-effective thiol-ene coupling and subsequent esterification reactions

    Hayashi, T; Kazlauciunas, A; Thornton, PD


    Linseed oil, a renewable material obtained from the ripened seeds of the flax plant, was conjugated with C. I. Disperse Red 1 to yield a coloured macromolecule in two experimentally-simplistic coupling steps. Firstly, the abundant presence of carbon-carbon double bonds in linseed oil was exploited to introduce carboxylic acid functionality to linseed oil via a thiol-ene reaction between linseed oil and 3-mercaptopropionic acid. C. I. Disperse Red 1 was then grafted to the carboxylic acid unit...

  15. Sm/TiCl4 (cat.) system-mediated intermolecular and intramolecular reductive coupling reactions of ketones with esters

    LIU Yun-kui; XU Dan-qian; XU Zhen-yuan; ZHANG Yong-min


    Sm/TiCl4 system could well integrate the high reactivity of samarium(Ⅱ) and high deoxygenation capacity of low valent titanium within one system. In this paper, the intermolecular and intramolecular reductive coupling reactions of ketones with esters mediated by metallic samarium (Sm) and a catalytic amount of titanium tetrachloride (TiCl4) were successfully developed. A series of substituted ketones and cyclic β-keto-esters were prepared in moderate to good yields under reflux and neutral conditions.

  16. Sequential decarboxylative azide–alkyne cycloaddition and dehydrogenative coupling reactions: one-pot synthesis of polycyclic fused triazoles

    Kuppusamy Bharathimohan


    Full Text Available Herein, we describe a one-pot protocol for the synthesis of a novel series of polycyclic triazole derivatives. Transition metal-catalyzed decarboxylative CuAAC and dehydrogenative cross coupling reactions are combined in a single flask and achieved good yields of the respective triazoles (up to 97% yield. This methodology is more convenient to produce the complex polycyclic molecules in a simple way.

  17. Evaluation of a single round polymerase chain reaction assay using dried blood spots for diagnosis of HIV-1 infection in infants in an African setting

    Ng'ayo Musa


    Full Text Available Abstract Background The aim of this study was to develop an economical 'in-house' single round polymerase chain reaction (PCR assay using filter paper-dried blood spots (FP-DBS for early infant HIV-1 diagnosis and to evaluate its performance in an African setting. Methods An 'in-house' single round PCR assay that targets conserved regions in the HIV-1 polymerase (pol gene was validated for use with FP-DBS; first we validated this assay using FP-DBS spiked with cell standards of known HIV-1 copy numbers. Next, we validated the assay by testing the archived FP-DBS (N = 115 from infants of known HIV-1 infection status. Subsequently this 'in-house' HIV-1 pol PCR FP-DBS assay was then established in Nairobi, Kenya for further evaluation on freshly collected FP-DBS (N = 186 from infants, and compared with findings from a reference laboratory using the Roche Amplicor® HIV-1 DNA Test, version 1.5 assay. Results The HIV-1 pol PCR FP-DBS assay could detect one HIV-1 proviral copy in 38.7% of tests, 2 copies in 46.9% of tests, 5 copies in 72.5% of tests and 10 copies in 98.1% of tests performed with spiked samples. Using the archived FP-DBS samples from infants of known infection status, this assay was 92.8% sensitive and 98.3% specific for HIV-1 infant diagnosis. Using 186 FP-DBS collected from infants recently defined as HIV-1 positive using the commercially available Roche Amplicor v1.5 assay, 178 FP-DBS tested positive by this 'in-house' single-round HIV-1 pol PCR FP-DBS PCR assay. Upon subsequent retesting, the 8 infant FP-DBS samples that were discordant were confirmed as HIV-1 negative by both assays using a second blood sample. Conclusions HIV-1 was detected with high sensitivity and specificity using both archived and more recently collected samples. This suggests that this 'in-house' HIV-1 pol FP-DBS PCR assay can provide an alternative cost-effective, reliable and rapid method for early detection of HIV-1 infection in infants.

  18. Cu(OAc)2 catalyzed Sonogashira cross-coupling reaction in amines

    Sheng Mei Guo; Chen Liang Deng; Jin Heng Li


    A simple Cu(OAc)2 catalyzed Sonogashira coupling protocol is presented. It was found that the couplings of a variety of aryl halides with terminal alkynes were conducted smoothly to afford the corresponding desired products in moderate to excellent yields, using Cu(OAc)2 as the catalyst and Et3N as the solvent.

  19. A modified molecular beacons-based multiplex real-time PCR assay for simultaneous detection of eight foodborne pathogens in a single reaction and its application.

    Hu, Qinghua; Lyu, Dongyue; Shi, Xiaolu; Jiang, Yixiang; Lin, Yiman; Li, Yinghui; Qiu, Yaqun; He, Lianhua; Zhang, Ran; Li, Qingge


    Foodborne disease outbreaks are often caused by one of the major pathogens. Early identification of the causal pathogen is crucial for disease control and prevention. We describe a real-time polymerase chain reaction (rtPCR) assay that can identify, in a single reaction, up to eight common foodborne bacterial pathogens, including Salmonella enterica subsp. enterica, Listeria monocytogenes, Escherichia coli O157, Vibrio parahaemolyticus, V. vulnificus, Campylobacter jejuni, Enterobacter sakazakii, and Shigella spp. This multiplex rtPCR assay takes advantage of modified molecular beacons and the multicolor combinational probe coding strategy to discriminate each pathogen and the homo-tag assisted non-dimer (HAND) system to prevent dimer formation. The detection limits of the assay ranged from 1.3×10(3) colony-forming units (CFU)/g stool (L. monocytogenes) to 1.6×10(4) CFU/g stool (Shigella spp.). The target genes were 100% specific as assessed on 986 reference strains covering 41 species since no cross-reactions were observed. The assay was applied to the detection of foodborne pathogens in 11,167 clinical samples and the results were compared with culture methods for further validation. The sensitivity and specificity of the rtPCR were 100% and 99%, respectively. When performed in a 96-well rtPCR system, more than 90 samples could be analyzed within 3 h. Given the high accuracy, sensitivity, specificity, and short turn-around time, the established assay could be used for the rapid and reliable identification of the causative pathogens responsible for a certain foodborne disease outbreak and rapid screening of these major foodborne pathogens in laboratory-based surveillance of outpatient clinical samples or even food samples.

  20. Improvement and optimization of a multiplex real-time reverse transcription polymerase chain reaction assay for the detection and typing of Vesicular stomatitis virus.

    Hole, Kate; Velazquez-Salinas, Lauro; Velazques-Salinas, Lauro; Clavijo, Alfonso


    An improvement to a previously reported real-time reverse transcription polymerase chain reaction (real-time RT-PCR) assay for the detection of Vesicular stomatitis virus (VSV) is described. Results indicate that the new assay is capable of detecting a panel of genetically representative strains of VSV present in North, Central, and South America. The assay is specific for VSV and allows for simultaneous differentiation between Vesicular stomatitis Indiana virus and Vesicular stomatitis New Jersey virus. This real-time RT-PCR is able to detect current circulating strains of VSV and can be used for rapid diagnosis of VSV and differentiation of VSV from other vesicular diseases, such as foot-and-mouth disease.

  1. Loop mediated isothermal amplification assay using hydroxy naphthol blue, conventional polymerase chain reaction and real-time PCR in the diagnosis of intraocular tuberculosis.

    Balne, P K; Basu, S; Rath, S; Barik, M R; Sharma, S


    This study is a comparative evaluation (Chi-square test) of a closed tube loop mediated isothermal amplification assay using hydroxy naphthol blue dye (HNB-LAMP), real-time polymerase chain reaction (PCR) and conventional PCR in the diagnosis of intraocular tuberculosis. Considering clinical presentation as the gold standard in 33 patients, the sensitivity of HNB-LAMP assay (75.8%) was higher (not significant, P value 0.2) than conventional PCR (57.6%) and lower than real-time PCR (90.9%). Specificity was 100% by all three methods. No amplification was observed in negative controls (n = 20) by all three methods. The cost of the HNB-LAMP assay was Rs. 500.00 and it does not require thermocycler, therefore, it can be used as an alternative to conventional PCR in resource-poor settings.

  2. Loop mediated isothermal amplification assay using hydroxy naphthol blue, conventional polymerase chain reaction and real-time PCR in the diagnosis of intraocular tuberculosis

    P K Balne


    Full Text Available This study is a comparative evaluation (Chi-square test of a closed tube loop mediated isothermal amplification assay using hydroxy naphthol blue dye (HNB-LAMP, real-time polymerase chain reaction (PCR and conventional PCR in the diagnosis of intraocular tuberculosis. Considering clinical presentation as the gold standard in 33 patients, the sensitivity of HNB-LAMP assay (75.8% was higher (not significant, P value 0.2 than conventional PCR (57.6% and lower than real-time PCR (90.9%. Specificity was 100% by all three methods. No amplification was observed in negative controls (n = 20 by all three methods. The cost of the HNB-LAMP assay was Rs. 500.00 and it does not require thermocycler, therefore, it can be used as an alternative to conventional PCR in resource-poor settings.

  3. A novel polymerase chain reaction (PCR based assay for authentication of cell lines or tissues from human, pig and chicken origin



    Full Text Available A polymerase chain reaction based assay was developed for authentication of cell lines or tissues from human, pig and chicken origin. Specificity was achieved by species specific primer design targeting the mitochondrial D-loop sequence. Amplicon sizes were 114 bp, 169 bp and 645-648 bp for chicken, human and pig derived cell lines, respectively. Primers were tested for species specificity and non-specificity between haplogroups of the same organisms using BLAST tool and subsequently for cross amplification DNA extracted from human, chicken and pig venous blood as a positive control. Primers were also amplifying specific products in DNA extracted from individual cell line in both functional cell models and intentionally mixed cell lines consisting functional cell models. The PCR assay developed in this study represents a low-cost species specific end-point PCR based assay of the mitochondrial D-loop for the authentication of the cell line origin.

  4. Cycloaddition Reaction of Vinylphenylfurans and Dimethyl Acetylenedicarboxylate to [8 + 2] Isomers via Tandem [4 + 2]/Diradical Alkene-Alkene Coupling/[1,3]-H Shift Reactions: Experimental Exploration and DFT Understanding of Reaction Mechanisms.

    Chen, Kai; Wu, Feng; Ye, Lijuan; Tian, Zi-You; Yu, Zhi-Xiang; Zhu, Shifa


    An experimental test of designed [8 + 2] reaction of vinylphenylfuran and dimethyl acetylenedicarboxylate (DMAD) has been carried out, showing that the reaction gave unexpected addition products under different conditions. When the reaction was conducted under thermal conditions in toluene, expoxyphenanthrene, which was named as a [8 + 2] isomer, was generated. The scope of this reaction has been investigated in the present study. In addition, experiments and DFT calculations have been conducted to investigate how the reaction between vinylphenylfuran and DMAD took place. Surprisingly, the reaction did not involve the expected [8 + 2] intermediate, o-quinodimethane. Instead, the reaction starts from intermolecular Diels-Alder reactions between DMAD and the furan moiety of vinylphenylfuran, followed by unexpected intramolecular alkene-alkene coupling. This step generates a diradical species, which then undergoes [1,3]-H shift to give the experimentally observed expoxyphenanthrene. DFT calculations revealed that, the [8 + 2] cycloadduct cannot be obtained because the [1,5]-H shift process from the [1,5]-vinyl shift intermediate is disfavored kinetically compared to the [1,3]-H shift to the [8 + 2] isomer.

  5. Detection of Morganella morganii, a prolific histamine former, by the polymerase chain reaction assay with 16S rDNA-targeted primers.

    Kim, Shin-Hee; An, Haejung; Field, Katharine G; Wei, Cheng-I; Velazquez, Jorge Barros; Ben-Gigirey, Begoña; Morrissey, Michael T; Price, Robert J; Pitta, Thomas P


    A polymerase chain reaction (PCR) assay for the rapid and sensitive detection of the most prolific histamine former, Morganella morganii, was developed. 16S rDNA targeted PCR primers were designed, and the primer specificity and sensitivity of the PCR assay were evaluated. The 16S rDNA sequence (1,503 bp) for M. morganii showed 95% identity to those for enteric bacteria, i.e., Enterobacter spp., Klebsiella spp., Citrobacter spp., Hafnia alvei, Proteus spp., and Providencia spp. The unique primers for M. morganii were designed on the basis of the variable regions in the 16S rDNA sequence. The primers showed positive reactions with all M. morganii strains tested. However, PCR amplification was not detected when the primers were tested with other enteric or marine bacteria. When the sensitivity of the assay was evaluated, M. morganii was detected at levels ranging from 10(6) to 10(8) CFU/ml in albacore homogenate after the PCR amplification. The sensitivity of the assay was greatly improved with the enrichment of samples, and 9 CFU of M. morganii per ml of albacore homogenate was detected after 6 h of enrichment at 37 degrees C.

  6. Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

    Cannon, William R.; Baker, Scott E.


    Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants. When used to model deterministic systems, the method corresponds to a rescaling of the time dependent reactions in such a way that steady states can be reached on the same time scale but with significantly fewer computational steps. The relationships between reaction affinities, free energy changes and generalized detailed balance are central to the discussion. The significance for applications in systems biology are discussed as is the concept and assumption of maximum entropy production rate as a biological principle that links thermodynamics to natural selection.

  7. Efficient Synthesis of Bi-butenolides Derivatives through Oxidative Dimeric Cyclizing-Coupling Reaction of 2,3-Allenoic Acids

    MA Sheng-Ming; YU Zhan-Qian


    @@ Allenes are three carbon functional groups possessing two perpendicular π-orbitals. Their unique reaction be havior is spread over three carbon atoms, which shows great potential in organic synthesis in terms of chirality transfer and diversity, as a result of the axial chirality as well as the substituent-loading capability. Recently, we devoted ourselves to establish a new area of oxidative cyclization-dimerization reactions between two functionalized allenes to give interesting bicyclic compounds in a single step. The formidable challenges are to match the reactivities of two allenes, and regenerate the catalyst, which would be reduced after reductive-elimination. In this paper we wish to disclose our recent studies on the synthesis of bi-butenolides from oxidative cyclization self-coupling reaction of 2,3 allenoic acids, in which a new system (PdCl2/RI/air) for regeneration of the palladium(Ⅱ) species was observed.

  8. Bifurcation and pattern formation in a coupled higher autocatalator reaction diffusion system


    Spatiotemporal structures arising in two identical cells, which are governed by higher autocatalator kinetics and coupled via diffusive interchange of autocatalyst,are discussed.The stability of the unique homogeneous steady state is obtained by the linearized theory.A necessary condition for bifurcations in spatially non-uniform solutions in uncoupled and coupled systems is given.Further information about Turing pattern solutions near bifurcation points is obtained by weakly nonlinear theory.Finally, the stability of equilibrium points of the amplitude equation is discussed by weakly nonlinear theory, with the bifurcation branches of the weakly coupled system.

  9. Methane coupling reaction in an oxy-steam stream through an OH radical pathway by using supported alkali metal catalysts

    Liang, Yin


    A universal reaction mechanism involved in the oxidative coupling of methane (OCM) is demonstrated under oxy-steam conditions using alkali-metal-based catalysts. Rigorous kinetic measurements indicated a reaction mechanism that is consistent with OH radical formation from a H 2O-O2 reaction followed by C-H activation in CH 4 with an OH radical. Thus, the presence of water enhances both the CH4 conversion rate and the C2 selectivity. This OH radical pathway that is selective for the OCM was observed for the catalyst without Mn, which suggests clearly that Mn is not the essential component in a selective OCM catalyst. The experiments with different catalyst compositions revealed that the OH.-mediated pathway proceeded in the presence of catalysts with different alkali metals (Na, K) and different oxo anions (W, Mo). This difference in catalytic activity for OH radical generation accounts for the different OCM selectivities. As a result, a high C2 yield is achievable by using Na2WO4/SiO2, which catalyzes the OH.-mediated pathway selectively. Make it methane: A universal reaction mechanism involved in the oxidative coupling of methane is demonstrated under oxy-stream conditions by using alkali-metal-based catalysts. Rigorous kinetic measurements indicated a reaction mechanism that is consistent with OH radical formation from an H2O-O2 reaction, followed by C-H activation in CH4 with an OH radical. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Investigation of thermochemistry associated with the carbon-carbon coupling reactions of furan and furfural using ab initio methods.

    Liu, Cong; Assary, Rajeev S; Curtiss, Larry A


    Upgrading furan and small oxygenates obtained from the decomposition of cellulosic materials via formation of carbon-carbon bonds is critical to effective conversion of biomass to liquid transportation fuels. Simulation-driven molecular level understanding of carbon-carbon bond formation is required to design efficient catalysts and processes. Accurate quantum chemical methods are utilized here to predict the reaction energetics for conversion of furan (C4H4O) to C5-C8 ethers and the transformation of furfural (C5H6O2) to C13-C26 alkanes. Furan can be coupled with various C1 to C4 low molecular weight carbohydrates obtained from the pyrolysis via Diels-Alder type reactions in the gas phase to produce C5-C8 cyclic ethers. The computed reaction barriers for these reactions (∼25 kcal/mol) are lower than the cellulose activation or decomposition reactions (∼50 kcal/mol). Cycloaddition of C5-C8 cyclo ethers with furans can also occur in the gas phase, and the computed activation energy is similar to that of the first Diels-Alder reaction. Furfural, obtained from biomass, can be coupled with aldehydes or ketones with α-hydrogen atoms to form longer chain aldol products, and these aldol products can undergo vapor phase hydrocycloaddition (activation barrier of ∼20 kcal/mol) to form the precursors of C26 cyclic hydrocarbons. These thermochemical studies provide the basis for further vapor phase catalytic studies required for upgrading of furans/furfurals to longer chain hydrocarbons.

  11. Development of two real-time polymerase chain reaction assays to detect Actinobacillus pleuropneumoniae serovars 1-9-11 and serovar 2.

    Marois-Créhan, Corinne; Lacouture, Sonia; Jacques, Mario; Fittipaldi, Nahuel; Kobisch, Marylène; Gottschalk, Marcelo


    Two real-time, or quantitative, polymerase chain reaction (qPCR) assays were developed to detect Actinobacillus pleuropneumoniae serovars 1-9-11 (highly related serovars with similar virulence potential) and serovar 2, respectively. The specificity of these assays was verified on a collection of 294 strains, which included all 16 reference A. pleuropneumoniae strains (including serovars 5a and 5b), 263 A. pleuropneumoniae field strains isolated between 1992 and 2009 in different countries, and 15 bacterial strains other than A. pleuropneumoniae. The detection levels of both qPCR tests were evaluated using 10-fold dilutions of chromosomal DNA from reference strains of A. pleuropneumoniae serovars 1 and 2, and the detection limit for both assays was 50 fg per assay. The analytical sensitivities of the qPCR tests were also estimated by using pure cultures and tonsils experimentally spiked with A. pleuropneumoniae. The detection threshold was 2.5 × 10(4) colony forming units (CFU)/ml and 2.9 × 10(5) CFU/0.1 g of tonsil, respectively, for both assays. These specific and sensitive tests can be used for the serotyping of A. pleuropneumoniae in diagnostic laboratories to control porcine pleuropneumonia.

  12. A capsid gene-based real-time reverse transcription polymerase chain reaction assay for the detection of marine vesiviruses in the Caliciviridae

    McClenahan, Shasta D.; Bok, Karin; Neill, John D.; Smith, Alvin W.; Rhodes, Crystal R.; Sosnovtsev, Stanislav V.; Green, Kim Y.; Romero, Carlos H.


    A real-time reverse transcription polymerase chain reaction (rtRT-PCR) assay was developed for the identification of marine vesiviruses. The primers were designed to target a 176-nucleotide fragment within a highly conserved region of the San Miguel sea lion viruses (SMSVs) capsid gene. The assay detected viral RNA from nine marine vesivirus serotypes described previously, including two serotypes (SMSV-8 and SMSV-12) not identified with presently available molecular assays, a highly-related bovine vesivirus strain (Bos-1), a mink vesivirus strain (MCV), and two novel genotypes isolated recently from Steller sea lions (SSL V810 and V1415). The real-time assay did not amplify sequences from the corresponding genomic regions of feline calicivirus (also in the genus Vesivirus) and representative members of the genus Norovirus. The rtRT-PCR assay described below may prove useful as a diagnostic tool for the detection of currently circulating, emerging and previously described marine vesiviruses in clinical samples, especially when large numbers are screened in surveillance studies of these restricted viruses. PMID:19410604

  13. Development of conventional and real-time reverse transcription polymerase chain reaction assays to detect Tembusu virus in Culex tarsalis mosquitoes.

    Petz, Lawrence N; Turell, Michael J; Padilla, Susana; Long, Lewis S; Reinbold-Wasson, Drew D; Smith, Darci R; O'Guinn, Monica L; Melanson, Vanessa R; Lee, John S


    Tembusu virus (TMUV) is an important emerging arthropod-borne virus that may cause encephalitis in humans and has been isolated in regions of southeast Asia, including Malaysia, Thailand, and China. Currently, detection and identification of TMUV are limited to research laboratories, because quantitative rapid diagnostic assays for the virus do not exist. We describe the development of sensitive and specific conventional and real-time quantitative reverse transcription polymerase chain reaction assays for detecting TMUV RNA in infected cell culture supernatant and Culex tarsalis mosquitoes. We used this assay to document the replication of TMUV in Cx. tarsalis, where titers increased 1,000-fold 5 days after inoculation. These assays resulted in the detection of virus-specific RNA in the presence of copurified mosquito nucleic acids. The use of these rapid diagnostic assays may have future applications for field pathogen surveillance and may assist in early detection, diagnosis, and control of the associated arthropod-borne pathogens. © The American Society of Tropical Medicine and Hygiene.

  14. Science Letters:Evaluation of a kinetic uricase method for serum uric acid assay by predicting background absorbance of uricase reaction solution with an integrated method

    LIAO Fei; ZHAO Yun-sheng; ZHAO Li-na; TAO Jia; ZHU Xiao-yun; LIU Lan


    A patented kinetic uricase method was evaluated for serum uric acid assay. Initial absorbance of the reaction mixture before uricase action (A0) was obtained by correcting the absorbance at 293 nm measured before the addition of uricase solution,and background absorbance (Ab) was predicted by an integrated method. Uric acid concentration in reaction solution was calculated from △A, the difference between A0 and Ab, using the absorptivity preset for uric acid. This kinetic uricase method exhibited CV<4.3% and recovery of 100%. Lipids, bilirubin, hemoglobin, ascorbic acid, reduced glutathione and xanthine <0.32 mmol/L in serum had no significant effects. △A linearly responded to 1.2 to 37.5 μmol/L uric acid in reaction solution containing 15 μl serum.The slope of linear response was consistent with the absorptivity preset for uric acid while the intercept was consistent with that for serum alone. Uric acid concentrations in clinic sera by different uricase methods positively correlated to each other. By Bland-Altman analysis, this kinetic uricase method accorded with that by quantifying the total change of UV absorbance on the completion of uricase reaction. These results demonstrated that this kinetic uricase method is reliable for serum uric acid assay with enhanced resistance to both xanthine and other common errors, wider range of linear response and much lower cost.

  15. Nonequilibrium thermodynamics in the strong coupling and non-Markovian regime based on a reaction coordinate mapping

    Strasberg, Philipp; Schaller, Gernot; Lambert, Neill; Brandes, Tobias


    We propose a method to study the thermodynamic behaviour of small systems beyond the weak coupling and Markovian approximation, which is different in spirit from conventional approaches. The idea is to redefine the system and environment such that the effective, redefined system is again coupled weakly to Markovian residual baths and thus, allows to derive a consistent thermodynamic framework for this new system-environment partition. To achieve this goal we make use of the reaction coordinate (RC) mapping, which is a general method in the sense that it can be applied to an arbitrary (quantum or classical and even time-dependent) system coupled linearly to an arbitrary number of harmonic oscillator reservoirs. The core of the method relies on an appropriate identification of a part of the environment (the RC), which is subsequently included as a part of the system. We demonstrate the power of this concept by showing that non-Markovian effects can significantly enhance the steady state efficiency of a three-level-maser heat engine, even in the regime of weak system-bath coupling. Furthermore, we show for a single electron transistor coupled to vibrations that our method allows one to justify master equations derived in a polaron transformed reference frame.

  16. Evaluation of a novel real-time fluorescent polymerase chain reaction assay for high-risk human papilloma virus DNA genotypes in cytological cervical screening.

    Cheng, Jiaoying; Bian, Meilu; Cong, Xiao; Sun, Aiping; Li, Min; Ma, Li; Chen, Ying; Liu, Jun


    It has been confirmed that detection of high-risk human papillomavirus (HR HPV) DNA is useful in cervical cancer (CC) screening. Recently, a new real-time fluorescent polymerase chain reaction (PCR) assay was developed to detect HR HPV. This assay can synchronize nucleic acid amplification and testing using specific primers for 13 types of HR HPV genomes, combined with specific TaqMan fluorescent marker probe techniques through the fluorescence automatic PCR instrument. Furthermore, it uses TaqGold™ DNA polymerase, which minimizes the amount of non-specific amplification and increases the sensitivity of the assay. The aim of this study was to evaluate the analytical and clinical performance of the real-time fluorescent PCR assay in CC screening, compared to the Qiagen Hybrid Capture(®) II High-Risk HPV DNA test(®) (HC II). In total, 1,252 cervical specimens were collected from women between 19 and 71 years of age. The specimens were examined with three different assays, real-time fluorescent PCR assay and HC II for HR HPV detection combined with liquid-based cytology. Women with cytological abnormalities or HR HPV-positive results underwent colposcopy and cervical biopsy. This study demonstrated good overall agreement between HC II and real-time fluorescent PCR assay (overall agreement, 92.25%; Cohen's κ=0.814). For the detection of high-grade cervical intraepithelial neoplasias (CIN) and CC, the sensitivity of HC II and real-time fluorescent PCR was 94.48 and 92.82%, respectively, and the negative predictive value was 98.85 and 98.54%, respectively. High HR HPV infection rate of the high-grade CIN and CC group was detected (PHPV detection and could be used in CC screening in clinic.

  17. Triplex real-time polymerase chain reaction assay for detection and quantification of norovirus (GI and GII) and sapovirus.

    Niwa, Shoichi; Tsukagoshi, Hiroyuki; Ishioka, Taisei; Sasaki, Yoshiko; Yoshizumi, Masakazu; Morita, Yukio; Kimura, Hirokazu; Kozawa, Kunihisa


    To improve detection of norovirus (NoVGI, NoVGII) and sapovirus (SaV), a simultaneous quantitative RT-PCR method was established. This triplex real-time PCR method was evaluated using a combination of optimized specific primers and probes. The performance of the developed PCR assay was equivalent to that of monoplex real-time PCR across a broad dynamic range of 10(2) -10(7) copies/assay using plasmid DNA standards. The limit of detection was 10(2) copies/assay. The quantitative value was comparable with that of monoplex real-time PCR of stool samples. Our triplex real-time PCR is useful for detection of NoV and SaV infections. © 2013 The Societies and Wiley Publishing Asia Pty Ltd.

  18. A Quantitative Polymerase Chain Reaction Assay for the Detection and Quantification of Epizootic Epitheliotropic Disease Virus (EEDV; Salmonid Herpesvirus 3).

    Glenney, Gavin W; Barbash, Patricia A; Coll, John A


    Epizootic epitheliotropic disease virus (EEDV; salmonid herpesvirus [SalHV3]; family Alloherpesviridae) causes a systemic disease of juvenile and yearling Lake Trout Salvelinus namaycush. No cell lines are currently available for the culture and propagation of EEDV, so primary diagnosis is limited to PCR and electron microscopy. To better understand the pervasiveness of EEDV (carrier or latent state of infection) in domesticated and wild Lake Trout populations, we developed a sensitive TaqMan quantitative PCR (qPCR) assay to detect the presence of the EEDV terminase gene in Lake Trout tissues. This assay was able to detect a linear standard curve over nine logs of plasmid dilution and was sensitive enough to detect single-digit copies of EEDV. The efficiency of the PCR assay was 99.4 ± 0.06% (mean ± SD), with a 95% confidence limit of 0.0296 (R(2) = 0.994). Methods were successfully applied to collect preliminary data from a number of species and water bodies in the states of Pennsylvania, New York, and Vermont, indicating that EEDV is more common in wild fish than previously known. In addition, through the development of this qPCR assay, we detected EEDV in a new salmonid species, the Cisco Coregonus artedi. The qPCR assay was unexpectedly able to detect two additional herpesviruses, the Atlantic Salmon papillomatosis virus (ASPV; SalHV4) and the Namaycush herpesvirus (NamHV; SalHV5), which both share high sequence identity with the EEDV terminase gene. With these unexpected findings, we subsequently designed three primer sets to confirm initial TaqMan qPCR assay positives and to differentiate among EEDV, ASPV, and NamHV by detecting the glycoprotein genes via SYBR Green qPCR. Received April 20, 2015; accepted November 10, 2015.

  19. Validation of high-throughput real time polymerase chain reaction assays for simultaneous detection of invasive citrus pathogens.

    Saponari, Maria; Loconsole, Giuliana; Liao, Hui-Hong; Jiang, Bo; Savino, Vito; Yokomi, Raymond K


    A number of important citrus pathogens are spread by graft propagation, arthropod vector transmission and inadvertent import and dissemination of infected plants. For these reasons, citrus disease management and clean stock programs require pathogen detection systems which are economical and sensitive to maintain a healthy industry. To this end, multiplex quantitative real-time PCR (qPCR) assays were developed allowing high-throughput and simultaneous detection of some major invasive citrus pathogens. Automated high-throughput extraction comparing several bead-based commercial extraction kits were tested and compared with tissue print and manual extraction to obtain nucleic acids from healthy and pathogen-infected citrus trees from greenhouse in planta collections and field. Total nucleic acids were used as templates for pathogen detection. Multiplex reverse transcription-qPCR (RT-qPCR) assays were developed for simultaneous detection of six targets including a virus, two viroids, a bacterium associated with huanglongbing and a citrus RNA internal control. Specifically, two one-step TaqMan-based multiplex RT-qPCR assays were developed and tested with target templates to determine sensitivity and detection efficiency. The first assay included primers and probes for 'Candidatus Liberibacter asiaticus' (CLas) and Citrus tristeza virus (CTV) broad spectrum detection and genotype differentiation (VT- and T3-like genotypes). The second assay contained primers and probes for Hop stunt viroid (HSVd), Citrus exocortis viroid (CEVd) and the mitochondrial NADH dehydrogenase (nad5) mRNA as an internal citrus host control. Primers and TaqMan probes for the viroids were designed in this work; whereas those for the other pathogens were from reports of others. Based on quantitation cycle values, automated high-throughput extraction of samples proved to be as suitable as manual extraction. The multiplex RT-qPCR assays detected both RNA and DNA pathogens in the same dilution series

  20. Unexpected hydrodeiodo Sonogashira-Heck-Casser coupling reaction of 2,2'-diiodobiphenyls with acetylenes.

    Chou, Meng-Yen; Mandal, Ashis Baran; Leung, Man-kit


    2,2'-Diiodobiphenyl-4,4'-dicarboxylic acid dimethyl ester (3) undergoes either a ring-closure reaction with phenylacetylene to give 4 or hydrodeiodo phenylethynylation to give 5 under the catalytic conditions of Pd(OAc)(2)/CuI/phosphine in amines. In these reactions, the amine and the phosphine ligands play important roles in controlling the reactivity. Among the ligands we used, tris(o-tolyl)phosphine is the best ligand for hydrodeiodo phenylethynylation, while the bidentate phosphine ligand retards both of the reactions. On the basis of our results, we propose that 5 is formed through a fast hydrodeiodination, followed by a Sonogashira phenylethynylation. The results of the deuterium labeling experiments show that proton exchange between the acetylenic proton and the alkyl protons of amine occurs effectively under the reaction conditions. In addition, the hydrogen that replaces the iodide in the hydrodeiodination process arises mainly from the acetylenic proton.

  1. Elimination of competing hydrolysis and coupling side reactions of a cyclodextrin glucanotransferase by directed evolution

    Kelly, Ronan M.; Leemhuis, Hans; Rozeboom, Henriette J.; van Oosterwijk, Niels; Dijkstra, Bauke W.; Dijkhuizen, Lubbert


    Thermoanaerobacterium thermosulfurigenes cyclodextrin glucanotransferase primarily catalyses the formation of cyclic alpha-(1,4)-linked oligosaccharides (cyclodextrins) from starch. This enzyme also possesses unusually high hydrolytic activity as a side reaction, thought to be due to partial retenti

  2. Averaging methods for stochastic dynamics of complex reaction networks: description of multi-scale couplings

    Plyasunov, S


    This paper is concerned with classes of models of stochastic reaction dynamics with time-scales separation. We demonstrate that the existence of the time-scale separation naturally leads to the application of the averaging principle and elimination of degrees of freedom via the renormalization of transition rates of slow reactions. The method suggested in this work is more general than other approaches presented previously: it is not limited to a particular type of stochastic processes and can be applied to different types of processes describing fast dynamics, and also provides crossover to the case when separation of time scales is not well pronounced. We derive a family of exact fluctuation-dissipation relations which establish the connection between effective rates and the statistics of the reaction events in fast reaction channels. An illustration of the technique is provided. Examples show that renormalized transition rates exhibit in general non-exponential relaxation behavior with a broad range of pos...

  3. Effect of coupling in the 28Si+154Sm reaction studied by quasi-elastic scattering

    Kaur, Gurpreet; Behera, B. R.; Jhingan, A.; Nayak, B. K.; Dubey, R.; Sharma, Priya; Thakur, Meenu; Mahajan, Ruchi; Saneesh, N.; Banerjee, Tathagata; Khushboo, Kumar, A.; Mandal, S.; Saxena, A.; Sugathan, P.; Rowley, N.


    The study of the coupling to collective states of the 28Si projectile and 154Sm target in fusion mechanism is reported. Understanding such couplings is important as they influence the barrier height and the formation probability of the compound nuclei, which in turn may be related to the synthesis of superheavy elements in heavier systems. In the present work, before performing the coupled-channel calculations, we wish to obtain an experimental signature of coupling to projectile and target excitation through barrier distribution (BD) study. To this end, the BDs of the 28Si+154Sm and 16O+154Sm systems have been compared using existing fusion data, scaled to compensate for the differences between the nominal Coulomb barriers and the respective coupling strengths. However, the large error bars on the high-energy side of the fusion BD prevent any definite identification of such signatures. We have, therefore, performed a quasi-elastic (QE) scattering experiment for the heavier 28Si+154Sm system and compared its results with existing QE data for the 16O projectile. Since QE BDs are precise at higher energies, the comparison has shown that the BD of 28Si+154Sm is similar to that of 16O+154Sm to a large extent except for a peaklike structure on the higher energy side. The similarity shows that the 154Sm deformation plays a major role in the fusion mechanism of 28Si+154Sm system. The peaklike structure is attributed to 28Si excitation. In contrast with previous studies, it is found that a coupled-channel calculation with vibrational coupling to the first 2+ state of 28Si reproduces this structure rather well. However, an almost identical result is found with the rotational coupling scheme if one considers the large positive hexadecapole deformation of the projectile. A value around that given by Möller and Nix (β4≈0.25 ) leads to a strong cancellation in the re-orientation term that couples the 2+ state back to itself, making that state look vibrational in this

  4. C(sp2)–C(sp2) cross coupling reaction catalyzed by a palladacycle phosphine complex: A simple and sustainable protocol in aqueous media

    Seyyed Javad Sabounchei; Marjan Hosseinzadeh


    The Heck reactions of various aryl halides with olefins using {[Ph2PCH2PPh2CH=C(O)(C10H7)] PdCl2} as efficient catalyst has been investigated. The mononuclear palladacycle complex showed excellent activity in aqueous phase including the C(sp2)–C(sp2) cross coupling reactions. The advantages of the protocol are high yields, short reaction time, a cleaner reaction profile and notable simplicity.

  5. A new multiplex polymerase chain reaction assay for the identification a panel of bacteria involved in bacteremia

    Hossein Fazzeli


    Conclusions: The presented multiplex PCR offers a rapid and accurate molecular diagnostic tool for simultaneous detection of some pathogenic microorganisms. The IC exists in the multiplex PCR accompanied by other primers in the system, can serve as a simple, cost- effective internal control for the multiplex PCR assay.

  6. Miswak mediated green synthesized palladium nanoparticles as effective catalysts for the Suzuki coupling reactions in aqueous media

    Mujeeb Khan


    Full Text Available Green and eco-friendly synthesis of palladium nanoparticles NPs is carried out under facile and eco-friendly conditions using an aqueous solution of Salvadora persica L. (SP root extract (RE as a bioreductant, which is commonly known as Miswak. The as-synthesized Pd NPs were characterized using various spectroscopic and microscopic techniques, including, UV–Vis spectroscopy, FT-IR spectroscopy, XRD, ICP-MS and TEM. Detailed investigations of the Pd NPs have confirmed that the polyphenolic phytomolecules present in the RE of Miswak not only act as a bioreductant by facilitating the reduction and growth of Pd NPs, but they also functionalize the surface of Pd NPs and stabilized them in various solvents. Furthermore, the catalytic activity of the green synthesized Pd NPs was also tested toward the Suzuki coupling reactions of various aryl halides in aqueous media. The as-prepared Pd NPs exhibited superior catalytic activity and reusability for the Suzuki coupling reaction in aqueous and aerobic conditions. The kinetics of the reaction studied by GC revealed that the conversion of various aryl halides to biphenyl takes place in a short time.

  7. Selective C-Arylation of 2,5-Dibromo-3-hexylthiophene via Suzuki Cross Coupling Reaction and Their Pharmacological Aspects

    Hafiz Mansoor Ikram


    Full Text Available The present study reports the synthesis of various new derivatives based on 5-aryl-2-bromo-3-hexylthiophene with moderate-to-good yields via a palladium-catalyzed Suzuki cross-coupling reaction. This coupling method involved the reaction of 2,5-dibromo-3-hexylthiophene with several arylboronic acids in order to synthesize corresponding thiophene derivatives under controlled and optimal reaction conditions. The different substituents (CH3, OCH3, Cl, F etc. present on arylboronic acids are found to have significant electronic effects on the overall properties of new products. The synthesized thiophene molecules were studied for their haemolytic, biofilm inhibition and anti-thrombolytic activities, and almost all products showed potentially good properties. The compound 2-bromo-5-(3-chloro-4-fluorophenyl-3-hexylthiophenein particular exhibited the highest values for haemolytic and bio-film inhibition activities among all newly synthesized derivatives. In addition, the compound 2-bromo-3-hexyl-5-(4-iodophenylthiophene also showed high anti-thrombolytic activity, suggesting the potential medicinal applications of these newly synthesized compounds.

  8. Effects of Molecular Oxygen, Solvent, and Light on Iridium-Photoredox/Nickel Dual-Catalyzed Cross-Coupling Reactions.

    Oderinde, Martins S; Varela-Alvarez, Adrian; Aquila, Brian; Robbins, Daniel W; Johannes, Jeffrey W


    In order to achieve reproducibility during iridium-photoredox and nickel dual-catalyzed sp(3)-sp(2) carbon-carbon bond-forming reactions, we investigated the role that molecular oxygen (O2), solvent and light-source (CF lamp or blue LED) play in a variety of Ir-photoredox mediated transformations. The presence of O2 was discovered to be important for catalyst activation when air-stable Ni(II) precatalysts were used in DMF under CF lamp irradiation; however, O2 was not required for catalysis when conducted with Ni(COD)2 in the same reaction system. O2 is believed to promote rapid reduction of the Ni(II) precatalyst by Ir(II) to Ni(0). In addition to O2, the effects that solvent and light-source have on the dual-catalyzed decarboxylative cross-coupling reactions will be discussed. These findings have enabled us to develop a more robust dual-catalyzed decarboxylative cross-coupling protocol.

  9. A novel assay method for the trace determination of Th and U in copper and lead using inductively coupled plasma mass spectrometry

    LaFerriere, Brian D.; Maiti, Tapas C.; Arnquist, Isaac J.; Hoppe, Eric W.


    This study describes a novel sample preparation and assay method developed in support of the MAJORANA DEMONSTRATOR experiment for the determination of thorium and uranium levels in copper and lead shielding components. Meticulously clean sample preparation methods combined with novel anion exchange separations for analyte pre-concentration and matrix removal were developed. Quantification was performed by inductively coupled plasma mass spectrometry. Detection limits of 0.0084 pg 232Th/g and 0.0106 pg 238U/g were determined for copper, while detection limits of 0.23 pg 232Th/g and 0.46 pg 238U/g were achieved for lead. These methods allow the Majorana Collaboration to accurately assay detector components and ensure that the experiment’s stringent radiopurity requirements are met.

  10. Analysis of Flavonoids in Lotus (Nelumbo nucifera) Leaves and Their Antioxidant Activity Using Macroporous Resin Chromatography Coupled with LC-MS/MS and Antioxidant Biochemical Assays.

    Zhu, Ming-Zhi; Wu, Wei; Jiao, Li-Li; Yang, Ping-Fang; Guo, Ming-Quan


    Lotus (Nelumbo nucifera) leaves, a traditional Chinese medicinal herb, are rich in flavonoids. In an effort to thoroughly analyze their flavonoid components, macroporous resin chromatography coupled with HPLC-MS/MS was employed to simultaneously enrich and identify flavonoids from lotus leaves. Flavonoids extracted from lotus leaves were selectively enriched in the macroporous resin column, eluted subsequently as fraction II, and successively subjected to analysis with the HPLC-MS/MS and bioactivity assays. Altogether, fourteen flavonoids were identified, four of which were identified from lotus leaves for the first time, including quercetin 3-O-rhamnopyranosyl-(1→2)-glucopyranoside, quercetin 3-O-arabinoside, diosmetin 7-O-hexose, and isorhamnetin 3-O-arabino- pyranosyl-(1→2)-glucopyranoside. Further bioactivity assays revealed that these flavonoids from lotus leaves possess strong antioxidant activity, and demonstrate very good potential to be explored as food supplements or even pharmaceutical products to improve human health.

  11. Analysis of Flavonoids in Lotus (Nelumbo nucifera Leaves and Their Antioxidant Activity Using Macroporous Resin Chromatography Coupled with LC-MS/MS and Antioxidant Biochemical Assays

    Ming-Zhi Zhu


    Full Text Available Lotus (Nelumbo nucifera leaves, a traditional Chinese medicinal herb, are rich in flavonoids. In an effort to thoroughly analyze their flavonoid components, macroporous resin chromatography coupled with HPLC-MS/MS was employed to simultaneously enrich and identify flavonoids from lotus leaves. Flavonoids extracted from lotus leaves were selectively enriched in the macroporous resin column, eluted subsequently as fraction II, and successively subjected to analysis with the HPLC-MS/MS and bioactivity assays. Altogether, fourteen flavonoids were identified, four of which were identified from lotus leaves for the first time, including quercetin 3-O-rhamnopyranosyl-(1→2-glucopyranoside, quercetin 3-O-arabinoside, diosmetin 7-O-hexose, and isorhamnetin 3-O-arabino- pyranosyl-(1→2-glucopyranoside. Further bioactivity assays revealed that these flavonoids from lotus leaves possess strong antioxidant activity, and demonstrate very good potential to be explored as food supplements or even pharmaceutical products to improve human health.

  12. Comparative evaluation of polymerase chain reaction assay with microscopy for detection of asymptomatic carrier state of theileriosis in a herd of crossbred cattle

    Charaya, Gaurav; Rakha, N. K.; Maan, Sushila; Kumar, Aman; Kumar, Tarun; Jhambh, Ricky


    Aim: This study aims to develop and to standardize a polymerase chain reaction (PCR) assay that will diagnose clinical as well as carrier state of the disease and to compare the results with conventional microscopy technique. Materials and Methods: A herd of crossbred cattle with the previous history of theileriosis in village Lahli, district Rohtak, Haryana, was selected for this study. A total of 29 blood samples were collected randomly from cows including five clinically ill cattle. Blood smears from all animals and lymph node biopsy smears from animal with swollen lymph nodes were examined microscopically after conventional Giemsa staining. Phenol chloroform isoamyl alcohol method was used for extracting DNA from blood. Previously published primers targeting cytochrome b gene sequence of Theileria annulata were used in the PCR assay that was standardized to use in the laboratory. Results: Out of 29 samples tested,18 (62.06%) were found positive for theileriosis by PCR assay, whereas only 10 (34.48%) samples were detected positive by conventional microscopic technique using Giemsa staining method. Conclusions: On the basis results of comparative studies, it can be concluded that PCR assay is a more sensitive than microscopic examination for detection of theileriosis. This can be attributed to the ability of PCR assay to detect small amounts of genomic DNA of T. annulata or low parasitemia in cows. Therefore, PCR assay can serve as a more sensitive tool to detect Theileria for detection of theileriosis even in asymptomatic carrier cattle which is important for the implementation of successful control programs. PMID:27733810

  13. Comparative evaluation of polymerase chain reaction assay with microscopy for detection of asymptomatic carrier state of theileriosis in a herd of crossbred cattle

    Gaurav Charaya


    Full Text Available Aim: This study aims to develop and to standardize a polymerase chain reaction (PCR assay that will diagnose clinical as well as carrier state of the disease and to compare the results with conventional microscopy technique. Materials and Methods: A herd of crossbred cattle with the previous history of theileriosis in village Lahli, district Rohtak, Haryana, was selected for this study. A total of 29 blood samples were collected randomly from cows including five clinically ill cattle. Blood smears from all animals and lymph node biopsy smears from animal with swollen lymph nodes were examined microscopically after conventional Giemsa staining. Phenol chloroform isoamyl alcohol method was used for extracting DNA from blood. Previously published primers targeting cytochrome b gene sequence of Theileria annulata were used in the PCR assay that was standardized to use in the laboratory. Results: Out of 29 samples tested,18 (62.06% were found positive for theileriosis by PCR assay, whereas only 10 (34.48% samples were detected positive by conventional microscopic technique using Giemsa staining method. Conclusions: On the basis results of comparative studies, it can be concluded that PCR assay is a more sensitive than microscopic examination for detection of theileriosis. This can be attributed to the ability of PCR assay to detect small amounts of genomic DNA of T. annulata or low parasitemia in cows. Therefore, PCR assay can serve as a more sensitive tool to detect Theileria for detection of theileriosis even in asymptomatic carrier cattle which is important for the implementation of successful control programs.

  14. Nafion-Teflon bimembrane-supported palladium catalysts for Suzuki coupling reactions


    Nafion-Teflon bimembrane was used as an efficient support for the preparation and application of heterogeneous palladium catalysts. The supported palladium catalysts exhibit high activity and stability in the Suzuki cross-coupling of aryl bromides with arylboronic acids to afford the corresponding biaryls in good to excellent yields, and can be readily recovered and reused several times without significant loss of activity.

  15. Applications of and alternatives to pi-electron-deficient azine organometallics in metal catalyzed cross-coupling reactions.

    Campeau, Louis-Charles; Fagnou, Keith


    While the use of pi-deficient azine halides in palladium catalyzed cross-coupling reactions is common, the use of pi-electron deficient azine organometallics has been less intensively examined. In recent years, important advances have been made that are beginning to address this deficiency and need. The purpose of this tutorial review is to highlight and discuss the innovations that facilitate the synthesis of azine-containing biaryls with a focus on the pyridine structural motif. Given the number of important compounds which exhibit azine-heterobiaryls and the wide use of cross-coupling methods in their synthesis, this review should be of interest among synthetic organic chemists and organometallic chemists alike.

  16. Preliminary Study of Coupling Electrical Energy to Detonation Reaction Zone of Primasheet-1000 Explosive


    200-kJ capacitor bank into the conductive zone behind the detonation front of Primasheet-1000 explosive reaction. Upon initiation of the from a 5.5 kV, 0.010 F, 200 kJ capacitor bank into the conductive zone behind the detonation front of Primasheet-1000 explosive reaction. Upon...explosive. The plates are 2.54 cm wide by 50 cm long by 1.27 cm thick. 55 kilojoules (KJ) of energy is transferred from a capacitor to a 22

  17. Reaction diffusion in Ni–Al diffusion couples in steady magnetic fields

    Li, Chuanjun, E-mail: [School of Materials Science and Engineering, Shanghai University, Shanghai 200072 (China); Yuan, Zhaojing; Guo, Rui; Xuan, Weidong; Ren, Zhongming; Zhong, Yunbo; Li, Xi [School of Materials Science and Engineering, Shanghai University, Shanghai 200072 (China); Wang, Hui; Wang, Qiuliang [Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190 (China)


    Highlights: • The Ni–Al diffusion couples were prepared by the electrodeposition technique. • The magnetic field reduced the growth rates of product layers in diffusion couples. • The effect of the magnetic field on diffusion depends on its intensity and direction. • The spiral motion of an atom in the magnetic field reduces diffusivity. - Abstract: The effect of a steady magnetic field on reactive diffusion in Ni–Al diffusion couples was investigated. The diffusion couples prepared by the electrodeposition technique were annealed in the temperature range of 530–590 °C with and without the magnetic field of 6 T. Regardless of the magnetic field, two intermetallic compounds, i.e., Ni{sub 2}Al{sub 3} and NiAl{sub 3}, were present in the product layers of diffusion couples. NiAl{sub 3} phase shows island-like structures at relatively lower temperatures while the Ni{sub 2}Al{sub 3} phase forms a typical layered structure. The growth of Ni{sub 2}Al{sub 3} layer was found to be parabolic. When the diffusion direction was perpendicular to the direction of the magnetic field, the external magnetic field reduced the growth rate of the Ni{sub 2}Al{sub 3} phase. Whereas the magnetic field had no obvious effect on the growth rate of Ni{sub 2}Al{sub 3} layers in the diffusion configuration of mutually parallel directions. The magnetic field intensity and direction dependence of growth rate of Ni{sub 2}Al{sub 3} intermetallic layers can be attributed to the change in number of collision of an atom with neighbors during diffusion due to spiral motion under the action of the Lorentz force, which leads to change the frequency factor, not activation energy, for layer growth.

  18. Development of a diagnostic real-time polymerase chain reaction assay for the detection of invasive Haemophilus influenzae in clinical samples.

    Meyler, Kenneth L


    Since the introduction of the Haemophilus influenzae serotype b vaccine, invasive H. influenzae disease has become dominated by nontypeable (NT) strains. Several widely used molecular diagnostic methods have been shown to lack sensitivity or specificity in the detection of some of these strains. Novel real-time assays targeting the fucK, licA, and ompP2 genes were developed and evaluated. The fucK assay detected all strains of H. influenzae tested (n = 116) and had an analytical sensitivity of 10 genome copies\\/polymerase chain reaction (PCR). This assay detected both serotype b and NT H. influenzae in 12 previously positive specimens (culture and\\/or bexA PCR) and also detected H. influenzae in a further 5 of 883 culture-negative blood and cerebrospinal fluid (CSF) samples. The fucK assay has excellent potential as a diagnostic test for detection of typeable and nontypeable strains of invasive H. influenzae in clinical samples of blood and CSF.

  19. Development of an event-specific hydrolysis probe quantitative real-time polymerase chain reaction assay for Embrapa 5.1 genetically modified common bean (Phaseolus vulgaris).

    Treml, Diana; Venturelli, Gustavo L; Brod, Fábio C A; Faria, Josias C; Arisi, Ana C M


    A genetically modified (GM) common bean event, namely Embrapa 5.1, resistant to the bean golden mosaic virus (BGMV), was approved for commercialization in Brazil. Brazilian regulation for genetically modified organism (GMO) labeling requires that any food containing more than 1% GMO be labeled. The event-specific polymerase chain reaction (PCR) method has been the primary trend for GMO identification and quantitation because of its high specificity based on the flanking sequence. This work reports the development of an event-specific assay, named FGM, for Embrapa 5.1 detection and quantitation by use of SYBR Green or hydrolysis probe. The FGM assay specificity was tested for Embrapa 2.3 event (a noncommercial GM common bean also resistant to BGMV), 46 non-GM common bean varieties, and other crop species including maize, GM maize, soybean, and GM soybean. The FGM assay showed high specificity to detect the Embrapa 5.1 event. Standard curves for the FGM assay presented a mean efficiency of 95% and a limit of detection (LOD) of 100 genome copies in the presence of background DNA. The primers and probe developed are suitable for the detection and quantitation of Embrapa 5.1.

  20. Development of a real-time polymerase chain reaction assay for the detection of the invasive Mediterranean fanworm, Sabella spallanzanii, in environmental samples.

    Wood, Susanna A; Zaiko, Anastasija; Richter, Ingrid; Inglis, Graeme J; Pochon, Xavier


    The Mediterranean fanworm, Sabella spallanzanii Gmelin 1791, was first detected in the Southern Hemisphere in the 1990s and is now abundant in many parts of southern Australia and in several locations around northern New Zealand. Once established, it can proliferate rapidly, reaching high densities with potential ecological and economic impacts. Early detection of new S. spallanzanii incursions is important to prevent its spread, guide eradication or control efforts and to increase knowledge on the species' dispersal pathways. In this study, we developed a TaqMan probe real-time polymerase chain reaction assay targeting a region of the mitochondrial cytochrome oxidase I gene. The assay was validated in silico and in vitro using DNA from New Zealand and Australian Sabellidae with no cross-reactivity detected. The assay has a linear range of detection over seven orders of magnitude with a limit of detection reached at 12.4 × 10(-4) ng/μL of DNA. We analysed 145 environmental (water, sediment and biofouling) samples and obtained positive detections only from spiked samples and those collected at a port where S. spallanzanii is known to be established. This assay has the potential to enhance current morphological and molecular-based methods, through its ability to rapidly and accurately identify S. spallanzanii in environmental samples.

  1. Development and inter-laboratory transfer of a decaplex polymerase chain reaction assay combined with capillary electrophoresis for the simultaneous detection of ten food allergens.

    Cheng, Fang; Wu, Jiajie; Zhang, Jin; Pan, Aihu; Quan, Sheng; Zhang, Dabing; Kim, HaeYeong; Li, Xiang; Zhou, Shan; Yang, Litao


    Food allergies cause health risks to susceptible consumers and regulations on labeling of food allergen contents have been implemented in many countries and regions. To achieve timely and accurate food allergen labeling, the development of fast and effective allergen detection methods is very important. Herein, a decaplex polymerase chain reaction (PCR) assay combined with capillary electrophoresis was developed to detect simultaneously 10 common food allergens from hazelnut, pistachio, oat, sesame, peanut, cashew, barley, wheat, soybean and pecan. The absolute limit of detection (LODa) of this system is between 2 and 20 copies of haploid genome, and the relative LOD (LODr) is as low as 0.005% (w/w) in simulated food mixtures. The developed assay was subsequently applied to 20 commercial food products and verified the allergen ingredients stated on the labels. Furthermore, results using this decaplex PCR assay was successfully replicated in three other laboratories, demonstrating the repeatability and applicability of this assay in routine analysis of the 10 food allergens.

  2. Use of ImageJ to recover information from individual cells in a G protein-coupled receptor assay.

    Trabuco, João R C; Martins, Sofia Aires M; Prazeres, Duarte Miguel F


    Live-cell assays used in GPCR research often rely on fluorescence techniques that generate large amounts of raw image data. Consequently, the capacity to accurately and timely extract useful information from image and video data has become more and more important. Image J is an open-source program that provides powerful tools with a simple interface designed to fit the needs of image analysis of most researchers. In this chapter, Image J routines to extract information from individual cells in a calcium GPCR assay are described. In these routines, individual cells in the same image/video data can be separated using either a progressive threshold or a local threshold method. Both methods can be optimized to either a maximum number of selection or maximum area selected resulting in conceptually distinct selections.

  3. Assay of calcium borogluconate veterinary medicines for calcium gluconate, boric acid, phosphorus, and magnesium by using inductively coupled plasma emission spectrometry

    Lyons, D.J.; Spann, K.P.


    An inductively coupled plasma spectrometric method is described for the determination of 4 elements (Ca, B, P, and Mg) in calcium borogluconate veterinary medicines. Samples are diluted, acidified, and sprayed directly into the plasma. Reproducibility relative confidence intervals for a single sample assay are +/- 1.4% (calcium), +/- 1.8% (boron), +/- 2.6% (phosphorus), and +/- 1.4% (magnesium). The total element concentrations for each of 4 elements compared favorably with concentrations determined by alternative methods. Formulation estimates of levels of calcium gluconate, boric acid, phosphorus, and magnesium salts can be made from the analytical data.

  4. A cAMP Biosensor-Based High-Throughput Screening Assay for Identification of Gs-Coupled GPCR Ligands and Phosphodiesterase Inhibitors

    Vedel, Line; Bräuner-Osborne, Hans; Mathiesen, Jesper Mosolff


    resulted in prolonged signaling and enabled detection of weak partial agonists and/or ligands with low potency, which is highly advantageous in large HTS settings and hit identification. In addition, the assay enabled detection of β2AR inverse agonists and PDE inhibitors. High signal-to-noise ratios were...... in living cells. We used the β2-adrenergic receptor (β2AR) as a representative Gs-coupled receptor and characterized two cell lines with different expression levels. Low receptor expression allowed detection of desensitization kinetics and delineation of partial agonism, whereas high receptor expression...

  5. Live Cell Bioluminescence Imaging in Temporal Reaction of G Protein-Coupled Receptor for High-Throughput Screening and Analysis.

    Hattori, Mitsuru; Ozawa, Takeaki


    G protein-coupled receptors (GPCRs) are notable targets of basic therapeutics. Many screening methods have been established to identify novel agents for GPCR signaling in a high-throughput manner. However, information related to the temporal reaction of GPCR with specific ligands remains poor. We recently developed a bioluminescence method for the quantitative detection of the interaction between GPCR and β-arrestin using split luciferase complementation. To monitor time-course variation of the interactions, a new imaging system contributes to the accurate evaluation of drugs for GPCRs in a high-throughput manner.

  6. Crawling and turning in a minimal reaction-diffusion cell motility model: Coupling cell shape and biochemistry

    Camley, Brian A.; Zhao, Yanxiang; Li, Bo; Levine, Herbert; Rappel, Wouter-Jan


    We study a minimal model of a crawling eukaryotic cell with a chemical polarity controlled by a reaction-diffusion mechanism describing Rho GTPase dynamics. The size, shape, and speed of the cell emerge from the combination of the chemical polarity, which controls the locations where actin polymerization occurs, and the physical properties of the cell, including its membrane tension. We find in our model both highly persistent trajectories, in which the cell crawls in a straight line, and turning trajectories, where the cell transitions from crawling in a line to crawling in a circle. We discuss the controlling variables for this turning instability and argue that turning arises from a coupling between the reaction-diffusion mechanism and the shape of the cell. This emphasizes the surprising features that can arise from simple links between cell mechanics and biochemistry. Our results suggest that similar instabilities may be present in a broad class of biochemical descriptions of cell polarity.

  7. Crawling and turning in a minimal reaction-diffusion cell motility model: coupling cell shape and biochemistry

    Camley, Brian A; Li, Bo; Levine, Herbert; Rappel, Wouter-Jan


    We study a minimal model of a crawling eukaryotic cell with a chemical polarity controlled by a reaction-diffusion mechanism describing Rho GTPase dynamics. The size, shape, and speed of the cell emerge from the combination of the chemical polarity, which controls the locations where actin polymerization occurs, and the physical properties of the cell, including its membrane tension. We find in our model both highly persistent trajectories, in which the cell crawls in a straight line, and turning trajectories, where the cell transitions from crawling in a line to crawling in a circle. We discuss the controlling variables for this turning instability, and argue that turning arises from a coupling between the reaction-diffusion mechanism and the shape of the cell. This emphasizes the surprising features that can arise from simple links between cell mechanics and biochemistry. Our results suggest that similar instabilities may be present in a broad class of biochemical descriptions of cell polarity.

  8. Comparison of nested and ELISA based polymerase chain reaction assays for detecting Chlamydia trachomatis in pregnant women with preterm complications.

    Sulaiman, S; Chong, P P; Mokhtarudin, R; Lye, M S; Wan Hassan, W H


    Identification of pregnant women infected with Chlamydia trachomatis is essential to allow early antibiotic treatment in order to prevent adverse pregnancy outcomes. In this study, two nucleic acid amplification tests (NAAT) namely nested PCR (BioSewoom, Korea) and Amplicor CT/NG (Roche Diagnostic, USA) were evaluated in terms of sensitivity and specificity for the detection of C. trachomatis DNA in pregnant women with preterm complications. A cross-sectional study was carried out in two public hospitals in Southern Selangor, Malaysia. Endocervical swabs obtained were subjected to DNA amplification using nested PCR (BioSewoom, Korea) and Amplicor CT/NG (Roche Diagnostic, USA). A total of 83 endocervical swabs obtained from pregnant women of less than 37 weeks gestation and presented with preterm complications were subjected to chlamydial DNA detection using both assays. The study shows that Amplicor CT/NG assay is more effective in the detection of C. trachomatis DNA from endocervical swabs compared to Biosewoom nested PCR kit. Agreement between the two assays were poor (kappa=0.094) with nested PCR showing a low sensitivity of 10.81% and a 97.83% specificity when compared to Amplicor CT/NG. The results obtained indicated that BioSewoom nested PCR was less sensitive than Amplicor CT/ NG for detecting C. trachomatis in endocervical specimens and that another more reliable test is required for confirmatory result.

  9. Novel TaqMan real-time polymerase chain reaction assay for verifying the authenticity of meat and commercial meat products from game birds.

    Rojas, María; González, Isabel; Pavón, Miguel Angel; Pegels, Nicolette; Lago, Adriana; Hernández, Pablo E; García, Teresa; Martín, Rosario


    Species-specific real-time polymerase chain reaction (PCR) assays using TaqMan probes have been developed for verifying the labeling of meat and commercial meat products from game birds, including quail, pheasant, partridge, guinea fowl, pigeon, Eurasian woodcock and song thrush. The method combines the use of species-specific primers and TaqMan probes that amplify small fragments (amplicons <150 base pairs) of the mitochondrial 12S rRNA gene, and an endogenous control primer pair that amplifies a 141-bp fragment of the nuclear 18S rRNA gene from eukaryotic DNA. Analysis of experimental raw and heat-treated binary mixtures as well as of commercial meat products from the target species demonstrated the suitability of the assay for the detection of the target DNAs.

  10. Giardia and Cryptosporidium spp. dissemination during wastewater treatment and comparative detection via immunofluorescence assay (IFA), nested polymerase chain reaction (nested PCR) and loop mediated isothermal amplification (LAMP).

    Gallas-Lindemann, Carmen; Sotiriadou, Isaia; Plutzer, Judit; Noack, Michael J; Mahmoudi, Mohammad Reza; Karanis, Panagiotis


    Environmental water samples from the Lower Rhine area in Germany were investigated via immunofluorescence assays (IFAs), nested polymerase chain reaction (nested PCR) and loop-mediated isothermal amplification (LAMP) to detect the presence of Giardia spp. (n=185) and Cryptosporidium spp. (n=227). The samples were concentrated through filtration or flocculation, and oocysts were purified via centrifugation through a sucrose density gradient. For all samples, IFA was performed first, followed by DNA extraction for the nested PCR and LAMP assays. Giardia cysts were detected in 105 samples (56.8%) by IFA, 62 samples (33.5%) by nested PCR and 79 samples (42.7%) by LAMP. Cryptosporidium spp. were detected in 69 samples (30.4%) by IFA, 95 samples (41.9%) by nested PCR and 99 samples (43.6%) by LAMP. According to these results, the three detection methods are complementary for monitoring Giardia and Cryptosporidium in environmental waters.

  11. Development of a locked nucleic acid real-time polymerase chain reaction assay for the detection of Pinus armandii in mixed species pine nut samples associated with dysgeusia.

    Handy, Sara M; Timme, Ruth E; Jacob, Salena M; Deeds, Jonathan R


    Recent work has shown that the presence of the species Pinus armandii , even when occurring as species mixtures of pine nuts, is correlated with taste disturbance (dysgeusia), also referred to as "pine mouth". Because of this known possibility of pine nut mixtures, a need was identified for a rapid streamlined assay to detect the presence of this species in the presence of other types of pine nuts. A locked nucleic acid probe was employed in a real-time polymerase chain reaction (RT-PCR) format to detect a single nucleotide polymorphism (SNP) unique to this species. This assay was able to detect P. armandii in homogenates down to ∼1% concentration (the lowest level tested) in the presence of several commonly co-occurring and closely related species of pine and should prove to be a useful tool for the detection of this species in food products.

  12. kinetics of the coupled gas-iron reactions involving silicon and carbon



    Sep 1, 1985 ... and a gas phase consisting carbon monoxide, silicon monoxide and carbon dioxide. ... limited by oxygen in the metal boundary layer at the slag- ... the furnace into the reaction chamber the carbon monoxide acting as both a ...


    To elucidate the binding mechanism of the herbicide bentazon (3-isopropyl-1H-2,1,3-benzothiadiazine-4(3H)-one 2,2-dioxide) with humic monomers in the presence of an oxidative enzyme, the reaction of bentazon with catechol, caffeic acid, protocatechuic...

  14. Sensitive and specific colorimetric DNA detection by invasive reaction coupled with nicking endonuclease-assisted nanoparticles amplification.

    Zou, Bingjie; Cao, Xiaomei; Wu, Haiping; Song, Qinxin; Wang, Jianping; Kajiyama, Tomoharu; Kambara, Hideki; Zhou, Guohua


    Colorimetric DNA detection is preferable to methods in clinical molecular diagnostics, because no expensive equipment is required. Although many gold nanoparticle-based colorimetric DNA detection strategies have been developed to analyze DNA sequences of interest, few of them can detect somatic mutations due to their insufficient specificity. In this study, we proposed a colorimetric DNA detection method by coupling invasive reaction with nicking endonuclease-assisted nanoparticles amplification (IR-NEANA). A target DNA firstly produces many flaps by invasive reaction. Then the flaps are converted to targets of nicking reaction-assisted nanoparticles amplification by ligation reaction to produce the color change of AuNPs, which can be observed by naked eyes. The detection limit of IR-NEANA was determined as 1pM. Most importantly, the specificity of the method is high enough to pick up as low as 1% mutant from a large amount of wild-type DNA backgrounds. The EGFR gene mutated at c.2573 T>G in 9 tissue samples from non-small cell lung cancer patients were successfully detected by using IR-NEANA, suggesting that our proposed method can be used to detect somatic mutations in biological samples.

  15. Separation of electron-transfer and coupled chemical reaction components of biocatalytic processes using Fourier transform ac voltammetry.

    Fleming, Barry D; Zhang, Jie; Bond, Alan M; Bell, Stephen G; Wong, Luet-Lok


    The underlying electron-transfer and coupled chemical processes associated with biologically important catalytic reactions can be resolved using a combination of Fourier transform ac voltammetry with an analysis of the separated dc and ac components. This outcome can be achieved because the response associated with generation of the catalytic current is essentially confined to the steady-state dc component, whereas the electron-transfer step is dominant in the fundamental and higher harmonics. For the mediated oxidation of glucose with glucose oxidase, it was found that the underlying reversible redox chemistry of the mediator, ferrocenemonocarboxylic acid, as detected in the third and higher harmonics, was totally unaffected by introduction of the catalytic process. In contrast, for the catalytic reduction of molecular oxygen by cytochrome P450, slight changes in the P450 redox process were detected when the catalytic reaction was present. Simulations of a simple catalytic reaction scheme support the fidelity of this novel FT ac voltammetric approach for examining mechanistic nuances of catalytic forms of electrochemical reaction schemes.

  16. Proton-coupled electron transfer in tyrosine and a β-hairpin maquette: reaction dynamics on the picosecond time scale.

    Pagba, Cynthia V; Chi, San-Hui; Perry, Joseph; Barry, Bridgette A


    In proteins, proton-coupled electron transfer (PCET) can involve the transient oxidation and reduction of the aromatic amino acid tyrosine. Due to the short life time of tyrosyl radical intermediates, transient absorption spectroscopy provides an important tool in deciphering electron-transfer mechanisms. In this report, the photoionization of solution tyrosine and tyrosinate was investigated using transient, picosecond absorption spectroscopy. The results were compared to data acquired from a tyrosine-containing β-hairpin peptide. This maquette, peptide A, is an 18-mer that exhibits π-π interaction between tyrosine (Y5) and histidine (H14). Y5 and H14 carry out an orthogonal PCET reaction when Y5 is oxidized in the mid-pH range. Photolysis of all samples (280 nm, instrument response: 360 fs) generated a solvated electron signal within 3 ps. A signal from the S1 state and a 410 nm signal from the neutral tyrosyl radical were also formed in 3 ps. Fits to S1 and tyrosyl radical decay profiles revealed biphasic kinetics with time constants of 10-50 and 400-1300 ps. The PCET reaction at pH 9 was associated with a significant decrease in the rate of tyrosyl radical and S1 decay compared to electron transfer (ET) alone (pH 11). This pH dependence was observed both in solution and peptide samples. The pH 9 reaction may occur with a sequential electron-transfer, proton-transfer (ETPT) mechanism. Alternatively, the pH 9 reaction may occur by coupled proton and electron transfer (CPET). CPET would be associated with a reorganization energy larger than that of the pH 11 reaction. Significantly, the decay kinetics of S1 and the tyrosyl radical were accelerated in peptide A compared to solution samples at both pH values. These data suggest either an increase in electronic coupling or a specific, sequence-dependent interaction, which facilitates ET and PCET in the β hairpin.

  17. Detection of Citrus leprosis virus C using specific primers and TaqMan probe in one-step real-time reverse-transcription polymerase chain reaction assays.

    Choudhary, Nandlal; Wei, G; Govindarajulu, A; Roy, Avijit; Li, Wenbin; Picton, Deric D; Nakhla, M K; Levy, L; Brlansky, R H


    Citrus leprosis virus C (CiLV-C), a causal agent of the leprosis disease in citrus, is mostly present in the South and Central America and spreading toward the North America. To enable better diagnosis and inhibit the further spread of this re-emerging virus a quantitative (q) real-time reverse transcription polymerase chain reaction (qRT-PCR) assay is needed for early detection of CiLV-C when the virus is present in low titer in citrus leprosis samples. Using the genomic sequence of CiLV-C, specific primers and probe were designed and synthesized to amplify a 73 nt amplicon from the movement protein (MP) gene. A standard curve of the 73 nt amplicon MP gene was developed using known 10(10)-10(1) copies of in vitro synthesized RNA transcript to estimate the copy number of RNA transcript in the citrus leprosis samples. The one-step qRT-PCR detection assays for CiLV-C were determined to be 1000 times more sensitive when compared to the one-step conventional reverse transcription polymerase chain reaction (RT-PCR) CiLV-C detection method. To evaluate the quality of the total RNA extracts, NADH dehydrogenase gene specific primers (nad5) and probe were included in reactions as an internal control. The one-step qRT-PCR specificity was successfully validated by testing for the presence of CiLV-C in the total RNA extracts of the citrus leprosis samples collected from Belize, Costa Rica, Mexico and Panama. Implementation of the one-step qRT-PCR assays for CiLV-C diagnosis should assist regulatory agencies in surveillance activities to monitor the distribution pattern of CiLV-C in countries where it is present and to prevent further dissemination into citrus growing countries where there is no report of CiLV-C presence.

  18. Metal- and reagent-free highly selective anodic cross-coupling reaction of phenols.

    Elsler, Bernd; Schollmeyer, Dieter; Dyballa, Katrin Marie; Franke, Robert; Waldvogel, Siegfried R


    The direct oxidative cross-coupling of phenols is a very challenging transformation, as homo-coupling is usually strongly preferred. Electrochemical methods circumvent the use of oxidizing reagents or metal catalysts and are therefore highly attractive. Employing electrolytes with a high capacity for hydrogen bonding, such as methanol with formic acid or 1,1,1,3,3,3-hexafluoro-2-propanol, a direct electrolysis in an undivided cell provides mixed 2,2'-biphenols with high selectivity. This mild method tolerates a variety of moieties, for example, tert-butyl groups, which are not compatible with other strong electrophilic media but vital for later catalytic applications of the formed products. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Microwave-assisted Palladium-micelle-catalyzed Suzuki Cross-coupling Reaction in Water

    LIN Li; LI Sheng-hai; JIANG Ri-hua


    A microwave-accelerated Suzuki coupling procedure was developed via guanidinium ionic liquids(GILs)stabilized Pd-micelle.The Pd micelle/GILs play a key role in enhancing the activity,due to the highly dispersed Pd active sites and the phase transfer function of GILs,which ensures the adsorption of reactants and facilitates the translation of the intermediates to the surface of the micelle.

  20. Coupling IR Thermography and BIA to analyse body reaction after one acupuncture session

    Piquemal, M.


    Coupling both thermography and bio-Impedance, some biophysical acupuncture mechanisms are statically studied on a small population of 18 subjects. Results show that a possible way of understanding acupuncture, in an electrical way, should be to consider ionic flux redistribution between vascular and extra cell compartments. This is a two steps mechanism. The first one is starting with needles insertion and the second one is lasting with more intensity after removing them from skin.

  1. An investigation of genital ulcers in Jackson, Mississippi, with use of a multiplex polymerase chain reaction assay: high prevalence of chancroid and human immunodeficiency virus infection.

    Mertz, K J; Weiss, J B; Webb, R M; Levine, W C; Lewis, J S; Orle, K A; Totten, P A; Overbaugh, J; Morse, S A; Currier, M M; Fishbein, M; St Louis, M E


    In 1994, an apparent outbreak of atypical genital ulcers was noted by clinicians at the sexually transmitted disease clinic in Jackson, Mississippi. Of 143 patients with ulcers tested with a multiplex polymerase chain reaction (PCR) assay, 56 (39%) were positive for Haemophilus ducreyi, 44 (31%) for herpes simplex virus, and 27 (19%) for Treponema pallidum; 12 (8%) were positive for > 1 organism. Of 136 patients tested for human immunodeficiency virus (HIV) by serology, 14 (10%) were HIV-seropositive, compared with none of 200 patients without ulcers (P genital ulcers and HIV infection in this population highlights the urgency of preventing genital ulcers in the southern United States.

  2. Chiral PEPPSI Complexes: Synthesis, Characterization, and Application in Asymmetric Suzuki–Miyaura Coupling Reactions

    Benhamou, Laure


    PEPPSI complexes incorporating chiral N-heterocyclic carbene (NHC) ligands based on 2,2-dimethyl-1-(o-substituted aryl)propan-1-amines were synthesized. Two complexes, with one saturated and one unsaturated NHC ligand, were structurally characterized. The chiral PEPPSI complexes were used in asymmetric Suzuki-Miyaura reactions, giving atropisomeric biaryl products in modest to good enantiomeric ratios. © 2013 American Chemical Society.

  3. Diversity-oriented synthesis of dihydrobenzoxazepinones by coupling the Ugi multicomponent reaction with a Mitsunobu cyclization

    Lisa Moni


    Full Text Available An operationally simple protocol for the synthesis of 2,3-dihydrobenzo[f][1,4]oxazepin-3-ones, based on an Ugi reaction of an ortho-(benzyloxybenzylamine, glycolic acid, an isocyanide and an aldehyde, followed by an intramolecular Mitsunobu substitution was developed. The required ortho-(benzyloxybenzylamines have been in situ generated from the corresponding azides, in turn prepared in high yields from salicylic derivatives.

  4. Development of a multiplex polymerase chain reaction assay for simultaneous identification of human enterovirus 71 and coxsackievirus A16

    Thao, Nguyen Thi Thanh; Ngoc, Nguyen Thi Kim; Tú, Phan Văn; Thúy, Trần Thi; Cardosa, Mary Jane; McMinn, Peter Charles; Phuektes, Patchara


    Human enterovirus 71 (HEV71) and coxsackievirus A16 (CVA16) are two major aetiological agents of hand, foot and mouth disease (HFMD) in children. Recently there have been several large outbreaks of HFMD in Vietnam and the Asia-Pacific region. In this study, a multiplex RT-PCR assay was developed in order to detect simultaneously HEV71, CVA16 and other human enteroviruses. Enterovirus detection was performed with a mixture of three pairs of oligonucleotide primers: one pair of published primer...

  5. Electronic Coupling of Cobalt Nanoparticles to Nitrogen-Doped Graphene for Oxygen Reduction and Evolution Reactions.

    Xu, Chaohe; Lu, Meihua; Yan, Binggong; Zhan, Yi; Balaya, Palani; Lu, Li; Lee, Jim Yang


    The rational design of nonprecious-metal electrocatalysts with activities comparable to or greater than that of platinum is extremely valuable to the development of high energy density metal-air batteries. Herein, the two-step preparation of a highly active oxygen electrocatalyst based on ultrasmall cobalt nanoparticles stabilized in a nitrogen-doped graphene matrix is reported. The catalyst performs as well as the commercial Pt/C catalyst in the oxygen reduction reaction, and better than the Pt/C catalyst in the oxygen evolution reaction. This particular electrocatalyst could significantly lower the overpotentials of oxygen electrochemical reactions in aqueous lithium-air batteries to attain a round-trip efficiency of about 79.0 % at a current density of 0.1 mA cm(-2) , thereby surpassing the performance of the commercial Pt/C catalyst. The good performance may be attributed to strong metal-support interactions, maximized by a high dispersion of ultrasmall cobalt nanocrystals in a nitrogen-doped graphene matrix, which yields electrocatalytic properties greater than the sum of its parts. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Analytical validation of a quantitative reverse transcriptase polymerase chain reaction assay for evaluation of T-cell targeted immunosuppressive therapy in the dog.

    Riggs, C; Archer, T; Fellman, C; Figueiredo, A S; Follows, J; Stokes, J; Wills, R; Mackin, A; Bulla, C


    Cyclosporine is an immunosuppressive agent that inhibits T-cell function by decreasing production of cytokines such as interleukin-2 (IL-2) and interferon-γ(IFN-γ). In dogs, there is currently no reliable analytical method for determining effective cyclosporine dosages in individual patients. Our laboratory has developed a quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assay that measures IL-2 and IFN-γ gene expression, with the goal of quantifying immunosuppression in dogs treated with cyclosporine. This study focuses on analytical validation of our assay, and on the effects of sample storage conditions on cyclosporine-exposed samples. Heparinized whole blood collected from healthy adult dogs was exposed to a typical post-treatment blood concentration for cyclosporine(500 ng/mL) for 1 h, and then stored for 0, 24, and 48 h at both room temperature and 4 ◦C.The study was then repeated using a cyclosporine concentration of 75 ng/mL, with sample storage for 0, 24, and 48 h at 4 ◦C. Cytokine gene expression was measured using RT-qPCR,and assay efficiency and inter- and intra-assay variability were determined. Storage for upto 24 h at room temperature, and up to 48 h at 4 ◦C, did not significantly alter results compared to samples that were processed immediately. Validation studies showed our assay to be highly efficient and reproducible and robust enough to be feasible under standard practice submission conditions. © 2013 Elsevier B.V. All rights reserved.

  7. Real-time polymerase chain reaction detection of cauliflower mosaic virus to complement the 35S screening assay for genetically modified organisms.

    Cankar, Katarina; Ravnikar, Maja; Zel, Jana; Gruden, Kristina; Toplak, Natasa


    Labeling of genetically modified organisms (GMOs) is now in place in many countries, including the European Union, in order to guarantee the consumer's choice between GM and non-GM products. Screening of samples is performed by polymerase chain reaction (PCR) amplification of regulatory sequences frequently introduced into genetically modified plants. Primers for the 35S promoter from Cauliflower mosaic virus (CaMV) are those most frequently used. In virus-infected plants or in samples contaminated with plant material carrying the virus, false-positive results can consequently occur. A system for real-time PCR using a TaqMan minor groove binder probe was designed that allows recognition of virus coat protein in the sample, thus allowing differentiation between transgenic and virus-infected samples. We measured the efficiency of PCR amplification, limits of detection and quantification, range of linearity, and repeatability of the assay in order to assess the applicability of the assay for routine analysis. The specificity of the detection system was tested on various virus isolates and plant species. All 8 CaMV isolates were successfully amplified using the designed system. No cross-reactivity was detected with DNA from 3 isolates of the closely related Carnation etched ring virus. Primers do not amplify plant DNA from available genetically modified maize and soybean lines or from different species of Brassicaceae or Solanaceae that are natural hosts for CaMV. We evaluated the assay for different food matrixes by spiking CaMV DNA into DNA from food samples and have successfully amplified CaMV from all samples. The assay was tested on rapeseed samples from routine GMO testing that were positive in the 35S screening assay, and the presence of the virus was confirmed.

  8. A sensitive and quantitative polymerase chain reaction-based cell free in vitro non-homologous end joining assay for hematopoietic stem cells.

    Lijian Shao

    Full Text Available Hematopoietic stem cells (HSCs are responsible for sustaining hematopoietic homeostasis and regeneration after injury for the entire lifespan of an organism. Maintenance of genomic stability is crucial for the preservation of HSCs, which depends on their efficient repair of DNA damage, particularly DNA double strand breaks (DSBs. Because of the paucity of HSCs and lack of sensitive assays, directly measuring the ability of HSCs to repair DSBs has been difficult. Therefore, we developed a sensitive and quantitative cell free in vitro non-homologous end joining (NHEJ assay using linearized plasmids as the substrates and quantitative polymerase chain reaction (qPCR technique. This assay can sensitively detect DSB repair via NHEJ in less than 1 µg 293T cell nuclear proteins or nuclear extracts from about 5,000 to 10,000 human BM CD34(+ hematopoietic cells. Using this assay, we confirmed that human bone marrow HSCs (CD34(+CD38(- cells are less proficient in the repair of DSBs by NHEJ than HPCs (CD34(+CD38(+ cells. In contrast, mouse quiescent HSCs (Pyronin-Y(low LKS(+ cells and cycling HSCs (Pyronin-Y(hi LKS(+ cells repaired the damage more efficiently than HPCs (LKS(- cells. The difference in the abilities of human and mouse HSCs and HPCs to repair DSBs through NHEJ is likely attributed to their differential expression of key NHEJ DNA damage repair genes such as LIG4. These findings suggest that the qPCR-based cell free in vitro NHEJ assay can be used to sensitively measure the ability of human and mouse HSCs to repair DSBs.

  9. Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples

    Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.


    During summer and early fall 2010, 15 river samples and 6 fecal-source samples were collected in West Virginia. These samples were analyzed by three laboratories for three microbial source tracking (MST) markers: AllBac, a general fecal indicator; BacHum, a human-associated fecal indicator; and BoBac, a ruminant-associated fecal indicator. MST markers were analyzed by means of the quantitative polymerase chain reaction (qPCR) method. The aim was to assess interlaboratory precision when the three laboratories used the same MST marker and shared deoxyribonucleic acid (DNA) extracts of the samples, but different equipment, reagents, and analyst experience levels. The term assay refers to both the markers and the procedure differences listed above. Interlaboratory precision was best for all three MST assays when using the geometric mean absolute relative percent difference (ARPD) and Friedman's statistical test as a measure of interlaboratory precision. Adjustment factors (one for each MST assay) were calculated using results from fecal-source samples analyzed by all three laboratories and applied retrospectively to sample concentrations to account for differences in qPCR results among labs using different standards and procedures. Following the application of adjustment factors to qPCR results, ARPDs were lower; however, statistically significant differences between labs were still observed for the BacHum and BoBac assays. This was a small study and two of the MST assays had 52 percent of samples with concentrations at or below the limit of accurate quantification; hence, more testing could be done to determine if the adjustment factors would work better if the majority of sample concentrations were above the quantification limit.

  10. Development of a multiplex real-time PCR assay for the detection of Bordetella pertussis and Bordetella parapertussis in a single tube reaction.

    Arbefeville, Sophie; Levi, Michael H; Ferrieri, Patricia


    Pertussis is an infectious respiratory disease caused by the fastidious bacterium Bordetella pertussis, which may infect unvaccinated, previously vaccinated children, and adults in whom immunity has waned. Infants are at a particular risk for severe disease and complications. Bordetella parapertussis may cause a similar illness, however the symptoms are less severe and of shorter duration. Pertussis is a highly contagious disease and early diagnosis is essential. Studies have shown that PCR is 2-4 times more likely than culture to detect Bordetella pertussis. We developed a multiplex, real-time PCR assay using analyte-specific reagent (ASR) primers and probes dispensed in a convenient lyophilized bead format that targeted the multi-copy insertion sequences IS481 and IS1001 of B. pertussis and B. parapertussis, respectively. These specific ASRs were used in conjunction with Cepheid Smartmix. Included in the ASRs is a competitive internal control to evaluate the performance of the PCR reaction. After DNA extraction, amplification and detection were done on the Smart Cycler System, which performs integrated amplification and detection automatically in a single step. Specificity of the assay was confirmed using multiple distinct bacterial strains. Sensitivity of the assay and extraction efficiency were evaluated on DNA isolated from pure bacterial cultures and on spiked respiratory specimens. We also spiked different swab types and transport media to evaluate for interfering substances. To assess accuracy, we studied different patient specimen types received from two outside laboratories that used similar or different methods to detect B. pertussis and B. parapertussis. The sensitivity and the specificity of the assay for B. pertussis were 90% and 96%, respectively, and for B. parapertussis 71% (only 7 positive specimens were available for testing) and 100%, respectively. Our assay was found to be a valid method for the simultaneous detection of B. pertussis and B

  11. Mixed convection flow of couple stress fluid between rotating discs with chemical reaction and double diffusion effects

    Kaladhar, K.; Srinivasacharya, D.


    The chemical reaction, Soret and Dufour effects on steady flow of a couple stress fluid between two rotating disks are studied. The lower disc is rotating with angular velocity Ω1 where as the upper disc is rotating with Ω2. The density variation in centrifugal and Coriolis force terms are taken into consideration by invoking a linear density-temperature relation and Boussinesq approximation to account the buoyancy effects. The non-linear governing partial differential equations are transformed into system of ordinary differential equations by using the similarity transformations. Homotopy Analysis Method (HAM) has been used to solve the resulting equations. Graphical illustrations of the dimensionless velocity, concentration and temperature profiles are presented at different values of the emerging parameter of the present study. It has been found that as an increase in couple stresses leads to the decrease in velocity, temperature and increase in concentration of the fluid. Flow velocities, temperature and concentration profiles are decreases with an increase in reaction parameter.

  12. A Study of Gas Diffusion Electrodes for the Coupled Reaction of Water Electrolysis and Electrocatalytic Benzene Hydrogenation

    HuangHaiyan; YuYing; WangJing


    Gas diffusion electrodes are applied to the coupled reaction of water electrolysis and electrocatalytic benzene hydrogenation. The effects of the preparation conditions of electrodes, electrolyte acidity, the concentration of benzene and water vapor, and the flow rate of N2 are investigated by evaluating the efficiency of the current. Furthermore, the optimal operational conditions have been ascertained. The results of our experiment show that gas diffusion electrodes have good performance when the content of PTFE is 10% (wt) and that of Nation is 0.75mg/cm2. The optimal operational conditions are as follows: The temperature of electrolysis is 70℃, acidity 0.5tool/L, the concentration of benzene 26%,the concentration of vapor 10%, the flow rate of N2 80mL/min-240mL/min. The efficiency of the current can reach 35% under optimal operational conditions. Then, a conclusion can be drawn that gas diffusion electrodes can improve the rate of the coupled reaction effectively.

  13. A chip-type thin-layer electrochemical cell coupled with capillary electrophoresis for online separation of electrode reaction products

    He, Jian-Bo, E-mail:; Cui, Ting; Zhang, Wen-Wen; Deng, Ning


    Graphical abstract: -- Highlights: •A new coupling of thin-layer electrolysis with capillary electrophoresis (CE). •Rapid electrolysis, direct sampling followed by online CE separation. •At least 13 products of quercetin oxidation were separated. •Thermodynamic and kinetic parameters were determined from CE peak areas. -- Abstract: A coupling technique of thin-layer electrolysis with high-performance capillary electrophoresis/UV–vis technique(EC/HPCE/UV–vis) is developed for online separation and determination of electrode reaction products. A chip-type thin-layer electrolytic (CTE) cell was designed and fabricated, which contains a capillary channel and a background electrolyte reservoir, allowing rapid electrolysis, direct sampling and online electrophoretic separation. This chip-type setup was characterized based on an electrophoresis expression of Nernst equation that was applied to the redox equilibrium of o-tolidine at different potentials. The utility of the method was demonstrated by separating and determining the electro-oxidation products of quercetin in different pH media. Two main products were always found in the studied time, potential and pH ranges. The variety of products increased not only with increasing potential but also with increasing pH value, and in total, at least 13 products were observed in the electropherograms. This work illustrates a novel example of capillary electrophoresis used online with thin-layer electrolysis to separate and detect electrode reaction products.

  14. Boron-mediated sequential alkyne insertion and C–C coupling reactions affording extended π-conjugated molecules

    Shoji, Yoshiaki; Tanaka, Naoki; Muranaka, Sho; Shigeno, Naoki; Sugiyama, Haruka; Takenouchi, Kumiko; Hajjaj, Fatin; Fukushima, Takanori


    C–C bond coupling reactions illustrate the wealth of organic transformations, which are usually mediated by organotransition metal complexes. Here, we show that a borafluorene with a B–Cl moiety can mediate sequential alkyne insertion (1,2-carboboration) and deborylation/Csp2–Csp2 coupling reactions, leading to aromatic molecules. The first step, which affords a borepin derivative, proceeds very efficiently between the borafluorene and various alkynes by simply mixing these two components. The second step is triggered by a one-electron oxidation of the borepin derivative, which results in the formation of a phenanthrene framework. When an excess amount of oxidant is used in the second step, the phenanthrene derivatives can be further transformed in situ to afford dibenzo[g,p]chrysene derivatives. The results presented herein will substantially expand the understanding of main group chemistry and provide a powerful synthetic tool for the construction of a wide variety of extended π-conjugated systems. PMID:27581519

  15. Organic aqueous tunable solvents (OATS): a vehicle for coupling reactions and separations.

    Pollet, Pamela; Hart, Ryan J; Eckert, Charles A; Liotta, Charles L


    In laboratory-based chemical synthesis, the choice of the solvent and the means of product purification are rarely determined by cost or environmental impact considerations. When a reaction is scaled up for industrial applications, however, these choices are critical: the separation of product from the solvent, starting materials, and byproduct usually constitutes 60-80% of the overall cost of a process. In response, researchers have developed solvents and solvent-handling methods to optimize both the reaction and the subsequent separation steps on the manufacturing scale. These include "switchable" solvents, which are designed so that their physical properties can be changed abruptly, as well as "tunable" solvents, wherein the solvent's properties change continuously through the application of an external stimulus. In this Account, we describe the organic aqueous tunable solvent (OATS) system, examining two instructive and successful areas of application of OATS as well as its clear potential for further refinement. OATS systems address the limitations of biphasic processes by optimizing reactions and separations simultaneously. The reaction is performed homogeneously in a miscible aqueous-organic solvent mixture, such as water-tetrahydrofuran (THF). The efficient product separation is conducted heterogeneously by the simple addition of modest pressures of CO(2) (50-60 bar) to the system. Under these conditions, the water-THF phase splits into two relatively immiscible phases: the organic THF phase contains the hydrophobic product, and the aqueous phase contains the hydrophilic catalyst. We take advantage of the unique properties of OATS to develop environmentally benign and cost-competitive processes relevant in industrial applications. Specifically, we describe the use of OATS for optimizing the reaction, separation, design, and recycling of (i) Rh-catalyzed hydroformylation of olefins such as 1-octene and (ii) enzyme-catalyzed hydrolysis of 2-phenylacetate. We

  16. A Pentaplex Real-Time Polymerase Chain Reaction Assay for Detection of Four Species of Soil-Transmitted Helminths

    Basuni, Madihah; Muhi, Jamail; Othman, Nurulhasanah; Verweij, Jaco J.; Ahmad, Maimunah; Miswan, Noorizan; Rahumatullah, Anizah; Aziz, Farhanah Abdul; Zainudin, Nurul Shazalina; Noordin, Rahmah


    Soil-transmitted helminth infections remain a major public health burden in low- and middle-income countries. The traditional diagnosis by microscopic examination of fecal samples is insensitive and time-consuming. In this study, a pentaplex real-time polymerase chain reaction (PCR) was evaluated for the simultaneous detection of Ancylostoma, Necator americanus, Ascaris lumbricoides, and Strongyloides stercoralis. The results were compared with those obtained by conventional parasitological d...

  17. A convenient route to symmetrically and unsymmetrically substituted 3,5-diaryl-2,4,6-trimethylpyridines via Suzuki–Miyaura cross-coupling reaction

    Szawkało, Joanna; Czarnocki, Zbigniew


    Summary A series of differently substituted 3,5-diaryl-2,4,6-trimethylpyridines were prepared and characterized using the Suzuki–Miyaura coupling reaction with accordingly selected bromo-derivatives and arylboronic acids. The reaction conditions were carefully optimized allowing high yield of isolated products and also the construction of unsymmetrically substituted diarylpyridines, difficult to access by other methods. PMID:27340474

  18. Palladium-catalyzed cross-coupling reaction of diazo compounds and vinyl boronic acids: an approach to 1,3-diene compounds.

    Xia, Yamu; Xia, Ying; Liu, Zhen; Zhang, Yan; Wang, Jianbo


    A palladium-catalyzed oxidative cross-coupling of vinyl boronic acids and cyclic α-diazocarbonyl compounds has been reported. The reaction constitutes an efficient method for the synthesis of 1,3-diene compounds bearing a ring structure. Mechanistically, the reaction involves migratory insertion of palladium carbene as the key step.

  19. Detection of Maillard reaction products by a coupled HPLC-Fraction collector technique and FTIR characterization of Cu(II)-complexation with the isolated species

    Ioannou, Aristos; Daskalakis, Vangelis; Varotsis, Constantinos


    The isolation of reaction products of asparagine with reducing sugars at alkaline pH and high temperature has been probed by a combination of high performance liquid chromatography (HPLC) coupled with a Fraction Collector. The UV-vis and FTIR spectra of the isolated Maillard reaction products showed structure-sensitive changes as depicted by deamination events and formation of asparagine-saccharide conjugates. The initial reaction species of the Asn-Gluc reaction were also characterized by Density Functional Theory (DFT) methods. Evidence for Cu (II) metal ion complexation with the Maillard reaction products is supported by UV-vis and FTIR spectroscopy.

  20. Effects of doping in 25-atom bimetallic nanocluster catalysts for carbon–carbon coupling reaction of iodoanisole and phenylacetylene

    Zhimin Li


    Full Text Available We here report the catalytic effects of foreign atoms (Cu, Ag, and Pt doped into well-defined 25-gold-atom nanoclusters. Using the carbon-carbon coupling reaction of p-iodoanisole and phenylacetylene as a model reaction, the gold-based bimetallic MxAu25−x(SR18 (–SR=–SCH2CH2Ph nanoclusters (supported on titania were found to exhibit distinct effects on the conversion of p-iodoanisole as well as the selectivity for the Sonogashira cross-coupling product, 1-methoxy-4-(2-phenylethynylbenzene. Compared to Au25(SR18, the centrally doped Pt1Au24(SR18 causes a drop in catalytic activity but with the selectivity retained, while the AgxAu25−x(SR18 nanoclusters gave an overall performance comparable to Au25(SR18. Interestingly, CuxAu25−x(SR18 nanoclusters prefer the Ullmann homo-coupling pathway and give rise to product 4,4′-dimethoxy-1,1′-biphenyl, which is in opposite to the other three nanocluster catalysts. Our overall conclusion is that the conversion of p-iodoanisole is largely affected by the electronic effect in the bimetallic nanoclusters’ 13-atom core (i.e., Pt1Au12, CuxAu13−x, and Au13, with the exception of Ag doping, and that the selectivity is primarily determined by the type of atoms on the MxAu12−x shell (M=Ag, Cu, and Au in the nanocluster catalysts.

  1. An alternative to fully coupled reactive transport simulations for long-term prediction of chemical reactions in complex geological systems

    De Lucia, Marco; Kempka, Thomas; Kühn, Michael


    Fully-coupled reactive transport simulations involving multiphase hydrodynamics and chemical reactions in heterogeneous settings are extremely challenging from a computational point of view. This often leads to oversimplification of the investigated system: coarse spatial discretization, to keep the number of elements in the order of few thousands; simplified chemistry, disregarding many potentially important reactions. A novel approach for coupling non-reactive hydrodynamic simulations with the outcome of single batch geochemical simulations was therefore introduced to assess the potential long-term mineral trapping at the Ketzin pilot site for underground CO2 storage in Germany [1],[2]. The advantage of the coupling is the ability to use multi-million grid non-reactive hydrodynamics simulations on one side and few batch 0D geochemical simulations on the other, so that the complexity of both systems does not need to be reduced. This contribution shows the approach which was taken to validate this simplified coupling scheme. The procedure involved batch simulations of the reference geochemical model, then performing both non-reactive and fully coupled 1D and 3D reactive transport simulations and finally applying the simplified coupling scheme based on the non-reactive and geochemical batch model. The TOUGHREACT/ECO2N [3] simulator was adopted for the validation. The degree of refinement of the spatial grid and the complexity and velocity of the mineral reactions, along with a cut-off value for the minimum concentration of dissolved CO2 allowed to originate precipitates in the simplified approach were found out to be the governing parameters for the convergence of the two schemes. Systematic discrepancies between the approaches are not reducible, simply because there is no feedback between chemistry and hydrodynamics, and can reach 20 % - 30 % in unfavourable cases. However, even such discrepancy is completely acceptable, in our opinion, given the amount of

  2. Application of “Boomerang” Linear Polystyrene-Stabilized Pd Nanoparticles to a Series of C-C Coupling Reactions in Water

    Atsushi Ohtaka


    Full Text Available The application of a catch-and-release system for soluble Pd species between water (reaction medium and polystyrene (polymer support was examined in the Suzuki coupling reaction with 2-bromothiophene and the Heck reaction with styrene or bromobenzene. Although a slight increase in particle size was observed by TEM after re-stabilization of the Pd species on linear polystyrene, no agglomeration was observed.

  3. Polymerase chain reaction assay for rapid, sensitive detection, and identification of Colletotrichum gloeosporioides causing greater yam anthracnose.

    Raj, Mithun; Jeeva, M L; Hegde, V; Vidyadharan, Pravi; Archana, P V; Senthil alias Sankar, M; Nath, S Vishnu


    Anthracnose caused by Colletotrichum gloeosporioides is an economically important disease which affects greater yam (Dioscorea alata L.) worldwide. Apart from airborne conidia, the pathogen propagules surviving in soil and planting material are the major sources of inoculum. A nested PCR assay has been developed for specific detection of C. gloeosporioides in soil and planting material. In conventional (single-round) PCR, the limit of detection was 20 pg, whereas in nested PCR the detection limit increased to 0.2 pg of DNA. The primers designed were found to be highly specific and could be used for accurate identification of the pathogen up to species level. The protocol was standardized for detection of the pathogen in artificially and naturally infected field samples.

  4. Biogenic synthesis of palladium nanoparticles using Pulicaria glutinosa extract and their catalytic activity towards the Suzuki coupling reaction.

    Khan, Mujeeb; Khan, Merajuddin; Kuniyil, Mufsir; Adil, Syed Farooq; Al-Warthan, Abdulrahman; Alkhathlan, Hamad Z; Tremel, Wolfgang; Tahir, Muhammad Nawaz; Siddiqui, Mohammed Rafiq H


    Green synthesis of nanomaterials finds the edge over chemical methods due to its environmental compatibility. Herein, we report a facile and eco-friendly method for the synthesis of palladium (Pd) nanoparticles (NPs) using an aqueous solution of Pulicaria glutinosa, a plant widely found in a large region of Saudi Arabia, as a bioreductant. The as-prepared Pd NPs were characterized using ultraviolet-visible (UV-vis) spectroscopy, powder X-ray diffraction (XRD), transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDX), and Fourier transform-infrared spectroscopy (FT-IR). The hydroxyl groups of the plant extract (PE) molecules were found mainly responsible for the reduction and growth of Pd NPs. FT-IR analysis confirmed the dual role of the PE, both as a bioreductant as well as a capping ligand, which stabilizes the surface of Pd NPs. The crystalline nature of the Pd NPs was identified using XRD analysis which confirmed the formation of a face-centered cubic structure (JCPDS: 87-0641, space group: Fm3m (225)). Furthermore, the as-synthesized Pd NPs demonstrated excellent catalytic activity towards the Suzuki coupling reaction under aqueous and aerobic conditions. Kinetic studies of the catalytic reaction monitored using GC confirmed that the reaction completes in less than 5 minutes.

  5. Carbon-supported palladium and ruthenium nanoparticles: application as catalysts in alcohol oxidation, cross-coupling and hydrogenation reactions.

    García-Suárez, Eduardo J; Lara, Patricia; García, Ana B; Philippot, Karine


    In the last fifteen-years, the application of metal nanoparticles as catalysts in organic synthesis has received a renewed interest. Therefore, much attention is currently being paid to the synthesis of metal nanoparticles in order to achieve the control of their characteristics in terms of size, shape and surface chemistry. Besides this, the recyclability as well as the recovery from the reaction medium still remain the major drawbacks to widespread the use of nanoparticles in catalysis. To overcome these problems, the immobilization of metal nanoparticles on solid supports appears as a promising alternative. In that context, carbon materials offer several advantages as solid supports such as availability, relatively low cost, high mechanical strength, chemical stability, and a pore structure along with an attractive surface chemistry which allows easy modifications, such as its functionalization, to suit the nanoparticles immobilization needs. Among the transition metals Palladium and Ruthenium are widely employed as efficient catalysts in many reactions. Herein, the most recent advances, from recent papers and patents, in relation to the preparation of carbon-supported Pd or Ru nanoparticles systems as well as their application as catalysts in alcohol oxidation, cross-coupling or hydrogenation reactions, are reviewed.

  6. Accuracy of a rapid real-time polymerase chain reaction assay for diagnosis of group B Streptococcus colonization in a cohort of HIV-infected pregnant women.

    Gouvea, Maria Isabel S; Joao, Esau C; Teixeira, Maria de Lourdes B; Read, Jennifer S; Fracalanzza, Sergio E L; Souza, Claudia T V; Souza, Maria José de; Torres Filho, Helio M; Leite, Cassiana C F; do Brasil, Pedro E A A


    There are limited data regarding Xpert performance to detect Group B Streptococcus (GBS) in HIV-infected pregnant women. We evaluated the accuracy of a rapid real-time polymerase chain reaction (PCR) test in a cohort of HIV-infected women. At 35-37 weeks of pregnancy, a pair of combined rectovaginal swabs were collected for two GBS assays in a cohort of sequentially included HIV-infected women in Rio de Janeiro: (1) culture; and (2) real-time PCR assay [GeneXpert GBS (Cepheid, Sunnyvale, CA)]. Using culture as the reference, sensitivity, specificity, positive and negative-likelihood ratios were estimated. From June 2012 to February 2015, 337 pregnant women met inclusion criteria. One woman was later excluded, due to failure to obtain a result in the index test; 336 were included in the analyses. The GBS colonization rate was 19.04%. Sensitivity and specificity of the GeneXpert GBS assay were 85.94% (95% CI: 75.38-92.42) and 94.85% (95% CI: 91.55-96.91), respectively. Positive and negative predictive values were 79.71% (95% CI: 68.78-87.51) and 96.63% (95% CI: 93.72-98.22), respectively. GeneXpert GBS is an acceptable test for the identification of GBS colonization in HIV-infected pregnant women and represents a reasonable option to detect GBS colonization in settings where culture is not feasible.

  7. Discriminating complement-mediated acute transfusion reaction for type O+ red blood cells transfused into a B+ recipient with the complement hemolysis using human erythrocytes (CHUHE) assay.

    Cunnion, Kenji M; Hair, Pamela S; Krishna, Neel K; Whitley, Pamela H; Goldberg, Corinne L; Fadeyi, Emmanuel A; Maes, Lanne Y


    A patient with B+ sickle cell disease received 3 units of red blood cells (RBCs) from two O+ donors and developed fever and hypotension after the first unit, consistent with an acute transfusion reaction (ATR). Anti-B titers in plasma from each O+ donor were markedly elevated and nondiscriminatory. In order to evaluate the potential for the transfused units to produce complement-mediated hemolysis of B+ RBCs, hemolytic complement testing was performed. Plasma from each donor was diluted in veronal buffer and incubated with B+ RBCs, and free hemoglobin was measured by spectrophotometer in the complement hemolysis using human erythrocytes (CHUHE) assay. Peptide inhibitor of complement C1 (PIC1) was used to confirm antibody-initiated complement pathway activation. A 96-fold difference (p = 0.014) in hemolysis was measured between plasma samples from the two O+ donors using the CHUHE assay. The extremely high degree of hemolysis produced by the one plasma was inhibited by PIC1 in a dose-dependent manner. These results indicate that hemolytic complement testing with the CHUHE assay can be used to assess the risk of antibody-initiated, complement-mediated hemolysis from a transfusion beyond what can be achieved with antibody titers alone. © 2016 AABB.

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

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


    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.

  9. Development of multiplex polymerase chain reaction assay for simultaneous detection of clostero-, badna- and mandari-viruses along with huanglongbing bacterium in citrus trees.

    Meena, Ram Prasnna; Baranwal, V K


    Citrus trees harbor a large number of viral and bacterial pathogens. Citrus yellow vein clearing virus (CYVCV), Indian citrus ringspot virus (ICRSV), Citrus yellow mosaic virus (CYMV), Citrus tristeza virus (CTV) and a bacterium, Candidatus Liberibacter asiaticus (CLa) associated with huanglongbing (HLB) disease, the most prevalent pathogens in citrus orchards of different regions in India and are responsible for debilitating citriculture. For detection of these viral and bacterial pathogens a quick, sensitive and cost effective detection method is required. With this objective a multiplex polymerase chain reaction (mPCR) assay was developed for simultaneous detection of four viruses and a bacterium in citrus. Several sets of primers were designed for each virus based on the retrieved reference sequences from the GenBank. A primer pair published previously was used for greening bacterium. Each pair of primers was evaluated for their sensitivity and differentiation by simplex and mPCR. The constant amplified products were identified on the basis of molecular size in mPCR and were compared with standard PCR. The amplicons were cloned and results were confirmed with sequencing analysis. The mPCR assay was validated using naturally infected field samples for one or more citrus viruses and the huanglongbing bacterium. The mPCR assay developed here will aid in the production of virus free planting materials and rapid indexing for certification of citrus budwood programme. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Evaluation of a real-time polymerase chain reaction (PCR) assay for detection of anisakis simplex parasite as a food-borne allergen source in seafood products.

    Lopez, Itziar; Pardo, Miguel Angel


    Anisakis simplex has been recognized as an important cause of disease in humans and as a food-borne allergen source. Actually, this food-borne parasite was recently identified as an emerging food safety risk. An A. simplex -specific primer-probe system based on a real-time polymerase chain reaction (PCR) detection assay has been successfully optimized and validated with seafood samples. In addition, a DNA extraction procedure has been optimized to detect the presence of the nematode in food samples. The assay is a very reliable, specific, and sensitive methodology to detect the presence of traces of this parasite in seafood products, including highly processed samples. As a result, 13 sequences of cytochrome c oxidase II gene were obtained and scrutinized to calculate intra- and interspecific variabilities of 0 and 35-67%, respectively. Finally, an efficiency of 2.07 +/- 0.14 of the assay was calculated, and a limit of detection of 40 ppm parasite in 25 g of sample was also optimized. Actually, the presence of this parasite in several seafood products has been demonstrated, enforcing the necessity of a design for a good manufacturing practice protocol for the processing industry to minimize the presence of this parasite as a food-borne allergen source in seafood products.

  11. Variation in Bluetongue virus real-time reverse transcription polymerase chain reaction assay results in blood samples of sheep, cattle, and alpaca.

    Brito, Barbara P; Gardner, Ian A; Hietala, Sharon K; Crossley, Beate M


    Bluetongue is a vector-borne viral disease that affects domestic and wild ruminants. The epidemiology of this disease has recently changed, with occurrence in new geographic areas. Various real-time quantitative reverse transcription polymerase chain reaction (real-time qRT-PCR) assays are used to detect Bluetongue virus (BTV); however, the impact of biologic differences between New World camelids and domestic ruminant samples on PCR efficiency, for which the BTV real-time qRT-PCR was initially validated are unknown. New world camelids are known to have important biologic differences in whole blood composition, including hemoglobin concentration, which can alter PCR performance. In the present study, sheep, cattle, and alpaca blood were spiked with BTV serotypes 10, 11, 13, and 17 and analyzed in 10-fold dilutions by real-time qRT-PCR to determine if species affected nucleic acid recovery and assay performance. A separate experiment was performed using spiked alpaca blood subsequently diluted in 10-fold series in sheep blood to assess the influence of alpaca blood on performance efficiency of the BTV real-time qRT-PCR assay. Results showed that BTV-specific nucleic acid detection from alpaca blood was consistently 1-2 logs lower than from sheep and cattle blood, and results were similar for each of the 4 BTV serotypes analyzed.

  12. Flame Atmospheric Pressure Chemical Ionization Coupled with Negative Electrospray Ionization Mass Spectrometry for Ion Molecule Reactions

    Cheng, Sy-Chyi; Bhat, Suhail Muzaffar; Shiea, Jentaie


    Flame atmospheric pressure chemical ionization (FAPCI) combined with negative electrospray ionization (ESI) mass spectrometry was developed to detect the ion/molecule reactions (IMRs) products between nitric acid (HNO3) and negatively charged amino acid, angiotensin I (AI) and angiotensin II (AII), and insulin ions. Nitrate and HNO3-nitrate ions were detected in the oxyacetylene flame, suggesting that a large quantity of nitric acid (HNO3) was produced in the flame. The HNO3 and negatively charged analyte ions produced by a negative ESI source were delivered into each arm of a Y-shaped stainless steel tube where they merged and reacted. The products were subsequently characterized with an ion trap mass analyzer attached to the exit of the Y-tube. HNO3 showed the strongest affinity to histidine and formed (Mhistidine-H+HNO3)- complex ions, whereas some amino acids did not react with HNO3 at all. Reactions between HNO3 and histidine residues in AI and AII resulted in the formation of dominant [MAI-H+(HNO3)]- and [MAII-H+(HNO3)]- ions. Results from analyses of AAs and insulin indicated that HNO3 could not only react with basic amino acid residues, but also with disulfide bonds to form [M-3H+(HNO3)n]3- complex ions. This approach is useful for obtaining information about the number of basic amino acid residues and disulfide bonds in peptides and proteins.




    BACKGROUND: We have modified a polymerase chain reaction (PCR)-aided transcript titration assay (1) in order to allow quantitation of low amounts of DNA topoisomerase II alpha mRNA in small RNA samples. EXPERIMENTAL DESIGN: The titration assay was used to quantitate the amount of DNA topoisomerase I

  14. Two novel nonradioactive polymerase chain reaction-based assays of dried blood spots, genomic DNA, or whole cells for fast, reliable detection of Z and S mutations in the alpha 1-antitrypsin gene

    Andresen, B S; Knudsen, I; Jensen, P K;


    Two new nonradioactive polymerase chain reaction (PCR)-based assays for the Z and S mutations in the alpha 1-antitrypsin gene are presented. The assays take advantage of PCR-mediated mutagenesis, creating new diagnostic restriction enzyme sites for unambiguous discrimination between test samples...

  15. Development of a quantitative real-time polymerase chain reaction assay to target a novel group of ammonia-producing bacteria found in poultry litter.

    Rothrock, M J; Cook, K L; Lovanh, N; Warren, J G; Sistani, K


    Ammonia production in poultry houses has serious implications for flock health and performance, nutrient value of poultry litter, and energy costs for running poultry operations. In poultry litter, the conversion of organic N (uric acid and urea) to NH(4)-N is a microbially mediated process. The urease enzyme is responsible for the final step in the conversion of urea to NH(4)-N. Cloning and analysis of 168 urease sequences from extracted genomic DNA from poultry litter samples revealed the presence of a novel, dominant group of ureolytic microbes (representing 90% of the urease clone library). Specific primers and a probe were designed to target this novel poultry litter urease producer (PLUP) group, and a new quantitative real-time PCR assay was developed. The assay allowed for the detection of 10(2) copies of target urease sequences per PCR reaction (approximately 1 x 10(4) cells per gram of poultry litter), and the reaction was linear over 8 orders of magnitude. Our PLUP group was present only in poultry litter and was not present in environmental samples from diverse agricultural settings. This novel PLUP group represented between 0.1 to 3.1% of the total microbial populations (6.0 x 10(6) to 2.4 x 10(8) PLUP cells per gram of litter) from diverse poultry litter types. The PLUP cell concentrations were directly correlated to the total cell concentrations in the poultry litter and were found to be influenced by the physical parameters of the litters (bedding material, moisture content, pH), as well as the NH(4)-N content of the litters, based on principal component analysis. Chemical parameters (organic N, total N, total C) were not found to be influential in the concentrations of our PLUP group in the diverse poultry litters Future applications of this assay could include determining the efficacy of current NH(4)-N-reducing litter amendments or in designing more efficient treatment protocols.

  16. A broad G protein-coupled receptor internalization assay that combines SNAP-tag labeling, diffusion-enhanced resonance energy transfer, and a highly emissive terbium cryptate acceptor

    Angélique eLEVOYE


    Full Text Available Although G protein-coupled receptor (GPCR internalization has long been considered a major aspect of the desensitization process that tunes ligand responsiveness, internalization is also involved in receptor resensitization and signaling, as well as the ligand scavenging function of some atypical receptors. Internalization thus contributes to the diversity of GPCR-dependent signaling, and its dynamics and quantification in living cells has generated considerable interest. We developed a robust and sensitive assay to follow and quantify ligand-induced and constitutive GPCR internalization but also receptor recycling in living cells. This assay is based on diffusion-enhanced resonance energy transfer (DERET between cell surface GPCRs labeled with a luminescent terbium cryptate donor and a fluorescein acceptor present in the culture medium. GPCR internalization results in a quantifiable reduction of energy transfer. This method yields a high signal-to-noise ratio due to time-resolved measurements. For various GPCRs belonging to different classes, we demonstrated that constitutive and ligand-induced internalization could be monitored as a function of time and ligand concentration, thus allowing accurate quantitative determination of kinetics of receptor internalization but also half-maximal effective or inhibitory concentrations of compounds. In addition to its selectivity and sensitivity, we provided evidence that DERET-based internalization assay is particularly suitable for characterizing biased ligands. Furthermore, the determination of a Z’-factor value of 0.45 indicates the quality and suitability of DERET-based internalization assay for high-throughput screening (HTS of compounds that may modulate GPCRs internalization.

  17. A Broad G Protein-Coupled Receptor Internalization Assay that Combines SNAP-Tag Labeling, Diffusion-Enhanced Resonance Energy Transfer, and a Highly Emissive Terbium Cryptate.

    Levoye, Angélique; Zwier, Jurriaan M; Jaracz-Ros, Agnieszka; Klipfel, Laurence; Cottet, Martin; Maurel, Damien; Bdioui, Sara; Balabanian, Karl; Prézeau, Laurent; Trinquet, Eric; Durroux, Thierry; Bachelerie, Françoise


    Although G protein-coupled receptor (GPCR) internalization has long been considered as a major aspect of the desensitization process that tunes ligand responsiveness, internalization is also involved in receptor resensitization and signaling, as well as the ligand scavenging function of some atypical receptors. Internalization thus contributes to the diversity of GPCR-dependent signaling, and its dynamics and quantification in living cells has generated considerable interest. We developed a robust and sensitive assay to follow and quantify ligand-induced and constitutive-induced GPCR internalization but also receptor recycling in living cells. This assay is based on diffusion-enhanced resonance energy transfer (DERET) between cell surface GPCRs labeled with a luminescent terbium cryptate donor and a fluorescein acceptor present in the culture medium. GPCR internalization results in a quantifiable reduction of energy transfer. This method yields a high signal-to-noise ratio due to time-resolved measurements. For various GPCRs belonging to different classes, we demonstrated that constitutive and ligand-induced internalization could be monitored as a function of time and ligand concentration, thus allowing accurate quantitative determination of kinetics of receptor internalization but also half-maximal effective or inhibitory concentrations of compounds. In addition to its selectivity and sensitivity, we provided evidence that DERET-based internalization assay is particularly suitable for characterizing biased ligands. Furthermore, the determination of a Z'-factor value of 0.45 indicates the quality and suitability of DERET-based internalization assay for high-throughput screening (HTS) of compounds that may modulate GPCRs internalization.

  18. Assessment of the effects of metabolism on the estrogenic activity of xenoestrogens: a two-stage approach coupling human liver microsomes and a yeast estrogenicity assay.

    Elsby, R; Maggs, J L; Ashby, J; Paton, D; Sumpter, J P; Park, B K


    Concern that the reproductive health of humans is being affected by exposure to xenoestrogens has led to the development of various in vitro and in vivo screening assays for the identification of suspected xenoestrogens. However, the estrogenic activity of a chemical determined in vitro may not necessarily predict its activity in vivo if the chemical is metabolized during the assay and/or in vivo. Therefore, to investigate the role of metabolism in modulating the estrogenic activity of suspected xenoestrogens, we have devised a two-stage approach coupling incubations with either human or rat hepatic microsomes with a yeast estrogenicity (transcription) assay. We have assessed the activity of the proestrogenic pesticide 99.5% methoxychlor [1,1,1-trichloro-2,2-bis-(4-methoxyphenyl)ethane, MXC] (EC(50) = 4.45 +/- 1.9 ,icroM, n = 6) and a structural analog, methoxybisphenol A [2,2-bis-(4-methoxyphenyl) propane, MBPA], in the yeast estrogenicity assay and also established that yeast (Saccharomyces cerevisiae), unlike human liver microsomes, are not able to demethylate MXC or MBPA to estrogenic metabolites. This indicates that the proestrogen MXC has weak intrinsic estrogenic activity. Using 99.5% MXC and 17beta-estradiol as paradigms, we have demonstrated how metabolism can enhance or suppress, respectively, estrogenic activity. The effect of metabolism on the activities of the weak xenoestrogens 3,17beta-bisdesoxyestradiol [1,3,5(10)-estratriene] and 6-hydroxytetralin (5,6,7,8-tetrahydro-2-naphthol) was also assessed. This two-stage approach can distinguish the estrogenic activity of a suspect chemical from the activity due to its more, or less, active metabolites and will aid in the evaluation of novel xenoestrogens and, more importantly, proestrogens.

  19. Consecutive cross-coupling reactions of 2,2-difluoro-1-iodoethenyl tosylate with boronic acids: efficient synthesis of 1,1-diaryl-2,2-difluoroethenes

    Ju Hee Kim


    Full Text Available The cross-coupling reactions of 2,2-difluoro-1-iodoethenyl tosylate (2 with 2 equiv of boronic acids in the presence of catalytic amounts of Pd(OAc2 and Na2CO3 afforded the mono-coupled products 3 and 5 in high yields. The use of 4 equiv of boronic acids in the presence of catalytic amount of Pd(PPh32Cl2 and Na2CO3 in this reaction resulted in the formation of symmetrical di-coupled products 4 in high yields. Unsymmetrical di-coupled products 4 were obtained in high yields from the reactions of 3 with 2 equiv of boronic acids in the presence of catalytic amounts of Pd(OAc2 and Na2CO3.

  20. Consecutive cross-coupling reactions of 2,2-difluoro-1-iodoethenyl tosylate with boronic acids: efficient synthesis of 1,1-diaryl-2,2-difluoroethenes.

    Kim, Ju Hee; Choi, Su Jeong; Jeong, In Howa


    The cross-coupling reactions of 2,2-difluoro-1-iodoethenyl tosylate (2) with 2 equiv of boronic acids in the presence of catalytic amounts of Pd(OAc)2 and Na2CO3 afforded the mono-coupled products 3 and 5 in high yields. The use of 4 equiv of boronic acids in the presence of catalytic amount of Pd(PPh3)2Cl2 and Na2CO3 in this reaction resulted in the formation of symmetrical di-coupled products 4 in high yields. Unsymmetrical di-coupled products 4 were obtained in high yields from the reactions of 3 with 2 equiv of boronic acids in the presence of catalytic amounts of Pd(OAc)2 and Na2CO3.