Real-Time Duplex Applications of Loop-Mediated AMPlification (LAMP) by Assimilating Probes

Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP) are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for λ-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field.     

Photopolymerization synthesis of poly(N-isopropylacrylamide) hydrogels

Poly(N-isopropylacrylamide) (NIPAAm) gels were formed by photopolymerization of NIPAAm in the absence of a crosslinker using a water solvent at 25°C. Factors affecting formation were the wavelength region of irradiated light, the type of photoinitiators, and the concentrations of the photoinitiator and monomer. A high-pressure mercury lamp (400 W) was used as a light source. An NIPAAm concentration of 10 wt % and irradiation time of 15 h was used for the photopolymerization. The gel (68% yield) was formed when the quartz glass system was used, but no gelation was observed for the Pyrex glass system that transmits light with π > 290 nm. The gel (100% yield) was easily formed, even in the latter system, when 30 mmol/L of hydrogen peroxide and potassium persulfate were used as the photoinitiator. Water soluble photoinitiators such as ferric chloride and sodium anthraquinone-2,7-disulfonate were not effective for the gel formation. Yield of the gel increased with increasing the potassium persulfate concentration (1–30 mmol/L), but it decreased when a high concentration of hydrogen peroxide (60 mmol/L) was used. The gel yield increased with the NIPAAm concentration (5–20 wt %). The degree of swelling of the resultant poly(NIPAAm) gels, which was measured by immersing the gels in water at various temperatures (0–50°C) for 24 h, steeply decreased at about 30°C with increasing temperature, exhibiting a temperature-responsive character. The gels swelled and shrank in water below and above the temperature, respectively. The extent of the character depended on the concentrations of hydrogen peroxide and monomer. The formation mechanism of the gel in the photopolymerization of NIPAAm using hydrogen peroxide photoinitiator was discussed. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 65:1313–1318, 1997     

Cell interaction study of amyloid by using luminescent conjugated polythiophene: implication that amyloid cytotoxicity is correlated with prolonged cellular binding

Needles and noodles: Studying amyloid toxicity is important for understanding protein misfolding diseases. Using a luminescent conjugated polythiophene, we found that cell binding of nontoxic filamentous amyloids of insulin and β2-microglobulin was less efficient than that of toxic fibrillar amyloids; this suggests a correlation between amyloid toxicity and cell binding.     

Nile blue adsorbed onto silica gel modified with niobium oxide for electrocatalytic oxidation of NADH

A study of modified carbon paste electrode employing Nile blue (NB) adsorbed on silica gel modified with niobium oxide (SN) for electrocatalytic oxidation of reduced nicotinamide adenine dinucleotide (NADH) is described. The adsorbed organic dye on SN was used to prepare a modified carbon paste electrode to investigate its electrochemical properties. The formal potential (E°′) of the adsorbed NB (−230 mV vs. saturated calomel electrode, SCE) showed a shift of 70 mV towards a more positive potential value, compared to NB dissolved in aqueous solution. In solutions with pH between 6.0 and 8.0 did stability and E°′ remained almost constant. However, for a solution pH lower than 6.0 the E°′ was affected by the acidity of the contacting solution, shifting the E°′ towards more positive values. For the solution pHs between 6.0 and 8.0 the electrocatalytic activity remained almost constant. A linear response range for NADH between 1.0×10⁻⁵ and 5.2×10⁻⁴ mol l⁻¹, at pH 7.0, was observed for the electrode, with an applied potential of −200 mV versus SCE. The formation of an intermediate charge transfer (CT) complex was proposed to the CT reaction between NADH and adsorbed NB. The heterogeneous electron transfer rate, k_obs, was 1400 M⁻¹ s⁻¹ and the apparent Michaelis-Menten constant, was 0.21 mM at pH 7.0 evaluated from rotating disk electrode (RDE) experiments with an electrode coverage of about 5.2×10⁻⁹ mol cm⁻². The increase in the reaction rate between NADH and the immobilized NB compared to those obtained with dissolved NB was assigned to the shift of the E°′ towards more positive values.     

Synthesis of AlPO4 Molecular Sieves with AFI and AEL Structures by Dry-Gel Conversion Method and Catalytic Application of Their SAPO Counterparts on Isopropylation of Biphenyl

AlPO₄-5 and AlPO₄-11 were synthesized by dry-gel conversion (DGC) method. Steam-assisted conversion (SAC) and vapor-phase transport (VPT) techniques were applied for this purpose. The synthesis was successful in presence of a certain minimum amount of external bulk water, without which the crystallization failed. Crystallization by VPT method was slower than corresponding SAC and HTS method. SAPO analogs of the samples, SAPO-5 and SAPO-11 were also synthesized by DGC method. Samples made by DGC methods had higher yield than the conventional hydrothermal synthesis (HTS); otherwise the samples showed similar characteristics as that made by HTS. XRD, SEM and N₂-adsorption results showed high crystallinity and purity of the samples made by DGC, and ²⁷Al MAS NMR spectra indicated the tetrahedral framework nature of Al. SAPO-5 and SAPO-11 were tested for their catalytic activity in isopropylation of biphenyl, and in terms of conversion and selectivity, SAPO-5 was found to be suitable for this application.     

Effect of polymer density on polyethylene hollow fiber membrane formation via thermally induced phase separation

Microporous high‐density polyethylene (HDPE) and low‐density polyethylene (LDPE) hollow fiber membranes were prepared from polyethylene–diisodecyl phthalate solution via thermally induced phase separation. Effect of the polyethylene density on the membrane structure and performance was investigated. The HDPE membrane showed about five times higher water permeability than the LDPE membrane because it had the larger pore and the higher porosity at the outer membrane surface. The formation of the larger pore was owing to both the initial larger structure formed by spinodal decomposition and the suppression of the diluent evaporation from the outer membrane surface due to the higher solution viscosity. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 471–474, 2004     

Design of new catalysts for ecological high-quality transportation fuels by combinatorial computational chemistry and tight-binding quantum chemical molecular dynamics approaches

Recently, we introduced a concept of combinatorial chemistry to computational chemistry and proposed a new method called “combinatorial computational chemistry”, which enables us to perform a theoretical high-throughput screening of catalysts. In the present paper, we reviewed our recent application of our combinatorial computational chemistry approach to the design of new catalysts for high-quality transportation fuels. By using our combinatorial computational chemistry techniques, we succeeded to predict new catalysts for methanol synthesis and Fischer–Tropsch synthesis. Moreover, we have succeeded in the development of chemical reaction dynamics simulator based on our original tight-binding quantum chemical molecular dynamics method. This program realizes more than 5000 times acceleration compared to the regular first-principles molecular dynamics method. Electronic- and atomic-level information on the catalytic reaction dynamics at reaction temperatures significantly contributes the catalyst design and development. Hence, we also summarized our recent applications of the above quantum chemical molecular dynamics method to the clarification of the methanol synthesis dynamics in this review.