Multiplex PCR with minisequencing as an effective high-throughput SNP typing method for formalin-fixed tissue

Extensive collections of formalin-fixed paraffin-embedded (FFPE) tissues exist that could be exploited for genetic analyses in order to provide important insights into the genetic basis of disease or host/pathogen cointeractions. We report here an evaluation of a 44 SNP multiplex genotyping method, multiplex PCR with minisequencing (MPMS), on 92 DNA extractions performed on six archival FFPE samples of variable DNA quality, which date between 9 and 25 years old. On the three extracts with highest quality, we found the assay efficiency to be near 100%. However, the efficiency of the lowest quality extracts varied significantly. In this study, we demonstrate that although direct measures of DNA concentration in the extracts provide no useful information with regard to subsequent MPMS success, the success of the assay can be determined to some degree a priori, through initial screening of the DNA quality using a simple quantitative real-time PCR (qPCR) assay for nuclear DNA, and/or an assay of the maximum PCR amplifiable size of nuclear DNA. MPMS promises to be of significant use in future genetic studies on FFPE material. It provides a streamlined approach for retrieving a large amount of genetic information using simple, single reactions and minute amounts of archival tissue/DNA. In the light of this evidence, we suggest that the systematic screening of FFPE collections may in the future provide valuable insights into the past.     

2-Amino-7-nitro-fluorenes in neat and mixed solvents-optical band shapes and solvatochromism

Femtosecond transient absorption spectroscopy of amino-nitro-fluorenes in the UV-visible range shows that the dynamic Stokes shift of the emission band is sensitive to infrared-active modes of the solvent. Bandshapes for stationary absorption and emission are needed to quantify the observed spectral evolution. They are reported for 2-amino-7-nitro-fluorene (ANF), 2-dimethylamino-7-nitro-fluorene (dM-ANF), and 2-di(n-butyl)amino-7-nitro-9-di(n-propyl)-fluorene (dBdP-ANF) in a variety of solvents. Bands broaden systematically with increasing solvent polarity. This effect is taken into account in an improved location of band positions. The resulting solvatochromic plots differ significantly from those that use peak positions of absorption spectra and fluorescence quantum distributions. Absorption spectra were also measured in aqueous solvent mixtures, and shifts are described by binding curves for hydrogen bonding and stepwise solvent exchange.     

A new multicomponent reaction catalyzed by a [Lewis Acid](+)[Co(CO)(4)](-) catalyst: stereospecific synthesis of 1,3-oxazinane-2,4-diones from epoxides, isocyanates, and CO

The use of mechanistic information to develop a new, catalytic multicomponent reaction is described. The complex [(salph)Al(THF)2]+[Co(CO)4]- (1, salph = N,N'-o-phenylenebis(3,5-di-tert-butylsalicylideneimine), THF = tetrahydrofuran), which is known to carbonylate epoxides, aziridines, and beta-lactones, was used to catalyze the synthesis of 1,3-oxazinane-2,4-diones from epoxides, isocyanates, and CO. Under optimized conditions, the reaction was both selective and high-yielding. 1,3-Oxazinane-2,4-diones were synthesized from a variety of epoxides and isocyanates, including some epoxides that do not undergo simple ring-expansion carbonylation. The best results were obtained using highly electrophilic isocyanates. The mechanism of the multicomponent reaction was investigated using labeling and stereochemistry, and the data obtained were consistent with the 1-catalyzed formation of beta-lactone and 1,3-oxazinane-2,4-dione from a common intermediate.     

Synthesis and characterization of new mesomorphic octakis(alkylthio)-substituted lead phthalocyanines and their films

The syntheses of new octakis (alkylthio)-substituted phthalocyanines of Pb(II) (1a and 2a) are described. These compounds are very soluble in most common organic solvents. They have been fully characterized using elemental analysis, NMR, infrared and UV–Vis spectroscopy. The mesogenic properties of these new materials were studied by differential scanning calorimetry and optical microscopy. These phthalocyanine derivatives are liquid at room temperature and form columnar-hexagonal (Col_h) mesophases below −10 °C. It has been indicated that the addition of methylene bridges to the phthalocyanine (Pc) core increases the clearing point temperatures. Also, the coordination of Pb²⁺ with the phthalocyanine core decreases the clearing point temperatures and the liquid crystal phase transition temperatures. Thin films of octakis(alkylthio)-substituted Pb(II) phthalocyanines 1a and 2a were prepared by the method of spin-coating. To obtain films with an ordered structure the film of 1a was slowly cooled from room temperature down to −10 °C. Sandwich structures of the form Au/PbPc(1a)/Au were prepared for the investigation of their electrical properties. It was shown that a slowly cooled Au/PbPc(1a)/Au structure demonstrates repeatable and stable electrical switching behaviour for applied bias voltages between −1 V and +1 V.     

Coding a coordination-driven self-assembly via a hydrogen bond-directed solid-state synthesis: an unexpected chiral tetrahedral capsule

An achiral ligand, synthesized in the solid state via a coded hydrogen bond-directed organic synthesis, self-assembles with Cu(II) ions to form a chiral tetrahedral capsule that hosts an anion as a guest.     

Synthesis and in-vitro antitumor activity of 1-[3-(indol-1-yl)prop-1-yn-1-yl]phthalazines and related compounds

A series of novel 3-(indol-1-yl)prop-1-yn-1-yl-substituted phthalazines and related azines was prepared via a concise pathway by palladium-catalyzed cross-coupling of appropriate halo-azines and N-propargylindoles. Some of the compounds exhibited significant antitumor activity in an in-vitro assay.     

Effect of halogenated fluorescent compounds on bioluminescent reactions

The paper investigates an application of luminescent bioassays to monitor the toxicity of organic halides. Effects of xanthene dyes (fluorescein, eosin Y, and erythrosin B), used as model compounds, on bioluminescent reactions of firefly Luciola mingrelica, marine bacteria Photobacterium leiognathi, and hydroid polyp Obelia longissima were studied. Dependence of bioluminescence quenching constants on the atomic weight of halogen substituents in dye molecules was demonstrated. Bacterial bioluminescence was shown to be most sensitive to heavy halogen atoms involved in molecular structure; hence, it is suitable for construction of sensors to monitor toxicity of halogenated compounds. Mechanisms of bioluminescence quenching—energy transfer processes, collisional interactions, and enzyme–dye binding—were considered. Changes of bioluminescence (BL) spectra in the presence of the dyes were analyzed. Interactions of the dyes with enzymes were studied using fluorescence characteristics of the dyes in steady-state and time-resolved experiments. The dependences of fluorescence anisotropy of enzyme-bound dyes, the average fluorescence lifetime, and the number of exponential components in fluorescence decay on the atomic weight of halogen substituents were demonstrated. The results are discussed in terms of “dark effect of heavy halogen atom” in the process of enzyme–dye binding; hydrophobic interactions were assumed to be responsible for the effect.     

Compressed-air flow control system

We present the construction and operation of a compressed-air driven flow system that can be used for a variety of microfluidic applications that require rapid dynamic response and precise control of multiple inlet streams. With the use of inexpensive and readily available parts, we describe how to assemble this versatile control system and further explore its utility in continuous- and pulsed-flow microfluidic procedures for the synthesis and analysis of microparticles.     

Magnetic field-induced reactions on the surface of chloroaluminum phthalocyanine thin films

The μ-(oxo)bis[phthalocyaninato] aluminum(III) (AlPc)(2)O films, with the crystallites oriented preferably in one direction, were obtained via chemical transformation of chloroaluminum(III) phthalocyanine AlClPc film upon its annealing in magnetic field. A comparative analysis of the influence of postdeposition annealing without and under applied magnetic field of 1 T on composition and morphology of AlClPc films has been carried out. The chemical transformation of AlClPc to (AlPc)(2)O on the substrate surface is studied by the methods of UV-vis and infrared spectroscopies, Raman, x-ray photoelectron spectroscopy as well as atomic force microscopy. Two interesting effects were observed upon heating the AlClPc films in magnetic field of 1 T. First, the temperature of the chemical transformation of AlClPc to (AlPc)(2)O decreased from 300 °C to 200 °C when magnetic field was applied during postdeposition annealing. Second, the formation of (AlPc)(2)O films with elongated crystallites with a preferential orientation was observed. The heating of (AlPc)(2)O films in a magnetic field at the same conditions did not demonstrate any effect on the structure and morphology of these films.     

Thermogravimetric analysis of walnut shell as pyrolysis feedstock

Thermal degradation behavior and kinetics of a biomass waste material, namely walnut shell, were investigated by using a thermogravimetric analyzer. The desired final temperature of 800 °C was achieved at three different heating rates (2, 10, and 15 °C min^?1) under nitrogen flow (50 mL min^?1). The TG and DTG curves exhibited three distinct zones that can mainly be attributed to removal of water, decomposition of hemicellulose + cellulose, and decomposition of lignin, respectively. The kinetic parameters (activation energy, pre-exponential factor, and reaction order) of active pyrolysis zone were determined by applying Arrhenius, Coats?CRedfern, and Horowitz?CMetzger methods to TG results. The values of activation energies were found to be between 45.6 and 78.4 kJ mol^?1. There was a great agreement between the results of Arrhenius and Coats?CRedfern methods while Horowitz?CMetzger method yielded relatively higher results. The existence of kinetic compensation effect was evident.