Automatic analysis of multiplex ligation-dependent probe amplification products (exemplified by a commercial kit for prenatal aneuploidy detection)

For use in routine prenatal diagnostics, we developed software and methods for automatic aneuploidy detection based on a commercial multiplex ligation-dependent probe amplification (MLPA) kit. Software and methods ensure a reliable, objective, and fast workflow, and may be applied to other types of MLPA kits. Following CE of MLPA amplification products, the software automatically identified the peak area for each probe, normalized it in relation to the neighboring peak areas of the test sample, computed the ratio relative to a reference created from normal samples, and compensated the ratio for a side effect of the normalization procedure that scaled all chromosomally normal DNA peak areas slightly up or down depending on the kind of aneuploidy present. For the chromosomes 13, 18, 21, X, and Y, probe reliability weighted mean ratio values and corresponding SDs were calculated, and the significance for being outside a reference interval around ratio 1.0 was tested. p < or = 1% suggested aneuploidy and 1 < p < or = 5% suggested potential aneuploidy. Individual peaks, where the normalized area was situated more than 4 SD from the corresponding reference, suggested possible partial deletion or gain. Sample quality was automatically assessed. Control probes were not required. Having used the software and methods for two years, we conclude that a reliable, objective, and fast workflow is obtained.     

The Sialons MLn[Si4−xAlxOxN7−x] with M = Eu,Sr, Ba and Ln = Ho‐Yb – Twelve Substitution Variants with the MYb[Si4N7] Structure Type

The oxonitridoalumosilicates (so‐called sialons) MLn[Si_4?xAl_xO_xN_7?x] with M = Eu, Sr, Ba and Ln =Ho, Er, Tm, Yb were obtained by the reaction of the respective lanthanoid metal, the alkaline earth carbonates or europium carbonate, resp., AlN, “Si(NH)₂” and MCl₂ as a flux in a radiofrequency furnace at temperatures around 2100 °C. The compounds MLn[Si_4?xAl_xO_xN_7?x] are relevant for the investigation of substitutional effects on the materials properties due to their ability of tolerating a comparatively large phase width up to x ≈ 2.0(5). The crystal structures of the twelve compounds were refined from X‐ray single crystal data and X‐ray powder data and are found to be isotypic to the MYb[Si₄N₇] structure type. The compounds crystallize in space group P6₃mc (no. 186, hexagonal) and are made up of chains of so‐called starlike units [N^[4](SiN₃)₄] or [N^[4]((Si,Al)(O,N)₃)₄], respectively. These units are formed by four (Si,Al)(N/O)₄ tetrahedra sharing a common central nitrogen atom. The structure refinement was performed utilizing an O/N‐distribution model according to Paulings rules, i.e. nitrogen was positioned on the four‐fold bridging site and nitrogen and oxygen were distributed equally on both of the two‐fold bridging sites, resulting in charge neutrality of the compound. The Si and Al atoms were distributed equally on their two crystallographic sites, referring to their elemental proportion in the compound, due to being poorly distinguishable by X‐ray methods. The chemical compositions of the compounds were derived from electron probe micro analyses (EPMA).     

Comparison of the Structural Information on Sol-Gel Systems Provided by Pyrene Labeled Fluorescent Probes

The influence of the acid catalyst concentration on the structural evolution of a sol-gel system was studied by doping TEOS based starting solutions with two fluorescent probes: a polystyrene chain (M _n =1700) and a much shorter alkane chain (M=172), both of them labeled at both ends with 1-pyrenyl. For this purpose, each probe was incorporated in two TEOS∶H₂O∶C₂H₅OH mixtures (molar ratios 1∶4∶1), one at pH 1.2 and the other at pH 2.5 (respectively below and above the isoelectric point of silica). Very low concentrations of the probes were used (≤10⁻⁶ M), so the pyrene dimmers and excimers were formed only intramolecularly. The ratios of excimer to monomer fluorescence intensities at excitation wavelength of 360 nm (where mainly the ground state pyrene dimmers are excited) were studied as a function of time. Different evolutions of these ratios were observed, which allowed us to predict that the silica structure developsvia the formation of primary particles, even at pH values below the isoelectric point of silica, where it is not possible to directly detect their formation.     

Speed of Sound, Isentropic Compressibilities, and Excess Molar Volumes of Binary Mixtures Containing p-Dioxane

The speed of sound u in and densities of eight binary mixtures of p-dioxane (p-C₄H₈O₂) with methylcyclohexane (c-C₆H₁₁CH₃), 1-chlorohexane (C₆H₁₃C1), 1-bromohexane (C₆H₁₃Br), p-xylene [C₆H₄(CH₃)₂], propylbenzene (C₆H₅C₃H₇), methyl acetate CH₃COOCH₃), butyl acetate (CH₃COOC₄H₉), and amyl acetate (CH₃COOC₅H₁₁) were measured over the whole composition range at 30°C. Isentropic compressibilities (K _S), Rao's molar sound functions (R), excess molar volumes (V ^E), excess isentropic compressibilities (K _S ^E ) together with relative change in volume V/₁₂ values, have been obtained for all measured mole fractions. The excess partial molar volume (V₁-V ₁ ⁰ ) of p-dioxane in different solvents have also been estimated. The experimental results have been analyzed in terms of the Prigogine–Flory–Patterson theory of solutions.     

In situ determination of adsorption kinetics of proteins in a finite bath

A method for fast in situ measurement of adsorption kinetics based on a finite bath was developed. We modified the conventional finite bath by replacing the external loop by a dip probe which enables in situ measurement of the concentration change in the contactor. Deposition of adsorbent particles on the reflection surface of the dip probe compromised measurements. Different membranes, a polyamide, a polypropylene and a nylon membrane were tested to protect the internal reflection surface of the dip probe from fouling with adsorbent particles. The nylon membrane provided efficient protection and high mass transfer evaluated by response time experiments. Unspecific adsorption of the model protein on the membrane could also be excluded. To corroborate the measurements of the dip probe the results were compared to a conventional finite bath and to a shallow-bed. The uptake curves for human polyclonal IgG at different concentrationes (0.1-3 g/l) on rProtein A Sepharose FF and MabSelect were used as model system. The effective diffusion coefficients were determined using a pore diffusion model. These values were in good agreement for all methods.     

The sound velocity in ideal liquid mixtures from thermal volume fluctuations.

The selection of the correct mixing rule for sound velocity in ideal liquid mixtures determines the interpretation of the sound velocity in real mixtures. This is especially important for the determination of apparent properties of solutes, such as their apparent compressibility. There are different approaches reported in the literature, and this article presents a new derivation of the mixing rule based on statistical mechanics. It is shown that the correlation of volume fluctuations between adjacent components has a crucial influence on the ideal mixing rule.     

The microenvironment in polymer solids with added plasticizers. An attempt to measure the size and distribution of free volume in poly(methyl methacrylate) solids

Various amounts of n-alkylbenzenes (C_n: C₆H₅-C_nH_2n+1 (n = 3-16)) were doped into poly(methyl methacrylate) (PMMA) films, and the emission and thermal properties of each film were measured in detail together with their solid-state ¹³C NMR spectra. The aim of the present work was to estimate the size distribution of free volume in amorphous regions of polymer solids heavily doped with plasticizers by using C_n as models of a plasticizer. The excimer fluorescence yields of C_n in PMMA were found to depend on both the amount of C_n and the length of the alkyl chains of C_n, although the fluorescence spectra of all of the C_ns in dilute fluid solution were almost the same. The quantitative analysis showed: (1) C_n with n ? 12 induces a phase separation in PMMA, in which almost all of the C_n molecules are in a separated phase, and thus they cannot penetrate regions in which PMMA chains are aggregated. This means that C_n with n ? 12 cannot enlarge the space between PMMA chains. (2) Smaller C_n (n < 11) can enter free volumes between PMMA chains that correspond to their molecular size, but they can enlarge them only to a limited extent. Thus, the amount by which plasticization can increase the free volume of PMMA is limited by the size of the dopant and the inherent free volume of the polymer matrix. (3) The efficiency of excimer formation was found to reveal the maximum amount of C_n that could fit in the free volume of PMMA. Thus our fluorescence measurements showed that PMMA solids that were plasticized to their limit had a free volume that was larger than the volume occupied by all the conformers of C₅ and smaller than the volume occupied by almost all the conformers of C₁₂. In conclusion, we were able to obtain information on plasticization and to demonstrate a method of monitoring microenvironments in polymer solids after they have been doped with plasticizers.     

Brillouin light scattering from a biopolymer gel: hypersonic sound waves in gelatin

Rayleigh-Brillouin light scattering experiments were performed on gelatin gels in order to obtain the (hypersonic) sound velocity and sound attenuation as a function of gelatin concentration. The results show that in the high frequency regime there is a strong coupling in the gel between the dynamics of the network and that of the fluid. The network sound velocity varies with ^1/2. Sound attenuation increases with increasing gelatin concentration.     

X-ray emission spectroscopy with EPMA applied to high Tc Superconductors using new spectrometer crystals

The High Temperature Superconductors are characterized by a very anisotropical structure and by typical arrangements of Cu- and O-atoms within CuO₂-planes. In studying the electronic structure of these compounds there is a strong demand for high resolution valence band spectroscopy. Using an electron probe microanalyzer we study the X-ray emission of O-K_ga and Cu-L emerging from polycrystalline YBa₂Cu₃O₇ and Tl₂Ba₂Ca₂Cu₃O₁₀. The O-K emission band is analyzed using a chlinochlore crystal in (001) orientation (2d = 28.4 Å). For the Cu-L emission band we use a beryl crystal in (10¯10) orientation (2d = 15.9 Å). Furthermore, orientation dependent X-ray emission spectroscopy of single-crystalline YBa₂Cu₃O₇ and Tl₂Ba₂Ca₁Cu₂O₈ specimens was performed. We present the partial O-K spectra which represent the O-2p ( = x, y, z) electronic densities of states of the valence band and compare them with calculated data.     

Distance-dependent fluorescence quenching ofN-acetyl-l-tryptophanamide by acrylamide

We examined the time-dependent intensity decays ofN-acetyl-l-tryptophanamide (NATA) when collisionally quenched by acrylamide in propylene glycol over a range of temperatures. The intensity decays of NATA became increasingly heterogeneous in the presence of acrylamide. The NATA intensity decays were not consistent with the Collins-Kimball radiation boundary condition (RBC) model for quenching. The steady-state Stern-Volmer plots show significant upward curvature, and quenching of NATA by acrylamide was observed even in vitrified propylene glycol, where translational diffusion cannot occur during the lifetime of the excited state. These frequencydomain and steady-state data indicate a through-space quenching interaction between NATA and acrylamide, and the results are consistent with a rate constant for quenching that depends exponentially on the fluorophore-quencher separation distance. The exponential distance-dependent rate of quenching also explains the upward curvature of the Stern-Volmer plot, and the steady-state data aid in determining the interaction distance between NATA and acrylamide. These results suggest that the distance-dependent quenching rates need to be considered in the interpretation of acrylamide quenching of proteins.