Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

Background: MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample.Results: Through simulation studies we have shown that our proposed method outperforms two existing methods that are based on simple threshold rules or iterative regression. We have illustrated the method using a controlled MLPA assay in which targeted regions are variable in copy number in individuals suffering from different disorders such as Prader-Willi, DiGeorge or Autism showing the best performace.Conclusion: Using the proposed mixed-model, we are able to determine thresholds to decide whether a region is altered. These threholds are specific for each individual, incorporating experimental variability, resulting in improved sensitivity and specificity as the examples with real data have revealed.

Specific delineation of BK polyomavirus in kidney tissue with a digoxigenin-labeled DNA probe.

The detection of BK polyomavirus (BK virus, BKV) in kidney tissue is hampered by nonspecificity of antibodies suited to immunohistochemistry, and nonspecific background with in situ hybridization. The biotin-labeled DNA probe that is commercially available (Enzo Life Sciences, Inc.) shows good signal, but the intrinsic background in kidney tissue is high. We determined that the intrinsic background is due to endogenous biotin or biotin-binding activity in the renal tubular epithelium. Neither antibody blocking procedures nor an avidin/biotin block were entirely satisfactory for eliminating this background staining. We developed a digoxigenin-labeled DNA probe, and protocol, for detecting BK virus in formalin-fixed, paraffin embedded, kidney tissue obtained at autopsy. The hybridization signal is strong and there is no perceptible background staining. Eleven negative control kidneys all failed to hybridize. Conditions for low stringency hybridization may be employed, detecting both the related JC polyomavirus and BKV. Alternatively, high stringency hybridization conditions may be utilized, detecting BKV only. BK associated tubular necrosis is clearly demonstrated in two cases of BK nephritis.

Electron probe microanalysis: principles and applications

This article summarizes the basic principles of electron probe microanalysis, with examples of applications in materials science and geology that illustrate the capabilities of the technique.

Diradicals acting through diamagnetic phenylene vinylene bridges: Raman spectroscopy as a probe to characterize spin delocalization

We present a complete Raman spectroscopic study in two structurally well-defined diradical species of different lengths incorporating oligo p-phenylene vinylene bridges between two polychlorinated triphenylmethyl radical units, a disposition that allows sizeable conjugation between the two radicals through and with the bridge. The spectroscopic data are interpreted and supported by quantum chemical calculations. We focus the attention on the Raman frequency changes, interpretable in terms of: (i) bridge length (conjugation length); (ii) bridge conformational structure; and (iii) electronic coupling between the terminal radical units with the bridge and through the bridge, which could delineate through-bond spin polarization, or spin delocalization. These items are addressed by using the"oligomer approach" in conjunction with pressure and temperature dependent Raman spectroscopic data. In summary, we have attempted to translate the well-known strategy to study the electron (charge) structure of π−conjugated molecules by Raman spectroscopy to the case of electron (spin) interactions via the spin delocalization mechanism.

Scrfl restriction fragment length polymorphism at the D7S23 locus (probe pKM.19), closely linked to cystic fibrosis

Source/Description: pKM.19 is a 1.0 kb EcoRI genomic fragment in pUC13 (ref. 1,2). pPl was isolated independently but contains the same fragment as pKM.19 (ref. 3)...

Electrical pump & probe and injected carrier losses quantification in Er doped Si slot waveguides

Electrically driven Er3+ doped Si slot waveguides emitting at 1530 nm are demonstrated. Two different Er3+ doped active layers were fabricated in the slot region: a pure SiO2 and a Si-rich oxide. Pulsed polarization driving of the waveguides was used to characterize the time response of the electroluminescence (EL) and of the signal probe transmission in 1 mm long waveguides. Injected carrier absorption losses modulate the EL signal and, since the carrier lifetime is much smaller than that of Er3+ ions, a sharp EL peak was observed when the polarization was switched off. A time-resolved electrical pump & probe measurement in combination with lock-in amplifier techniques allowed to quantify the injected carrier absorption losses. We found an extinction ratio of 6 dB, passive propagation losses of about 4 dB/mm, and a spectral bandwidth > 25 nm at an effective d.c. power consumption of 120 μW. All these performances suggest the usage of these devices as electro-optical modulators.

A polymorphic DNA probe from chromosome 7 (7q22)

Source/Description: p6a-l is a O.9 kb HindIII/BamHl genomic fragment subclone or cosmic cNX.6a in pUC13. cNX.6a was isolated from a non-methylated enriched library from the CMGT cell line Cll (1,2).

Electron scattering in isotonic chains as a probe of the proton shell structure of unstable nuclei

Electron scattering on unstable nuclei is planned in future facilities of the GSI and RIKEN upgrades. Motivated by this fact, we study theoretical predictions for elastic electron scattering in the N=82, N=50, and N=14 isotonic chains from very proton-deficient to very proton-rich isotones. We compute the scattering observables by performing Dirac partial-wave calculations. The charge density of the nucleus is obtained with a covariant nuclear mean-field model that accounts for the low-energy electromagnetic structure of the nucleon. For the discussion of the dependence of scattering observables at low-momentum transfer on the gross properties of the charge density, we fit Helm model distributions to the self-consistent mean-field densities. We find that the changes shown by the electric charge form factor along each isotonic chain are strongly correlated with the underlying proton shell structure of the isotones. We conclude that elastic electron scattering experiments on isotones can provide valuable information about the filling order and occupation of the single-particle levels of protons.

Hyperpolarized (6) Li as a probe for hemoglobin oxygenation level.

Hyperpolarization by dissolution dynamic nuclear polarization (DNP) is a versatile technique to dramatically enhance the nuclear magnetic resonance (NMR) signal intensity of insensitive long-T1 nuclear spins such as (6) Li. The (6) Li longitudinal relaxation of lithium ions in aqueous solutions strongly depends on the concentration of paramagnetic species, even if they are present in minute amounts. We herein demonstrate that blood oxygenation can be readily detected by taking advantage of the (6) Li signal enhancement provided by dissolution DNP, together with the more than 10% decrease in (6) Li longitudinal relaxation as a consequence of the presence of paramagnetic deoxyhemoglobin. Copyright © 2015 John Wiley & Sons, Ltd.

A new method for intraoperative localization of epilepsy focus by means of a gamma probe

Objective To evaluate the utility of a new multimodal image-guided intervention technique to detect epileptogenic areas with a gamma probe as compared with intraoperative electrocorticography. Materials and Methods Two symptomatic patients with refractory epilepsy underwent magnetic resonance imaging, videoelectroencephalography, brain SPECT scan, neuropsychological evaluation and were submitted to gamma probe-assisted surgery. Results In patient 1, maximum radioactive count was initially observed on the temporal gyrus at about 3.5 cm posteriorly to the tip of the left temporal lobe. After corticotomy, the gamma probe indicated maximum count at the head of the hippocampus, in agreement with the findings of intraoperative electrocorticography. In patient 2, maximum count was observed in the occipital region at the transition between the temporal and parietal lobes (right hemisphere). During the surgery, the area of epileptogenic activity mapped at electrocorticography was also delimited, demarcated, and compared with the gamma probe findings. After lesionectomy, new radioactive counts were performed both in the patients and on the surgical specimens (ex-vivo). Conclusion The comparison between intraoperative electrocorticography and gamma probe-assisted surgery showed similarity of both methods. The advantages of gamma probe include: noninvasiveness, low cost and capacity to demonstrate decrease in the radioactive activity at the site of excision after lesionectomy.

Three Wavelength Optical Probe for Surface Roughness Measurements of Paper Samples

In the present diploma work optical inspection methods were used to investigate surface roughness of paper samples. A special measurement setup, which includes three laser light sources of three different wavelengths, photodetector and goniometer, was used to measure the reflected laser light properties. The intensity of the light reflected in specular direction was measured versus the laser incidence angle for reference metal sample. The value of roughness was estimated and compared to initially known value of metal sample roughness. Thus, the measurement equipment and method were validated. Then the reflected intensity was measured versus reflection angle at constant incidence angle for the same metal sample and paper samples under investigation. The final values of the surface roughness were obtained from the analysis of the reflected intensity dependence. The results are in good correlation with other research groups.

Fe3+-SELECTIVE ENHANCED FLUORESCENCE PROBE BASED ON A RHODAMINE DERIVATIVE

A novel Fe3+-selective and turn-on fluorescent probe 1 incorporating a rhodamine fluorophore and quinoline subunit was synthesized. Probe 1 displayed high selectivity for Fe3+ in CH3CN–H2O (95:5 v/v) in the presence of other relevant metal cations. Interaction with Fe3+ in 1:1 stoichiometry could trigger a significant fluorescence enhancement due to the formation of the ring-open form. The fluorescent response images were investigated by a novel Euclidean distance method based on red, green, and blue values. A linear relationship was observed between fluorescence intensity changes and Fe3+ concentrations from 7.3 × 10−7 to 3.6 × 10−5 mol L−1.

A fluorescence probe study of gemini surfactants in aqueous solution: a comparison between n-2-n and n-6-n series of the alkanediyl-a,w-bis (dimethylalkylammonium bromides)

Two series of alkanediyl-a,w-bis (dimethylalkylammonium bromide (n-2-n and n-6-n; n=8, 10,12, and 16) have been synthesized and their micelles properties studied in aqueous solution using pyrene, pyrenecarboxaldehyde (PCA) and 1,8 anilinonaphtalene sulfonic acid sodium salt (ANS) as fluorescent probes. The micelles from these surfactants have been characterized on the basis of the information provided by micelle-solubilized fluorescent probes. The obtained results indicated that the surfactant concentration at which a marked decrease in l max parameter of pyrenecarboxaldehyde (PCA) occurs corresponds to the CMC determined by conductimetric measurements. Changes in the emission spectra of ANS and PCA observed in the submicellar range for both surfactants series (n-2-n and n-6-n) were interpreted as formation of pre-aggregates. It was found that the dimeric surfactants with long spacer (s= 6) form more hydrated aggregates when compared with those formed by the n-2-n and CnTAB surfactants series. This was attributed to a more difficult packing of n-6-n surfactant molecules to form micelles.