BRCA1 mutation screening using restriction endonuclease fingerprinting-single-strand conformation polymorphism in an automated capillary electrophoresis system

Efficient mutation scanning techniques are needed for the rapid detection of novel disease-associated mutations and rare-sequence variants of putative importance. The large size of the breast cancer 1 gene (BRCA1) and the many mutations found throughout its entire coding sequence make screening for mutations in this gene particularly challenging. We have developed a method for screening exon 11 of the BRCA1 gene based on restriction enzyme digestion of fluorescence-labeled polymerase chain reaction (PCR) products followed by single-strand conformation polymorphism (SSCP) using an automated capillary electrophoresis system, denoted capillary restriction endonuclease fingerprinting (REF)-SSCP electrophoresis. Using this strategy on a control set of samples, we were able to detect 17 of 18 known sequence alterations. The method was then applied to screen 73 Norwegian females with family histories of breast and/or ovarian cancer. A total of 172 sequence alterations were detected, including substitutions, insertions, and deletions. One novel substitution of unknown function was identified. Sequencing of all samples negative in the capillary REF-SSCP system gave no additional mutations confirming the high sensitivity of the described methodology. Capillary REF-SSCP electrophoresis appeared as a technically convenient technique, requiring amplification of fewer PCR fragments than traditional SSCP. The novel strategy allows high-throughput mutation scanning without radioactive labeling and polyacrylamide gel electrophoresis (PAGE).     

Markov processes in single molecule fluorescence

This article examines the current status of Markov processes in single molecule fluorescence. For molecular dynamics to be described by a Markov process, the Markov process must include all states involved in the dynamics and the first-passage time (FPT) distributions out of those states must be describable by a simple exponential law. The observation of non-exponential FPT distributions or other evidence of non-Markovian dynamics is common in single molecule studies and offers an opportunity to expand the Markov model to include new dynamics or states that improve understanding of the system.     

LaNi4.7Al0.3单颗粒微电极电化学行为的研究

报道了一种单颗粒微电极制备新方法, 并研究了LaNi4.7Al0.3球形单颗粒微电极的电化学行为.     

Single cell manipulation, analytics, and label-free protein detection in microfluidic devices for systems nanobiology

Single cell analytics for proteomic analysis is considered a key method in the framework of systems nanobiology which allows a novel proteomics without being subjected to ensemble-averaging, cell-cycle, or cell-population effects. We are currently developing a single cell analytical method for protein fingerprinting combining a structured microfluidic device with latest optical laser technology for single cell manipulation (trapping and steering), free-solution electrophoretical protein separation, and (label-free) protein detection. In this paper we report on first results of this novel analytical device focusing on three main issues. First, single biological cells were trapped, injected, steered, and deposited by means of optical tweezers in a poly(dimethylsiloxane) microfluidic device and consecutively lysed with SDS at a predefined position. Second, separation and detection of fluorescent dyes, amino acids, and proteins were achieved with LIF detection in the visible (VIS) (488 nm) as well as in the deep UV (266 nm) spectral range for label-free, native protein detection. Minute concentrations of 100 fM injected fluorescein could be detected in the VIS and a first protein separation and label-free detection could be achieved in the UV spectral range. Third, first analytical experiments with single Sf9 insect cells (Spodoptera frugiperda) in a tailored microfluidic device exhibiting distinct electropherograms of a green fluorescent protein-construct proved the validity of the concept. Thus, the presented microfluidic concept allows novel and fascinating single cell experiments for systems nanobiology in the future.     

New understanding of the nature of OH adsorption on Pt(1 1 1) electrodes

The adsorption of hydroxyl on Pt(1 1 1) single crystal electrodes from aqueous acidic solutions is carefully reinvestigated. The effect of small additions (10⁻⁸–10⁻⁵ M) of chloride and bisulphate anions on the OH adsorption region in perchloric acid solution has been studied. Two regions can be differentiated in the voltammetric profile, that behave differently after the addition of the foreign anion. The initial broad adsorption process is unaffected until the highest concentration is attained. However, the sharper peak at higher potentials is affected even at the lower anion concentration. Since mass transport limitations allow to discard the anion adsorption as the main process giving this peak, we propose that the two processes are due to the dissociative adsorption of two different kinds of water, that are affected by the anion in a different way. From this idea, a new model, based on the Frumkin adsorption isotherm, is proposed, which gives an excellent fit of the experimental results.     

集成滤波器在谱图信号除噪中的应用

本文提出了一种由神经元网络与线性自适应滤波器组成的集成滤波器的实现方法，用于谱图信号除噪处理。     

Resolution method for overlapping peaks based on the fractional-order differential

Equations between the differential order and the maximum of the fractional-order differential for the specified peak signals are developed based on the variation of the maximum of the specified peak signals at different orders. Also, equations between the differential order and the zero-crossing of the fractional-order differential of the specified peak signals are proposed according to the variation of the zero-crossing of the specified peak signals at different orders. Characteristic paramters of the Gaus- sian peak, Lorentzian peak, and Tsallis peak can be estimated using estimator I and estimator II which are obtained by the equations above. As a result, a new method is presented to resolve the overlapped peaks signal. Firstly, a fractional-order differential of the specified peak signals is obtained with the fractional-order differentiation filter. Then, characteristic paramters of the specified peak signals can be extracted using estimator I and estimator II. Finally, the Tsallis peak is used as a model to assign the overlapping peak signals correctly. Experimental results show that the proposed method is efficient and effective for the simulated overlapping peaks and detected overlapping voltammetric peak signals.     

Insights on the origin of the structural phase transition in BaV10O15 from electronic structure calculations and the effect of Ti-doping on its structure and electrical transport properties

Band structure calculations at the level of LMTO-ASA provide insight into the electronic structure of BaV₁₀O₁₅ and the origin of the structural phase transition. A crystal orbital Hamiltonian population/integrated crystal orbital Hamiltonian population analysis provides evidence that the crystallographic phase transition is driven by V-V bond formation. As well, the energy bands near the Fermi level are very narrow, <1 eV, consistent with the fact that the observed insulating behavior can be due to electron localization via either Mott-Hubbard correlation and/or Anderson disorder. The partial solid solution, BaV_10−xTi_xO₁₅, was examined to study the effect of Ti-doping at the V sites on the structure and electronic transport properties. In spite of the non-existence of “BaTi₁₀O₁₅”, the limiting x=8, as indicated by a monotonic increase in the cell volume and systematic changes in properties. This limit may be due to the difficulty of stabilizing Ti²⁺ in this structure. For x=0.5 both the first order structural phase transition and the magnetic transition at 40 K are quenched. The samples obey the Curie-Weiss law to x=3 with nearly spin only effective moments along with θ values which range from −1090 K (x=0.5) to −1629 K (x=3). For x>3 a very large, ∼2×10⁻³ emu/mol, temperature independent (TIP) contribution dominates. Conductivity measurements on sintered, polycrystalline samples show semiconducting behavior for all compositions. Activation energies for Mott hopping derived from high temperature data range from ∼0.1 eV for x=0-1 and fall to a plateau of 0.06 eV for x=3-7. Low temperature data for x=3, 5 and 7 show evidence for Mott variable range hoping (VRH) with a T^1/4 law and in one case between 5 and 17 K, a Efros-Shklovskii correlated hopping, T^1/2 law, was seen, in sharp contrast to BaV₁₀O₁₅ where only the E-S law was observed up to 75 K. Seebeck coefficients are small (<35 μV/K), positive, roughly TIP and increase with increasing x up to x=5. This may point to a Heikes hopping of holes but a simple single carrier model is impossible. The compositions for x>3 are remarkable in that local moment behavior is lost, yet a metallic state is not reached. The failure of this system to be driven metallic even at such high doping levels is not fully understood but it seems clear that disorder induced carrier localization plays a major role.     

A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data

Single nucleotide polymorphism (SNP) arrays were used to detect chromosomal regions with DNA copy number alterations. Current statistical methods for microarray-based comparative genomic hybridization (array-CGH) analysis generally assume certain relationships among adjacent markers on the same chromosome, and these assumptions may be questionable. For an SNP-array-based CGH study, multiple normal reference SNP arrays were collected. In order to utilize these normal reference SNP arrays, we derived an empirical distribution of signal ratios for each SNP marker. With an assumed threshold value for the overall error rate control and the defined signal ratio ranges for chromosomal amplification and deletion, we proposed a procedure to identify chromosomal alteration regions based on several bootstrapped one-sample t-tests and the false discovery rate control. When we have multiple arrays for different individuals with the same disease, our method can also be used to detect SNP markers for chromosomal alteration regions that are common among these individuals. We applied our method to a published SNP array data set for breast carcinoma cell lines. For an individual with breast cancer, numerous chromosomal alteration regions were identified. Compared to results of previous studies, our method identified more chromosomal alteration regions, with some being implicated in the literature to harbor genes associated with breast cancer. For multiple cancer arrays, our results suggested the existence of common chromosomal alteration regions. However, a high proportion of false positives also indicated that genetic variations among different individuals with breast cancer can be present.     

Simultaneous measurement of glucose and glutamine in aqueous solutions by near infrared spectroscopy

A method is described for measuring the concentrations of both glucose and glutamine in binary mixtures from near infrared (NIR) absorption spectra. Spectra are collected over the range from 5000–4000/cm (2.0–2.5μm) with a 1-mm optical path length. Glucose absorbance features at 4710, 4400, and 4300/cm and glutamine features at 4700, 4580, and 4390/cm provide the analytical information required for the measurement. Multivariate calibration models are generated by using partial least squares (PLS) regression alone and PLS regression combined with a preprocessing digital Fourier filtering step. The ideal number of PLS factors and spectral range are identified separately for each analyte. In addition, the optimum Fourier filter parameters are established for both compounds. The best overall analytical performance is obtained by combining Fourier filtering and PLS regression. Glucose measurements are established over the concentration range from 1.66–59.91 mM, with a standard error of prediction (SEP) of 0.32 mM and a mean percent error of 1.84%. Glutamine can be measured over the concentration range from 1.10–30.65 mM with a SEP of 0.75 mM and a mean percent error of 6.67%. These results demonstrate the analytical utility of NIR spectroscopy for monitoring glucose and glutamine levels in mammalian and insect cell cultures.