Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria

DNA fingerprinting has attracted considerable interest as means for identifying, tracing and preventing the dissemination of infectious agents. Various methods have been developed for typing of pathogenic bacteria, which differ in discriminative power, reproducibility and ease of interpretation. During recent years a typing method, which uses the information provided by whole genome sequencing of bacterial species, has gained increased attention. Short sequence repeat (SSR) motifs are known to undergo frequent variation in the number of repeated units through cellular mechanisms most commonly active during chromosome replication. A class of SSRs, named variable number of tandem repeats (VNTRs), has proven to be a suitable target for assessing genetic polymorphisms within bacterial species. This review attempts to give an overview of bacterial agents where VNTR-based typing, or multiple-locus variant-repeat analysis (MLVA) has been developed for typing purposes, together with addressing advantages and drawbacks associated with the use of tandem repeated DNA motifs as targets for bacterial typing and identification.     

A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm

Rational drug design involves finding solutions to large combinatorial problems for which an exhaustive search is impractical. Genetic algorithms provide a novel tool for the investigation of such problems. These are a class of algorithms that mimic some of the major characteristics of Darwinian evolution. LEA has been designed in order to conceive novel small organic molecules which satisfy quantitative structure-activity relationship based rules (fitness). The fitness consists of a sum of constraints that are range properties. The algorithm takes an initial set of fragments and iteratively improves them by means of crossover and mutation operators that are related to those involved in Darwinian evolution. The basis of the algorithm, its implementation and parameterization, are described together with an application in de novo molecular design of new retinoids. The results may be promising for chemical synthesis and show that this tool may find extensive applications in de novo drug design projects.     

双波长分光光度法测定湿法炼锌净化液中的痕量锗

选择水杨基荧光酮－乳化剂ＯＰ－盐酸为显色体系，应用双波长分光光度法扣除硫酸锌的基体干扰，不分离直接测定了湿法炼锌过程中硫酸锌净化液中的痕量锗。测定范围在０－４０ｍｇ／Ｌ。本法应用于株洲冶炼厂锌净化液中锗的测定，结果与该厂长期的萃取－比色法结果相吻合，而测定速度较萃取－比色法至少提高了一倍。     

Enhancement of signal-to-noise level by synchronized dual wavelength modulation for light emitting diode fluorimetry in a liquid-core-waveguide microfluidic capillary electrophoresis system

The signal-to-noise level of light emitting diode (LED) fluorimetry using a liquid-core-waveguide (LCW)-based microfluidic capillary electrophoresis system was significantly enhanced using a synchronized dual wavelength modulation (SDWM) approach. A blue LED was used as excitation source and a red LED as reference source for background-noise compensation in a microfluidic capillary electrophoresis (CE) system. A Teflon AF-coated silica capillary served as both the separation channel and LCW for light transfer, and blue and red LEDs were used as excitation and reference sources, respectively, both radially illuminating the detection point of the separation channel. The two LEDs were synchronously modulated at the same frequency, but with 180°-phase shift, alternatingly driven by a same constant current source. The LCW transferred the fluorescence emission, as well as the excitation and reference lights that strayed through the optical system to a photomultiplier tube; a lock-in amplifier demodulated the combined signal, significantly reducing its noise level. To test the system, fluorescein isothiocyanate (FITC)-labeled amino acids were separated by capillary electrophoresis and detected by SDWM and single wavelength modulation, respectively. Five-fold improvement in S/N ratio was achieved by dual wavelength modulation, compared with single wavelength modulation; and over 100-fold improvement in S/N ratio was achieved compared with a similar LCW-CE system reported previously using non-modulated LED excitation. A detection limit (S/N = 3) of 10 nM FITC-labeled arginine was obtained in this work. The effects of modulation frequency on S/N level and on the rejection of noise caused by LED-driver current and detector were also studied.     

基于近红外光谱的维生素C片无损鉴别分析

基于近红外光谱技术与化学计量学方法,建立了一种国内外不同品牌维生素C片的无损鉴别方法。采集了国内外8个品牌的维生素C片共计40个样本的近红外光谱数据,比较了完整样品以及粉末样品的近红外光谱,采用连续小波变换技术消除背景干扰和基线漂移,基于标准偏差与相对标准偏差的变量筛选方法筛选出具有代表性的波数点,结合主成分分析方法对国内外不同品牌维生素C片进行鉴别分析。结果表明:原始光谱存在着明显的背景干扰和基线漂移现象,且粉末样品的重现性要优于完整样品;单纯使用原始光谱无法辨别来自不同品牌的维生素C片;连续小波变换可以有效消除背景干扰,提高模型鉴别能力;完整样品的鉴别准确率优于粉末样品,说明国内外不同品牌维生素C片主要成分基本一致,可能是辅剂和工艺上存在细微差异。通过结合近红外光谱分析技术与化学计量学方法,可实现对国产以及进口不同品牌维生素C片的鉴别分析。     

Application of recombinant phage display antibody system in study of Codakia orbicularis gill proteins

We used the recombinant phage display antibody system (RPAS) to obtain chimeric single-chain fragment variable (ScFv) antibodies to gill proteins of the white clam Codakia orbicularis (Linné, 1758). After three rounds of selection on immunotubes loaded with total gill protein extract, recombinant phages exhibiting antibodies to gill proteins were isolated and tested by enzyme-linked immunosorbent assay (ELISA). Clones exhibiting a high affinity for the mollusk proteins were selected for production of soluble ScFv antibodies, which were purified for subsequent analysis. ScFv antibodies exhibited a reaction specific for a protein whose molecular mass was about 15,000 Daltons and that was detected by the antigen capture technique followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blotting.     

Comparative analysis of affine scaling algorithms based on simplifying assumptions

We analyze several affine potential reduction algorithms for linear programming based on simplifying assumptions. We show that, under a strong probabilistic assumption regarding the distribution of the data in an iteration, the decrease in the primal potential function will be with high probability, compared to the guaranteed(1). ( 2n is a parameter in the potential function andn is the number of variables.) Under the same assumption, we further show that the objective reduction rate of Dikin's affine scaling algorithm is with high probability, compared to no guaranteed convergence rate.Research supported in part by NSF Grant DDM-8922636.     

Bonferroni-type inequalities; Chebyshev-type inequalities for the distributions on [0, n]

An elementary majorant-minorant method to construct the most stringent Bonferroni-type inequalities is presented. These are essentially Chebyshev-type inequalities for discrete probability distributions on the set {0, 1,..., n}, where n is the number of concerned events, and polynomials with specific properties on the set lead to the inequalities. All the known results are proved easily by this method. Further, the inequalities in terms of all the lower moments are completely solved by the method. As examples, the most stringent new inequalities of degrees three and four are obtained. Simpler expressions of Mrgritescu's inequality (1987, Stud. Cerc. Mat., 39, 246–251), improving Galambos' inequality, are given.