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).     

Purification and properties of a β-galactosidase with potential application as a digestive supplement

Functional-based screening of crude β-galactosidase activities from 42 yeast strains resulted in the selection of a single enzyme of potential interest as a digestive supplement. β-Galactosidase produced by Kluyveromyces marxianus DSM5418 was purified to homogeneity by a combination of gel filtration, ion-exchange, and hydroxylapatite chromatographies. The denatured (123 kDa) and native molecular masses (251 kDa) suggest that the enzyme is a homodimer. The optimum pH and temperature of the purified enzyme were 6.8 and 37°C, respectively. The unpurified β-galactosidase in particular displayed a high level of stability when exposed to simulated intestinal conditions in vitro for 4 h. Matrix-assisted laser desorption ionization mass sectrometry analysis revealed that the enzyme's trypsin-generated peptide mass fingerprint shares several peptide fragment hits with β-galactosidases from Kluyveromyces lactis. This confirms the enzyme's identity and indicates that significant sequence homology exists between these enzymes.     

A comparative study of solvent extraction of total petroleum hydrocarbons in soil

Three non-specific methods for the extraction of total petroleum hydrocarbons (TPH) from soil into organic solvent were compared. The techniques used for sample preparation were Soxhlet extraction, closed-vessel microwave-assisted extraction, and CEN shake extraction. The total concentrations of extracted compounds in the boiling point range of C10–C40 were determined by gas chromatography with flame ionization detection. The best recovery (99%) and repeatability (±3%) from standard oil mixtures were obtained with microwave-assisted extraction. However, the different extraction methods exhibited different behaviour when spiked soil samples were extracted. The best repeatability was obtained with CEN shake extraction (±6%) but the repeatability values for Soxhlet and microwave-assisted methods were quite high (>20%). However, the larger uncertainties of the latter extraction methods does not necessarily limit the applicability of these methods to the determination of petroleum hydrocarbons in soil, as in the assessment of soil contamination the expanded uncertainty of the result is usually not limited by analytical uncertainty, but rather by the uncertainty of the primary sampling stage. However, distinctive variation found in the chromatographic profiles illustrates that discretion should be obeyed when chromatograms obtained after application of different extraction methods on petroleum contaminated samples are to be used in the fingerprinting or age dating studies. Otherwise, misleading conclusions concerning the age of spillage could be drawn.     

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.     

基于移动代理的多播水印协议

 提出1个基于移动代理的位置无关的多播水印协议(MAMWP),使用移动代理来实现每个组成员接收到的是不同的数据流拷贝.该协议可以解决多播和指纹的矛盾,实现多播系统中的盗版源跟踪或泄密者识别.MAMWP不依赖于中间实体的安全性和计算能力,在实现上可以独立于现有的任何多播体系,有很好的扩展性,并且支持动态的组成员身份.MAMWP可作为多播安全系统的一个可选组成部分.     

Metabolic Profile of Agropyron repens (L.) P. Beauv. Rhizome Herbal Tea by HPLC-PDA-ESI-MS/MS Analysis

Agropyron repens (L.) P. Beauv. (couch grass) is a world-wide infesting rhizomatous plant with pharmacological applications. Chemical research is focused on its allelopathic and anti-inflammatory components, which are mainly present in the essential oil. Conversely, the aqueous extracts have been sparingly investigated, although the herbal tea is by far the most used formulation. To fill the gap, the metabolic profile of Agropyron repens rhizome herbal tea was investigated by electrospray ionization (ESI) tandem–mass spectrometry (MS/MS); the phenolic profile was investigated by HPLC-PDA-ESI-MS/MS. ESI-MS fingerprinting was provided, evidencing diagnostic ions for saccharides, organic acids and amino acids. The HPLC-PDA-ESI-MS/MS analysis evidenced at least 20 characteristic phenolic compounds, the most representative being caffeoyl and feruloyl quinic esters, followed by coumaric, caffeic and ferulic acids, and hesperidin among flavonoids. In addition, the essential amino acid tryptophan was identified for the first time. The results suggest new perspectives of applications for Agropyron repens rhizome.     

数字指纹的技术分析与模型改进

数字指纹作为数字作品版权保护的一种新型技术,越来越得到人们的重视。首先介绍了研究数字指纹的功能与特征,然后分析了指纹的多种编码方案以及指纹协议的演进过程,最后提出了一种数字指纹的系统模型,该模型可用于一些数字作品的版权保护。     

生物净化槽中茵群结构在梭鱼草(Pontederia cordata L)不同生长期的动态变化

为探究引入植物对生物净化槽处理黑臭河水的影响及机理,结合水质理化指标的动态变化,采用了ERIC-PCR指纹图谱技术来分析生物净化槽内的微生物群落结构在植物不同生长阶段的变化特征,比较植物与填料不同工艺组合对微生物群落结构的影响.结果发现:引种梭鱼草(Pontederia cordata L)的生物净化槽对主要污染物COD_(cr),NH_3-N和TP的去除率分别提高了19.8%～69.4%,18.2%～68%和23.9%～77.2%;微生物群落结构随植物不同生长发育阶段而变化,分蘖期优势菌群的种类和数量最多,同期净化效果也最好;从三种工艺的运行效果来看,植物+组合填料搭配最合适.     

Study on detection of mutation DNA fragment in gastric cancer by restriction endonuclease fingerprinting with capillary electrophoresis

The DNA fragment detection focusing technique has further enhanced the sensitivity and information of DNA targets. The DNA fragment detection method was established by capillary electrophoresis with laser‐induced fluorescence detection and restriction endonuclease chromatographic fingerprinting (CE‐LIF‐REF) in our experiment. The silica capillary column was coated with short linear polyarclarylamide (SLPA) using nongel sieving technology. The excision product of various restricted enzymes of DNA fragments was obtained by REF with the molecular biology software Primer Premier 5. The PBR322/BsuRI DNA marker was used to establish the optimization method. The markers were focused electrophoretically and detected by CE‐LIF. The results demonstrate that the CE‐LIF‐REF with SLPA can improve separation, sensitivity and speed of analysis. This technique may be applied to analysis of the excision product of various restricted enzymes of prokaryotic plasmid (pIRES2), eukaryote plasmid (pcDNA3.1) and the PCR product of codon 248 region of gastric cancer tissue. The results suggest that this method could very sensitively separate the excision products of various restricted enzymes at a much better resolution than the traditional agarose electrophoresis. Copyright © 2011 John Wiley & Sons, Ltd.     

Quantitative fingerprinting by headspace—Two-dimensional comprehensive gas chromatography–mass spectrometry of solid matrices: Some challenging aspects of the exhaustive assessment of food volatiles

The study proposes an investigation strategy that simultaneously provides detailed profiling and quantitative fingerprinting of food volatiles, through a “comprehensive” analytical platform that includes sample preparation by Headspace Solid Phase Microextraction (HS-SPME), separation by two-dimensional comprehensive gas chromatography coupled with mass spectrometry detection (GC × GC–MS) and data processing using advanced fingerprinting approaches.