Screening of ligands for redox-active europium using magnetic resonance imaging

We report a screening procedure to predict ligand coordination to Eu^II and Eu^III using magnetic resonance imaging in which bright images indicate complexation and dark images indicate no complexation. Here, paramagnetic Gd^III is used as a surrogate for Eu^III in the screening procedure to enable detection with magnetic resonance imaging. The screening procedure was tested using a set of eight ligands with known coordination to Eu^II and Eu^III, and results were found to be consistent with expected binding. Validation of the screening procedure with known coordination chemistry enables use with new ligands in the future.     

The application of a sequential procedure with elimination as a method for the screening for metabolic diseases

A sequential classification procedure with early elimination, for the screening for metabolic diseases, is presented. Asymptotic properties of the procedure are derived in the Appendix and it is shown that the procedure is asymptotically distribution-free under certain assumptions, and asymptotically at least as efficient as a comparable fixed-sample procedure. With the use of data obtained from 36 mentally retarded patients, the procedure was evaluated by means of a bootstrap simulation. The procedure was then applied to this set of data, with satisfactory results and a considerable economy in observations.     

Selection of monoclonal antibodies for immunoaffinity chromatography: model studies with antibodies against soy bean trypsin inhibitor

To facilitate selection of monoclonal antibodies for immunoaffinity chromatography, an ELISA screening procedure was developed. The assay is based on the avidin-biotin system and provides a profile of the monoclonal antibody which is based on the binding characteristics of the antigen binding site when exposed to different elution reagents. The elution profiles of 5 monoclonal antibodies to soy bean trypsin inhibitor (SBTI) were determined and for 2 of the antibodies the results obtained in the ELISA were verified using column experiments. The affinity constants were determined for the same 5 monoclonal antibodies and no correlation was seen with the ease of elution. The elution profiles presented here are easily obtained and the results indicate that a general screening procedure for suitable combinations of antibodies and elution conditions can be carried out using an elution ELISA assay when modified as described herein.     

A simplified immunofluorescence technique for antibody to varicella-zoster membrane antigen (FAMA)

Indirect fluorescent antibody to varicella-zoster membrane antigens (FAMA) was measured by a new technique. The procedure gives rapid, sensitive and accurate results and is suitable for use in diagnosis or screening of susceptibility to varicella-zoster virus (VZV) infection. The test procedure was simplified by using Terasaki tissue culture plates for the reaction and for direct observation by fluorescence microscopy. Preparations of VZV-infected Vero cells stored in liquid nitrogen could be used as antigen in this FAMA-test.     

Docking and scoring with alternative side-chain conformations

We describe a scoring and modeling procedure for docking ligands into protein models that have either modeled or flexible side-chain conformations. Our methodical contribution comprises a procedure for generating new potentials of mean force for the ROTA scoring function which we have introduced previously for optimizing side-chain conformations with the tool IRECS. The ROTA potentials are specially trained to tolerate small-scale positional errors of atoms that are characteristic of (i) side-chain conformations that are modeled using a sparse rotamer library and (ii) ligand conformations that are generated using a docking program. We generated both rigid and flexible protein models with our side-chain prediction tool IRECS and docked ligands to proteins using the scoring function ROTA and the docking programs FlexX (for rigid side chains) and FlexE (for flexible side chains). We validated our approach on the forty screening targets of the DUD database. The validation shows that the ROTA potentials are especially well suited for estimating the binding affinity of ligands to proteins. The results also show that our procedure can compensate for the performance decrease in screening that occurs when using protein models with side chains modeled with a rotamer library instead of using X-ray structures. The average runtime per ligand of our method is 168 seconds on an Opteron V20z, which is fast enough to allow virtual screening of compound libraries for drug candidates.     

Feature screening with latent responses

A novel feature screening method is proposed to examine the correlation between latent responses and potential predictors in ultrahigh-dimensional data analysis. First, a confirmatory factor analysis (CFA) model is used to characterize latent responses through multiple observed variables. The expectation-maximization algorithm is employed to estimate the parameters in the CFA model. Second, R-Vector (RV) correlation is used to measure the dependence between the multivariate latent responses and covariates of interest. Third, a feature screening procedure is proposed on the basis of an unbiased estimator of the RV coefficient. The sure screening property of the proposed screening procedure is established under certain mild conditions. Monte Carlo simulations are conducted to assess the finite-sample performance of the feature screening procedure. The proposed method is applied to an investigation of the relationship between psychological well-being and the human genome.     

Simplified Procedure for Recovery of Lignin Acidolysis Products for Determining the Lignin-Degrading Abilities of Microorganisms

A simplified procedure for the identification and measurement of single-ring aromatic products of lignin acidolysis is described. The procedure employed a 6-h hydrolysis of spruce milled wood lignin in acidic dioxane at 87°C, followed by a series of organic extractions to recover acidolysis products which were quantified by gas chromatography of trimethylsilyl derivatives. Complex gel permeation chromatography procedures utilized by other workers were avoided in the modified procedure, but equivalent results were obtained. The simplified procedure was utilized to hydrolyze sound and actinomycete-decayed spruce milled wood lignins and was shown to be useful as a technique for the rapid screening of microorganisms for their ability to alter lignin.     

Fluorometric assay for determining epoxide hydrolase activity

We have developed a rapid screening procedure that enables the screening of hundreds of enzyme samples or variants for epoxide hydrolase activity towards any substrate. The procedure detects the products of the enzymatic reaction via periodate cleavage and remaining fluorescence of carboxyfluorescein.     

Screening of xylanolytic bacteria using a colour plate method

A simple procedure is described for the screening and isolation of xylanolytic bacteria, able to degrade hemicellulose. Bagasse hemicellulose was purified, cross-linked with green dye for use as indicator, and used in a Petri dish assay for the determination of xylanolytic activity. Hydrolysis of the substrate causes the formation of transparent halos around bacterial colonies. The screening procedure was used to select thermoresistant bacteria. The four best isolates were characterized and classified as Bacillus species.     

Convenient method for detecting 14CO2 in multiple samples: application to rapid screening for mutants.

A procedure is presented for the rapid screening of bacterial colonies to detect mutants unable to produce 14CO2 from a labeled precursor. The method is especially useful for mass screening for mutants that cannot be easily detected by their phenotypic characteristics.     

噬菌体抗体库筛选技术研究进展

噬菌体抗体库技术是一项新兴的基因工程抗体技术,应用这项技术获得高特异性抗体的关键之一就是筛选环节。根据抗原性质以及筛选目的的不同,筛选方法的选择也不相同,各种筛选策略的优化对中和抗体的获得有至关重要的作用。     

A two-phase procedure for QTL mapping with regression models

It is typical in QTL mapping experiments that the number of markers under investigation is large. This poses a challenge to commonly used regression models since the number of feature variables is usually much larger than the sample size, especially, when epistasis effects are to be considered. The greedy nature of the conventional stepwise procedures is well known and is even more conspicuous in such cases. In this article, we propose a two-phase procedure based on penalized likelihood techniques and extended Bayes information criterion (EBIC) for QTL mapping. The procedure consists of a screening phase and a selection phase. In the screening phase, the main and interaction features are alternatively screened by a penalized likelihood mechanism. In the selection phase, a low-dimensional approach using EBIC is applied to the features retained in the screening phase to identify QTL. The two-phase procedure has the asymptotic property that its positive detection rate (PDR) and false discovery rate (FDR) converge to 1 and 0, respectively, as sample size goes to infinity. The two-phase procedure is compared with both traditional and recently developed approaches by simulation studies. A real data analysis is presented to demonstrate the application of the two-phase procedure.     

Development and application of a DNA microarray-based yeast two-hybrid system

The yeast two-hybrid (Y2H) system is the most widely applied methodology for systematic protein–protein interaction (PPI) screening and the generation of comprehensive interaction networks. We developed a novel Y2H interaction screening procedure using DNA microarrays for high-throughput quantitative PPI detection. Applying a global pooling and selection scheme to a large collection of human open reading frames, proof-of-principle Y2H interaction screens were performed for the human neurodegenerative disease proteins huntingtin and ataxin-1. Using systematic controls for unspecific Y2H results and quantitative benchmarking, we identified and scored a large number of known and novel partner proteins for both huntingtin and ataxin-1. Moreover, we show that this parallelized screening procedure and the global inspection of Y2H interaction data are uniquely suited to define specific PPI patterns and their alteration by disease-causing mutations in huntingtin and ataxin-1. This approach takes advantage of the specificity and flexibility of DNA microarrays and of the existence of solid-related statistical methods for the analysis of DNA microarray data, and allows a quantitative approach toward interaction screens in human and in model organisms.     

Controlled search for the producers of ionophore antibiotics among Streptomycetes

A procedure was developed for directed screening of cultures producing ionophore antibiotics among streptomycetes. The procedure is based on measuring the membrane potential generated in the presence of the Men+/nH+ = -expchanger-protonophore couple. It provided isolation of cultures producing ionophore antibiotics at the fermentation broth stage. It was possible to use the procedure in screening both electrogenic and nonelectrogenic ionophores and to rapidly differentiate them. 5 cultures producing ionophore antibiotics were detected with this procedure; 3 of them carry out nonelectrogenic transport of the cations. The cation transport in the other two cultures was electrogenic. Cation selectivity of the antibiotics produced by the cultures was determined with the procedure. An antibiotic identical to indanomycin was isolated from the culture fluid of Streptomyces chromogenes.     

Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli

Based on the results of a systematic study of factors affecting plasmid yield and purity, a procedure suitable for the rapid screening for and isolation of covalently closed circular DNA from Streptomyces lividans and Escherichia coli was developed. The method consists of lysis of lysozyme-treated bacteria combined with alkaline denaturation of DNA at high temperature. Renaturation of CCC DNA and precipitation of single-stranded DNA together with protein is achieved by the addition of a minimal amount of phenol/chloroform. The screening procedure uses only a single tube and the samples can be analyzed by agarose gel electrophoresis about 30 min after lysis. Removal of phenol and further purification of the plasmid preparation is achieved by consecutive precipitations with isopropanol and spermine, followed by extraction with ethanol, producing samples suitable for restriction endonuclease digestion, ligation, and transformation of S. lividans protoplasts or competent E. coli cells in about 2 h. All steps of the procedure are explained in detail with information about the effects of changing parameters. This should help the experimenter to obtain reproducible results and may be useful if the method has to be adapted to new strains or plasmids.     

A note of feature screening via a rank-based coefficient of correlation

Feature screening is a useful and popular tool to detect informative predictors for ultrahigh-dimensional data before developing statistical analysis or constructing statistical models. While a large body of feature screening procedures has been developed, most methods are restricted to examine either continuous or discrete responses. Moreover, even though many model-free feature screening methods have been proposed, additional assumptions are imposed in those methods to ensure their theoretical results. To address those difficulties and provide simple implementation, in this paper we extend the rank-based coefficient of correlation to develop a feature screening procedure. We show that this new screening criterion is able to deal with continuous and binary responses. Theoretically, the sure screening property is established to justify the proposed method. Simulation studies demonstrate that the predictors with nonlinear and oscillatory trajectories are successfully retained regardless of the distribution of the response. Finally, the proposed method is implemented to analyze two microarray datasets.     

Detection of mitochondrial DNA deletions by a screening procedure using the Polymerase Chain Reaction

We describe an accurate procedure for a rapid diagnosis of heteroplasmic mtDNA deletions based on the polymerase chain reaction (PCR). For a selective amplification of deleted mtDNA across the breakpoints of the deletion, we used seven combinations of primers surrounding the most common deleted region between the two origins of mtDNA replication. This procedure was performed on muscle biopsies of twenty patients harboring a single mtDNA deletion and one patient with multiple mtDNA deletions. The results were compared with Southern-blotting analysis. We conclude that this PCR procedure is a sensitive and convenient screening method for the detection of mtDNA deletions. (Mol Cell Biochem 174: 221–225, 1997)     

Investigation of 208 consecutive cases of cervical cone biopsies with regard to indication, negative samples and quality control

OBJECTIVE: To analyze factors in preoperative management and cytologic screening leading to a conization specimen free of neoplasia. STUDY DESIGN: From January 2001 through December 2003, cervical conization was performed on 208 consecutive cases at the Gynecologic Department, Krankenhaus Lainz, Vienna. Indications for cone biopsy were based on suspicious internal and/or external conventional cytologic screening results followed by punch biopsies in selected cases. RESULTS: Benign cervical lesions were diagnosed in 22 women (10.6%). Histologic results in negative cone biopsies were cervicitis (n = 12), infection with HPV without cervical intraepithelial neoplasia (n = 1), tubal metaplasia (n = 4) and combined diagnoses indicating no neoplasia (n = 5). Regarding cytologic screening results prior to conization, long-lasting infections with HPV can cause repeated findings of cells of unknown origin or reversible mild to moderate dysplasia eventually leading to conization specimens free of neoplasia. Furthermore, tubal metaplasia is a frequent pitfall in misinterpretation of cytologic smears. CONCLUSION: Reevaluation of cytologic screening results after the final histologic diagnosis becomes available following cone biopsy is a key issue in continuous quality assurance for the diagnostic procedure. In this article we also present a method of stratifying screening results according to the correctness of the results. Along with other established measures of diagnostic performance, this may support benchmarking and interpretation of the overall cytologic screening quality.     

Evaluation of Disinfectants for Hospital Housekeeping Use

A use-dilution procedure and screening method are proposed to aid the hospital bacteriologist in selecting the most effective disinfectants. Sixteen disinfectants were tested with and without organic material on six different organisms. Sporadic results usually obtained with quaternaries tested by the procedure of the Association of Official Agricultural Chemists (AOAC) were eliminated by the methods of this study. The use-dilution procedure employs the material upon which the disinfectant is to be used, rather than stainless steel, as in the AOAC use-dilution test. The importance of testing each disinfectant against several organisms and in the presence of organic material is discussed.     

噬菌体cDNA文库筛选方法的改良

cDNA文库的构建和简便、快速的筛选是获得全长基因的重要途径,基于PCR的筛库方法具有快捷、灵敏的特点。研究改进了基于PCR的噬菌体cDNA文库筛选方法,用液体分装的方法,替代了文库筛选的关键步骤——涂板分区,省去了噬菌体文库铺平板、浸染、培养、划块洗脱的操作过程,使筛库的工作量减少,进一步提高了筛选速度和获得阳性克隆的效率。