A simple method to determine released acetylcholine in the presence of choline

In experiments where the release of labeled acetylcholine is to be determined, the addition of choline oxidase to the incubation medium prevents any reuptake of choline. In addition, since betaine, the oxidation product of choline is not extractable into tetraphenylboron - butyronitrile, no further procedure to eliminate choline is required.     

Familial high myopia: evidence of an autosomal dominant mode of inheritance and genetic heterogeneity.

High myopia, defined as a refractive error inferior to -6 diopters, often appears as a familial disease. In order to precise its genetic background, we performed a segregation analysis on 32 French families (320 subjects including 120 individuals with clinical data) containing at least one high myopic person in their genealogy. Under the assumption of a two-alleles single gene model, the autosomal dominant transmission mode showed a much greater likelihood than the autosomal recessive mode, which therefore was rejected. From the segregation model obtained, a two-point linkage analysis was made on 18 families (107 subjects), among the 32 used for the segregation analysis. Different candidate loci were tested: collagen genes including Stickler syndrome types 1 and 2, proteoglycan genes, Marfan 1 syndrome and a Marfan like disorder localised in 3p24.2-p25. No evidence of linkage was found with any of the studied markers. In addition, the absence of linkage with chromosome 18p11.31 markers, a locus linked to familial high myopia in 6 North American families and 1 family of Chinese descent, demonstrated the genetic heterogeneity of the disease.     

Peakmatch: a simple and robust method for peak list matching

Peak lists are commonly used in NMR as input data for various software tools such as automatic assignment and structure calculation programs. Inconsistencies of chemical shift referencing among different peak lists or between peak and chemical shift lists can cause severe problems during peak assignment. Here we present a simple and robust tool to achieve self-consistency of the chemical shift referencing among a set of peak lists. The Peakmatch algorithm matches a set of peak lists to a specified reference peak list, neither of which have to be assigned. The chemical shift referencing offset between two peak lists is determined by optimizing an assignment-free match score function using either a complete grid search or downhill simplex optimization. It is shown that peak lists from many different types of spectra can be matched reliably as long as they contain at least two corresponding dimensions. Using a simulated peak list, the Peakmatch algorithm can also be used to obtain the optimal agreement between a chemical shift list and experimental peak lists. Combining these features makes Peakmatch a useful tool that can be applied routinely before automatic assignment or structure calculation in order to obtain an optimized input data set.     

A simple method to detect and estimate heterogeneity: application to Huntington disease, diabetes, and HIV seroconversion.

The traditional method for calculating risk in prospective and retrospective studies is based on the assumption that the study population is homogeneous. Risk is therefore estimated as an overall average for the entire population, when in fact some individuals may be at high risk and others at little or no risk. This paper introduces an alternate approach to risk estimation. The calculations are equally simple and utilize the same data. Yet, the new approach allows for heterogeneity and can detect it when it exists. The new method was applied to HIV seroconversion data from a follow-up study, age-at-onset distribution for Huntington disease, and age-specific prevalence of insulin-treated diabetes. These analyses were intended to demonstrate both applicability of the method to different types of data and the accuracy of the estimates when compared with the known parameters. The HIV analysis predicted a high-risk subgroup constituting about 17% of the cohort. This estimate closely approximates the actual 16% who reportedly engaged in high-risk activities and had a 15-fold higher seroconversion rate than the rest of the cohort. There is no evidence from genetic linkage studies for heterogeneity in Huntington disease. The present results, however, suggested that 14%-18% of individuals who are susceptible to the disease have a much lower risk than others. Diabetes data was chosen because the model is clearly too simplistic for this disease, and the analysis did reveal lack of fit of the model.     

A simple method to determine the enantiomeric ratio in enantioselective biocatalysis

The enantiomeric ratio (E) is commonly used to characterize the enantioselectivity in enzyme-catalyzed kinetic resolution. In this paper this parameter is directly derived from the enantiomeric excess of substrate and product. This is formally more correct than using Chen's equation after calculating the degree of conversion from both ee values using the relation of Sih and Wu. New expressions and useful graphs have been generated for reversible and irreversible uni-uni reactions. The theoretical predictions have been verified experimentally for various reactions. Values for E and the thermodynamic equilibrium constant,K_EQ, were obtained for a ( -dehalogenase-catalyzed dehalogenation, a hydrolysis reaction by porcine pancreatic lipase, and for C. Cylindracea lipase-catalyzed esterification and transesterification. In view of the current developments in the field of chiral analysis, this method is an easily available tool in the quantitative treatment of enzyme-catalyzed resolution of enantiomers.     

A simple and robust statistical test for detecting the presence of recombination

Recombination is a powerful evolutionary force that merges historically distinct genotypes. But the extent of recombination within many organisms is unknown, and even determining its presence within a set of homologous sequences is a difficult question. Here we develop a new statistic, phi(w), that can be used to test for recombination. We show through simulation that our test can discriminate effectively between the presence and absence of recombination, even in diverse situations such as exponential growth (star-like topologies) and patterns of substitution rate correlation. A number of other tests, Max chi2, NSS, a coalescent-based likelihood permutation test (from LDHat), and correlation of linkage disequilibrium (both r2 and /D'/) with distance, all tend to underestimate the presence of recombination under strong population growth. Moreover, both Max chi2 and NSS falsely infer the presence of recombination under a simple model of mutation rate correlation. Results on empirical data show that our test can be used to detect recombination between closely as well as distantly related samples, regardless of the suspected rate of recombination. The results suggest that phi(w) is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances.     

A simple and rapid method to determine the zygosity of uPA-transgenic SCID mice

Successful transplantation of xenogeneic hepatocytes into uPA-transgenic SCID mice depends on the zygosity of the recipient mice. Normally, the difference between homozygous and heterozygous animals is determined via a quantitative Southern blot. We sequenced a part of the mouse genome that is eliminated upon integration of the transgene in the genome. Based on that sequence we developed a multiplex PCR that allows the unambiguous discrimination of negative, heterozygous, and homozygous uPA-transgenic SCID mice in a single day procedure. The speed of the procedure is an essential quality because transplantation of xenogeneic hepatocytes into uPA-SCID mice should be done as soon as possible after birth.     

Adaptation of the phosphotungstate method to determine reduced and oxidized vitamin C in blood plasma

The phosphotungstate reagent (PTR) was used for quantitative spectrophotometric determination of physiological forms of vitamin C in blood plasma. An immediate action of PTR on the first half of the tested samples allowed to determine reduced vitamin C concentrations (I) at 700 nm. 10 mM dithiothreitol added to the second half of the samples reduced oxidized vitamin C in it--hence the total amount of this vitamin was reduced with a concentration (II) determined as above (remains of dithiothreitol were removed with N-ethylmaleimide). The difference of results (II) and (I) gave the concentration of oxidized vitamin C. The method is characterised by fault-less analytical parameters: correlation coefficients of analytical curves > 0.99, recovery factor 100.5%, variation coefficients intra- and inter-serial < 3% and < 5%, respectively, detection limit 0.05 microM. The simplicity of the method enables an easy control of the ratio of oxidized and reduced vitamin C concentrations in blood plasma--the biomarker of the level of oxidative damage to cells.     

A simple and robust method for preparation of cDNA nylon microarrays.

DNA array technology has made remarkable progress in recent years and has become an indispensable tool in molecular biology research. However, preparing high-quality custom-made DNA arrays at a reasonable cost is still an important concern because we cannot abandon the use of DNA array systems designed for specific purposes. To address these problems, we here report the use of rolling circle amplification products of cDNA plasmids dissolved in 80% formamide as DNA probes immobilized on a nylon membrane. First, because formamide is practically non-volatile under ambient conditions and nucleic acids are easily dissolved in it, the use of formamide as a DNA solvent ensures that the DNA concentration of the solution will not change during arraying, which often takes several hours to a day depending on the number of DNA spots and arrays to produce. Secondly, the use of rolling circle amplification technology greatly reduced the labor needed to prepare the spotted DNA. The results in this study demonstrate that the introduction of these two modifications in preparation of nylon DNA array greatly improved its quality.     

A simple method to determine concentration of enantiomers in enzyme-catalyzed kinetic resolution

Kinetic resolutions play important roles in industrial biotransformations for production of optical pure compounds from racemic substrates. A simple method, based on enantiomeric excess of both substrate (ee _S) and the corresponding product (ee _P), was developed for determination of concentration of enantiomers in kinetic resolution. Since only relative quantity (ee) was required in the proposed method, calibration and cumbersome quantitative sample handling can be avoided and analytical accuracy can be greatly improved.     

Between-generation differences in ascertainment and penetrance: relevance to genetic hypotheses in fragile X

Between-generation differences in ascertainment were examined in 54 extended fragile X pedigrees, where all available members were clinically, psychometrically, and cytogenetically investigated. In 24 families a diagnosis was verified by molecular characterization using the pfxa3 fragile X-specific probe. We found considerable differences between generations in relative proportions of affected fragile X subjects versus non-penetrant carriers. We also found deviation in the segregation ratio in unbiased samples of relatives in pedigrees. We claim that these irregularites are influenced by different rates of ascertainment, depending on the clinical expression of the condition (penetrance) and the fertility of fragile X individuals in a pedigree, as well as by the thoroughness of clinical investigation in individual families. Penetrance and fertilty were estimated in fragile X females assessed by psychometric tests, and they were compared with earlier estimates based on a subjective judgement of their intellectual status. We suggest that the standard correction for ascertainment bias, such as has been applied in segregation analysis of this condition, is not sufficient to adjust for all types of bias.     

A simple and efficient method to determine the terminal sequences of restriction fragments containing known sequences.

We present an improvement of the inverse PCR method for the determination of end sequences of restriction fragments containing unknown DNA sequences flanked by known segments. In this approach, a short "bridge" DNA is inserted during the self-ligation step of the inverse PCR technique. This bridge DNA acts as primer annealing sites for amplification and subsequent direct sequencing. Successive PCR amplifications enable selective amplification of the unknown sequences from a complex mixture. Unlike previously described methods, our method does not require special materials, such as synthetic adapters or biotinylated primers that must be prepared each time to adapt the target. Furthermore, no complex steps such as dephosphorylation or purification are needed. Our method can save time and reduce the cost of cloning unknown sequences; it is ideal for routine, rapid gene walking. We applied this method to a GC-rich bacterial genome and succeeded in determining the end sequences of a 4.5-kb fragment.     

A simple general method to determine the proportion of active ribosomes in eukaryotic cells

The resistance of 80S ribosomes derived from active polyribosomes to dissociation in high KCl cone, can conveniently be used to assay the proportion of active ribosomes in eukaryotic cells. The method described has been useful in studies of organisms as diverse as fungi (yeast), protozoa (Tetrahymena), higher plants (barley), echinoderms (sea urchin), insects (Musca), birds (chick) and mammals (mouse, rat). The technique is relatively insensitive to the use of harsh mechanical treatments for cell disruption or the presence of endogenous ribonuclease activity.     

The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes

The linear polymerase chain reaction was used to sequence amplified RNA genes from strains of Bacillus, Thermus and Legionella. The technique described is simple and reproducible and it works well with double standard product which has been PEG precipitated directly from PCR reactions.     

A simple and fast method to determine the parameters for fuzzy c-means cluster analysis

MOTIVATION: Fuzzy c-means clustering is widely used to identify cluster structures in high-dimensional datasets, such as those obtained in DNA microarray and quantitative proteomics experiments. One of its main limitations is the lack of a computationally fast method to set optimal values of algorithm parameters. Wrong parameter values may either lead to the inclusion of purely random fluctuations in the results or ignore potentially important data. The optimal solution has parameter values for which the clustering does not yield any results for a purely random dataset but which detects cluster formation with maximum resolution on the edge of randomness. RESULTS: Estimation of the optimal parameter values is achieved by evaluation of the results of the clustering procedure applied to randomized datasets. In this case, the optimal value of the fuzzifier follows common rules that depend only on the main properties of the dataset. Taking the dimension of the set and the number of objects as input values instead of evaluating the entire dataset allows us to propose a functional relationship determining the fuzzifier directly. This result speaks strongly against using a predefined fuzzifier as typically done in many previous studies. Validation indices are generally used for the estimation of the optimal number of clusters. A comparison shows that the minimum distance between the centroids provides results that are at least equivalent or better than those obtained by other computationally more expensive indices.     

A method to determine the mode of binding for GCPII inhibitors using bio-layer interferometry

The rapid dilution of the enzyme-inhibitor complex assay to monitor the recovery of enzyme activity is a well-established assay to determine the reversibility of inhibition. Our laboratory has previously employed this method to ascertain the reversibility of known glutamate carboxypeptidase II (GCPII)-targeting agents. Due to the tedious and time-consuming nature of the assay, we sought to develop a facile method to determine the reversibility of well-characterized GCPII inhibitors using bio-layer interferometry (BLI). The results from the BLI assay are in agreement with the rapid dilution method. Herein, we report for the first time, a rapid, novel real-time BLI method to determine reversibility of inhibition.