Cloning genes from a library using a clustering strategy and PCR

A new polymerase chain reaction (PCR)-based method is described for the isolation of clones of interest from a library when only part of a sequence is available. In actuality, this occurs with many genomes that have been partially sequenced using a random strategy. The method presented here, discriminating clusters by PCR (DCbyPCR), is a nonradioactive and improved alternative to colony hybridization.     

Prediction of ATP/GTP-binding motif: a comparison of a perceptron type neural network and a consensus sequence method [corrected

Neural networks have been applied to a number of protein structure problems. In some applications their success has not been substantiated by a comparison with the performance of a suitable alternative statistical method on the same data. In this paper, a two-layer feed-forward neural network has been trained to recognize ATP/GTP-binding [corrected] local sequence motifs. The neural network correctly classified 78% of the 349 sequences used. This was much better than a simple motif-searching program. A more sophisticated statistical method was developed, however, which performed marginally better (80% correct classification) than the neural network. The neural network and the statistical method performed similarly on sequences of varying degrees of homology. These results do not imply that neural networks, especially those with hidden layers, are not useful tools, but they do suggest that two-layer networks in particular should be carefully tested against other statistical methods.     

Relative Elemental Rates and Anisotropy of Growth in Area: a Computer Programme

A method of analysis of growth patterns in two dimensions haspreviously been proposed by Richarads and Kavanagh (1943),whichconsists of evaluating the divergence of velocity by vectoranalysis. The method has been adpted for solution by numericalmethods, and has been programmed for an electronic computer.The method and the programme are described, and applied to theanalysis of leaf growth in Xanthium. These preliminary resultssuggest that the system could be successfully applied to a widevariety of problem of 2-dimensional growth.     

Determination of free choline in plasma and erythrocyte samples and choline derived from membrane phosphatidylcholine by a chemiluminescence method

A sensitive chemiluminescence method for assay of choline which has been developed for analysis of erythrocyte and plasma levels of choline is reported here. This method includes a charcoal purification step which yields consistent results with plasma and erythrocyte extracts. Further, choline derived from membrane phosphatidylcholine may also be measured by an extension of this method following digestion with phospholipase D. This method has been used to study abnormal levels of erythrocyte choline that occur in cluster headache patients compared to control subjects and migraine patients. In addition, the time course of changes in plasma and erythrocyte choline following a fatty meal have been monitored. Plasma choline levels rise to a maximum between 1 and 3 h after the meal and this is followed by a rise in erythrocyte choline levels which are maximal 3 h after the meal.     

Microscopic instrumentation and analysis of laser-tissue interaction in a skin flap model

A dorsal skin flap model for microcirculatory studies has been modified for "in vivo" studies of laser-tissue interaction with microcirculation. An experimental apparatus has been built implementing a laser delivery system, video microscopy during irradiation, and thermal recordings. This model has been used to study irradiation effects on microcirculation using the argon laser (488 and 514.5 nm) and the argon pumped dye laser at 577 nm. The results include: measurements of the optical properties of the model; dosimetry measurements for the production of embolized and stationary coaguli in arterioles and venules; and focal vessel disappearance of venules irradiated with the argon or the argon pumped dye laser at 577 nm; a method to determine light attenuation in the model; a unique method for measurements of blood flow velocity in arterioles and venules and measurements obtained with this method; measurements of transient and steady state temperatures during irradiation and a study of laser induced photorelaxation phenomena in venules.     

Designing of highly effective complementary and mismatch siRNAs for silencing a gene

In past, numerous methods have been developed for predicting efficacy of short interfering RNA (siRNA). However these methods have been developed for predicting efficacy of fully complementary siRNA against a gene. Best of author's knowledge no method has been developed for predicting efficacy of mismatch siRNA against a gene. In this study, a systematic attempt has been made to identify highly effective complementary as well as mismatch siRNAs for silencing a gene.Support vector machine (SVM) based models have been developed for predicting efficacy of siRNAs using composition, binary and hybrid pattern siRNAs. We achieved maximum correlation 0.67 between predicted and actual efficacy of siRNAs using hybrid model. All models were trained and tested on a dataset of 2182 siRNAs and performance was evaluated using five-fold cross validation techniques. The performance of our method desiRm is comparable to other well-known methods. In this study, first time attempt has been made to design mutant siRNAs (mismatch siRNAs). In this approach we mutated a given siRNA on all possible sites/positions with all possible nucleotides. Efficacy of each mutated siRNA is predicted using our method desiRm. It is well known from literature that mismatches between siRNA and target affects the silencing efficacy. Thus we have incorporated the rules derived from base mismatches experimental data to find out over all efficacy of mutated or mismatch siRNAs. Finally we developed a webserver, desiRm (http://www.imtech.res.in/raghava/desirm/) for designing highly effective siRNA for silencing a gene. This tool will be helpful to design siRNA to degrade disease isoform of heterozygous single nucleotide polymorphism gene without depleting the wild type protein.     

The design of a diagnostic test system based on magnetic sorbents and liposomes

The results obtained in the study of the possibility of using magnetic sorbents for the construction of a diagnostic assay system based on the antigen-antibody interaction are presented. As a model, Yersinia pestis capsular antigen and immunoglobulins to it have been used. A solid-phase immunofluorescent liposomal assay method has been developed; this method can be used for the detection of biopolymers in the sample under study and for the determination of their activity.     

Colloidal gold, a useful marker for transmission and scanning electron microscopy.

Electron dense markers of a size suitable for transmission electron microscopy and scanning electron microscopy have been prepared with gold granules labeled with a monolayer of specific macromolecules. The optimum conditions for preparing the markers have been ascertained. The method is simple, rapid and seems to be general since gold granules have been labeled with polysaccharides and proteins. As homogeneous populations of gold granules having different sizes can be prepared, the method is also suitable for double marking experiments. The gold technique is illustrated by the localization of polysaccharides and glycoproteins on yeast cell walls and erythrocyte membranes by transmission electron microscopy and on yeast cells and intact erythrocytes by scanning electron microscopy. Good spatial resolution of the marker was achieved in all cases. The method is also suitable for marking thin sections. Spectrophotometric measurements were used to determine the number of gold granules adsorbed per cell.     

Tattooing in reconstruction of the nipple and areola: a new method

In order to produce the characteristic color of the nipple-areola complex and in unilateral reconstructions to match the other side, a modified tattooing method has been introduced. The quite different requirements between reconstruction and ornamental studio tattooing can only be satisfied by different techniques. For the first time, pigment particles have been suspended in a gel rather than adsorbed on an opaque mineral. Our porcine study has shown how the pigment is distributed in the dermis without penetration of the gel particles. The first 16 of the authors' 29 patients have been reviewed with an analysis of their appearance. Using this new method, a third achieved a completely natural appearance and two-thirds were judged to be intermediate, compared with an unnatural, although sometimes acceptable, result in all the earlier conventional tattoos.     

Plasmid uptake by bacteria: a comparison of methods and efficiencies

The ability to introduce individual molecules of plasmid DNA into cells by transformation has been of central importance to the recent rapid advancement of plasmid biology and to the development of DNA cloning methods. Molecular genetic manipulation of bacteria requires the development of plasmid-mediated transformation systems that include (1) chemical transformation, (2) electro-transformation, (3) biolistic transformation, and (4) sonic transformation, leading to the introduction of exogenous plasmid DNA into bacterial cells. In this review, the manipulation properties and transformation efficiencies of these techniques are described. In addition to these methods, a conceptually novel transformation technique, namely the hydrogel exposure method, was developed. The hydrogel exposure method, based on the Yoshida effect, provides a significant advance over chemical means for transforming many strains of Escherichia coli and a variety of other bacterial species. The new term “tribos transformation” has been proposed for this novel technique. We also determined that, compared to conventional methods, the hydrogel exposure method is a novel and convenient method by which to transform bacteria.     

Improved calculations of compactness and a reevaluation of continuous compact units

A new method for calculating compactness (Z) that uses look-up table-based algorithms for area and volume computations is introduced. These algorithms can be used in any iterative area orvolume calculation, are more than 1000 times faster than the originalalgorithms, and have equal or better precision. With the faster algorithms it is now possible to calculate the compactness of all continuous units in a protein, and to precisely locate the optimal compact units without the screening functions and limited resolution used previously. These methods have been incorporated into a fully automatic domain finding algorithm, and this method has been applied to the 21 proteins originally analyzed as well as 12 additional proteins. This method is robust, and yields similar units even when applied to coordinates of protein crystals grown under different experimental conditions. © 1993 Wiley-Liss, Inc.     

Transferrin microheterogeneity as a probe in normal and disease states

Isoelectric focusing of iron saturated serum has been established as a convenient method for showing transferrin glycan microheterogeneity. In a clinical setting, the method is used in the detection of cerebrospinal fluid leakage, the screening for surreptitious alcohol abuse and in the diagnosis of the carbohydrate deficient glycoprotein syndrome. In normal physiological states it can also be used as a tool to probe for changes in N-glycosylation.     

Modification of a method of passive immune hemolysis on a solid medium for detecting the production of thermolabile enterotoxins by Vibrio cholerae and Escherichia coli strains

A modification of the passive immune hemolysis method for the determination of the production of thermolabile enterotoxins by V. cholerae and E. coli is proposed. This modification permits the use of solid culture media. Experiments with cholera enterotoxin have demonstrated that the sensitivity of the modified method is 8-10 times higher than that of the Elek method. Similar results have been obtained with the use of the proposed method in the study of the capacity of different V. cholerae and E. coli strains for producing enterotoxins. The results obtained with the use of this method have been found to correlate with those obtained by means of the skin test and passive immune hemolysis in a liquid medium. We have used the modified method in the study of the production of thermolabile enterotoxin in transconjugants obtained by the hybridization of E. coli strain GA 107 carrying plasmid pCG86 which determines the synthesis of thermolabile and thermostable enterotoxins and E. coli strain K12 C600 R. The results obtained in the study of toxin formation in 99 transconjugants, carried out with the use of the proposed method, the skin test and passive immune hemolysis, have been shown to coincide.     

18O labeling over a coffee break: a rapid strategy for quantitative proteomics

Proteomics-based quantification methods for differential protein expression measurements are among the most important and challenging techniques in the field of mass spectrometry. Though numerous quantification methods have been established, no method meets all the demands for measuring accurate protein expression levels. Of the various relative quantification methods by isotopic labeling, (18)O labeling method has been shown to be simple, specific, cost-effective and applicable to a wide range of analyses. However, some researchers refrain from using the method due to long incubation periods required during the labeling process. To address this problem, we demonstrate a method by which the labeling procedure can be completed in 15 min. We digested and labeled samples using immobilized trypsin on micro-spin columns to speed up the enzyme-mediated oxygen substitution, thereby completing the labeling process within 15 min with high labeling efficiency. We demonstrate the efficiency and accuracy of the method using a four protein mixture and whole cell lysate from rat vascular endothelial cells.     

Isolation of glycosylated hemoglobins by a combination of ion-exchange and gel-filtration chromatographies: a pilot study

The techniques of ion exchange and gel filtration have been combined in a single chromatographic column which allows the simultaneous isolation of hemoglobins glycosylated at their beta-amino termini from other hemoglobin species as well as from molecules differing in size from the hemoglobins. This method is unique because it makes possible isolation of preparative quantities of glycosylated hemoglobins within approximately 15 min. The method works most efficiently with a dry weight-to-weight ratio of Biorex 70 to Sephadex G25 of 1.4 to 1.0. The technique was applied to the determination of the apparent first-order rate constant for the deglycosylation of the labile form of hemoglobin AIc.     

Development and validation of a liquid chromatography-tandem mass spectrometry for the determination of Kendine 91, a novel histone deacetylase inhibitor, in mice plasma and tissues: application to a pharmacokinetic study

A liquid chromatography-tandem mass spectrometric method (LC-MS/MS) has been developed and validated to determine the concentration of Kendine 91 in mice plasma and tissues. Simvastatin was employed as the internal standard. Separation was performed on a C8 column, with a mobile phase consisting of methanol and aqueous 10 mM formic acid (73:27 v/v). Both analyte and internal standard were determined using electrospray ionization and the MS data acquisition was via multiple-reaction monitoring (MRM) in positive scanning mode. Quantification was performed using the transitions m/z 444-->169 and 441-->325 for Kendine 91 and simvastatin, respectively. The method was validated with respect to linearity, accuracy, precision, recovery and stability. This assay has been successfully applied to a pharmacokinetic study after intravenous injection of Kendine 91 in mice in a dose of 10mg/kg.     

Development of a carbon dioxide-capture assay in microtiter plate for aspartyl-beta-hydroxylase.

CO2-capture methods have been used for assaying many decarboxylating enzymes including hydroxylation-coupled decarboxylation reactions. The traditional CO2-capture method involves performing the reaction in capped tubes and radiometric measurement of trapped 14CO2 by scintillation counting. In this report, a 14CO2-capture method in a 96-well microtiter plate format has been developed and a phosphor imaging system has been employed for sample measurement. The new assay method has been used successfully to assay aspartyl-beta-hydroxylase activity in microtiter plate format. The results obtained here compare favorably with those obtained from the traditional tube method. The method is sensitive, suitable for high throughput, and generally applicable to many CO2-releasing enzyme assays.     

Use of 9-aminoacridine as a probe in a kinetic study of DNA-poly-L-lysine interaction

An attempt has been made to use a fluorescent dye as a probe in a kinetic study of DNA-poly-L-lysine interaction by the stopped-flow method. It is found that 9-aminoacridine is suitable for this purpose. The results have indicated that polylysine binds to DNA at least in two steps; a slow unimolecular process (τ ～ 2 msec) being preceded by a rapid bimolecular one (τ ? 1 msec). The usefulness of this method for the kinetic study of the interaction between DNA and basic polypeptides has been emphasized.