OB-fold: growing bigger with functional consistency

It was predicted that the folding space for various protein sequences is restricted and a maximum of 1000 protein folds could be expected. Although, there were about 648 folds identified, general functional features of individual folds is not thoroughly studied. We selected OB-fold, which is supposed to be an oligonucleotide and oligosaccharide binding fold to study the general functional features. OB-fold is a small beta-barrel fold formed from 5 strands connected by modulating loops. We observed consistently 2 or 3 loops on the same face of barrel acting as clamps to bind to their ligands. Depending on the ligand, which could be a single or double stranded DNA/RNA or an oligosaccharide, and their conformational properties the loops change in length and sequence to accommodate various ligands. Different classes of OB-folded proteins were analyzed and found that the functional features are retained in spite of negligible sequence homology among various proteins studied.     

Extended applications of electric cell-substrate impedance sensing for assessment of the structure-function of α2β1 integrin

Electric cell-substrate impedance sensing (ECIS) was applied to assess the structure-function of α2β1 integrin, receptor for collagen and laminin. On collagen-coated gold electrodes, expression of this integrin on human rhabdomyosarcoma (RD) cells (RDX2C2) yielded a five-fold increase in resistance when compared with mock transfected RD (RDpF) cells (34.5±5.2 versus 6.5±0.8 Ω/cell). An intermediate level of 16±2 Ω/cell was measured upon expression of an α2β1 mutant that lacked the α2 cytoplasmic domain (RDX2CO). On laminin, the resistance measured for RDX2C2 cells was also higher but only twice that of RDpF cells at 71±4 and 37±4 Ω/cell, respectively. In comparison, RDX2CO cells (38±4 Ω/cell), exhibiting no enhanced adhesive function, yielded a similar result to that of RDpF cells. On fibronectin, RDX2C2 and RDpF cells, exhibiting comparable levels of adhesion, were similar in resistance measurements at 85±5and 89±7 Ω/cell, respectively. It has been shown that deletion of α2 cytoplasmic domain results in dysregulated recruitment of the α2β1 mutant to focal adhesion complexes that mediate binding of fibronectin. RDX2CO cells on fibronectin, exhibiting reduced adhesive function, was associated with noticeably lower resistance (60±4 Ω/cell). Monitoring electroporation of the RD plasma membrane also indirectly validated cell attachment as reflected by the resistance measured. Results from this study demonstrated the potential of ECIS for study of the structure-function of βl integrin adhesion receptors.     

The compensation effect: A fact or a fiction

In this article, the facts and fictions surrounding the compensation effect is explored. False compensation effect occurs mainly due to: propagation of computational and experimental errors resulting in inaccurate estimates of the Arrhenius parameters; and, the natural compensation between InA andE. Since Arrhenius parameters are sensitive to errors in temperature; the errors due to uncertainty in temperature should be minimized to eliminate false compensation effect. Increasing the experimental temperature range is helpful in minimizing errors due to uncertainty in temperature. A point of concurrence in a plot of Ink and 1/T establishes the occurrence of true compensation effect. True compensation effect has been shown to be a useful tool in chemical research for: identifying the governing reaction mechanism; predicting the effects of various reaction parameters; and, correlating and reducing experimental data.

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Zusammenfassung In dieser Mitteilung werden Fakten und Vorstellungen betreffs des Kompensationseffektes untersucht. Falsche Kompensationseffekte werden hauptsächlich verursacht durch: eine ungenaue Ermittlung der Arrheniusparameter durch die Fortpflanzung von rechnerischen und experimentellen Fehlern sowie dem natürlichen Kompensationseffektes zwischen InA undE. Das Arrheniusparameter gegenüber Fehler im Temperaturwert sehr empfindlich sind, sollten Temperaturungenäuigkeitsfehler zur Vermeidung eines falschen Kompensationseffektes minimalisiert werden. Zur Verminderung der aus der Temperaturungenauigkeit resultierenden Fehler ist es von Nutzen, den Temperaturbereich des Experimentes zu erweitern. Ein wahrer Kompensationseffekt wird durch einen Schnittpunkt in einem Ink-1/T Diagramm angezeigt. Es wird gezeigt, daß der wahre Kompensationseffekt ein nutzvolles Mittel in der chemischen Forschung darstellt: zur Feststellung des dominierenden Reaktionsmechanismus, zur Vorhersage der einflüsse verschiedener Reaktionsparameter und zur Aufarbeitung und Schlußfolgerung von bzw. aus experimentellen Daten.

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, . , , lnA E. , , . . Ink-1/T . , , , .

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The author would like to thank the reviewer for his constructive criticisms.     

An approximate max-flow min-cut relation for undirected multicommodity flow,with applications

In this paper, we prove the first approximate max-flow min-cut theorem for undirected multicommodity flow. We show that for a feasible flow to exist in a multicommodity problem, it is sufficient that every cut's capacity exceeds its demand by a factor ofO(logClogD), whereC is the sum of all finite capacities andD is the sum of demands. Moreover, our theorem yields an algorithm for finding a cut that is approximately minimumrelative to the flow that must cross it. We use this result to obtain an approximation algorithm for T. C. Hu's generalization of the multiway-cut problem. This algorithm can in turn be applied to obtain approximation algorithms for minimum deletion of clauses of a 2-CNF formula, via minimization, and other problems. We also generalize the theorem to hypergraph networks; using this generalization, we can handle CNF clauses with an arbitrary number of literals per clause.Most of the results in this paper were presented in preliminary form in Approximation through multicommodity flow,Proceedings, 31th Annual Symposium on Foundations of Computer Science (1990), pp. 726–737.Research supported by the National Science Foundation under NSF grant CDA 8722809, by the Office of Naval and the Defense Advanced Research Projects Agency under contract N00014-83-K-0146, and ARPA Order No. 6320, Amendament 1.Research supported by NSF grant CCR-9012357 and by an NSF Presidential Young Investigator Award.     

Validation of LC/MS electrospray ionisation method for the estimation of ursodiol in human plasma and its application in bioequivalence study

A novel High Performance Liquid Chromatography-electrospray mass spectrometric method has been developed for the estimation of Ursodiol (Ursodeoxycholic acid)--a bile acid, in human plasma using Ornidazole as internal standard. The methodology involved solid phase extraction of the analyte from human plasma matrix. The chromatographic separation was achieved within seven minutes by an isocratic mobile phase containing 1.0 mM ammonium acetate and Acetonitrile (65:35, v/v), flowing through XTerra MS C18, 100 x 2.1, 3.5 microm analytical column, at a flow rate of 0.2 ml/min. Ion signals were measured in negative mode for Ursodiol and internal standard at m/z 391.3 and 278.1, respectively. A detailed validation of the method was performed as per USFDA guidelines and the standard curves were found to be linear in the range 50.0 ng/ml to 3000.0 ng/ml with the mean correlation coefficient more than 0.99. The absolute recovery was more than 54.90% for Ursodiol and 76.51% for internal standard. Ursodiol was stable for sixty-nine days at -70 degrees C and for eight hours at ambient temperature. After extraction from plasma, the reconstituted samples of Ursodiol were stable in autosampler at 10 degrees C for forty-eight hours. Upon subjecting to three freeze thaw cycles, there was no change in the recovery of the analyte. The integrity of the plasma samples remained unaffected even upon four-fold dilution with drug free human plasma. The method was simple, specific, sensitive, precise, accurate and suitable for bioequivalence and pharmacokinetic studies. It was successfully applied to the pilot bioequivalence study of Ursodiol in male human subjects.     

Extraction and micro-determination of manganese(II) with oxine and aliquat 336

A sensitive and selective method has been developed for the micro-determination of Mn(II) by the selective extraction of the yellow Mn(II)-8-hydroxyquinolinate complex with a liquid ion-exchanger, Aliquat 336, from basic medium. The molar absorptivity of the complex is 2.2 x 10(4)1.mole(-1).cm(-1) at 420 nm and the colour system obeys Beer's law in the range 0.1-3.5 ppm Mn(II) in the final solution. The composition and stability of the complex are discussed. Potential interferents have been examined and the method is applied to analysis of standard steel and bronze samples.     

Spectrophotometric determination of isoproturon using p-aminoacetophenone and its application in environmental and biological samples

A simple and sensitive method for the determination of isoproturon, a widely used herbicide is described here which is based on alkaline hydrolysis of isoproturon to its corresponding primary amine followed by diazotization and coupling with p-aminoacetophenone in alkaline medium. The absorption maxima of the coloured compound formed is measured at 525 nm. Beer's law is obeyed over the concentration range of 0.5-5.0 mug in a final solution volume of 25 ml (0.02-0.2 ppm). The molar absorptivity and Sandell's sensitivity were found to be 8.6x10(5) l mol(-1) cm(-1) and 0.0002 mug cm(-2), respectively. The method has been satisfactorily applied to the determination of isoproturon in environmental and biological samples.     

A study of equilibrium between cadmium cyanide and alkali halides and thiocyanate by solubility measurements

Summary A study of the Cd(CN)₂ +x X^– [Cd(CN)₂X _x ] ^x– equilibrium (where X = Cl, Br or CNS) has been carried out at 18° and 38° by measuring the solubility of cadmium cyanide in potassium chloride, bromide and thiocyanate at various concentrations, and at a high ionic strength (6 M) maintained with sodium perchlorate to minimise the effect of activity coefficients. Equilibrium constants forx = 1 and 2 have been calculated and clearly favour the situation wherex = 1. H values for the dissociation of [Cd(CN)₂X]^– have also been calculated.     

Stability-Indicating HPLC Method for the Determination of Metadoxine as Bulk Drug and in Pharmaceutical Dosage Form

A sensitive and reproducible method is described for the quantitative determination of metadoxine in the presence of its degradation products. The method was based on high performance liquid chromatographic separation of the drug from its degradation products on the reversed phase, kromasil column [C₁₈ (5-micron, 25 cm × 4.6 mm, i.d.)] at ambient temperature using a mobile phase consisting of methanol and water (50: 50, v/v). Flow rate was 1.0 mL min^?1 with an average operating pressure of 180 kg cm^?2 and t _R was found to be 2.85 ± 0.05 min. Quantitation was achieved with UV detection at 286 nm based on peak area with linear calibration curves at concentration range 10–100 μg mL^?1. This method has been successively applied to pharmaceutical formulation. No chromatographic interference from the tablet excipients was found. The method was validated in terms of precision, robustness, recovery and limits of detection and quantitation. Drug was subjected to acid, alkali and neutral hydrolysis, oxidation, dry heat, wet heat treatment and photo and UV degradation. As the proposed method could effectively separate the drug from its degradation products, it can be employed as stability indicating one. Moreover, the proposed HPLC method was utilized to investigate the kinetics of the acidic, alkaline and oxidative degradation processes at different temperatures and their respective apparent pseudo first order rare constant, half-life and activation energy was calculated with the help of Arrhenius plot. In addition the pH-rate profile of degradation of metadoxine in constant ionic strength buffer solutions with in the pH range 2–11 was studied.