Colorimetric endpoint assay for enzyme-catalyzed iodide ion release for high-throughput screening in microtiter plates

Efforts are being made to engineer enzymes with enhanced activities against haloalkanes, a toxicologically important class of compounds widely used and frequently occurring in the environment. Here we describe a facile, inexpensive, and robust method for the screening of libraries of mutated enzymes with iodoalkane substrates. Iodide formed in the enzymatic reaction is oxidized to iodine, which in the presence of starch gives blue color that can be measured at 610nm or scored with the human eye. The assay can be performed with enzymes in crude cell lysates in 96-wells microtiter plates. Expression clones of several glutathione transferases showed diverse activities with different iodoalkanes, and a mutant library of human glutathione transferase A1-1 expressed variants with enhanced substrate selectivities.

Calcium-binding to lens βB2- and βA3-crystallins suggests that all β-crystallins are calcium-binding proteins

Crystallins are the major proteins of a mammalian eye lens. The topologically similar eye lens proteins, beta- and gamma-crystallins, are the prototype and founding members of the betagamma-crystallin superfamily. Betagamma-crystallins have until recently been regarded as structural proteins. However, the calcium-binding properties of a few members and the potential role of betagamma-crystallins in fertility are being investigated. Because the calcium-binding elements of other member proteins, such as spherulin 3a, are not present in betaB2-crystallin and other betagamma-crystallins from fish and mammalian genomes, it was argued that lens betagamma-crystallins should not bind calcium. In order to probe whether beta-crystallins can bind calcium, we selected one basic (betaB2) and one acidic (betaA3) beta-crystallin for calcium-binding studies. Using calcium-binding assays such as 45Ca overlay, terbium binding, Stains-All and isothermal titration calorimetry, we established that both betaB2- and betaA3-crystallin bind calcium with moderate affinity. There was no significant change in their conformation upon binding calcium as monitored by fluorescence and circular dichroism spectroscopy. However, 15N-1H heteronuclear single quantum correlation NMR spectroscopy revealed that amide environment of several residues underwent changes indicating calcium ligation. With the corroboration of calcium-binding to betaB2- and betaA3-crystallins, we suggest that all beta-crystallins bind calcium. Our results have important implications for understanding the calcium-related cataractogenesis and maintenance of ionic homeostasis in the lens.

Advances in the analysis of isothermal titration calorimetry data for ligand-DNA interactions

Isothermal titration calorimetry (ITC) is a well established technique for the study of biological interactions. The strength of ITC is that it directly measures enthalpy changes associated with interactions. Experiments can also yield binding isotherms allowing quantification of equilibrium binding constants, hence an almost complete thermodynamic profile can be established. Principles and application of ITC have been well documented over recent years, experimentally the technique is simple to use and in ideal scenarios data analysis is trivial. However, ITC experiments can be designed such that previously inaccessible parameters can be evaluated. We outline some of these advances, including (1) exploiting different experimental conditions; (2) low affinity systems; (3) high affinity systems and displacement assays. In addition we ask the question: What if data cannot be fit using the fitting functions incorporated in the data-analysis software that came with your ITC? Examples where such data might be generated include systems following non 1:n binding patterns and systems where binding is coupled to other events such as ligand dissociation. Models dealing with such data are now appearing in literature and we summarise examples relevant for the study of ligand-DNA interactions.

Statistical criteria to establish optimal antibody dilution in flow cytometry analysis

BACKGROUND

In direct techniques of flow cytometry, the optimal antibody dilution or titer point is established from the plateau area of the antibody titration curve. However, the plateau area is defined without any statistical criteria, which may lead to an incorrect selection of antibody dilution. Herein, we report statistical criteria to establish the optimal antibody dilution for CD14, CD8, CD4, and CD3 analysis by flow cytometry in peripheral whole blood.

METHODS

The unpaired t-test (two-tail P value) was used as statistical criteria to analyze the titration curve of the following monoclonal antibody panels: CD14-FITC, CD8-FITC, CD4-RD1, and CD3-PC5.

RESULTS

Using the unpaired t-test (two-tail P value), the plateau area from the antibody titration curve was fitted when two consecutive antibody volumes showed mean peak of channel fluorescence (MPCF) values not significantly different. When the antibody was used at volume corresponding to that of the antibody titration point, the flow cytometry analysis of whole blood samples with different density of cell antigens can be correctly discriminated.

CONCLUSION

This statistical criteria allows the fitting of the plateau area of MPCF versus antibody volume and consequently, to define the optimal antibody dilution.

Isothermal titration calorimetry to determine association constants for high-affinity ligands

An important goal in drug development is to engineer inhibitors and ligands that have high binding affinities for their target molecules. In optimizing these interactions, the precise determination of the binding affinity becomes progressively difficult once it approaches and surpasses the nanomolar level. Isothermal titration calorimetry (ITC) can be used to determine the complete binding thermodynamics of a ligand down to the picomolar range by using an experimental mode called displacement titration. In a displacement titration, the association constant of a high-affinity ligand that cannot be measured directly is artificially lowered to a measurable level by premixing the protein with a weaker competitive ligand. To perform this protocol, two titrations must be carried out: a direct titration of the weak ligand to the target macromolecule and a displacement titration of the high-affinity ligand to the weak ligand-target macromolecule complex. This protocol takes approximately 5 h.

Benzimidazo[1,2-c][1,2,3]thiadiazole-7-sulfonamides as inhibitors of carbonic anhydrase

A series of benzimidazo[1,2-c][1,2,3]thiadiazole-7-sulfonamides were synthesized and their binding to two carbonic anhydrase isozymes measured by isothermal titration calorimetry (ITC). Human carbonic anhydrase I (hCAI) and bovine carbonic anhydrase II (bCAII) bound the inhibitors with observed association constants in the range from 1.1 x 10(6) to 2.6 x 10(7) M(-1).

Chemical force titrations of antigen- and antibody-modified poly(methylmethacrylate)

Poly(methylmethacrylate) (PMMA) is a versatile polymer that displays desirable properties for development of cheap and disposable microfluidic devices for sensing biomolecular interactions. Atomic force microscopy (AFM) and chemical force titrations were used to determine the efficacy of surface modifications made to accommodate protein-substrate linkage. AFM images show the effects on surface morphology of carboxylated-, amine-, hCG antigen- and anti-hCG antibody-modified PMMA substrates. Confocal microscopy was used to determine the fluorescent intensity of labeled antibody species on the PMMA substrate, confirming the success of surface antigen/antibody immobilization. Surface pK(1/2) value for carboxylic acid and amine species grafted on PMMA were determined. When carboxylic acid or amine-terminated tips were titrated against PMMA samples terminated with the hCG antigen and anti-hCG antibody, peaks appeared in the force titration curve consistent with the pI range of the antigen or antibody species. Strong adhesive forces were present at pH values above 7.0 when the antigen was present on the PMMA substrate, and these were attributed to hydrophobic interactions between the antigen and the alkane "linker" chain attaching the amine or carboxylate group to the AFM tip. Such hydrophobic interactions were not observed with the carboxylic acid or amine/antibody combinations suggesting that the surface-linked antibody was more resistant to denaturation under higher pH. The results demonstrated the feasibility of using AFM approaches for interrogating protein grafting strategies in the fabrication of PMMA-based microsystems.

Solubility measurement of polymorphic compounds via the pH-metric titration technique

In drug development, the thermodynamically most stable form of a compound is preferred because metastable forms are prone to transform to the stable form during processing, formulation, or storage [Guillory, J.K., 1999. Generation of polymorphs, hydrates, solvates, and amorphous solids. In: Brittain, H.G. (Ed.), Polymorphism in Pharmaceutical Solids. Marcel Dekker, New York, pp. 183-226]. It is therefore important to discover and characterize the stable form as early as possible. One of the most important properties to determine is thermodynamic solubility. However, due to compound and time constraints this solubility value is usually not determined until late in discovery. This report explores the ability of the pH-metric titration method to measure intrinsic solubility of the stable form of compounds that exist in one or more polymorphic forms. One metastable form and the stable form of eight compounds were examined. Intrinsic solubility was measured via pH-metric titration. The technique was performed on a larger scale in order to monitor polymorphic form changes by powder X-ray diffraction. Shake-flask solubility and corresponding X-ray diffraction data of each form was also determined. The results of this study indicate that, in general, when starting with a metastable polymorph, the pH-metric titration method is able to achieve the solubility of the stable form by the third titration, while the traditional shake-flask solubility method is unable to consistently determine the stable form solubility.

A Titration Strategy Is Needed To Manage Breakthrough Cancer Pain Effectively: Observations from Data Pooled from Three Clinical Trials

BACKGROUND

Breakthrough pain is a prevalent and serious problem in patients with cancer. However, it is not known how best to predict the effective dose of breakthrough opioid for any given patient.

METHODS

Data were pooled and reanalyzed from three large, randomized clinical trials of the rapidly absorbed oral transmucosal fentanyl citrate lozenges (OTFC) in which patients were carefully titrated to an optimal OTFC dose. The relationships between the optimal OTFC dose, patients' previous opioid dose, 24-hour total opioid, and patient characteristics were explored to determine whether the optimal OTFC dose can be predicted based on pretreatment clinical factors.

RESULTS

The cohort included 188 patients within the three trials whose breakthrough pain was effectively managed with OTFC. Prior to entry into the trial, the average breakthrough opioid dose in the 188 patients was 12% of the daily dose of scheduled opioid but strikingly, ranged from 1%-72%. The optimal OTFC dose was poorly correlated with patients' scheduled or previous breakthrough opioid doses. The only clinically meaningful correlation was that the average final OTFC dose significantly decreased with increasing age. Overall, there was enormous interindividual variability in patients' dose requirements for breakthrough pain.

CONCLUSIONS

This is the largest study to date of the relationship between clinical variables and the effective dose of OTFC when titrated to effect for breakthrough cancer pain. These results suggest that use of breakthrough medication should routinely be individualized with a titration strategy separate from the around-the-clock medication, according to each patient's response to their breakthrough opioid.

Quantifying the sequence-dependent species barrier between hamster and mouse prions

Prion diseases are transmissible neurodegenerative disorders. It is widely accepted that prions are the infectious agents responsible for disease transmission, and the sequence homology between the infectious prion and the host prion protein determines its transmission efficiency across species. However, previous studies have often reported different results regarding seeding efficiency, the efficiency of initiating amyloid propagation by adding pre-existing amyloid fibrils as seed. In the present study, we used synthetic peptides as a simple system to determine the sequence-dependent transmission barrier between hamster and mouse. We found that the heterologous seeding efficiency of hamster and mouse prion peptides was 4 times less than that of homologous seeding. Moreover, residue 139 was not the only residue in determining seeding efficiency. When the seed had Ile at this position, the homology at this position between seed and monomer determined the seeding efficiency. When the seed had Met at this position, homology at residues 109 and 112 determined the seeding efficiency.

Reliability and uncertainty in the estimation of pKa by least squares nonlinear regression analysis of multiwavelength spectrophotometric pH titration data

When drugs are poorly soluble then, instead of the potentiometric determination of dissociation constants, pH-spectrophotometric titration can be used along with nonlinear regression of the absorbance response surface data. Generally, regression models are extremely useful for extracting the essential features from a multiwavelength set of data. Regression diagnostics represent procedures for examining the regression triplet (data, model, method) in order to check (a) the data quality for a proposed model; (b) the model quality for a given set of data; and (c) that all of the assumptions used for least squares hold. In the interactive, PC-assisted diagnosis of data, models and estimation methods, the examination of data quality involves the detection of influential points, outliers and high leverages, that cause many problems when regression fitting the absorbance response hyperplane. All graphically oriented techniques are suitable for the rapid estimation of influential points. The reliability of the dissociation constants for the acid drug silybin may be proven with goodness-of-fit tests of the multiwavelength spectrophotometric pH-titration data. The uncertainty in the measurement of the pK (a) of a weak acid obtained by the least squares nonlinear regression analysis of absorption spectra is calculated. The procedure takes into account the drift in pH measurement, the drift in spectral measurement, and all of the drifts in analytical operations, as well as the relative importance of each source of uncertainty. The most important source of uncertainty in the experimental set-up for the example is the uncertainty in the pH measurement. The influences of various sources of uncertainty on the accuracy and precision are discussed using the example of the mixed dissociation constants of silybin, obtained using the SQUAD(84) and SPECFIT/32 regression programs.

A rigorous multiple independent binding site model for determining cell-based equilibrium dissociation constants

A new 4-parameter nonlinear equation based on the standard multiple independent binding site model (MIBS) is presented for fitting cell-based ligand titration data in order to calculate the ligand/cell receptor equilibrium dissociation constant and the number of receptors/cell. The most commonly used linear (Scatchard Plot) or nonlinear 2-parameter model (a single binding site model found in commercial programs like Prism(R)) used for analysis of ligand/receptor binding data assumes only the K(D) influences the shape of the titration curve. We demonstrate using simulated data sets that, depending upon the cell surface receptor expression level, the number of cells titrated, and the magnitude of the K(D) being measured, this assumption of always being under K(D)-controlled conditions can be erroneous and can lead to unreliable estimates for the binding parameters. We also compare and contrast the fitting of simulated data sets to the commonly used cell-based binding equation versus our more rigorous 4-parameter nonlinear MIBS model. It is shown through these simulations that the new 4-parameter MIBS model, when used for cell-based titrations under optimal conditions, yields highly accurate estimates of all binding parameters and hence should be the preferred model to fit cell-based experimental nonlinear titration data.

Monitoring denitrification by pH-Stat titration

An improved pH-stat titrimetric procedure was developed, validated, and extensively applied to monitor biological heterotrophic denitrification in a lab-scale sequencing batch reactor (SBR). So far, titrimetric procedures were not successful in monitoring denitrification processes in full-scale wastewater (WW) treatment plants, mainly because the stoichiometric ratio between proton production and nitrate reduction is highly variable due to variability of both biomass and influent WW characteristics. In this article, a new titration procedure is proposed where a simple calibration step is performed before each experimental test. This procedure allows for the assessment of (i) nitrate content in a sample of mixed liquor; (ii) the maximum denitrification rate of sludge when fed on acetate; and (iii) the denitrification potential (DNP) of different substrates. As for (i), validation by comparison with spectrophotometric measures indicated an average discrepancy of less than 3% on more than 40 samples; as for (ii) and (iii) collected values compared well with literature data. The titrimetric method proposed here is also capable of assessing the biomass anoxic yield in a very simple way, since it does not require any analytical nitrate determination. According to the results of this experimentation, titrimetry appeared to be a simple, inexpensive, and powerful tool for monitoring and operating denitrification processes in WW treatment plants.

Evaluation of methods for the determination of water in substances with unknown chemical and thermal behaviour

The water content of six different substances was determined by means of five different methods. The methods used were loss on drying, thermogravimetry (coupled with DSC), a new phosphorous-pentoxide method, direct Karl-Fischer titration and the Karl-Fischer oven. A combination of direct Karl-Fischer titration and the KF-oven method was found to be the optimal technique for water determination of substances of unidentified chemical and thermal behaviour based on detailed considerations about selectivity, type of water binding, sample properties and efficiency.

Simple but Effective Way to Sense Pyrophosphate and Inorganic Phosphate by Fluorescence Changes

A new fluorescent chemosensor based on the acridine-Zn(II) derivative effectively recognizes pyrophosphate and inorganic phosphate at pH 7.4. Acridine derivative 1 displayed a fluorescent quenching effect with pyrophosphate; on the other hand, a large fluorescent enhancement was observed with inorganic phosphate. [structure: see text].

Oral rapid loading of valproic acid—An alternative to the usual saturation scheme?

Valproic acid (VPA) is considered to be a drug of first choice for the therapy of generalized and focal epilepsies. Due to its broad field of application and its good compatibility, VPA is one of the most frequently prescribed antiepileptic drugs (AED) worldwide. Previous studies have examined the safety and tolerability of rapid intravenous-loaded VPA in the treatment of epilepsy and status epilepticus, but rapid oral loading has not been evaluated in paediatrics systematically in the past. The standard titration scheme takes 10-14 days, some physicians prefer a slower titration of up to 4 weeks. At many institutes, especially children are treated as inpatients until the desired dosage is reached. This causes high costs to the health system and is very inconvenient for the families affected. We have developed a new loading scheme to achieve a therapeutic serum level on the third day of treatment, in order to minimize the time between the beginning of the therapy and reaching the therapeutic serum level. This is the first attempt at doing this with VPA for children with epilepsy.

Accelerated nuclei preparation and methods for analysis of histone modifications in yeast

The continuing identification of new histone post-translational modifications and ongoing discovery of their roles in nuclear processes has increased the demand for quick, efficient, and precise methods for their analysis. In the budding yeast Saccharomyces cerevisiae, a variety of methods exist for the characterization of histone modifications on a global scale. However, a wide gap in preparation time and histone purity exists between the most widely used extraction methods, which include a simple whole cell extraction (WCE) and an intensive histone extraction. In this work we evaluate various published WCE buffers for their relative effectiveness in the detection of histone modifications by Western blot analysis. We also present a precise, yet time-efficient method for the detection of subtle changes in histone modification levels. Lastly, we present a protocol for the rapid small-scale purification of nuclei that improves the performance of antibodies that do not work efficiently in WCE. These new methods are ideal for the analysis of histone modifications and could be applied to the analysis and improved detection of other nuclear proteins.

Study of the near-neutral pH-sensitivity of chitosan/gelatin hydrogels by turbidimetry and microcantilever deflection

The fundamental properties and pH-sensitivity of chitosan/gelating hydrogels were investigated using spectroscopic and microelectro mechanical (MEMS) measurement approaches. Turbidimetric titration revealed that there were electrostatic attractive interactions between tripolyphosphate (TPP), chitosan, and gelatin in the acidic pH range, depending on their degree of ionization. The pH-sensitive swelling behavior of the hydrogels was investigated by monitoring the deflection of hydrogel-coated microcantilevers, which exhibited a sensitive and repeatable response to solution pH. The deflection of the microcantilever increased as the pH decreased, and the response speed of the system exhibited a nearly linear relationship with pH. The effects of the pH and concentration of TPP solution, as well as the ratio of chitosan to gelatin in gel precursor solutions, on the pH sensitivity of the hydrogels were also investigated. It was found that the swelling of the hydrogel is mainly a result of chain relaxation of chitosan-TPP complexes caused by protonation of free amino groups in chitosan, which depends on the crosslinking density set during the formation of the network. An increase in initial crosslink density induced a decrease in swelling and pH sensitivity. It can be concluded from this study that pH-sensitive chitosan gel properties can be tuned by preparatory conditions and inclusion of gelatin. Furthermore, microcantilevers can be used as a platform for gaining increased understanding of environmentally sensitive polymers.

Oral transmucosal fentanyl citrate for cancer breakthrough pain: a review

PURPOSE/OBJECTIVES

To review the dose titration, efficacy, and safety of oral transmucosal fentanyl citrate (OTFC).

DATA SOURCES

Phase I and II clinical trial abstracts and evidence-based review articles.

DATA SYNTHESIS

OTFC has an onset, peak, and duration of action similar to that of an IV dose of an opioid and has been demonstrated to be effective and well tolerated for the management of breakthrough pain in patients with cancer.

CONCLUSIONS

Studies of OTFC demonstrate that it is easy to use,noninvasive, effective, safe, and acceptable to patients, caregivers, and healthcare providers. However, OTFC is expensive and approved for use only in opioid-tolerant patients with cancer.

IMPLICATIONS FOR NURSING

Breakthrough pain in patients with cancer is a common problem with characteristics that make it difficult to treat. Oncology nurses should familiarize themselves with OTFC's unique characteristics to be able to best help patients manage their therapy.

Enthalpy of the B-to-Z conformational transition of a DNA oligonucleotide determined by isothermal titration calorimetry

The influence of high concentrations of Na(+) or [Co(NH(3))(6)](3+) on the conformation of two related DNA oligomers was investigated by circular dichroism spectropolarimetry (CD), isothermal titration calorimetry (ITC), and differential scanning calorimetry (DSC). As revealed by CD, DNA oligomers, (dC-dG)(4) and (dm(5)C-dG)(4), both form right-handed double helical structures (B-DNA) in standard phosphate buffer with 115 mM Na(+) at 25 degrees C. However, at 2.0 M Na(+) or 200 microM [Co(NH(3))(6)](3+), (dm(5)C-dG)(4) assumes a left-handed double helical structure (Z-DNA), whereas the unmethylated (dC-dG)(4) analog remains right-handed under those conditions. ITC was then used to determine the enthalpy change upon increasing the concentration of either Na(+) or [Co(NH(3))(6)](3+) for both DNA oligomers at 25 degrees C. The titration with Na(+) resulted in endothermic isotherms with (dm(5)C-dG)(4) being more endothermic than (dC-dG)(4) by 700 cal/mol basepair. In contrast, titration with [Co(NH(3))(6)](3+) resulted in exothermic isotherms with (dC-dG)(4) being more exothermic than (dm(5)C-dG)(4) by 720 cal/mol basepair. We attribute the enthalpy difference to the conformational transition from B-form DNA to Z-form DNA for (dm(5)C-dG)(4), a transition which does not occur for the unmethylated (dC-dG)(4). The value of approximately 700 cal/mol basepair for the enthalpy of the B-Z transition compares favorably with previously published results obtained by different techniques. DSC was used to monitor the duplex to single strand transitions for both oligomers under the different concentrations. These results indicated that methylation of the cytidine destabilizes (dm(5)C-dG)(4) relative to (dC-dG)(4). Coupling the DSC data with the ITC data allowed construction of a thermodynamic cycle which gives insight into the influence of both temperature and ionic strength on the heat content of the two DNA systems studied. Further, this study reveals the utility of using ITC for determinations of transition enthalpies with the appropriate choice of control.

Odorant binding protein has the biochemical properties of a scavenger for 4-hydroxy-2-nonenal in mammalian nasal mucosa

Odorant binding proteins (OBP) are soluble lipocalins produced in large amounts in the nasal mucosa of several mammalian species. Although OBPs can bind a large variety of odorous compounds, direct and exclusive involvement of these proteins in olfactory perception has not been clearly demonstrated. This study investigated the binding properties and chemical resistance of OBP to the chemically reactive lipid peroxidation end-product 4-hydroxy-2-nonenal (HNE), in an attempt to establish a functional relationship between this protein and the molecular mechanisms combating free radical cellular damage. Experiments were carried out on recombinant porcine and bovine OBPs and results showed that both forms were able to bind HNE with affinities comparable with those of typical OBP ligands (K(d) = 4.9 and 9.0 microm for porcine and bovine OBP, respectively). Furthermore, OBP functionality, as determined by measuring the binding of the fluorescent ligand 1-aminoanthracene, was partially lost only when incubating HNE levels and exposure time to HNE exceeded physiological values in nasal mucosa. Finally, preliminary experiments in a simplified model resembling nasal epithelium showed that extracellular OBP can preserve the viability of an epithelial cell line derived from bovine turbinates exposed to toxic amounts of the aldehyde. These results suggest that OBP, which is expressed at millimolar levels, might reduce HNE toxicity by removing from the nasal mucus a significant fraction of the aldehyde that is produced as a consequence of direct exposure to the oxygen present in inhaled air.