DESIGN: computerized optimization of experimental design for estimating Kd and Bmax in ligand binding experiments. I. Homologous and heterologous binding to one or two classes of sites

We have developed a versatile computer program for optimization of ligand binding experiments (e.g., radioreceptor assay system for hormones, drugs, etc.). This optimization algorithm is based on an overall measure of precision of the parameter estimates (D-optimality). The program DESIGN uses an exact mathematical model of the equilibrium ligand binding system with up to two ligands binding to any number of classes of binding sites. The program produces a minimal list of the optimal ligand concentrations for use in the binding experiment. This potentially reduces the time and cost necessary to perform a binding experiment. The program allows comparison of any proposed experimental design with the D-optimal design or with assay protocols in current use. The level of nonspecific binding is regarded as an unknown parameter of the system, along with the affinity constant (Kd) and binding capacity (Bmax). Selected parameters can be fixed at constant values and thereby excluded from the optimization algorithm. Emphasis may be placed on improving the precision of a single parameter or on improving the precision of all the parameters simultaneously. We present optimal designs for several of the more commonly used assay protocols (saturation binding with a single labeled ligand, competition or displacement curve, one or two classes of binding sites), and evaluate the robustness of these designs to changes in parameter values of the underlying models. We also derive the theoretical D-optimal design for the saturation binding experiment with a homogeneous receptor class.

Use of a simian virus 40-based shuttle vector to analyze enhanced mutagenesis in mitomycin C-treated monkey cells

When monkey cells were treated with mitomycin C 24 h before transfection with UV-irradiated pZ189 (a simian virus 40-based shuttle vector), there was a twofold increase in the frequency of mutations in the supF gene of the vector. These results suggest the existence of an enhancible mutagenesis pathway in mammalian cells. However, DNA sequence analysis of the SupF- mutants suggested no dramatic changes in the mechanisms of mutagenesis due to mitomycin C treatment of the cells.

Vasopressin and oxytocin receptors in vagina, myometrium, and oviduct of rabbits

In view of the presence of distinct oxytocin (OT) and vasopressin (VP) receptors in the male genital tract (porcine) we have reexamined the receptors for OT and AVP in the classical OT target tissue, female genital tract (rabbit). Neurohypophysial hormone receptors have been investigated in vagina, myometrium, and oviduct using quantitative ligand binding, adenylate cyclase, and contractility studies. Our results clearly indicate the presence of distinct OT and V1 VP receptors in the myometrium, while only the latter was detected in vagina and oviduct. In myometrium, estrogen treatment increases the density of OT and AVP receptors, while progesterone administration inhibits the estrogen effect. At the time of spontaneous delivery a dramatic (17-fold) increase was observed for the OT sites, while the AVP sites were unchanged. AVP receptors in vagina were sensitive to sex steroid administration and were reduced during pregnancy and delivery. Isometric contractility studies suggest that not just OT, but AVP can stimulate uterine strips, an effect that is partially reversible by the V1 antagonist d(CH2)5TyrMeAVP. In vagina only AVP is effective in inducing contractions at nanomolar concentrations. These results suggest a role for AVP as well as OT in regulation of the motility of female genital tract.

A versatile method for simultaneous analysis of families of curves

We have developed a versatile new approach to the simultaneous analysis of families of curves, which combines the simplicity of empirical methods with several of the advantages of mathematical modeling, including objective comparison of curves and statistical hypothesis testing. The method uses weighted smoothing cubic splines; the degree of smoothing is adjusted automatically to satisfy constraints on curve chape (monotonicity, number of inflection points). By simultaneous analysis of a family of curves, one can extract the shape common to all the curves. Up to four linear scaling parameters are used to match the shape to each curve, and to provide optimal superimposition of the several curves. By applying constraints to these scaling factors, one can test a variety of hypotheses concerning comparisons of curves (e.g., identity, parallelism, or similarity of shape of two or more curves), and thus evaluate the effects of experimental manipulation. By optimal pooling of data one can avoid the need for arbitrary selection of a typical experiment, and can detect subtle but reproducible effects that might otherwise be overlooked. This approach can facilitate the development of an appropriate model. The method has been implemented in a Turbo-Pascal program for IBM-PC compatible microcomputers, and in FORTRAN-77 for the DEC-10 mainframe, and has been utilized successfully in a wide variety of applications.

An exact correction to the "Cheng-Prusoff" correction

The use of graphical estimation techniques in pharmacology is well entrenched, yet can sometimes lead to confusion and errors. The widely used Cheng-Prusoff correction for obtaining the inhibition constant Ki from the graphical mid point or ED50 of a displacement or inhibition curve is not exact, contrary to popular belief. We show that under many commonly used experimental conditions, the Cheng-Prusoff rule can lead to a substantial 3- to 6-fold or larger error in the estimate of Ki. Surprisingly, an explicit, relatively simple exact correction rule is available. We derive this rule and show the conditions under which its use is required.

Test of models for the sequence specificity of UV-induced mutations in mammalian cells

We have used mathematical modeling and statistical analysis to examine the correlation between UV-induced DNA damage and resulting base-substitution mutations in mammalian cells. The frequency and site specificity of UV-induced photoproducts in the supF gene of the pZ189 shuttle vector plasmid were compared with the frequency and site specificity of base-substitution mutations induced upon passage of the UV-irradiated vector in monkey cells. The hypothesis that the observed mutational spectrum is due to a preferential insertion of adenosine opposite UV photoproducts in the DNA template was found to best explain the mutational data. Models in which it was postulated that only (6-4) photoproducts, and not cyclobutane dimers, are mutagenic, or that the relative frequency of photoproduct formation does not influence mutation frequencies, fit the data much less well. This analysis demonstrates that molecular mechanisms of mutagenesis in mammalian cells can be deduced from mutational data obtained with a shuttle vector system.

Naloxonazine effects on the interaction of enkephalin analogs with mu-1, mu and delta opioid binding sites in rat brain membranes

The authors have characterized the opioid receptors of rat brain membranes using self- and cross-displacement studies with both tritiated and unlabeled [D-Ala2, D-Leu5]-enkephalin and [D-Ala2, MePhe4, Gly-ol5]-enkephalin. Mathematical modeling demonstrated the presence of three classes of binding sites, corresponding to mu, delta and the putative mu-1 classes of site. Unlabeled naloxonazine shows high affinity for all three classes of sites, with highest affinity for the mu-1 sites. Membranes were preincubated with 50 nM naloxonazine or with controls (50 nM naloxone or buffer) for 30 min. Preincubation of membranes with 50 nM naloxonazine resulted in a dramatic, nearly 2-fold reduction in the binding of [3H][D-Ala2, D-Leu5]-enkephalin and [3H][D-Ala2, MePhe4, Gly-ol5]-enkephalin relative to the controls. Quantitative analyses using mathematical modeling with program "LIGAND" suggested that this effect was primarily "competitive," i.e., attributable to changes in affinity, with no apparent or detectable noncompetitive or irreversible effects on binding capacities for the three classes of sites.

A model-free approach to estimation of relative potency in dose-response curve analysis

We have developed a new, general approach to analysis of dose-response curves from bioassay, immunoassay (including radioimmunoassay, immunoradiouretic assay, enzyme-linked immunosorbent assay), and other experimental procedures. It provides a test for parallelism, similarity of shape, and a measure of relative potency for any set of two or more curves. The method uses a constrained smoothing spline function to estimate the curve shape, together with a nonlinear least-squares fitting technique to estimate parameters for relative potency and slope. The use of "constrained splines" permits the analysis of nonlinear dose-response curves that cannot be described by a simple model or equation such as the symmetric four-parameter logistic. A microcomputer program is used for the analysis, providing relative potencies and their SE and evaluation of goodness of fit.

UV light-induced cyclobutane pyrimidine dimers are mutagenic in mammalian cells

We used a simian virus 40-based shuttle vector plasmid, pZ189, to determine the role of pyrimidine cyclobutane dimers in UV light-induced mutagenesis in monkey cells. The vector DNA was UV irradiated and then introduced into monkey cells by transfection. After replication, vector DNA was recovered from the cells and tested for mutations in its supF suppressor tRNA marker gene by transformation of Escherichia coli carrying a nonsense mutation in the beta-galactosidase gene. When the irradiated vector was treated with E. coli photolyase prior to transfection, pyrimidine cyclobutane dimers were removed selectively. Removal of approximately 90% of the pyrimidine cyclobutane dimers increased the biological activity of the vector by 75% and reduced its mutation frequency by 80%. Sequence analysis of 72 mutants recovered indicated that there were significantly fewer tandem double-base changes and G X C----A X T transitions (particularly at CC sites) after photoreactivation of the DNA. UV-induced photoproducts remained (although at greatly reduced levels) at all pyr-pyr sites after photoreactivation, but there was a relative increase in photoproducts at CC and TC sites and a relative decrease at TT and CT sites, presumably due to a persistence of (6-4) photoproducts at some CC and TC sites. These observations are consistent with the fact that mutations were found after photoreactivation at many sites at which only cyclobutane dimers would be expected to occur. From these results we conclude that UV-induced pyrimidine cyclobutane dimers are mutagenic in DNA replicated in monkey cells.

Denominator definition by the utilization correction factor method

Most clinical research in the United States has been carried out in atypical populations. This study, done in a network of primary care populations in Virginia, calculates the denominator by the utilization correction factor method and compares the demography with that of the population of the state. The demographic characteristics of the patients in the network are very similar to those of the underlying populations and on the same order of state-of-the-art sampling methods in current use.

Mu1: a very high affinity subtype of enkephalin binding sites in rat brain

Displacement studies of [3H]-[D-Ala2-MePhe4-Gly-ol5]-enkephalin ([3H]-DAGO) and [3H]-[D-Ala2-D-Leu5]-enkephalin ([3H]-DADL) by the corresponding unlabeled ligands show that there are at least three classes of sites which bind these enkephalin analogs with high affinity. Using computer modeling, the introduction of the third site significantly improved the goodness of fit in ten consecutive experiments. These sites appear to correspond to the mu, delta and mu 1 sites, with mean dissociation constants of 11, 1.3 and 0.9 nM for DADL and 2.5, 300 and 0.3 nM for DAGO, respectively.

Increased affinity and selectivity of enkephalin tripeptide (Tyr-D-Ala-Gly) dimers

The binding of alkylendiamide dimers of the three N-terminal residues of [D-Ala2,D-Leu5]enkephalin (DADL) to rat brain and Ng108-15 neuroblastoma-glioma cell membranes was compared with that of DADL, Tyr-D-Ala-Gly-NMe-Phe-Gly-ol (DAGO) and morphiceptin. Tritiated DADL and DAGO were used as labeled ligands for delta- and mu-receptors, respectively. Dimerization of the tripeptides resulted in dramatic increases in both mu and delta binding. The binding to mu-receptors showed two peaks at an alkyl chain length of n = 2 and approximately n = 16. In contrast, delta binding (NG108-15 cells) increased steadily with increasing chain length. The dimers with n less than 18 were mu-preferential, and the one with n = 2 showed the most dramatic increase in mu selectivity with a 400 fold higher affinity to mu- than to delta-receptors. For long-chain alkyl spacers the compounds became delta selective.

Endocrine, renal, and hemodynamic responses to graded dopamine infusions in normal men

The present study was performed to determine the hemodynamic, hormonal, and natriuretic responses to infusions of dopamine (DA) that reflect physiological as well as pharmacological levels in blood or tissue. In six normal men, DA was infused for 2 h at three fixed dosages (0.03 or 0.1, 0.3, and 3.0 micrograms/kg X min) on three separate occasions, which resulted in increases in mean plasma DA concentrations from basal levels of less than 0.03 ng/ml to 0.69 +/- 0.12, 3.73 +/- 0.40, and 38.4 +/- 3.80 (+/- SE) ng/ml. Mean plasma PRL decreased and DA excretion increased significantly from basal levels during all three DA infusions. Plasma LH decreased and norepinephrine (NE) excretion increased during both the middle and high dose infusions, while sodium excretion, plasma NE, and heart rate increased only during the high dose DA infusion. Basal plasma aldosterone values were low and did not change with DA treatment. PRA, TSH, and FSH also did not change. GH responses were difficult to assess because of the frequency of episodic secretions. Since DA concentrations in hypophysial-portal blood may equal or exceed 1 ng/ml, these results support a role for DA in the acute regulation of PRL, and possibly LH, in normal men. As a natriuretic response occurred only at supraphysiological concentrations of circulating DA, if DA has a physiological role in modulating sodium excretion during normal sodium intake, it must be released from dopaminergic neurons or otherwise locally produced in very high concentrations in the kidney.

Separation of different UDP glucuronosyltransferase activities according to charge heterogeneity by chromatofocusing using mouse liver microsomes. Three major types of aglycones

Hepatic UDP glucuronosyltransferase (EC 2.4.1.17) (GT) enzymes in control, phenobarbital- and 3-methylcholanthrene-induced microsomes from C57BL/6N mice have been fractionated according to charge heterogeneity on a chromatofocusing system using a pH 9.5 to 6 gradient. Transferase activities for eleven different substrates were determined on column fractions. Activities toward 3-hydroxybenzo[a]pyrene, phenolphthalein and estrone (type 1 substrates) were enhanced by both effector compounds and always eluted primarily at pH 8.5. In control and phenobarbital-induced microsomes, activities toward testosterone, 4-hydroxybiphenyl, morphine, naphthol and 9-hydroxybenzo[a]pyrene (type 2 substrates) eluted primarily at about pH 6.7. Activities toward p-nitrophenol, 4-methylumbelliferone and 2-hydroxybiphenyl (type 3 substrates) in control and phenobarbital-induced microsomes exhibited two peaks which eluted at pH 8.5 and 6.7. 3-Methylcholanthrene treatment increased almost exclusively activities which eluted at pH 8.5 for each of the three types of substrates. The pH value of elution corresponds to the approximate isoelectric point of the eluted protein. Immunoabsorption studies with an antibody preparation raised against a purified low pI form confirmed that a 51,000-dalton transferase form, GTM1, eluted primarily at pH 6.7 and that a 54,000-dalton form, GTM2, eluted at pH 8.5. A mathematical treatment of the ratios of activity after 3-methylcholanthrene treatment to that after phenobarbital treatment versus pH produced six patterns of activity. A minimum of two enzymes at the low pH region and one enzyme at the high pH region, all with broad-substrate specificity, could account for these patterns.

Serotoninergic system in scrapie-infected hamsters

Hamsters inoculated with scrapie virus show a dramatic hypersensitivity to serotoninergic drugs, developing a behavioral syndrome not unlike that obtained with pharmacologically induced lesions of the raphe nuclei. In an attempt to explain the state of hypersensitivity and to determine whether or not serotoninergic neurons were targets of the scrapie virus, pre- and postsynaptic serotoninergic sites were studied in the cerebral cortices of scrapie-infected and sham-inoculated hamsters. [3H]Imipramine binding and the uptake of endogenous 5-hydroxytryptamine (5-HT, serotonin) in synaptosomes prepared from scrapie-inoculated animals were not different from those of controls. This suggests integrity of the serotoninergic neurons in scrapie-infected hamsters. In contrast, affinity for the 5-HT1 receptor (which modulates inhibitory response) was diminished whereas that for the 5-HT2 receptor (which modulates excitatory response) was increased. This "imbalance" between the two receptors which is amplified in in vivo responses may account for the 5-HT hypersensitivity. The alteration in the affinity of the two postsynaptic 5-HT receptors supports the observation that scrapie virus alters cell plasma membranes.

A very high affinity opioid binding site in rat brain: demonstration by computer modeling

We present substantial new evidence for at least four distinct types of opioid receptors in rat brain, using quantitative ligand binding studies and mathematical modeling. Three of these binding sites are consistent with the well established "mu", "delta" and "kappa" receptors. The fourth has two distinctive features: 1) extremely high affinity (dissociation constant less than 1 nM); 2) almost complete lack of specificity for the classical "delta" or "mu" selective ligands. These properties are consistent with the putative "mu1" receptor described by Pasternak and coworkers.

Development of a friendly, self-teaching, interactive statistical package for analysis of clinical research data. The BRIGHT STAT-PACK

We have developed a new statistical analysis package for use by the clinical investigator, the clinician, and the laboratory researcher. This package attempts to implement the following philosophy: The programs should be essentially self-teaching, friendly, and forgiving; the programs should educate the user regarding the underlying theory, assumptions, and interpretation of the statistical methods involved; the programs should automatically test relevant assumptions and warn the user when these assumptions appear to have been violated; the programs should make recommendations about the availability of alternative statistical methods and automatically perform such analyses when indicated; the programs should interpret the results; and the programs should mimic, insofar as possible, the logic used in a routine, elementary statistical consultation. Several programs have been developed, extensively tested, and used.

Changes in the status of neurotransmitter receptors in a rabbit model of hepatic encephalopathy

It has previously been shown in an animal model of hepatic encephalopathy (HE) that the number of receptors for the inhibitory neurotransmitter, gamma-aminobutyric acid (GABA), increases and that the number of receptors for the excitatory neurotransmitter, glutamate, decreases. To determine the functional status of other neurotransmitter systems in HE, measurements were made of the specific binding of other neurotransmitters to synaptic membranes prepared from the brains of normal rabbits and rabbits in HE due to galactosamine-induced acute liver failure. The development of HE was associated with: (i) a decrease in the density (Bmax) of receptors for the two excitatory amino acid neurotransmitters, aspartate and kainic acid; (ii) an increase in the Bmax of both the low and high affinity binding site for strychnine, a marker for the inhibitory neurotransmitter glycine; (iii) a decrease in the affinity (Kd) of receptors for dopamine, and (iv) no appreciable change in either the specific binding of [3H]D-ala2-methionine enkephalinamide or [3H]naloxone, markers for opiate receptors, or in the Bmax or the Kd of receptors for acetylcholine. If it is assumed that the sensitivity of the brain to neurotransmitters varies directly with the density of neurotransmitter receptors, HE may be associated with increased sensitivity to inhibitory amino acid neurotransmitters and decreased sensitivity to excitatory amino acid neurotransmitters. Thus, the observed changes in neurotransmitter receptors in HE afford a feasible pathophysiological basis for the mediation of the neural inhibition of HE.

New methods for characterization of complex receptor systems involving 3 or more binding sites: application to brain opiate receptors

The problems of evaluating results based on the analysis of complex binding models are considered and new methods are proposed to provide independent confirmation of the existence of multiple sites. A new plotting format for the results from experiments involving two ligands is introduced, and its utility is demonstrated for a) finding initial estimates for nonlinear least squares curve fitting; b) presenting the results of multiple experiments; and c) giving a new means for evaluating the significance of a third site. The general problem of finding initial estimates for models involving three classes of sites, and strategies for using nonlinear least squares curve fitting algorithms to optimize the fit are considered.

Changes in glutamate receptors on synaptic membranes associated with hepatic encephalopathy or hyperammonemia in the rabbit

The status of the excitatory glutamatergic neurotransmitter system in hepatic encephalopathy has been studied. Synaptic membranes (SM) were prepared from the brains of normal rabbits, hyperammonemic normal rabbits, and rabbits with fulminant hepatic failure. Data on the specific binding of glutamate to SM indicated that fulminant hepatic failure was associated with a decrease in the number of glutamate receptors on SM from cerebral cortex, cerebellum, and particularly the hippocampus, without any associated change in the affinity of these receptors. In contrast, hyperammonemia was associated with an increase in the affinity and no decrease in the number of glutamate receptors on SM from the hippocampus. These findings indicate that the effects of hyperammonemia and fulminant hepatic failure on cerebral glutamate receptors are fundamentally different. The decreased number of glutamate receptors in hepatic encephalopathy might reflect a decreased sensitivity of glutamatergic neurons to glutamate-mediated neural excitation, a phenomenon that could contribute to the neural inhibition of hepatic encephalopathy.

Gamma-aminobutyric acid and benzodiazepine receptors in an animal model of fulminant hepatic failure

Hepatic encephalopathy (HE) is a syndrome of generalized neural inhibition, which complicates both acute and chronic liver failure. Since gamma-aminobutyric acid (GABA) is the principal inhibitory neurotransmitter of the brain and HE is associated with increased responsiveness to certain drugs (benzodiazepines and barbiturates) that mediate neural inhibition by binding to the GABA receptor complex on postsynaptic neural membranes, the status of this receptor complex in HE was investigated. Fulminant hepatic failure was induced in rabbits by the intravenous injection of galactosamine hydrochloride. Neural membranes were isolated from the brains of normal rabbits, rabbits in hepatic coma, and rabbits with another type of metabolic encephalopathy, uremic coma. To characterize GABA and benzodiazine receptors, measurements were made of the specific binding to neural membranes of 3H-GABA and 3H-flunitrazepam, respectively. Computer-assisted Scatchard plot analysis of the binding data suggested the presence of two independent receptors for GABA and a single class of receptor for benzodiazepines. Hepatic coma was associated with no changes in the affinities of these receptors but with significant increases in their densities: 0.34 vs. 0.60; 1.1 vs. 2.2; and 4.6 vs. 7.3 pmol/mg of membrane protein for the high-affinity GABA, low-affinity GABA and benzodiazepine receptors, respectively. Uremic coma was associated with no changes in the affinities or densities of GABA receptors. On the basis of these findings, it is suggested that (1) increased numbers of GABA receptors in liver failure may potentiate neural inhibition by increasing the sensitivity of the brain to GABA and (2) increased responsiveness to the sedative-hypnotic effects of benzodiazepines in liver failure may be mediated by increased numbers of receptors for this class of drug, permitting increased drug effect.

Designing learning experiences for teachers...and students

Guidelines for helping medical educators make decisions about designing learning activities are very few and non-specific. The author describes and illustrates four concepts that govern those decisions: personal anchor, objectifying the subjective experience, developing knowledge, and collective wisdom. Medical educators at the Medical College of Virginia have used these concepts to plan and implement their teaching activities.

Experimental artifacts and the analysis of ligand binding data: results of a computer simulation

Use of computerized analysis techniques for ligand binding data have recently become generally available, and are now used quite routinely. When used appropriately, these tools can improve the precision of the estimated parameters for binding affinity, K, and capacity, R. Furthermore, such programs can also calculate the uncertainty of the estimates e.g., as a percent coefficient of variation (%CV). However, because of unmeasured variability in specific activity, tracer purity, counting efficiency, counter background, efficiency of separation, etc., the actual uncertainty in the parameters K and R is usually much larger than stated. In an attempt to examine the effects of such artifacts, we have developed a computer program which simulates data arising from a number of commonly used experimental designs, and then intentionally distorted with each of these artifacts. Finally, the data are converted to B/F and B and plotted in the conventional Scatchard plot. Distortions revealed in this graph are indicative of the effect each artifact has on the parameter estimates. The computer program is generally written to stimulate the binding of 2 or more ligands to one, two or many classes of independent or cooperative specific sites as well as to nonspecific sites. Thus, the program is applicable in a wide variety of situations. Results show that low tracer purity ("bindability") or low filtration efficiency will significantly alter the measured R value. Poorly determined specific radioactivity may significantly alter the measured K value as well. Imprecise measurement of machine background may result in the spacious appearance of positive cooperativity, or of additional high or low affinity classes of binding sites. Finally, under some circumstances, it is possible to detect and correct for the presence of these artifacts.