A model of non-uniform lung parenchyma distortion

A finite element model of mammalian lung parenchyma is used to study the effect of large non-uniform distortions on lung elastic behaviour. The non-uniform distortion is a uni-axial stretch from an initial state of uniform pressure expansion. For small distortions, the parenchymal properties are linearly isotropic and described by two elastic moduli. However, for large distortions, the parenchyma has anisotropic non-linear elastic properties described by five independent elastic moduli dependent on the degree of distortion; they are computed for a range of distortions and initial pressures. Ez, the Young's modulus in the direction of stretch, increases significantly with distortion (epsilon(z)) while Ex, the Young's modulus in the plane perpendicular to the stretch, is approximately constant. The greater the initial pressure, the bigger the difference between the two moduli at larger distortion strains. The shear modulus G(xz) is approximately independent of degree of distortion except at the highest initial pressure. The Poisson's ratio, nu(xz) is approximately constant with distortion strain for lower initial pressures, but increases significantly with epsilon(z) at higher pressures. Model predictions of the relation between G(xz) and initial uniform inflation pressure show a good correlation with reported experimental data for small distortion strains in a range of species. The model also exhibits similar behaviour to the experimentally measured uni-axial large deformations of a tri-axially pre-loaded block of parenchyma (Hoppin et al., 1975, Journal of Applied Physiology 39, 742-751).     

Following FRET through five energy transfer steps: spectroscopic photobleaching, recovery of spectra, and a sequential mechanism of FRET.

We report the acquisition and analysis of spectrally resolved photobleaching data from a model system designed to exhibit FRET. Spectrally resolved photobleaching can be used to determine the presence of FRET in these systems and to investigate multi-step mechanisms of energy transfer. The model system was a previously described set of fluorescent beads consisting of a system of six fluorophores. In standard photobleaching experiments to determine FRET, bleaching of an acceptor molecule resulting in recovery of donor intensity or changes in photobleaching kinetics are used as indicators of FRET. Here, we use the Bateman equations to model growth and decay in a photobleaching experiment. Linked donor-acceptor growth and decay is used as an indicator of FRET. The apparatus required is relatively simple when compared to lifetime imaging systems. Several data analysis strategies, rigorous model building, global fitting procedures, and error analysis are presented. Using these procedures a five-step sequential mechanism of energy transfer was selected for these beads.     

Computer analysis of enzyme-substrate-inhibitor kinetic data with automatic model selection using IBM-PC compatible microcomputers

A weighted nonlinear least-squares curve-fitting program, implemented in compiled BASIC for the IBM-PC is described to estimate the parameters of enzyme kinetics obeying Michaelis-Menten kinetics and seven inhibition models. The effects of the inhibitor on the maximal velocity (Vm) and the Michaelis-Menten constant (Km) are used to select automatically the most plausible model of inhibition and to calculate initial estimates of parameters. The program is used to demonstrate that the inhibition of carbamyl-phenylalanine hydrolase by the product phenylalanine is consistent with the pure mixed noncompetitive model.     

Cytofluorometric quantification of the activity and reaction kinetics of acid phosphatase

Synopsis This paper describes how fluorogenic substrates derived from naphthol AS can be used for the microscopic demonstration and cytofluorometric quantification of the activity and reaction kinetics of acid phosphatase in single living cells.A special study has been made of acid naphthol AS-BI phosphatase. However, the method can be extended to other hydrolytic enzymes. The method is sensitive and accurate because: quantification of very low enzyme activity is possible; the reaction kinetics can be evaluated with a good degree of precision inasmuch as the initial reaction velocity is derived over short times; there is an absence of distributional error; and the errors due to extra-cellular diffusion of the hydrolysed substrate, to photo-decomposition, and to autofluorescence can be contained within very narrow limits.The procedures for determining enzyme activity and reaction kinetics, and the instrumental characteristics and devices required for carrying out these measurements, are described. Some possible applications are indicated.     

Automated kinetic analysis of pyruvate kinase

An apparatus for the automatic determination of enzyme kinetics of pyruvate kinase is described. A continuous plit of velocity versus substrate concentration is obtained using quantities of enzyme and substrates comparable to manual determinations. The automated procedure offers a number of advantages over manual methods including elimination of repetitive pipetting, simpler reaction temperature regulation, reduced analysis time, and possible on-line computer analysis. The apparatus utilizes a commercially available column uv flow monitor to measure NADH/NAD changes in the coupled lactic dehydrogenase reaction at 340 nm in a continuous flow system. The optical density changes are directly related to the velocity of the enzyme-catalyzed reaction. A linear substrate gradient is generated from a density gradient maker to provide the required relationship between velocity and substrate concentration. The system is calibrated by forming a gradient from a hemoglobin solution of known concentration. The procedure has been evaluated by determination of the kinetic parameters of three of the isozymes of pyruvate kinase. Values obtained by the continuous flow method are in close agreement with those obtained by individual point determination in a recording spectrophotometer.     

A quenched-flow apparatus which allows the measurement of the kinetics of a reaction in one stroke

A chemical quenched-flow apparatus is described which measures, in a unique stroke, enough data points (8–11) for establishing the kinetics curve of a reaction. Only very small volumes of reaction solutions (2 × 500 μl) are required. The time intervals between which the kinetic data may be measured range from 5 to 37 ms and from 120 to 450 ms with the corresponding mixing times of 0.6 and 5 ms, respectively. This apparatus was used to investigate the pre-steady-state domain of the aminoacylation reaction of tRNA^Val by valyl-tRNA synthetase from yeast.     

A versatile gel casting cum electrophoresis apparatus

A simple apparatus for vertical.,in situ, polyacrylamide or agarose gel casting as well as for the subsequent electrophoresis is described. The apparatus is completely leakproof and does not require any special device like clamps, O-rings, gaskets, grease etc. for sealing. Slab gels of various thickness (0.04 to 1.0 cm) can be made and the apparatus can be used for analytical or preparative purposes. Gel rods can also be cast and run in the device. Forward as well as reverse polarity electrophoresis of a sample can be run simultaneously in the apparatus. NCL Communication No.: 3077.     

Biosynthetic direction substrate kinetics and product inhibition studies on the first enzyme of histidine biosynthesis, adenosine triphosphate phosphoribosyltransferase.

Initial velocity steady-state substrate kinetics for the ATP phosphoribosyltransferase reaction in the biosynthetic direction were determined and are consistent with a sequential kinetic mechanism. To hold the fractions of magnesium-complexed substrates and products constant so as to avoid possible distortion of reciprocal velocity plots Mg²⁺ binding constants to the substrates ATP and phosphoribosylpyrophosphate and the product pyrophosphate were measured under assay conditions. Several conformational states of the phosphoribosyltransferase distinguishable by other criteria gave similar substrate kinetic behavior. Product inhibition studies were conducted to elucidate the binding order. Phosphoribosyl-ATP was competitive with respect to ATP and was non-competitive with respect to phosphoribosylpyrophosphate. Pyrophosphate was non-competitive with respect to both substrates. The data are consistent with the ordered Bi-Bi kinetic mechanism with ATP binding first to free enzyme and phosphoribosyl-ATP dissociating last from enzyme-product complexes.     

Nonlinear estimation of the parameters of Monod kinetics that best describe mineralization of several substrate concentrations by dissimilar bacterial densities

The kinetics of mineralization of a wide range of concentrations of benzoate, glucose, and benzylamine by Pseudomonas sp., Salmonella typhimurium, and microorganisms in acclimated sewage was studied. The treatment of initial substrate concentration and population density as independent variables in nonlinear regression analysis permitted the estimation of a single value for each of the parameters of Monod kinetics that best described the mineralization of substrate at each concentration by the pure cultures and the sewage microflora. One value for each of the parameters of Monod kinetics was used for each of the three compounds to produce theoretical curves which lay close to the observed data on mineralization. Statistically significant differences existed in the values of the parameters of Monod kinetics that best described mineralization in cultures differing only in initial substrate concentration and cell density. However, for the compounds tested, the variance left by analyses using one value for each parameter of Monod kinetics was less than double the unexplained variance left by individual analyses of the data from each treatment. Although significant, this increase is small compared with the amount of variance that could be explained using only one value for each parameter of Monod kinetics.     

Nonlinear estimation of the parameters of Monod kinetics that best describe mineralization of several substrate concentrations by dissimilar bacterial densities.

The kinetics of mineralization of a wide range of concentrations of benzoate, glucose, and benzylamine by Pseudomonas sp., Salmonella typhimurium, and microorganisms in acclimated sewage was studied. The treatment of initial substrate concentration and population density as independent variables in nonlinear regression analysis permitted the estimation of a single value for each of the parameters of Monod kinetics that best described the mineralization of substrate at each concentration by the pure cultures and the sewage microflora. One value for each of the parameters of Monod kinetics was used for each of the three compounds to produce theoretical curves which lay close to the observed data on mineralization. Statistically significant differences existed in the values of the parameters of Monod kinetics that best described mineralization in cultures differing only in initial substrate concentration and cell density. However, for the compounds tested, the variance left by analyses using one value for each parameter of Monod kinetics was less than double the unexplained variance left by individual analyses of the data from each treatment. Although significant, this increase is small compared with the amount of variance that could be explained using only one value for each parameter of Monod kinetics.     

Generation of equally sized particle plaques using solid-liquid suspensions

A device is presented for the generation of equally sized plaques of sensitive particles in a 96-well format. The resulting particle plaques can be used for the measurement of adsorption isotherms and uptake kinetics in protein chromatography or for immobilization reactions. The particle plaques are formed from suspensions with a vacuum device that is designed as a reusable sandwich module. The particles are retained by a mesh while the solvent is removed by the vacuum. As most particles used for protein chromatography are sensitive to mechanical stress and dehydration, the vacuum device is gentle enough to allow the use of these particles, thus eliminating the uncertainty of slurry preparation and pipetting. Apparatus characteristics and preparation procedures are described precisely. The physical intactness of the particles after the preparation procedure is proved by microscopic analysis. Data on the uniformity of the obtained resin plaques with respect to the reproducibility of their adsorption performance is given. Finally, adsorption isothermal and kinetic data of BSA on an ordinary HIC system obtained by high-throughput measurements are shown as an application example.     

A new spectrophotometric cuvette holder for low temperature studies; Its application to the study of carbonmonoxyhemoglobin oxidation rate

A new spectrophotometric cuvette holder to be used for subzero temperature is described. The device is easily adaptable to a commercial spectrophotometer and it was checked down to --40 degrees C. Satisfactory mixing of the reactants contained in the cuvette at low temperatures is attained using a special stirrer and suitable solution volumes. The rate of carbonmonoxyhemoglobin oxidation by K3Fe(CN)6 at different subzero temperatures has been studied using this apparatus; the results are in agreement with the extrapolated data at room temperature.     

An MRI-based method to align the compressive loading axis for human cadaveric knees

There is a need to align the mechanical axis of the tibia with the axis of loading for studies involving tibiofemoral compression to interpret results and to ensure repeatability of loading within and among specimens. Therefore, the objectives of this study were (1) to develop a magnetic resonance imaging (MRI)-based alignment method for use with apparatuses applying tibiofemoral joint compression, (2) to demonstrate the usefulness of the method by aligning cadaveric knees in an apparatus that could apply tibiofemoral joint compression, and (3) to quantify the error associated with the alignment method. A four degree-of-freedom adjustable device was constructed to allow determination and alignment of the mechanical axis of the tibia of cadaveric knee joints with the axis of loading of an apparatus applying tibiofemoral joint compression. MRI was used to determine the locations of bony landmarks in three dimensions defining the mechanical axis of the tibia relative to an initial orientation of the four degree-of-freedom device. Adjustment values of the device were then computed and applied to the device to align the mechanical axis of the tibia with the axis of a compressive loading apparatus. To demonstrate the usefulness of the method, four cadaveric knees were aligned in the compressive loading apparatus. The vectors describing the mechanical axis of the tibia and the loading axis of the apparatus before and after adjustment of the four degree-of-freedom device were computed for each cadaveric knee. After adjustment of the four degree-of-freedom device, the mechanical axis of the tibia was collinear with the loading axis of the apparatus for each cadaveric knee. The errors in the adjustment values introduced by inaccuracies in the MR images were quantified using the Monte Carlo technique. The precisions in the translational and rotational adjustments were 1.20 mm and 0.90 deg respectively. The MR-based alignment method will allow consistent interpretation of results obtained during tibiofemoral compressive studies conducted using the apparatus described in this paper by providing a well-defined loading axis. The alignment method can also be adapted for use with other apparatuses applying tibiofemoral compression.     

Transient gene expression in maize, rice, and wheat cells using an airgun apparatus

An airgun apparatus has been constructed for transient gene expression studies of monocots. This device utilizes compressed air from a commercial airgun to propel macroprojectile and DNA-coated tungsten particles. The β-glucuronidase (GUS) reporter gene was used to monitor transient expression in three distinct cell types of maize (Zea mays), rice (Oryza sativa), and wheat (Triticum aestivum). The highest level of GUS activity in cultured maize cells was observed when distance between stopping plate and target cells was adjusted to 4.3 centimeters. Efficiency of transformation was estimated to be 4.4 × 10⁻³. In a partial vacuum of 700 millimeters Hg, velocity of macroprojectile was measured at 520 meters per second with a 6% reduction in velocity at atmospheric pressure. A polyethylene film placed in the breech before firing contributed to a 12% increase in muzzle velocity. A 700 millimeters Hg level of vacuum was necessary for maximum number of transfornants. GUS expression was also detected in wheat leaf base tissue of microdissected shoot apices. High levels of transient gene expression were also observed in hard, compact embryogenic callus of rice. These results show that the airgun apparatus is a convenient, safe, and low-cost device for rapid transient gene expression studies in cereals.     

A telemetry-based device to determine the force-displacement behaviour of materials in high impact loading situations

Meaningful testing of stab resistant body armour requires the use of realistic body tissue simulants. A device for the determination of the force-displacement behaviour of materials in high impact loading situations has been developed for the testing of such simulants. Force measurement is achieved with the use of electrical foil strain gauges applied to a cylindrical load cell. A piezo-resistive accelerometer (+/- 500 g) is used to calculate the displacement of the device through double integration of its signal, with the impact velocity used as a boundary condition. The signals from the strain gauge circuit and the accelerometer are sampled at 2500 Hz. The data are transmitted to a receiver via telemetry using a 418 MHz FM transmitter and from the receiver to a laptop PC via the serial port. Calibration of the device is described and sample results showing forces up to 2500 N and displacements up to 0.04 m are presented.     

An improved conductiometric standpipe technique for measuring interstitial seepage velocities

The measurement of the seepage velocity through river-bed gravels is required in many biological and chemical investigations concerned with chemical fluxes through the gravel interstices. An improved conductiometric technique is described which is based on an earlier electrolytic method. The apparatus is calibrated for a range of gravel types to yield a spatially-averaged seepage velocity rather than a Darcian bulk velocity. Problems of stratification of the electrolyte and the need for temperature monitoring have been eliminated. The apparatus is compact and, incorporating a micro-computer-based data aquisition system, is easy and rapid to use even in adverse field conditions.     

Effects of dissipation and external fields on the dynamics of conformational distortions in DNA

The dynamics of conformational distortions in DNA has been studied in the framework of the simple mathematical model based on the sine-Gordon equation with two additional terms. The first of the terms describes the effects of dissipation, and the second takes the action of external field into account. With the help of the energetic method, an analytical expression for the velocity of local conformational distortion as a function of time has been found, and conditions have been determined under which the influence of dissipation and constant external force are in a balance, providing the distortion to move with a constant velocity along the DNA. The graphs of changes in the velocity of movement of local conformational distortions in different homogeneous polynucleotide chains have been constructed using the model values of the parameters v0 = 189 (m/s), beta(DNA) = 4.25 x 10(-34) (J x s) and F0(DNA) = 3.12 x 10(-22) (J), which determine the initial velocity of the distortion, the coefficient of dissipation, and the value of the external generalized force, respectively. The accordance of the model values used with the experimental values available from the literature is discussed.     

Enzymic product formation curves with the normal or diffusion limited reaction mechanism and in the presence of substrate receptors

1. The enzymic product formation curves for several enzymes have been studied. 2. The product formation kinetics was related to the initial velocity kinetics and to the diffusion rate limited kinetics. 3. The time curves revealed new constants characterizing structural and binding properties of the enzymic systems which are not revealed from initial velocities. 4. The influence of selected inhibitors on the time curves has been studied. 5. The time curves revealed the specific substrate-receptor binding which was not revealed from initial velocities. 6. The product formation kinetics of acid phosphatase, beta-amylase and NADPH2 cytochrome-c reductase in the absence and in the presence of inhibitors, mercuric acetate and o-iodosobenzoate is described. 7. The time curves revealed the binding of cytochrome-c to the specific natural protein receptors. 8. The activation energies of acid phosphatase and beta-amylase were determined from the time curves.     

Dynamic concentration challenges for biosensor characterization

A method and apparatus are described for characterization of the steady state and dynamic response of biosensors. The apparatus produces a steady stream of homogeneously mixed analyte whose concentration can be fixed at discrete values or varied continously. The device is ideally suited for continously operated biosensors, but is also effective for biosensors that operate in discrete sampling modes. The system permits simultaneous testing of several sensors and determination of the accuracy, precision and repeatability of sensor response. The characteristics of this testing apparatus were validated with ferrocyanide and glucose as indicators. As an example of use of the apparatus, concentration ramps were created and used to complement conventional step changes for characterizing an implantable glucose sensor. The ramp rate can be adjusted easily by scaling the apparatus to simulate the rate of concentration change anticipated during actual monitoring situations.