Molecular packing parameters of bipolar lipids.

The bipolar lipid fractions extracted from the thermophilic archaeobacterium Sulfolobus solfataricus have different chemical structures and geometrical shapes. The conditions which lead to the formation of vesicles were investigated in order to study the self-assembly of these molecules. Such conditions are fulfilled when an appropriate mixture of two different molecular species (both bipolar or bipolar and monopolar) is used. According to the theory introduced by Israelachvili and co-workers, lipid self-assembly results from the balance of interaction free energy, entropy and molecular geometry. We have shown that this theory can be extended to bipolar lipids, in spite of their more complex nature, and the experimental results obtained combining 1H-NMR, light scattering and entrapped volume techniques closely match theoretical expectations. To carry out calculations, it was necessary to introduce hypotheses about the disposition of bipolar molecules in the vesicle membrane. These hypotheses have been tested indirectly by measuring the transport properties mediated by carriers or channels, whose transport mechanism can be considered to be a probe of the membrane structure.     

Myocardial blood perfusion and transport modeling using inert-tracer techniques: a review and recent investigations

The inert-gas clearance method for measuring blood perfusion in the heart may be useful in detecting and assessing coronary disease and myocardial infarctions. Estimating perfusion from clearance data requires a model of tracer transport. The tracer transport models in use are the compartmental model, the kinetic model, and more complex models which yield estimates by optimal estimation techniques. The implementation of one such complex model in which tissue need not be assumed homogeneous, and the resulting myocardial perfusion and diffusibility estimates, are discussed. Methods are reviewed which may be used to detect and assess coronary disease by average and regional myocardial-perfusion measurements. Possible explanations for the observed multicompartment myocardial clearance curve are discussed.     

Comparison of pressure chamber and psychrometer estimates of leaf water potential in rice

Summary The need to compare pressure-chamber estimates of leaf water potential with a psychrometric method has been established for several crop species. We investigated this relationship for rice (Oryza sativa L.) as well as the need to protect leaves from water loss during sampling and measuring period in the pressure chamber. Two rice cultivars grown in containers on a clay-loam soil were stressed to varying degrees by withholding water. Fully expanded leaves were sampled for estimation of leaf water potential by the dew point hygrometer and pressure-chamber techniques. The same leaf was used in both methods allowing direct comparison. Additionally, two alternative methods of leaf handling for measurement by the pressure chamber technique were compared. Protection of leaf samples against water loss during excision, transport and handling was found to be more important at higher leaf water potentials (>−1.0 MPa). The two cultivars used appeared to differ in their response to protection of the leaf sample. These results serve to further caution pressure chamber users on extrapolating comparisons between the two measurement methods and between tissue handling techniques even within a crop species.     

lambda-Repressor oligomerization kinetics at high concentrations using fluorescence correlation spectroscopy in zero-mode waveguides

Fluorescence correlation spectroscopy (FCS) has demonstrated its utility for measuring transport properties and kinetics at low fluorophore concentrations. In this article, we demonstrate that simple optical nanostructures, known as zero-mode waveguides, can be used to significantly reduce the FCS observation volume. This, in turn, allows FCS to be applied to solutions with significantly higher fluorophore concentrations. We derive an empirical FCS model accounting for one-dimensional diffusion in a finite tube with a simple exponential observation profile. This technique is used to measure the oligomerization of the bacteriophage lambda repressor protein at micromolar concentrations. The results agree with previous studies utilizing conventional techniques. Additionally, we demonstrate that the zero-mode waveguides can be used to assay biological activity by measuring changes in diffusion constant as a result of ligand binding.     

Introduction of a method for three-dimensional mapping of the charge motion in bacteriorhodopsin

Electric signals associated with the photocycle of bacteriorhodopsin carry valuable information about the proton transport process. Photocurrents measured by different experimental methods are interpreted in terms of intramolecular charge displacements. Permanent electrical asymmetry of the sample is considered to be a prerequisite for the detection of electric signals. The various photoelectric measuring techniques can be distinguished by the way of achievement of this asymmetry. A common feature of the available methods, however, is that the samples are cylindrically symmetric. Consequently, intramembraneous charge displacements can normally be monitored only along the axis of the membrane normal. We developed a novel method that allows also the detection of the in-plane components of the charge displacements. Samples containing oriented purple membrane fragments were used in the experiments, and the rotational symmetry was transiently broken via anisotropic excitation of the bR molecules by linearly polarized light. Kinetics of the normal and in-plane components were measured and interpreted as a result of spatial charge displacements associated with the proton transport process in bacteriorhodopsin.     

Robust numerical solution for the two parameter solute solvent transport model

Prediction of solute and solvent transport in cells is central to developing and testing cryopreservation protocols. As we show here, however, the models used can be difficult to accurately numerically integrate in some key cases, and thus are a challenge to implement when determining the time dependent cell state during cryoprotectant equilibration and cooling. Exact solution techniques exist for overcoming this problem, but their implementation is also challenging: inversion of a nonlinear function is required that negates much of the utility of the approach. This communication describes a simple approach for more robust numerical integration that can be implemented using any numerical differential equation solver, and can facilitate arbitrarily accurate solutions to transport models without the complication of inversion formulae or complicated numerical integration schemes. Further, a simple relevant example of red blood cell equilibration with 40% glycerol is presented with comments on extending the approach to other settings.     

Quantitative Measurement of Cell Membrane Transport: Technology and Applications

The transport of water and cryoprotective chemicals across cell membranes plays an absolutely fundamental role in the outcome of cryopreservation processing. The diversity of cell types as well as the remarkable range of perturbations that cells are subjected to as part of cryopreservation practices generate many interesting research questions. Simply stated, the extreme conditions typical of cryopreservation protocols extend the limits of membrane transport inquiry well beyond that considered in “normal” cell physiology. This paper provides a brief review of methods which have been used for measuring membrane transport properties, especially those methods developed during the past decade which allow us to measure coupled and uncoupled membrane transport properties of water and cryoprotective agents for individual cells in terms of classical Kedem–Katchalsky membrane transport theory. Representative results obtained from these new technologies will be offered to illustrate their utility and relevance to membrane transport issues arising in cryopreservation practice. Engineers have made significant contributions to this area of research primarily in terms of device development and the application of inverse methods to estimate membrane transport properties.     

Pulsed EPR Determination of Water Accessibility to Spin-Labeled Amino Acid Residues in LHCIIb

Membrane proteins reside in a structured environment in which some of their residues are accessible to water, some are in contact with alkyl chains of lipid molecules, and some are buried in the protein. Water accessibility of residues may change during folding or function-related structural dynamics. Several techniques based on the combination of pulsed electron paramagnetic resonance (EPR) with site-directed spin labeling can be used to quantify such water accessibility. Accessibility parameters for different residues in major plant light-harvesting complex IIb are determined by electron spin echo envelope modulation spectroscopy in the presence of deuterated water, deuterium contrast in transversal relaxation rates, analysis of longitudinal relaxation rates, and line shape analysis of electron-spin-echo-detected EPR spectra as well as by the conventional techniques of measuring the maximum hyperfine splitting and progressive saturation in continuous-wave EPR. Systematic comparison of these parameters allows for a more detailed characterization of the environment of the spin-labeled residues. These techniques are applicable independently of protein size and require ∼10-20 nmol of singly spin-labeled protein per sample. For a residue close to the N-terminus, in a domain unresolved in the existing x-ray structures of light-harvesting complex IIb, all methods indicate high water accessibility.     

A new methodological approach for studying axonal transport: cytofluorometric scanning of nerves

A new technique for studying axonal transport has been developed. The technique, which is based on histofluorescence techniques, enables the measurement of several different accumulated substances and parameters within a single nerve in relation to a nerve crush or local cooling. Any substance that can be made to fluoresce can be measured. The tissue is treated according to the formaldehyde-induced fluorescence method of Hillarp and Falck for visualization of monoamines, or according to the indirect immunofluorescence method. For immunofluorescence the nerve is cryostat-sectioned and various sections can be incubated with primary antisera against different antigens. After incubation and mounting the sections are placed in a cytofluorimeter (Leitz MPV II). They are passed under a measuring slit at a steady speed by a motor driven cross-table. The fluorescence intensity passing through the measuring slit is continuously registered by a recording unit with an integrator. This recorder produces a graphical nerve accumulation profile, and the area under the profile, relating to the fluorescence, is expressed in arbitrary units. This article presents data on the accumulation of noradrenaline, dopamine beta-hydroxylase, and tyrosine hydroxylase in crush-operated rat sciatic nerve. The time-course accumulations for noradrenaline (visualized by the Falck and Hillarp method) and dopamine beta-hydroxylase (visualized by immunofluorescence) demonstrated a striking similarity, which is to be expected since the two substances are stored in the same organelle. Tyrosine hydroxylase (visualized by immunofluorescence) showed a slower accumulation with time, but faster than would be expected had the enzyme been 100% soluble. Colchicine but not lumi-colchicine blocked the transport of noradrenaline organelles. With the new scanning technique we have the potential to study accumulation profiles of several different substances within a single nerve. Morphometric data, morphological observations, and photograph documentation of the same nerve section are also available.     

Solubility of retinoids in water

Spectrophotometric and radioactive techniques were used to measure the water solubility of retinaldehyde, retinol (vitamin A), and retinoic acid under physiological conditions. Hydration decreases the molar extinction coefficient of these substances and shifts their absorption peak bathochromically (10 nm for retinal and approximately 1 nm for the rest). We find their solubility to be about 0.1 microM at room temperature, pH 7.3 (with experimental values being 0.11 microM for retinaldehyde, 0.06 microM for retinol, and 0.21 microM for retinoic acid). To prevent oxidative degradation of retinol, which is the most labile retinoid, our argon-saturated buffer solutions contained physiological levels of ascorbate or alpha-tocopherol. To the best of our knowledge, water solubility of these compounds has not yet been previously reported. Although the measured solubilities are relatively low, they are significant and may account for the movement of retinoids through the aqueous phase as observed by others during exchange with binding proteins and during intervesicular transfer in the absence of binding proteins. Diffusion of uncomplexed retinoids through the aqueous phase can be a major pathway for transport over subcellular distances.     

Application of high-performance liquid chromatography-electrospray ionization-mass spectrometry to measure microsomal membrane transport of glucuronides

A primary reason for poor characterization of microsomal transport to date is the limitations of the measurement techniques used. Radiodetection provides sufficient sensitivity, but it can be applied only when labeled analogue is available. In this article, we report the novel application of high-performance liquid chromatography and electrospray tandem mass spectrometry (LC-MS/MS) in "rapid filtration" transport assays. The method was developed using glucuronides, but it is adaptable to any compound that can be measured with LC-MS/MS. Because of the high sensitivity and accuracy of this detection technique, the substrates can be used at their physiological concentration in the experiments. The new methodology does not require radiolabeling, so it remarkably widens the range of possible substrates to investigate and allows simultaneous detection as well as monitoring of substrate stability during the experiments.     

Activity assay of membrane transport proteins

Membrane transport proteins are integral membrane proteins and considered as potential drug targets. Activity assay of transport proteins is essential for developing drugs to target these proteins. Major issues related to activity assessment of transport proteins include availability of transporters, transport activity of transporters, and interactions between ligands and transporters. Researchers need to consider the physiological status of proteins (bound in lipid membranes or purified), availability and specificity of substrates, and the purpose of the activity assay (screening, identifying, or comparing substrates and inhibitors) before choosing appropriate assay strategies and techniques. Transport proteins bound in vesicular membranes can be assayed for transporting substrate across membranes by means of uptake assay or entrance counterflow assay. Alternatively, transport proteins can be assayed for interactions with ligands by using techniques such as isothermal titration calorimetry, nuclear magnetic resonance spectroscopy, or surface plasmon resonance. Other methods and techniques such as fluorometry, scintillation proximity assay, electrophysiologi-cal assay, or stopped-flow assay could also be used for activity assay of transport proteins. In this paper the major strategies and techniques for activity assessment of membrane transport proteins are reviewed.     

Application of the fluctuation theorem to motor proteins: from F<Subscript>1</Subscript>-ATPase to axonal cargo transport by kinesin and dynein

The fluctuation theorem is a representative theorem in non-equilibrium statistical physics actively studied in the 1990s. Relating to entropy production in non-equilibrium states, the theorem has been used to estimate the driving power of motor proteins from fluctuation in their motion. In this review, usage of the fluctuation theorem in experiments on motor proteins is illustrated for biologists, especially those who study mechanobiology, in which force measurement is a central issue. We first introduce the application of the fluctuation theorem in measuring the rotary torque of the rotary motor protein F₁-ATPase. Next, as an extension of this application, a recent trial estimating the force generated during cargo transport in vivo by the microtubule motors kinesin and dynein is introduced. Elucidation of the physical mechanism of such transport is important, especially for neurons, in which deficits in cargo transport are deeply related to neuronal diseases. Finally, perspectives on the fluctuation theorem as a new technique in the field of neuroscience are discussed.     

Measurement of cell proliferation by heavy water labeling

DNA replication occurs almost exclusively during S-phase of the cell cycle and represents a simple biochemical metric of cell division. Previous methods for measuring cell proliferation rates have important limitations. Here, we describe experimental protocols for measuring cell proliferation and death rates based on the incorporation of deuterium ((2)H) from heavy water ((2)H(2)O) into the deoxyribose moiety of purine deoxyribonucleotides in DNA of dividing cells. Label incorporation is measured by gas chromatography/mass spectrometry. Modifications of the basic protocol permit analysis of small cell samples (down to 2,000 cells). The theoretical basis and operational requirements for effective use of these methods to measure proliferation and death rates of cells in vivo are described. These methods are safe for use in humans, have technical and interpretation advantages over alternative techniques and can be used on small numbers of cells. The protocols enable definitive in vivo studies of the fraction or absolute number of newly divided cells and their subsequent survival kinetics in animals and humans.     

A novel method for the observation of membrane transporter dynamics.

A new method is proposed for measuring the dynamic properties of a membrane transporter by means of steady-state fluxes. Any voltage-sensitive transporter will give a flow of substrate in the presence of a steady-state periodic membrane potential. The periodic steady-state flow, averaged over one period, is a flux that can be measured by traditional steady-state techniques, such as the radioactive tracer method. The average flux, solely due to the periodic field, is described by a set of Lorentzian functions that depend on the applied periodic field amplitude and frequency. The normal mode amplitudes and frequencies of these Lorentzians are model-independent parameters of the transport mechanism. Measurement of the average flux as a function of the applied periodic frequency permits determination of system relaxation times as the reciprocals of the midpoints of the Lorentzian curves, which in turn can be used to estimate individual rate constants of specific models. It was found by simulation of a six-state model of the electrogenic Na+/glucose cotransporter, using published estimates of the model rate constants, that the periodic field effects can be large and rich with measurable details that can be used to study the mechanism thoroughly. The new method serves in this case to complement and expand on the information obtainable by means of the voltage clamp method. It was also found by means of simulations of a nonelectrogenic six-state cotransporter model that experimentally measurable effects are expected and that results can be used to distinguished among alternative kinetic models as well as to estimate individual rate constants.(ABSTRACT TRUNCATED AT 250 WORDS)     

A solid-supported membrane electrophysiology assay for efficient characterization of ion-coupled transport

Transport stoichiometry determination can provide great insight into the mechanism and function of ion-coupled transporters. Traditional reversal potential assays are a reliable, general method for determining the transport stoichiometry of ion-coupled transporters, but the time and material costs of this technique hinder investigations of transporter behavior under multiple experimental conditions. Solid-supported membrane electrophysiology (SSME) allows multiple recordings of liposomal or membrane samples adsorbed onto a sensor and is sensitive enough to detect transport currents from moderate-flux transporters that are inaccessible to traditional electrophysiology techniques. Here, we use SSME to develop a new method for measuring transport stoichiometry with greatly improved throughput. Using this technique, we were able to verify the recent report of a fixed 2:1 stoichiometry for the proton:guanidinium antiporter Gdx, reproduce the 1H⁺:2Cl⁻ antiport stoichiometry of CLC-ec1, and confirm loose proton:nitrate coupling for CLC-ec1. Furthermore, we were able to demonstrate quantitative exchange of internal contents of liposomes adsorbed onto SSME sensors to allow multiple experimental conditions to be tested on a single sample. Our SSME method provides a fast, easy, general method for measuring transport stoichiometry, which will facilitate future mechanistic and functional studies of ion-coupled transporters.     

Molecular interaction analysis in ligand design using mass transport,kinetic and thermodynamic methods

Ligand design in biotechnology is underpinned by the control of molecular affinity. Hence, measuring binding interactions is a key component in designing ligands for such uses as therapeutics, diagnostics, biomaterials and separation science. Mass transport, kinetic and thermodynamic methods have been used for macromolecular interaction analysis but also have potential applicability as direct methods for measuring small molecular interactions. They can enhance the ligand design process by providing the ability to choose ligands based on both their kinetic and thermodynamic binding properties.     

Zymographic techniques for the analysis of matrix metalloproteinases and their inhibitors

The balance between matrix metalloproteinases (MMPs) and their inhibitors, the tissue inhibitors of metalloproteinases (TIMPs), is largely responsible for the remodeling of tissues. Deregulation of this balance is a characteristic of extensive tissue degradation in certain degenerative diseases. To analyze the role of MMPs and TIMPs in tissue remodeling under normal and pathological conditions, it is important to have reliable detection methods. This review will focus on zymographical techniques for the analysis of MMPs and TIMPs. MMPs can be analyzed with several zymographical techniques, but substrate zymography is the most commonly used. This technique identifies MMPs by the degradation of their preferential substrate and by their molecular weight. Several substrates that can be used for zymography are described. Reverse zymography, which detects TIMPs by their ability to inhibit MMPs, is also discussed. Finally, in situ zymography is described, which is used to localize MMPs in tissue sections. Common problems encountered during sample preparation, zymography itself and the data analysis are discussed. Hints are given to improve the sensitivity and accuracy of zymographical methods. In conclusion, zymography is a valuable tool for research purposes and for the development of new diagnostic techniques and therapies for pathological conditions such as rheumatoid and osteoarthritis, and tumor progression.     

Detection of genetically altered copper levels in Drosophila tissues by synchrotron x-ray fluorescence microscopy

Tissue-specific manipulation of known copper transport genes in Drosophila tissues results in phenotypes that are presumably due to an alteration in copper levels in the targeted cells. However direct confirmation of this has to date been technically challenging. Measures of cellular copper content such as expression levels of copper-responsive genes or cuproenzyme activity levels, while useful, are indirect. First-generation copper-sensitive fluorophores show promise but currently lack the sensitivity required to detect subtle changes in copper levels. Moreover such techniques do not provide information regarding other relevant biometals such as zinc or iron. Traditional techniques for measuring elemental composition such as inductively coupled plasma mass spectroscopy are not sensitive enough for use with the small tissue amounts available in Drosophila research. Here we present synchrotron x-ray fluorescence microscopy analysis of two different Drosophila tissues, the larval wing imaginal disc, and sectioned adult fly heads and show that this technique can be used to detect changes in tissue copper levels caused by targeted manipulation of known copper homeostasis genes.