Measurements of the Plasma Parameters in a Mirror Trap by Means of Laser-Induced Fluorescence

Results of measurements of the absolute density of ArII ions in a mirror trap with a toroidal divertor are presented. The ion density was measured by the method of laser-induced fluorescence with the use of ArII metastable states. A technique is proposed to estimate the plasma electron temperature from the ratio of the fluorescence signals obtained by comparing the intensities of different optical transitions of ArII.     

Recovery of the Two-Dimensional Ion Distribution Function in a Magnetic Mirror from Measurements of Collective Thomson Scattering Spectra

Plasma Physics Reports - A method is proposed for tomography of the distribution function of energetic ions that are adiabatically trapped in an open magnetic trap, according to the diagnostic data...     

Automated System for Single Molecule Fluorescence Measurements of Surface-immobilized Biomolecules

Fluorescence Resonance Energy Transfer (FRET) microscopy has been widely used to study the structure and dynamics of molecules of biological interest, such as nucleic acids and proteins. Single molecule FRET (sm-FRET) measurements on immobilized molecules permit long observations of the system -effectively until both dyes photobleach- resulting in time-traces that report on biomolecular dynamics with a broad range of timescales from milliseconds to minutes. To facilitate the acquisition of large number of traces for statistical analyses, the process must be automated and the sample environment should be tightly controlled over the entire measurement time (~12 hours). This is accomplished using an automated scanning confocal microscope that allows the interrogation of thousands of single molecules overnight, and a microfluidic cell that permits the controlled exchange of buffer, with restricted oxygen content and maintains a constant temperature throughout the entire measuring period. Here we show how to assemble the microfluidic device and how to activate its surface for DNA immobilization. Then we explain how to prepare a buffer to maximize the photostability and lifetime of the fluorophores. Finally, we show the steps involved in preparing the setup for the automated acquisition of time-resolved single molecule FRET traces of DNA molecules.     

Remote Probing of Plant Photosynthetic Apparatus by Measuring Laser-Induced Fluorescence

Laser-induced fluorescence of birch, pine, and aspen trees was studied. The fluorescence of birch leaves, excited with a Xe–Cl laser at a wavelength of 308 nm, was measured under laboratory conditions. A persistent directly proportional dependence was found between the measured fluorescence signals and the chlorophyll content. An apparatus for measuring laser-induced fluorescence under field conditions was designed. Deciduous trees were found to have a wider range of fluorescence variability when compared to conifers, with the fluorescence intensity increasing in the leaves of deciduous trees before the autumn fall of leaves, during leaf yellowing. It is concluded that the method of lidar probing can be used for identifying tree species and assessing the condition of leaf and needle canopies.     

Overcoming the Problem of Non-Ideal Liquid Ion Exchanger Selectivity in Microelectrode Ion Flux Measurements

Ion-selective microelectrodes are a powerful tool in studies on various aspects of cell membrane biology in both animal and plant tissues. Further application of this technique is, however, limited to a large extent by the problem of non-ideal selectivity of the liquid ion exchanger used in the preparation of microelectrodes for ion flux measurements. Because of this problem, which is persistent in many commercial liquid ion exchangers, the microelectrode does not discriminate between the ion of interest and other interfering ions (for example, Mg²⁺ and Ca²⁺; Na⁺ and K⁺), thereby leading to inaccurate concentration readings and, consequently, inaccurate flux calculations. In this work we show that the existing analytical procedure to overcome this problem, using the inverted Nicolsky-Eisenman equation, is inadequate, and suggest an alternative analytical procedure that can be applied directly to the data obtained with commercially available liquid ion exchangers. We show that this alternative procedure allows accurate measurement of ionic concentrations with non-ideal ion-selective microelectrodes in the presence of interfering ions, and illustrate the method by direct experiment using Ca²⁺ and Mg²⁺ as a “case study”. Several more examples are given, further illustrating practical applications of the method for study of plant responses to salinity, osmotic and reactive oxygen species stresses.     

Kernel Estimates for One- and Two-Dimensional Ion Channel Dwell-Time Densities

In this paper, we compare nonparametric kernel estimates with smoothed histograms as methods for displaying logarithmically transformed dwell-time distributions. Kernel density plots provide a simpler means for producing estimates of the probability density function (pdf) and they have the advantage of being smoothed in a well-specified, carefully controlled manner. Smoothing is essential for multidimensional plots because, with realistic amounts of data, the number of counts per bin is small. Examples are presented for a 2-dimensional pdf and its associated dependency-difference plot that display the correlations between successive dwell times.     

Measurements of Photosynthetic Sulfide Oxidation by Chlorobium Using a Sulfide Ion Selective Electrode

A simple technique is described for using a sulfide sensitiveelectrode to measure the photooxidation of H₂S by a green sulfurbacterium, Chlorobium limicola forma thiosulfatophilum. Sulfidephotooxidation occurred only in the presence of bicarbonateat concentrations greater than 0.1 mM. This implies that therate-limiting carboxylating enzyme for CO₂ fixation in Chlorobiumhas a relatively low affinity for CO₂ compared to ribulose-1,5-biphosphatecarboxylase. Carbonyl cyanide-p-trifluoromethoxyphenyl-hydrazone(FCCP), an uncoupler of photophosphorylation, delays sulfideoxidation for about 15 sec after the onset of illumination at2 µM and is completely inhibitory at 10 µM. Theseeffects can be explained by the ATP requirement for CO₂ fixation.When the photooxidation of H₂S was prevented by 10 µMFCCP, a photoevolution of H₂S was observed. (Received December 24, 1981; Accepted September 10, 1982)     

Impact of Emission Anisotropy on Fluorescence Spectroscopy and FRET Distance Measurements

The objective of this report is to provide a practical and improved method for estimating Förster resonance energy transfer distance measurement error due to unknown angles in the dipole orientation factor based on emission anisotropy measurements. We improve on the method of Dale et al. (1979), which has minor mistakes and is frequently interpreted in overly optimistic ways in the literature. To facilitate proper fluorescence intensity measurements, we also evaluated instrument parameters that could impact the measurement. The apparent fluorescence intensity of isotropic samples depends on the sample emission anisotropy, fluorometer geometry, and optical apertures. We separate parameters of the sample, and those of the cylindrically symmetric illumination source and detector in the equations describing results of unpolarized and polarized fluorescence intensity measurements. This approach greatly simplifies calculations compared with the more universal method of Axelrod (1989). We provide a full computational method for calculating the Förster resonance energy transfer distance error and present a graph describing distance error in the simplest case.     

Temperature Effects on Pea Plants Probed by Simultaneous Measurements of the Kinetics of Prompt Fluorescence,Delayed Fluorescence and Modulated 820 nm Reflection

Simultaneous in vivo measurements of prompt fluorescence (PF), delayed fluorescence (DF) and 820-nm reflection (MR) were made to probe response of pea leaves to 40 s incubation at high temperatures (25–50°C). We interpret our observation to suggest that heat treatment provokes an inhibition of electron donation by the oxygen evolving complex. DF, in a time range from several microseconds to milliseconds, has been thought to reflect recombination, in the dark, between the reduced primary electron acceptor Q_A^– and the oxidized donor (P680⁺) of photosystem II (PSII). The lower electron transport rate through PSII after 45 and 50°C incubation also changed DF induction. We observed a decrease in the amplitude of the DF curve and a change in its shape and in its decay. Acceleration of P700⁺ and PC⁺ re-reduction was induced by 45°C treatment but after 50°C its reduction was slower, indicating inhibition of photosystem I. We suggest that simultaneous PF, MR and DF might provide useful information on assessing the degree of plant tolerance to different environmental stresses.     

Effect of Microvilli on Lateral Diffusion Measurements Made by the Fluorescence Photobleaching Recovery Technique

To consider the effect of surface microvilli on measurements of lateral diffusion by fluorescence photobleaching recovery, we have measured the diffusion of the lipid probe 3,3′-dihexadecyl indocarbocyanine iodide on the villated main body and unvillated budding polar body of unfertilized mouse eggs. On the main body we found D = (6.41 ± 0.62) × 10^-9 cm²/s with (77.0 ± 2.1)% recovery, and on the budding polar body we found D = (7.05 ± 0.75) × 10^-9 cm²/s with (84.7 ± 1.3)% recovery. We thus find only slight differences in diffusion in the two regions.     

Partitioning of the Leaf CO2 Exchange into Components Using CO2 Exchange and Fluorescence Measurements

Photorespiration was calculated from chlorophyll fluorescence and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) kinetics and compared with CO2 evolution rate in the light, measured by three gas-exchange methods in mature sunflower (Helianthus annuus L.) leaves. The gas-exchange methods were (a) postillumination CO2 burst at unchanged CO2 concentration, (b) postillumination CO2 burst with simultaneous transfer into CO2-free air, and (c) extrapolation of the CO2 uptake to zero CO2 concentration at Rubisco active sites. The steady-state CO2 compensation point was proportional to O2 concentration, revealing the Rubisco specificity coefficient (Ksp) of 86. Electron transport rate (ETR) was calculated from fluorescence, and photorespiration rate was calculated from ETR using CO2 and O2 concentrations, Ksp, and diffusion resistances. The values of the best-fit mesophyll diffusion resistance for CO2 ranged between 0.3 and 0.8 s cm-1. Comparison of the gas-exchange and fluorescence data showed that only ribulose-1,5-bisphosphate (RuBP) carboxylation and photorespiratory CO2 evolution were present at limiting CO2 concentrations. Carboxylation of a substrate other than RuBP, in addition to RuBP carboxylation, was detected at high CO2 concentrations. A simultaneous decarboxylation process not related to RuBP oxygenation was also detected at high CO2 concentrations in the light. We propose that these processes reflect carboxylation of phosphoenolpyruvate, formed from phosphoglyceric acid and the subsequent decarboxylation of malate.     

Assessment of Photosynthetic Performance of Prochloron in Lissoclinum patella in hospite by Chlorophyll Fluorescence Measurements

Two new PAM fluorometers (pulse amplitude modulated) were usedin an investigation of photosynthetic performance of Prochloronresident as a symbiont in the ascidian Lissoclinum patella,growing in a coral reef of Heron Island on the Great BarrierReef. With a new DIVING-PAM in situ measurements of effectivePSII quantum yield (     

The Early Stages of Photosystem II Assembly Monitored by Measurements of Fluorescence Lifetime, Fluorescence Induction and Isoelectric Focusing of Chlorophyll-Proteins in Barley Etiochloroplasts

The relationship between functional and structural aspects ofPSII formation during greening of etiolated barley leaves hasbeen investigated using fluorescence lifetime measurements,fluorescence kinetics analysis and analysis of chlorophyll-proteincomplexes by IEF-PAGE. Two phases of different character couldbe distinguished in the course of the greening process in dark-grownplants. An early phase covering the first 3–4 h afterthe onset of illumination and a late phase covering the subsequentgreening. During the first phase the formation of PSII reactioncenters and their minor antenna components was observed as manifestedby the IEF-PAGE polypeptide pattern. This was accompanied byshortening of the slow and middle components of the fluorescencelifetime, as well as by the rapid drop in the amplitude of theslow component. A room temperature emission band at 676 nm wasassociated with uncoupled chlorophyll and with the slow fluorescencelifetime component during the first hours of greening. Duringthe late greening phase peripheral light-harvesting complexesof PSII were formed concomitantly to an increase in lifetimeand amplitude of the fast component and to a further decreasein the lifetime of the middle component. The gradual increasein PSII complexity during both phases of greening was also manifestedby changes in proportion and kinetic properties of PSII     

Folding Study of Venus Reveals a Strong Ion Dependence of Its Yellow Fluorescence under Mildly Acidic Conditions

Venus is a yellow fluorescent protein that has been developed for its fast chromophore maturation rate and bright yellow fluorescence that is relatively insensitive to changes in pH and ion concentrations. Here, we present a detailed study of the stability and folding of Venus in the pH range from 6.0 to 8.0 using chemical denaturants and a variety of spectroscopic probes. By following hydrogen-deuterium exchange of ¹⁵N-labeled Venus using NMR spectroscopy over 13 months, residue-specific free energies of unfolding of some highly protected amide groups have been determined. Exchange rates of less than one per year are observed for some amide groups. A super-stable core is identified for Venus and compared with that previously reported for green fluorescent protein. These results are discussed in terms of the stability and folding of fluorescent proteins. Under mildly acidic conditions, we show that Venus undergoes a drastic decrease in yellow fluorescence at relatively low concentrations of guanidinium chloride. A detailed study of this effect establishes that it is due to pH-dependent, nonspecific interactions of ions with the protein. In contrast to previous studies on enhanced green fluorescence protein variant S65T/T203Y, which showed a specific halide ion-binding site, NMR chemical shift mapping shows no evidence for specific ion binding. Instead, chemical shift perturbations are observed for many residues primarily located in both lids of the β-barrel structure, which suggests that small scale structural rearrangements occur on increasing ionic strength under mildly acidic conditions and that these are propagated to the chromophore resulting in fluorescence quenching.     

Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, II: Fluorescence and Vibrational Spectroscopy Using a Cyanophenylalanine Probe

We demonstrate that cyano-phenylalanine (Phe_CN) can be utilized to probe the binding of the inhalational anesthetic halothane to an anesthetic-binding, model ion channel protein hbAP-Phe_CN. The Trp to Phe_CN mutation alters neither the α-helical conformation nor the 4-helix bundle structure. The halothane binding properties of this Phe_CN mutant hbAP-Phe_CN, based on fluorescence quenching, are consistent with those of the prototype, hbAP1. The dependence of fluorescence lifetime as a function of halothane concentration implies that the diffusion of halothane in the nonpolar core of the protein bundle is one-dimensional. As a consequence, at low halothane concentrations, the quenching of the fluorescence is dynamic, whereas at high concentrations the quenching becomes static. The 4-helix bundle structure present in aqueous detergent solution and at the air-water interface, is preserved in multilayer films of hbAP-Phe_CN, enabling vibrational spectroscopy of both the protein and its nitrile label (-CN). The nitrile groups' stretching vibration band shifts to higher frequency in the presence of halothane, and this blue-shift is largely reversible. Due to the complexity of this amphiphilic 4-helix bundle model membrane protein, where four Phe_CN probes are present adjacent to the designed cavity forming the binding site within each bundle, all contributing to the infrared absorption, molecular dynamics (MD) simulation is required to interpret the infrared results. The MD simulations indicate that the blue-shift of -CN stretching vibration induced by halothane arises from an indirect effect, namely an induced change in the electrostatic protein environment averaged over the four probe oscillators, rather than a direct interaction with the oscillators. hbAP-Phe_CN therefore provides a successful template for extending these investigations of the interactions of halothane with the model membrane protein via vibrational spectroscopy, using cyano-alanine residues to form the anesthetic binding cavity.     

Ion Channel Expression in the Developing Enteric Nervous System

The enteric nervous system arises from neural crest-derived cells (ENCCs) that migrate caudally along the embryonic gut. The expression of ion channels by ENCCs in embryonic mice was investigated using a PCR-based array, RT-PCR and immunohistochemistry. Many ion channels, including chloride, calcium, potassium and sodium channels were already expressed by ENCCs at E11.5. There was an increase in the expression of numerous ion channel genes between E11.5 and E14.5, which coincides with ENCC migration and the first extension of neurites by enteric neurons. Previous studies have shown that a variety of ion channels regulates neurite extension and migration of many cell types. Pharmacological inhibition of a range of chloride or calcium channels had no effect on ENCC migration in cultured explants or neuritogenesis in vitro. The non-selective potassium channel inhibitors, TEA and 4-AP, retarded ENCC migration and neuritogenesis, but only at concentrations that also resulted in cell death. In summary, a large range of ion channels is expressed while ENCCs are colonizing the gut, but we found no evidence that ENCC migration or neuritogenesis requires chloride, calcium or potassium channel activity. Many of the ion channels are likely to be involved in the development of electrical excitability of enteric neurons.