Theory of light quenching: effects of fluorescence polarization, intensity, and anisotropy decays.

Experimental studies have recently demonstrated that fluorescence emission can be quenched by laser light pulses from modern high repetition rate lasers, a phenomenon we call "light quenching." We now describe the theory of light quenching and some of its effects on the steady-state and time-resolved intensity and anisotropy decays of fluorophores. Light quenching can decrease or increase the steady-state or time-zero anisotropy. Remarkably, the light quenching can break the usual z axis symmetry of the excited-state population, and the emission polarization can range from -1 to +1 under selected conditions. The measured anisotropy (or polarization) depends upon whether the observation axis is parallel or perpendicular to the propagation direction of the light quenching beam. The effects of light quenching are different for a single pulse, which results in both excitation and quenching, as compared with a time-delayed quenching pulse. Time-delayed light quenching pulses can result in step-like changes in the time-dependent intensity or anisotropy and are predicted to cause oscillations in the frequency-domain intensity and anisotropy decays. The increasing availability of pulsed laser sources offers the opportunity for a new class of two-pulse or multiple-pulse experiments where the sample is prepared by an excitation pulse, the excited state population is modified by the quenching pulse(s), followed by time- or frequency-domain measurements of the resulting emission.     

Measurement of calcium channel inactivation is dependent upon the test pulse potential.

We have developed two methods to measure Ca2+ channel inactivation in Lymnaea neurons-one method, based upon the conventional double-pulse protocol, uses currents during a moderately large depolarizing pulse, and the other uses tail currents after a very strong activating pulse. Both methods avoid contamination by proton currents and are unaffected by rundown of Ca2+ current. The magnitude of inactivation measured differs for the two methods; this difference arises because the measurement of inactivation is inherently dependent upon the test pulse voltage used to monitor the Ca2+ channel conductance. We discuss two models that can generate such test pulse dependence of inactivation measurements-a two-channel model and a two-open-state model. The first model accounts for this by assuming the existence of two types of Ca2+ channels, different proportions of which are activated by the different test pulses. The second model assumes only one Ca2+ channel type, with two closed and open states; in this model, the test pulse dependence is due to the differential activation of channels in the two closed states by the test pulses. Test pulse dependence of inactivation measurements of Ca2+ channels may be a general phenomenon that has been overlooked in previous studies.     

Localization of calcium during somatic embryogenesis of carrot (Daucus carota L.)

Summary The distribution of free cytosolic Ca²⁺ was studied during somatic embryogenesis of carrot using confocal scanning laser microscopy with fluo-3 as a fluorescent Ca²⁺ indicator. Chlorotetracycline fluorescence, antimonate precipitation and proton induced X-ray emission analysis were used as additional methods to confirm the results obtained with fluo-3. The process of embryogenesis was found to coincide with a rise in the level of free cytosolic Ca²⁺. The level of Ca²⁺ was low in proembryogenic masses and relatively high in later stages of embryogenesis. The highest signal was found in the protoderm of embryos from the late globular to the torpedo-shaped stage. A gradient in fluorescence intensity was often observed along the longitudinal axis of the embryos. The most conspicuous intracellular signal was found in the nucleus. Other organelles did not take up the dye and were always without fluorescence. The changes in [Ca²⁺]_c are discussed in relation to physiological processes which are known to be important during somatic embryogenesis.This article is dedicated to the memory of the late Dr. Hans-Dieter Reiss.     

Asparagine of z8 Insert Is Critical for the Affinity,Conformation, and Acetylcholine Receptor-clustering Activity of Neural Agrin

Agrin isoforms with different bioactivities are synthesized by the nerve and the muscle. Neural agrin containing an 8-amino acid insert (z8) introduced by alternative splicing is the active form that induces synaptic differentiation at the neuromuscular junction. In addition to alternative splicing, extracellular calcium is also required for the activity of neural agrin. To understand better how the activity of agrin is regulated by alternative splicing, we have applied alanine substitution mutagenesis to the z8 insert and the calcium binding site in the minimally functional AgG3z8 fragment. Single alanine substitutions in the 4th through the 7th amino acid of the z8 splice insert significantly reduced the function of agrin, in terms of acetylcholine receptor clustering activity and the affinity for binding to the muscle surface. Mutation of the asparagine at the 4th position drastically reduces bioactivity such that it is equivalent to that of muscle form AgG3z0. These reduced activity mutants also show reduced magnitudes of the calcium-induced CD spectrum change from that observed in AgG3z8 fragments, indicating that cross-talk between calcium and the z8 insert is critical for the normal activity of agrin. However, removal of Ca²⁺ binding via mutation of both aspartic acids in the calcium binding site did not totally eliminate the activity of AgG3z8. These results suggest a model wherein the z8 insert is a Ca²⁺-responsive allosteric element that is essential in forming an active conformation in neuronal agrin.     

Metabolomic analysis using optimized NMR and statistical methods

NMR-based metabolomics requires robust automated methodologies, and the accuracy of NMR-based metabolomics data is greatly influenced by the reproducibility of data acquisition and processing methods. Effective water resonance signal suppression and reproducible spectral phasing and baseline traces across series of related samples are crucial for statistical analysis. We assess robustness, repeatability, sensitivity, selectivity, and practicality of commonly used solvent peak suppression methods in the NMR analysis of biofluids with respect to the automated processing of the NMR spectra and the impact of pulse sequence and data processing methods on the sensitivity of pattern recognition and statistical analysis of the metabolite profiles. We introduce two modifications to the excitation sculpting pulse sequence whereby the excitation solvent suppression pulse cascade is preceded by low-power water resonance presaturation pulses during the relaxation delay. Our analysis indicates that combining water presaturation with excitation sculpting water suppression delivers the most reproducible and information-rich NMR spectra of biofluids.     

Improved residual water suppression: WET180

Water suppression in biological NMR is frequently made inefficient by the presence of faraway water that is located near the edges of the RF coil and experiences significantly reduced RF field. WET180 (WET with 180 degrees pulse-toggling) is proposed to cancel the faraway water contribution to the residual solvent signal. The pulse sequence incorporates a modification of the last WET selective pulse to accommodate insertion of a toggled 180 degrees inversion pulse so that the original WET selective pulse angles are effectively preserved. Compared with existing WET methods, WET180 has the advantages of easy implementation, improved residual water suppression, clean spectral phase properties, and good signal intensity retention. WET180 is expected to be most useful in observing resonances close to water in samples containing biological molecules. In addition, the principle of WET180 can be applied in multidimensional experiments to improve residual water suppression and reduce artifacts around water.     

Determination of the number of water molecules in the proton pathway of bacteriorhodopsin using neutron diffraction data

It has been shown that water molecules participate in the proton pathway of bacteriorhodopsin. Large efforts have been made to determine with various biophysical methods the number of water molecules involved. Neutron diffraction H2O/D2O exchange experiments have been often used to reveal the position of water even with low-resolution diffraction data. With this technique, care must be taken with the limitations of the difference Fourier method which are commonly applied to analyze the data. In this paper we compare the results of the difference Fourier method applied to measured diffraction data (not presented here) and models with those from alternative methods introduced here: (1) a computer model calculation procedure to determine a label's scattering length density based on a comparison of intensity differences derived from models and intensity differences from our measurements; (2) a method based on the Parseval formula. Both alternative methods have been evaluated and tested using results of neutron diffraction experiments on purple membranes (Hauss et al. 1994). Our findings indicate that the difference Fourier method applied to low-resolution diffraction data can successfully determine the position of localized water molecules but underestimates their integrated scattering length density in the presence of labels in other positions. Furthermore, we present the results of neutron diffraction experiments on purple membranes performed to determine the number of water molecules in the projected area of the Schiff base at 86%, 75% and 57% relative humidity (r.h.). We found 19 +/- 2 exchangeable protons at 75% r.h., which means at least 8-9 water molecules are indispensable for normal pump function.     

Potential bias in NMR relaxation data introduced by peak intensity analysis and curve fitting methods

We present an evaluation of the accuracy and precision of relaxation rates calculated using a variety of methods, applied to data sets obtained for several very different protein systems. We show that common methods of data evaluation, such as the determination of peak heights and peak volumes, may be subject to bias, giving incorrect values for quantities such as R₁ and R₂. For example, one common method of peak-height determination, using a search routine to obtain the peak-height maximum in successive spectra, may be a source of significant systematic error in the relaxation rate. The alternative use of peak volumes or of a fixed coordinate position for the peak height in successive spectra gives more accurate results, particularly in cases where the signal/noise is low, but these methods have inherent problems of their own. For example, volumes are difficult to quantitate for overlapped peaks. We show that with any method of sampling the peak intensity, the choice of a 2- or 3-parameter equation to fit the exponential relaxation decay curves can dramatically affect both the accuracy and precision of the calculated relaxation rates. In general, a 2-parameter fit of relaxation decay curves is preferable. However, for very low intensity peaks a 3 parameter fit may be more appropriate.     

Mechano-Regulation of Alternative Splicing

Alternative splicing contributes to the complexity of proteome by producing multiple mRNAs from a single gene. Affymetrix exon arrays and experiments in vivo or in vitro demonstrated that alternative splicing was regulated by mechanical stress. Expression of mechano-growth factor (MGF) which is the splicing isoform of insulin-like growth factor 1(IGF-1) and vascular endothelial growth factor (VEGF) splicing variants such as VEGF₁₂₁, VEGF_165, VEGF₂₀₆, VEGF₁₈₉, VEGF₁₆₅ and VEGF₁₄₅ are regulated by mechanical stress. However, the mechanism of this process is not yet clear. Increasing evidences showed that the possible mechanism is related to Ca²⁺ signal pathway and phosphorylation signal pathway. This review proposes possible mechanisms of mechanical splicing regulation. This will contribute to the biomechanical study of alternative splicing.     

Galactosyl transferase: the role of manganese ions in the mechanism.

Double reciprocal plots for galactosyl transferase with UDP-galactose varying at several fixed Mn²⁺ concentrations are a series of straight lines. Different laboratories disagree as to whether the intercepts on the $\text{1}\text{v}$ axis are independent of Mn²⁺ or not. PbCl₂ added in a fixed proportion is shown theoretically to be incapable of introducing such a dependence on total metal ion concentration. A mechanism derived from extensive kinetic studies is presented, with alternative pathways for free UDP-galactose and the Mn²⁺ complex as substrates, following obligatory Mn²⁺ addition, and the conflicting results from different laboratories are explained on the basis of a different flux through the alternative pathways under different conditions.     

Correlation of nuclear acceptor sites for oestrogen receptors with gene transcription in vitro

1. Membrane particles prepared from ultrasonically-disrupted, aerobically-grown Escherichia coli were centrifuged on to a plastic film that was supported perpendicular to the centrifugal field to yield oriented membrane multilayers. In such preparations, there is a high degree of orientation of the planes of the membranes such that they lie parallel to each other and to the supporting film. 2. When dithionite- or succinate-reduced multilayers are rotated in the magnetic field of an e.p.r. spectrometer, about an axis lying in the membrane plane, angular-dependent signals from an iron-sulphur cluster at g(x)=1.92, g(y)=1.93 and g(z)=2.02 are seen. The g=1.93 signal has maximal amplitude when the plane of the multilayer is perpendicular to the magnetic field. Conversely, the g=2.02 signal is maximal when the plane of the multilayer is parallel with the magnetic field. 3. Computer simulations of the experimental data show that the cluster lies in the cytoplasmic membrane with the g(y) axis perpendicular to the membrane plane and with the g(x) and g(z) axes lying in the membrane plane. 4. In partially-oxidized multilayers, a signal resembling the mitochondrial high-potential iron-sulphur protein (Hipip) is seen whose g(z)=2.02 axis may be deduced as lying perpendicular to the membrane plane. 5. Appropriate choice of sample temperature and receiver gain reveals two further signals in partially-reduced multilayers: a g=2.09 signal arises from a cluster with its g(z) axis in the membrane plane, whereas a g=2.04 signal is from a cluster with the g(z) axis lying along the membrane normal. 6. Membrane particles from a glucose-grown, haem-deficient mutant contain dramatically-lowered levels of cytochromes and exhibit, in addition to the iron-sulphur clusters seen in the parental strain, a major signal at g=1.90. 7. Only the latter may be demonstrated to be oriented in multilayer preparations from the mutant. 8. Comparisons are drawn between the orientations of the iron-sulphur proteins in the cytoplasmic membrane of E. coli and those in mitochondrial membranes. The effects of diminished cytochrome content on the properties of the iron-sulphur proteins are discussed.     

Precipitation pulse use by an invasive woody legume: the role of soil texture and pulse size

Plant metabolic activity in arid and semi-arid environments is largely tied to episodic precipitation events or “pulses”. The ability of plants to take up and utilize rain pulses during the growing season in these water-limited ecosystems is determined in part by pulse timing, intensity and amount, and by hydrological properties of the soil that translate precipitation into plant-available soil moisture. We assessed the sensitivity of an invasive woody plant, velvet mesquite (Prosopis velutina Woot.), to large (35 mm) and small (10 mm) isotopically labeled irrigation pulses on two contrasting soil textures (sandy-loam vs. loamy-clay) in semi-desert grassland in southeastern Arizona, USA. Predawn leaf water potential (Ψ_pd), the isotopic abundance of deuterium in stem water (δD), the abundance of ¹³C in soluble leaf sugar (δ¹³C), and percent volumetric soil water content (θ_v) were measured prior to irrigation and repeatedly for 2 weeks following irrigation. Plant water potential and the percent of pulse water present in the stem xylem indicated that although mesquite trees on both coarse- and fine-textured soils quickly responded to the large irrigation pulse, the magnitude and duration of this response substantially differed between soil textures. After reaching a maximum 4 days after the irrigation, the fraction of pulse water in stem xylem decreased more rapidly on the loamy-clay soil than the sandy-loam soil. Similarly, on both soil textures mesquite significantly responded to the 10-mm pulse. However, the magnitude of this response was substantially greater for mesquite on the sandy-loam soil compared to loamy-clay soil. The relationship between Ψ_pd and δ¹³C of leaf-soluble carbohydrates over the pulse period did not differ between plants at the two sites, indicating that differences in photosynthetic response of mesquite trees to the moisture pulses was a function of soil water availability within the rooting zone rather than differences in plant biochemical or physiological constraints. Patterns of resource acquisition by mesquite during the dynamic wetting–drying cycle following rainfall pulses is controlled by a complex interaction between pulse size and soil hydraulic properties. A better understanding of how this interaction affects plant water availability and photosynthetic response is needed to predict how grassland structure and function will respond to climate change.     

The combination effects of phenolic compounds and fluconazole on the formation of ergosterol in Candida albicans determined by high-performance liquid chromatography/tandem mass spectrometry

A liquid chromatography/tandem mass spectrometry (LC/MS) with atmospheric pressure chemical ionization (APCI) for the quantification of ergosterol, lanosterol, and squalene was developed to evaluate the combination effects of phenolic compounds with fluconazole on ergosterol biosynthesis in Candida albicans. The three analytes were separated by a column of C18 and were quantified without interference with each other using positive mode tandem mass spectrometry (MS/MS). Molecular ions of ergosterol and lanosterol were detected as the [M+H-H2O]+ ion species at m/z 380 and 410, whereas squalene appeared as the [M+H]+ ion species at m/z 412. On fragmentation of ergosterol, lanosterol, and squalene, the product ions at m/z 69, 149, and 109, respectively, were present as major fragments. These product ions were used for the quantification of them in multiple reaction monitoring acquisition mode. The relationship between signal intensity and the analytes' concentration was linear over the concentration range of 0.05-10 microg/ml. Following the treatment of C. albicans with fluconazole in combination with albicanyl caffeate, resveratrol, and 3,4'-difluorostilbene, respectively, the content of ergosterol in both the sensitive and resistant C. albicans showed depletion, whereas the squalene showed accumulation especially in the sensitive isolates determined with the method developed.     

Technical evaluation of MALDI-TOF mass spectrometry for quantitative proteomic profiling matrix formulation and application

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has been recently used to identify disease markers by directly profiling and quantifying the peptide/proteins in biological samples under different physiological or experimental conditions. The information of reproducibility of such quantitative profiling method has not been available. It is important to evaluate and reduce error from technical variation. In this study, an unbiased signal acquisition strategy was used to evaluate the effects of three sample-matrix spotting methods and two matrix chemicals, α-cyano-4-hydroxycinnamic acid (CHCA) and sinapinic acid, on the reproducibility of the peptide/protein signal intensities. The sandwich spotting method using 0.1% nitrocellulose coating film and CHCA gave the best quantitative results for the standard peptides and proteins with mass<66.5 kDa. The normalized signal intensities of the standard peptides and proteins were directly proportional to their concentrations with intra-assay (within-day) coefficient of variations (CVs) ranging from 6.5% to 17%. When analyzing serum peptides <6000 m/z, the interassay (between-days) CVs of all the evaluated peptide peaks were <15%. These data indicate that with the right MS analysis conditions, MALDI-TOF MS appears to be a feasible tool for directly profiling and quantifying the peptide/ proteins in biological samples.     

Relative herbivory tolerance and competitive ability in two dominant : subordinate pairs of perennial grasses in a native grassland

We evaluated herbivory tolerance and competitive ability within twodominant : subordinate pairs of C₄, perennial grasses at each of twosites to determine the contribution of these processes to herbivore-inducedspecies replacement. Herbivory tolerance was assessed by cumulative regrowthfrom defoliated plants of each species and competitive ability was evaluated byrelative uptake of a ¹⁵N isotope placed into the soil between pairedspecies in the field. Herbivory tolerance was similar for the dominant andsubordinate species in both plant pairs and defoliation intensity had a greaterinfluence on herbivory tolerance than did defoliation pattern. Both specieswithin the Sorghastrum nutans : Schizachyriumscoparium pairs exhibited comparable nitrogen acquisition from a¹⁵N enriched pulse with or without defoliation. In contrast,S. scoparium acquired more ¹⁵N than did itssubordinate neighbor, Bothriochloa laguroides when thisspecies pair was undefoliated. Uniform defoliation of this species pair at adefoliation intensity removing 70% of the shoot mass accentuated this responsefurther demonstrating the greater competitive ability of the dominant comparedto the subordinate species. Although the 90% defoliation intensity reducednitrogen acquisition by the dominant relative to the subordinate species,B. laguroides, it did not reduce nitrogen acquisition bythe dominant below that of the subordinate neighbor. The occurrence of similarherbivory tolerance among dominant and subordinate species indicates thatselective herbivory suppressed the greater competitive ability, rather than thegreater herbivory tolerance, of the dominant grasses in this experimentaldesign. These data suggest that interspecific competitive ability may be ofequal or greater importance than herbivory tolerance in mediatingherbivore-induced species replacement in mesic grasslands and savannas.     

Development of separable electron spin resonance-computed tomography imaging for multiple radical species: an application to .OH and .NO

A method of separable ESR-CT (electron spin resonance-computed tomography) imaging for multiple radical species was developed and applied to imaging of .OH and .NO. The algorithm was improved by combining filtered back-projection with a modified algebraic reconstruction technique to enhance accuracy and shorten calculation time. With this algorithm, spectral-spatial images of the phantom consisting of 3-carbamoyl-2,2,5,5,-tetramethylpyrrolidine-N-oxyl and 2-phenyl-4,4,5,5,-tetramethylimidazoline-3-oxide-1-oxyl could be obtained in different directions by rotating the spatial axis. The spatial function of individual radicals was extracted by each of the two methods from each spectral-spatial image. The separative 2D images of each radical were individually constructed using the spatial function obtained with the two methods. By comparing the separative images with the phantom sample, the algorithm for separable ESR-CT imaging was established. This ESR-CT technique was combined with L-band ESR spectroscopy and applied to the separative imaging of .OH and .NO, which were spin trapped with 5, 5-dimethyl-1-pyrroline-N-oxide (DMPO) and Fe(2+)-N-methyl-D-glucamine dithiocarbamate complex, respectively. The ESR signal of DMPO-OH decreased gradually during data acquisition, and the decrease was calibrated by extrapolating the signal intensity to the beginning of data sampling. Both the position and size of the individual images for .OH and .NO were in very good agreement with the findings for the sample.     

Analysis of the principal g-tensors in single crystals of ferrimyoglobin complexes

This paper describes a method of determining the directions of the principal axes of the g-tensors in single crystals from measurements of the g-value variation in three crystalline planes (ab, bc*, ac) and of the principal values of g-tensors. Measurements of paramagnetic resonance spectra of ferrimyoglobin (Mb(Fe3+)) complexes (Mb(Fe3+).CN-, .N3-, .imidazole(Im.) and .OCN-) in single crystals provided detailed information on the electronic state of the Fe3+. The direction of the z axis in Mb(Fe3+).CN-, .N3- and .Im. is not parallel to that in Mb(Fe3+).H2O, which has been used as the haem normal, where the z axis is one of the principal axes of the g-tensors corresponding to the maximal (in low-spin state of Fe3+ in haem) or minimal (in high-spin state of Fe3+ in haem) g-value. In Mb(Fe3+).OCN-, however, which is in thermal equilibrium between high-spin and low-spin states, the directions of the z axis in both states seem to be perpendicular to the haem plane. The direction of the x axis is not parallel to the plane of the linked histidine ring.     

Male and female rats express similar blood pressure responses to "push-pull" gravitational stress.

Brief exposure to -G(z) ("push") reduces eye-level blood pressure (elbp) during subsequent exposure to +G(z) ("pull"). This is called the "push-pull effect." To evaluate the influence of gender and the axis of rotation (pitch vs. roll) on the push-pull effect, 10 isoflurane-anesthetized male and 10 female Sprague-Dawley rats were restrained supine on a heated tilt board. Rats were subjected to two G profiles: a control profile consisting of rotation from 0 G(z) to 90 degrees head-up tilt (+1 G(z)) for 10 s and a push-pull profile consisting of rotation from 0 G(z) to 90 degrees head-down tilt (-1 G(z)) for 2 s immediately preceding 10 s of +1 G(z) stress. A total of 16 tilts consisting of equal numbers of control and push-pull trials and equal numbers of pitch and roll rotations were imposed by using a counterbalanced design. Gender exerted a significant effect on baseline (0 G(z)) ELBP (pressure was approximately 4 mmHg higher in females). In males and females, ELBP rose to a similar extent ( approximately 8 mmHg) during push, fell to a similar extent (approximately 18 mmHg) during control +G(z) stress, and fell to a similar extent (approximately 22 mmHg) during push-pull +G(z) stress. Altering the axis of rotation between the x-axis (roll) and the y-axis (pitch) did not influence the results. Thus males and females exhibit a push-pull effect; however, gender and axis of rotation do not appear to influence the push-pull effect in anesthetized rats subjected to tilting.     

Effects of light quality and quantity on growth of the clonal plant Eichhornia crassipes

Summary Plant canopy shade reduces photosynthetic photon flux density (PPFD) and ratio of red to far-red light (z). Both effects can cause plants to increase potential for light acquisition through vertical growth and leaf area expansion. Clonal plants such as Eichhornia crassipes might alternatively increase light interception via horizontal growth of stolons or rhizomes and placement of new ramets in less shaded microsites. Effect of simulated canopy shade and component effects of PPFD and z were tested by filtering or adding light uniformly, to a whole group of connected ramets, or locally, to individual ramets within a group. In uniform treatments, low PPFD reduced total growth but low z did not. Low PPFD and low z independently reduced stolon and ramet production and caused etiolation of petioles; effect of low PPFD plus low z on ramet production was greater than that of either factor alone. Lateral clonal growth thus did not seem to be a response to uniform shading; instead, uniformly low PPFD or low z increased partitioning to established ramets. Low z changed partitioning without changing total growth. In local treatments, reduction of growth of individual ramets due to low PPFD and inhibition of new ramet production attributable to spectral composition of light were mitigated when connected ramets were unshaded; plants may respond differently to patchy than to uniform shade.