Quantal secretion from single visualized synaptic varicosities of sympathetic nerve terminals.
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Animals↗
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Effect of sequence length, sequence frequency, and data acquisition rate on the performance of a Hadamard transform time-of-flight mass spectrometer.
Various factors influencing the performance of a Hadamard transform time-of-flight mass spectrometer (HT-TOFMS) have been investigated. Using a nitrogen corona discharge to produce an ion stream of N2+, N3+, and N4+, it is found for spectra containing only N4+ that the signal-to-noise ratio (SNR) closely approaches the value calculated from the ion background by assuming that the ion background follows a Poisson distribution. In contrast, for a more intense beam containing N2+, N3+, and N4+, the SNR is less than its theoretical value because of the appearance of discrete spikes in the mass spectrum caused by deviations in the actual modulation sequence from the ideal one. These spikes can be reduced, however, by decreasing the modulation voltage. Under these optimized conditions, the pseudo-random sequence length is varied to understand how it alters SNR, mass resolution, and scan speed. When the length of the pseudo-random sequence is doubled, the SNR increases by the square root of 2 while the time necessary to record a mass spectrum also doubles. Mass resolution can be varied between 500 and 1200 at m/z = 609 as the sequence length, modulation speed (10 MHz, 25 MHz), and acquisition rate (up to 50 MHz) are changed. Scan speeds of 6000 passes per s can be obtained using a sequence containing 4095 elements modulated at 25 MHz. The capability to tailor the HT-TOFMS to increase the scan speed and resolution with a constant 50% duty cycle makes the technique extremely appealing as a mass analyzer for measuring rapid changes in the composition of an ion stream.
Algorithms↗
Processive interfacial catalytic turnover by Bacillus cereus sphingomyelinase on sphingomyelin vesicles.
Sphingomyelinase (SMase), a water-soluble enzyme from Bacillus cereus, is shown to bind with high affinity to vesicles of sphingomyelin (SM) but not to vesicles of phosphatidylcholine (PC). The reaction progress by SMase bound to SM vesicles occurs in the scooting mode with virtually infinite processivity of the successive interfacial turnover cycles. Three conditions for the microscopic steady state during the reaction progress at the interface are satisfied: the bound SMase does not leave the interface even after all the SM in the outer layer is converted to ceramide; the SMase-treated vesicles remain intact; and the ceramide product does not exchange with SM present in excess vesicles or in the inner layer of the hydrolyzed vesicle. Within these constraints, on accessibility and replenishment of the substrate, the extent of hydrolysis in the scooting mode reaction progress is a measure of the number of vesicles containing enzyme. The slope of the Poisson distribution plot, for the enzyme per vesicle versus the logarithm of the fraction of the total accessible substrate remaining unhydrolyzed in excess vesicles, shows that a single 32 kDa subunit of SMase is fully catalytically active. The maximum initial rate of hydrolysis, at the limit of the maximum possible substrate mol fraction, X(S)*=1, is 400 s(-1) in H(2)O and 220 s(-1) in D(2)O, which is consistent with the rate-limiting chemical step. The integrated reaction progress suggests that the ceramide product does not codisperse ideally on the hydrolyzed vesicles. Furthermore, complex reaction progress seen with covesicles of SM+PC are attributed to slow secondary changes in the partially hydrolyzed SM vesicles.
Animals↗
Rigid endoscopy in globus pharyngeus: how valuable is it?
The aim of this study was to assess the value of rigid endoscopy in patients presenting with globus symptoms. We conducted a retrospective analysis of 250 patients who underwent rigid endoscopy for globus symptoms over a 12-month period. In 217 patients (86.8 per cent) the examination of the larynx, pharynx and upper oesophagus was entirely normal. Abnormal findings included cricopharyngeal spasm in 12 patients (4.8 per cent), reflux in 11 (4.4 per cent), pharyngitis in two (0.8 per cent), web in two (0.8 per cent), and retention cyst in three (1.2 per cent). The 95 per cent confidence interval (CI) for the mean number of persons with malignancy based on the Poisson distribution is 0 and 3.7 (0 and 14.8 as rates per 1000). The relationship between the clinical diagnosis and endoscopic findings was examined using the chi-square test, with a p value of 0.0001. These results suggest that patients presenting with globus sensation are unlikely to harbour neoplastic lesions and therefore rigid endoscopy may well be an inappropriate investigation in this group. The risks, costs and discomfort associated with this intervention can often be avoided.
Adolescent↗
Synchronous neurite branchings in single goldfish retinal ganglion cells.
We have examined the time course of branch formation in neurites of retinal ganglion cells isolated from adult goldfish (Carassius auratus). These neurites elongate at approximately 13 microns/h, and usually branch by bifurcation of growth cones at their tips. The times elapsed between branchings in different neurites of single cells can be described by a Poisson distribution with a mean interval of approximately 2 h. As predicted by this distribution, a relatively large number of branchings occur simultaneously in different neurites of individual cells. Simultaneous branchings of neurites elongating at a common rate generate branch points that lay equidistant from their soma. Since similar branching patterns can be seen in dendrites of retinal ganglion and amacrine cells in situ, these results are consistent with the possibility that dendrites of individual neurons branch synchronously and grow at common rates during development.
Animals↗
Shared ITS DNA substitutions in isolates of opposite mating type reveal a recombining history for three presumed asexual species in the filamentous ascomycete genus Alternaria.
About 15,000 species of ascomycete fungi lack a known sexual state. For fungi with asexual states in the anamorph genera Embellisia, Ulocladium, and Alternaria, six species have known sexual states but more than 50 species do not. In sexual filamentous ascomycetes, opposite mating type information at the MAT1 locus regulates mating and the opposite mating type genes each have a clonal, non-recombining phylogenetic history. We used PCR to amplify and sequence fragments of the opposite mating type genes from three supposedly asexual species, A. brassicae, A. brassicicola and A. tenuissima. Each haploid fungal isolate had just one mating type, but both mating types were present in all the three species. We sequenced the ribosomal ITS regions for isolates of opposite mating type, for the three asexual species and four known related sexual species. In a phylogenetic analysis including other ITS sequences from GenBank, the three asexual species were not closely related to any of the known sexual species. Isolates of opposite mating type but the same species had identical ITS sequences. During any period of asexual evolutionary history, lineages of each mating type would have had a separate evolutionary history and any ITS substitutions shared between isolates of opposite mating type would have had to accumulate by convergence. Allowing for varying substitution rates and assuming a Poisson distribution of substitutions, the probability that isolates of opposite mating type shared an ITS substitution through convergence was low. This suggests that isolates of opposite mating type of A. brassicae, A. brassicicola and A. tenuissima were exchanging substitutions through sexual or parasexual reproduction while the ITS was evolving. If sexuality was lost, it was lost after the period of evolutionary history represented by the shared substitutions.
Alternaria↗
Single-molecule DNA amplification and analysis in an integrated microfluidic device.
Stochastic PCR amplification of single DNA template molecules followed by capillary electrophoretic (CE) analysis of the products is demonstrated in an integrated microfluidic device. The microdevice consists of submicroliter PCR chambers etched into a glass substrate that are directly connected to a microfabricated CE system. Valves and hydrophobic vents provide controlled and sensorless loading of the 280-nL PCR chambers; the low volume reactor, the low thermal mass, and the use of thin-film heaters permit cycle times as fast as 30 s. The amplified product, labeled with an intercalating fluorescent dye, is directly injected into the gel-filled capillary channel for electrophoretic analysis. Repetitive PCR analyses at the single DNA template molecule level exhibit quantized product peak areas; a histogram of the normalized peak areas reveals clusters of events caused by 0, 1, 2, and 3 viable template copies in the reactor and these event clusters are shown to fit a Poisson distribution. This device demonstrates the most sensitive PCR possible in a microfabricated device. The detection of single DNA molecules will also facilitate single-cell and single-molecule studies to expose the genetic variation underlying ensemble sequence and expression averages.
Base Sequence↗
Accurate analysis of fluorescence decays from single molecules in photon counting experiments.
In time-resolved, single-photon counting experiments, the standard method of nonlinear least-squares curve fitting incorrectly estimates the fluorescence lifetimes. Even for single-exponential data, errors may be up to +/- 15%, and for more complex fits, may be even higher, although the fitted line appears to describe the data. The origin of this error is not a result of the Poisson distribution, as is often stated, but is entirely due to the weighting of the fit. An alternative weighting method involving a minor change in the fitting method eliminates this problem, enabling accurate fitting even in difficult cases, including the small data sets observed in single molecule experiments and with a precision similar to that of maximum likelihood methods.
Journal Article↗
Synthesis/degradation ratio mass spectrometry for measuring relative dynamic protein turnover.
One of the major unanswered questions in quantitative proteomics is that of dynamic protein turnover in the cell. Here we present a new approach to quantitative proteomics that measures the relative dynamic turnover of proteins in cellular systems. In this approach, termed synthesis/degradation ratio mass spectrometry, stable isotope labeling is employed to calculate a relative synthesis/degradation ratio that reflects the relative rate at which 13C is incorporated into individual proteins in the cell. This synthesis/degradation ratio calculation is based on a Poisson distribution model that is designed to support high-throughput analysis. Protein separation and analysis is accomplished by utilizing one-dimensional SDS-PAGE gel electrophoresis followed by cutting the gel into a series of bands for in-gel digestion. The resulting peptide mixtures are analyzed via solid-phase MALDI LC-MS and LC-MS/MS using a tandem time-of-flight mass spectrometer. A portion of the soluble protein fraction from an E. coli K-12 strain was analyzed with synthesis/degradation ratios varying from approximately 0.1 to 4.4 for a variety of different proteins. Unlike other quantitative techniques, synthesis/degradation ratio mass spectrometry requires only a single cell culture to obtain useful biological information about the processes occurring inside a cell. This technique is highly amenable to shotgun proteomics-based approaches and thus should allow relative turnover measurements for whole proteomes in the future.
Bacterial Proteins↗
Electrogenerated chemiluminescence. 77. DNA hybridization detection at high amplification with [Ru(bpy)3]2+-containing microspheres.
An ultrasensitive DNA hybridization detection method based on electrogenerated chemiluminescence (ECL) using polystyrene microspheres/beads (PSB) as the carrier of the ECL labels, namely, tris(2,2'-bipyridyl)ruthenium(II) tetrakis(pentafluorophenyl)borate (Ru(bpy)3[B(C6F5)4]2), is reported. Probe single-stranded DNA (p-ssDNA) was attached to the surface of magnetic beads (MB) and hybridized with target-ssDNA (t-ssDNA) with immobilized PSB containing a large number of water insoluble Ru(bpy)3[B(C6F5)4]2 species (approximately 7.5 x 10(9) molecules/bead). With this approach a large amplification factor of Ru(bpy)3[B(C6F5)4]2 molecules for each t-ssDNA can be achieved, when each PSB is attached to a limited number of t-ssDNA. The p-ssDNA-MB <--> t-ssDNA-PSB/Ru(bpy)3(2+) conjugates formed were magnetically separated from the reaction media and dissolved in MeCN containing tri-n-propylamine (TPrA) as an ECL coreactant. ECL was produced with a potential scan from 0 to 3.0 V versus Ag/Ag+, and the integrated ECL intensity was found to be linearly proportional to the t-ssDNA concentration in a range of 1.0 fM to 10 nM under optimized conditions. ECL signals associated with two base pair mismatched ssDNA and noncomplementary ssDNA can be distinguished well from the ECL signal related to the complementary DNA hybridization. A Poisson distribution is followed when a large number of MB reacts with PSB, and the minimum number of 1.0- and 2.8-microm diameter MB required to bind and magnetically separate a single 10-microm diameter PSB from the reaction solution was estimated to be three and one, respectively. The principle described in this paper could be also applied to many other ECL analyses, such as immunoassays.
2,2'-Dipyridyl↗
Real-time PCR measurement by fluorescence anisotropy.
We have developed an instrument for monitoring real-time PCR using fluorescence anisotropy, enabling an assay chemistry in which the fluorescence from a labeled primer elucidates amplification. The instrument holds the sample temperature constant to within +/-0.03 degrees C during measurement in the extension phase of each PCR cycle and achieves 0.116 mP FA resolution. Primer conjugation with Alexa-Fluor 488, when compared with other fluorophores, is shown to provide the greatest FA range between primer and product. Comparable reproducibility and linearity of the crossing point for a range of target copy numbers is observed between the FA-based assay run in our instrument and the SYBR green assay run in commercial instrumentation. Reproducibility is also consistent with Poisson-distributed experimental error in aliquoting starting copies, a theoretical limit to instrument/assay performance.
Fluorescence Polarization↗
Excitation trap approach to analyze size and pigment-pigment coupling: reconstitution of LH1 antenna of Rhodobacter sphaeroides with Ni-substituted bacteriochlorophyll.
Replacement of the central Mg in chlorophylls by Ni opens an ultrafast (tens of femtoseconds time range) radiationless de-excitation path, while the principal ground-state absorption and coordination properties of the pigment are retained. A method has been developed for substituting the native bacteriochlorophyll a by Ni-bacteriochlorophyll a ([Ni]-BChl) in the light harvesting antenna of the core complex (LH1) from the purple bacterium, Rhodobacter (Rb.) sphaeroides, to investigate its unit size and excited state properties. The components of the complex have been extracted with an organic solvent from freeze-dried membranes of an LH1-only strain of Rb. sphaeroides and transferred into the micelles of n-octyl-beta-glucopyranoside (OG). Reconstitution was achieved by solubilization in 3.4% OG, followed by dilution, yielding a complex nearly identical to the native one, in terms of absorption, fluorescence, and circular dichroism spectra as well as energy transfer efficiency from carotenoid to bacteriochlorophyll. By adding increasing amounts of [Ni]-BChl to the reconstitution mixture, a series of LH1 complexes was obtained that contain increasing levels of this efficient excitation trap. In contrast to the nearly unchanged absorption, the presence of [Ni]-BChl in LH1 markedly affects the emission properties. Incorporation of only 3.2 and 20% [Ni]-BChl reduces the emission by 50% and nearly 100%, respectively. The subnanosecond fluorescence kinetics of the complexes were monoexponential, with the lifetime identical to that of the native complex, and its amplitude decreasing in parallel with the steady-state fluorescence yield. Quantitative analysis of the data, based on a Poisson distribution of the modified pigment in the reconstituted complex, suggests that the presence of a single excitation trap per LH1 unit suffices for efficient emission quenching and that this unit contains 20 +/- 1 BChl molecules.
Bacterial Proteins↗
Membrane permeability to macromolecules mediated by the membrane attack complex.
A simple and well-defined system of purified phospholipids and human complement proteins was used to study membrane permeability to macromolecules mediated by the membrane attack complex (MAC) of complement. Large unilamellar vesicles (LUVs) of phosphatidylcholine (PC) or phosphatidylserine (PS) containing trapped macromolecules [bovine pancreatic trypsin inhibitor (BPTI), thrombin, glucose-6-phosphate dehydrogenase (G6PD), and larger molecules] were used to monitor permeability. Membrane permeability to macromolecules was measured by thrombin inhibition by an external inhibitor or by separation of released molecules by gel filtration. Membrane-bound intermediates (C5b-8 or C5b-93) were stable for hours, and macromolecular permeability occurred without fragmentation, fusion, or aggregation of the vesicles. Quantitative membrane binding by C5b-7 as well as essentially quantitative release of thrombin was obtained for PS vesicles. MAC binding to PS-LUVs approximated the theoretical Poisson distribution curve for full release of vesicle contents by one complex per vesicle. Reactions with PC-LUVs occurred with some fluid-phase MAC assembly. Therefore, results from experiments with these vesicles were interpreted in a relative manner. However, the values obtained closely corroborated those obtained with PS-LUVs. At low C9/C5b-8 ratios, the size of the lesion was proportional to the C9 content of the MAC. Half-maximum release of BPTI, thrombin, and G6PD, by a single MAC per vesicle, required approximately 3,5, and 7 C9/C5b-8 (mol/mol), respectively. Larger molecules (greater than or equal to 118-A diameter) were not released from the vesicles. Release of G6PD (95.4-A diameter) required 45% of saturating C9. Therefore, it appeared that the last half of the bound C9 molecules did not increase pore size and the pore which released G6PD approached the diameter of the closed circular lesion measured (by others) in electron micrographs (approximately 100 A). The results were consistent with the formation of a stable membrane pore by a single complex per vesicle in which C9 molecules line only one side of the pore at low C9/C5b-8 ratios and maximum pore size is attained by incomplete, noncircular polymers of C9.
Cell Membrane Permeability↗
Proton permeation into single vesicles occurs via a sequential two-step mechanism and is heterogeneous.
This article describes the first single-vesicle study of proton permeability across the lipid membrane of small (approximately 100 nm) uni- and multilamellar vesicles, which were composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). To follow proton permeation into the internal volume of each vesicle, we encapsulated carboxyfluorescein, a pH-sensitive dye whose fluorescence was quenched in the presence of excess protons. A microfluidic platform was used for easy exchange of high- and low-pH solutions, and fluorescence quenching of single vesicles was detected with single-molecule total internal reflection fluorescence (TIRF) microscopy. Upon solution exchange and acidification of the extravesicular solution (from pH 9 to 3.5), we observed for each vesicle a biphasic decay in fluorescence. Through single-vesicle analysis, we found that rate constants for the first decay followed a Poisson distribution, whereas rate constants for the second decay followed a normal distribution. We propose that proton permeation into each vesicle first arose from formation of transient pores and then transitioned into the second decay phase, which occurred by the solubility-diffusion mechanism. Furthermore, for the bulk population of vesicles, the decay rate constant and vesicle intensity (dependent on size) correlated to give an average permeability coefficient; however, for individual vesicles, we found little correlation, which suggested that proton permeability among single vesicles was heterogeneous in our experiments.
Cell Membrane Permeability↗
Diffusion and cluster formation in one-dimensional systems with attractive interactions.
We study cluster formation in a finite one-dimensional model system where the particles experience long-range attractive forces. The particles are first placed in equidistant positions by a repulsive potential, which then is turned off, and only a weak long-range potential acts between the particles. It is shown that the mean-square deviation in distance between the colloids at first increases due to normal Brownian motion, followed by a crossover to anomalous diffusion governed by the long-range forces. Moreover, we also found that the subsequent cluster formation could be described by a Poisson distribution. The results presented here may help us understand diffusion and cluster formation in one-dimensional systems.
Journal Article↗
Iron wheels on silicon: wetting behavior and electronic structure of adsorbed organostannoxane clusters.
Atomic force microscopy and synchrotron radiation (SR) spectroscopy have been used to study the wetting behavior and electronic structure of thin films of a novel organometallic cluster--[BuSn(O)OC(O)Fc]6 ("Fc" = ferrocenyl)--on silicon substrates. This cluster comprises six ferrocene units connected to a stannoxane central core--"an iron wheel on a tin drum" (V. Chandrasekhar; et al. Angew. Chem., Int. Ed. 2000, 39, 1833). Thin films spin-cast onto native oxide-terminated silicon readily dewet the substrate. We have utilized advanced image analysis techniques based on Minkowski functionals to provide a detailed quantitative analysis of the morphology of the stannoxane overlayers. This analysis shows that the dewetting patterns are rather far removed from those expected to arise from a simple Poisson distribution of centers, and we discuss the implications of this finding in terms of nucleated and spinodal dewetting. Variations in both the surface roughness and the in-plane correlation length have been followed as a function of annealing time to probe the surface dewetting dynamics. SR valence band photoemission illustrates that the highest occupied molecular orbital (HOMO) of the cluster is found 2 eV below the Fermi level. Fe 2p --> 3d and Sn 3d --> 5p resonant photoemission spectroscopy have been used to enhance the cross sections of the partial density of states associated with the Fe and Sn atoms. Sn atoms make a large contribution to the HOMO of the cluster, whereas the Fe atoms are associated with an electronic environment seemingly very similar to that in the "parent" ferrocene molecule.
Journal Article↗
The functional relationship between in vivo bromodeoxyuridine labeling index and Ki-67 proliferation index in human breast cancer.
Proliferation indices are used, along with other parameters, to estimate the risk of recurrence of breast cancer for individual patients. Because it is unlikely one index will be practical for all patients, it is important to understand the relationship between various indices of proliferation. For this reason, we compared a proliferation index based on in vivo labeling of S-phase tumor cells with the thymidine analog bromodeoxyuridine (BrdUrd), to a proliferation index based on an estimate of the growth fraction with the MIB-1 antibody to the Ki-67 antigen. With informed consent, we gave 145 patients 200 mg/m2 BrdUrd intravenously just prior to surgical removal of breast cancer. On histology sections, we visually counted S-phase cells which had incorporated BrdUrd using the Br-3 antibody which is specific to DNA-incorporated BrdUrd, and we counted cells in the growth fraction using the MIB-1 antibody to the Ki-67 antigen. We found that both indices were positively correlated with tumor size, number of positive nodes, and tumor grade, and both were negatively correlated with age and estrogen-progesterone receptor positivity. Using a linear functional relationship model, we found that the best (i.e. the maximal) fit between the two indices (correlation coefficient 0.79; p < 0.0001) occurred when each index was square root transformed, as is appropriate when counts follow a Poisson distribution. When we used the median as a cutpoint for each index, the classification of 19 percent of data pairs changed depending upon which index was used. We also estimated that the Ki-67 intercept (1.02 +/- 0.25) was significantly greater than zero. We conclude that the BrdUrd index of DNA synthesis in S-phase correlates highly with the MIB-1 index of the growth fraction, and both indices correlate well with other parameters of tumor aggressiveness. Because this correlation is driven by concordance of the extremes of high and low counts, clinical comparison will be necessary to determine which is the better prognostic marker for human breast cancer.
Adult↗
Spike-frequency adaptation of a generalized leaky integrate-and-fire model neuron.
Although spike-frequency adaptation is a commonly observed property of neurons, its functional implications are still poorly understood. In this work, using a leaky integrate-and-fire neural model that includes a Ca2+-activated K+ current (IAHP), we develop a quantitative theory of adaptation temporal dynamics and compare our results with recent in vivo intracellular recordings from pyramidal cells in the cat visual cortex. Experimentally testable relations between the degree and the time constant of spike-frequency adaptation are predicted. We also contrast the IAHP model with an alternative adaptation model based on a dynamical firing threshold. Possible roles of adaptation in temporal computation are explored, as a a time-delayed neuronal self-inhibition mechanism. Our results include the following: (1) given the same firing rate, the variability of interspike intervals (ISIs) is either reduced or enhanced by adaptation, depending on whether the IAHP dynamics is fast or slow compared with the mean ISI in the output spike train; (2) when the inputs are Poisson-distributed (uncorrelated), adaptation generates temporal anticorrelation between ISIs, we suggest that measurement of this negative correlation provides a probe to assess the strength of IAHP in vivo; (3) the forward masking effect produced by the slow dynamics of IAHP is nonlinear and effective at selecting the strongest input among competing sources of input signals.
Action Potentials↗