Application of splines to the calculation of bacterial swimming speed distributions.

A new method of extracting information about bacterial speeds from photon correlation spectroscopy is presented. This method has the advantage that an estimation of the translational speed distribution is directly varied so as to achieve a best least-squares fit to the experimental autocorrelation function. The theory of spline approximations to continuous functions is briefly outlined. The importance of the previously disregarded diffusional component of bacterial motion is discussed. Experimental data from Salmonella at a low scattering angle is analyzed by this method of spline approximation and the distribution of translational speeds is obtained.     

A rotational diffusion coefficient of the 70S ribosome determined by depolarized laser light scattering

We have obtained a rotational diffusion coefficient of the 70S ribosome isolated from Escherichia-coli (MRE-600), from the depolarized light scattering spectrum measured by photon correlation spectroscopy. The intensity correlation function of depolarized scattered light contains contributions due to multiple scattered and anisotropy scattered light from the ribosomal particle. We discuss extensively the subtraction procedure used to obtain the rotational correlation time from the experimental correlation function. We have also obtained the translational diffusion coefficient from the same sample by determining the polarized correlation function. The hydrodynamic radius determined from the rotational diffusion coefficient is only slightly larger than the radius obtained from the translational diffusion coefficient. Therefore the ribosomal particle has a non-spherical shape. This conclusion, however, could be impaired by the effect of free draining of the ribosome.     

A rotational diffusion coefficient of the 70S ribosome determined by depolarized laser light scattering.

We have obtained a rotational diffusion coefficient of the 70S ribosome isolated from Escherichia-coli (MRE-600), from the depolarized light scattering spectrum measured by photon correlation spectroscopy. The intensity correlation function of depolarized scattered light contains contributions due to multiple scattered and anisotropy scattered light from the ribosomal particle. We discuss extensively the subtraction procedure used to obtain the rotational correlation from the time from the experimental correlation function. We have also obtained the translational diffusion coefficient from the same sample by determining the polarized correlation function. The hydrodynamic radius determined from the rotational diffusion coefficient is only slightly larger than the radius obtained from the translational diffusion coefficient. Therefore the ribosomal particle has a non-spherical shape. This conclusion, however, could be impaired by the effect of free draining of the ribosome.     

Comparison of molecular weight determination of sodium alginate by sedimentation-diffusion and light scattering

The weight average molecular weight, M̄_w, of sodium alginates were determined by the sedimentation-diffusion technique using photon correlation spectroscopy rather than boundary spreading in the analytical ultracentrifuge to determine the translational diffusion coefficients. This enables the diffusion coefficients to be determined easily and accurately. Excellent correlation is found between the observed zero concentration translational diffusion coefficient, D_O and the M̄_W values in a emphirical power law. The M̄_W obtained by sedimentation-diffusion and laser light scattering compare very favourably. The concentration dependence of the photon correlation spectroscopy data allowed determination of the coil overlap concentration, c*. The inverse proportionality of c* to both M̄_W and [η] is demonstrated.     

Fluorescence intensity multiple distributions analysis: concurrent determination of diffusion times and molecular brightness

Fluorescence correlation spectroscopy (FCS) has proven to be a powerful technique with single-molecule sensitivity. Recently, it has found a complement in the form of fluorescence intensity distribution analysis (FIDA). Here we introduce a fluorescence fluctuation method that combines the features of both techniques. It is based on the global analysis of a set of photon count number histograms, recorded with multiple widths of counting time intervals simultaneously. This fluorescence intensity multiple distributions analysis (FIMDA) distinguishes fluorescent species on the basis of both the specific molecular brightness and the translational diffusion time. The combined information, extracted from a single measurement, increases the readout effectively by one dimension and thus breaks the individual limits of FCS and FIDA. In this paper a theory is introduced that describes the dependence of photon count number distributions on diffusion coefficients. The theory is applied to a series of photon count number histograms corresponding to different widths of counting time intervals. Although the ability of the method to determine specific brightness values, diffusion times, and concentrations from mixtures is demonstrated on simulated data, its experimental utilization is shown by the determination of the binding constant of a protein-ligand interaction exemplifying its broad applicability in the life sciences.     

Bacterial assay for the rapid assessment of antifouling and fouling release properties of coatings and materials

An assay has been developed to accurately quantify the growth and release behaviour of bacterial biofilms on several test reference materials and coatings, using the marine bacterium Cobetia marina as a model organism. The assay can be used to investigate the inhibition of bacterial growth and release properties of many surfaces when compared to a reference. The method is based upon the staining of attached bacterial cells with the nucleic acid-binding, green fluorescent SYTO 13 stain. A strong linear correlation exists between the fluorescence of the bacterial suspension measured (RFU) using a plate reader and the total bacterial count measured with epifluorescence microscopy. This relationship allows the fluorescent technique to be used for the quantification of bacterial cells attached to surfaces. As the bacteria proliferate on the surface over a period of time, the relative fluorescence unit (RFU) measured using the plate reader also shows an increase with time. This was observed on all three test surfaces (glass, Epikote and Silastic T2) over a period of 4 h of bacterial growth, followed by a release assay, which was carried out by the application of hydrodynamic shear forces using a custom-made rotary device. Different fixed rotor speeds were tested, and based on the release analysis, 12 knots was used to provide standard shear force. The assay developed was then applied for assessing three different antifouling coatings of different surface roughness. The novel assay allows the rapid and sensitive enumeration of attached bacteria directly on the coated surface. This is the first plate reader assay technique that allows estimation of irreversibly attached bacterial cells directly on the coated surface without their removal from the surface or extraction of a stain into solution.     

Fluorescence correlation spectroscopy with high count rate and low background: analysis of translational diffusion

An epi-illuminated microscope configuration for use in fluorescence correlation spectroscopy in bulk solutions has been analyzed. For determining the effective sample dimensions the spatial distribution of the molecule detection efficiency has been computed and conditions for achieving quasi-cylindrical sample shape have been derived. Model experiments on translational diffusion of rhodamine 6G have been carried out using strong focusing of the laser beam, small pinhole size and an avalanche photodiode in single photon counting mode as the detector. A considerable decrease in background light intensity and measurement time has been observed. The background light is 40 times weaker than the fluorescence signal from one molecule of Rh6G, and the correlation function with signal-to-noise ratio of 150 can be collected in 1 second. The effect of the shape of the sample volume on the autocorrelation function has been discussed. Correspondence to: R. Rigler     

Two-photon fluorescence correlation spectroscopy: method and application to the intracellular environment.

We report on the application of two photon molecular excitation to fluorescence correlation spectroscopy. We demonstrate the first fluorescence correlation spectroscopy measurements of translational mobility in the cytoplasm of living cells. Two-photon excitation inherently excites small sample volumes in three dimensions, providing depth discrimination similar to confocal microscopy, without emission pinholes. We demonstrated accurate measurements of the diffusion constant, D, for particles of several different known sizes, in bulk solutions of different viscosity. We then showed measurements of translational diffusion for 7- and 15-nm radius latex beads in the cytoplasm of mouse fibroblast cells. We measured time-dependent diffusion coefficients. When first injected in the cells, the spheres moved from two to five times slower than in water, with average rates of 18 x 10(-8) cm2/s for the 7 nm and 5 x 10(-8) cm2/s for the 15 nm radius spheres. After a few hours, spheres stick to the cells, and the motion slows down 10 to 100 times.     

Application of Most-Probable-Number Statistics to Direct Enumeration of Microorganisms

A novel method for rapid determination of total microbial cell numbers was investigated. The method involves the application of most-probable-number estimation statistics to direct microscopic counting of microbial cells by using a particle sizing graticule. Its accuracy and reliability were tested with computer simulations of bacterial cell distributions encountered in ecological studies. Good estimates of cell numbers were obtained when the cell density varied from 3 to 6,000 cells per field, i.e., over 3 orders of magnitude. Low levels of contagion did not markedly influence cell estimates, although high levels, corresponding to discrete scattered microcolonies, did. However, these could be recognized visually. Estimates of cell numbers in Breed smears confirmed its speed and good correlation with the standard quadrat counting technique under real experimental conditions.     

Opticohydrodynamic properties of high-molecular-weight DNA. III. The effects of NaCl concentration

Excluded volume and persistence length of high-molecular-weight DNA from T2 bacteriophage have been evaluated over a range of NaCl concentrations from 0.005 to 2.0M using low-shear flow-birefringence and intrinsic-viscosity data. Uncertainty in persistence length due to ambiguity in the assignment of intrinsic birefringence has been avoided by calibrating the data at 0.2M NaCl using a recently reported persistence-length value based upon photon correlation spectroscopy [Jolly, D. & Eisenberg, H. (1976) Biopolymers 15 , 61]. Results at high salt concertrations are in satisfactory agreement with other estimates of excluded volume and chain flexibility in the literature, but at very low salt concentrations they reflect greater chain expansion than has heretofore been reported. The extinction-angle data imply a transition from a nondraining chain with excluded volume at 0.1M NaCl to an almost freely draining chain at 0.005M NaCl. Over this same salt range, the experimental persistencelength data agree very well with Flory's thermodynamic chain-expansion theory [Flory, P. J. (1953) J. Chem. Phys. 21 , 162], but are in generally poor agreement with other theoretical treatments. A detailed comparison of the results with other data in the literature suggests that the combined flow-birefringence-intrinsic-viscosity technique employed here may be more sensitive to the distribution of chain stiffness and excluded volume in polyelectroytechain expansion of DNA than are othe rhydrodynamic methods such as sedimentation or intrinsic viscosity alone.     

On the rotational brownian motion of a bacterial idle motor. II. Theory of fluorescence correlation spectroscopy

The photon flux autocorrelation function of a fluorescent label attached to a bacterial motor shaft is calculated for the case in which the bacterial motor is considered to be actively but idly rotating. It is shown that even when the fluorescent label has a very short lifetime, fluorescence correlation spectroscopy should provide a useful tool for determining the rate of revolution of the bacterial motor under various solution conditions.     

Standardization and validation of a new atomic absorption spectroscopy technique for determination and quantitation of Aluminium adjuvant in immunobiologicals

In the present study, Aluminium quantification in immunobiologicals has been described using atomic absorption spectroscopy (AAS) technique. The assay was found to be linear in 25-125 microg/ml Aluminium range. The procedure was found to be accurate for different vaccines with recoveries of external additions ranging between 93.26 and 103.41%. The mean Limit of Variation (L.V.) for both intra- and inter-assay precision was calculated to be 1.62 and 2.22%, respectively. Further the procedure was found to be robust in relation to digestion temperature, alteration in acid (HNO(3) and H(2)SO(4)) ratio used for sample digestion and storage of digested vaccine samples up to a period of 15 days. After validation, AAS method was compared for its equivalency with routinely used complexometric titration method. On simultaneously applying on seven different groups of both bacterial and viral vaccines, viz., DPT, DT, TT, Hepatitis-A and B, Antirabies vaccine (cell culture) and tetravalent DPT-Hib, a high degree of positive correlation (+0.85-0.998) among AAS and titration methods was observed. Further AAS method was found to have an edge over complexometric titration method that a group of vaccines, viz., ARV (cell culture, adsorbed) and Hepatitis-A, in which Aluminium estimation is not feasible by pharmacopoeial approved complexometric titration method (possibly due to some interference in the sample matrix), this newly described and validated AAS assay procedure delivered accurate and reproducible results.     

The standard deviation in fluorescence correlation spectroscopy

The standard deviation (SD) in fluorescence correlation spectroscopy (FCS) has been mostly neglected in applications. However, the knowledge of the correct SD is necessary for an accurate data evaluation, especially when fitting theoretical models to experimental data. In this work, an algorithm is presented that considers the essential features of FCS. It allows prediction of the performance of FCS measurements in various cases, which is important for finding optimal experimental conditions. The program calculates the SD of the experimental autocorrelation function online. This procedure leads to improved parameter estimation, compared to currently used theoretical approximations for the SD. Three methods for the calculation of the SD are presented and compared to earlier analytical solutions (D. E. Koppel. 1974. Phys. Rev. A. 10:1938-1945.), calculation directly from fluorescence intensity values, by averaging several FCS measurements, or by dividing one measurement into a set of shorter data packages. Although the averaging over several measurements yields accurate estimates for the SD, the other two methods are considerably less time consuming, can be run online, and yield comparable results.     

Determination of protein size in chromatography column eluants by on-line photon correlation spectroscopy

The dynamic light scattering technique of photon correlation spectroscopy has been used to determine biomacromolecule hydrodynamic radius in solutions flowing at rates similar to those experienced in liquid chromatographic separation systems. Such analyses can be performed rapidly (less than 5 s). The potential of the technique as an on-line noninvasive monitor for liquid chromatography is discussed.     

Treatment of mobile phase particulate matter in low-angle quasi-elastic light scattering

The method of quasi-elastic laser light scattering (QLS), particularly at low forward scattering angles, has been complicated by the transient presence of Mie or large Rayleigh scattering particles which contaminate the scattering volume. These large contaminating particles have substantial effects on photon correlation spectroscopy because the presence of these larger scatterers tends to decrease the value of the apparent diffusion coefficient of the particle of interest. A method is presented which yields more accurate diffusion constants by autocorrelation of selected photon count periods representative of minimal Mie or large Rayleigh particle contamination. This method was applied to the determination of the apparent diffusion constant for four proteins—ovalbumin, chymotrypsinogen-A, bovine serum albumin, and ribonuclease-A.     

Optimal running speed and the evolution of hominin hunting strategies

Recent discussion of the selective pressures leading to the evolution of modern human postcranial morphology, seen as early as Homo erectus, has focused on the relative importance of walking versus running. Specifically, these conversations have centered on which gait may have been used by early Homo to acquire prey. An element of the debate is the widespread belief that quadrupeds are constrained to run at optimally efficient speeds within each gait, whereas humans are equally efficient at all running speeds. The belief in the lack of optimal running speeds in humans is based, however, on a number of early studies with experimental designs inadequate for the purpose of evaluating optimality. Here we measured the energetic cost of human running (n = 9) at six different speeds for five minutes at each speed, with careful replicates and controls. We then compared the fit of linear versus curvilinear models to the data within each subject. We found that individual humans do, in fact, have speeds at which running is significantly less costly than at other speeds (i.e., an optimal running speed). In addition, we demonstrate that the use of persistence hunting methods to gain access to prey at any running speed, even the optimum, would be extremely costly energetically, more so than a persistence hunt at optimal walking speed. We argue that neither extinct nor extant hominin populations are as flexible in the chosen speeds of persistence hunting pursuits as other researchers have suggested. Variations in the efficiency of human locomotion appear to be similar to those of terrestrial quadrupeds.     

Laser light-scattering spectroscopy: a new application in the study of ciliary activity.

A uniquely precise and simple method to study ciliary activity by laser light-scattering spectroscopy has been developed and validated. A concurrent study of the effect of Ca2+ on ciliary activity in vitro by laser scattering spectroscopy and high speed cinematography has demonstrated that this new method is simpler and as accurate and reproducible as the high speed film technique.     

Loss of translational entropy in molecular associations

Molecular associations in solution are opposed by the loss of entropy (DeltaS) that results from the restriction of motion of each component in the complex. Theoretical estimates of DeltaS are essential for rationalizing binding affinities, as well as for calculating entropic contribution to enzyme catalysis. Recently a statistical-mechanical framework has been proposed for estimating efficiently the translational entropy loss (DeltaS(trsl)), while taking explicitly into account the complex intermolecular interactions between the solute and the solvent. This framework relates the translational entropy of a solute in solution to its "free volume," defined as the volume accessible to the center of mass of the solute in the presence of the solvent and calculated by using an extension of the cell model (CM) for condensed phases. The translational entropy of pure water, estimated with the CM algorithm, shows good agreement with the experimental information. The free volume of various solutes in water, calculated within the CM by using molecular dynamics simulations with explicit solvent, displays a strong correlation with the solutes' polar and total surface areas. This correlation is used to propose a parameterization that can be used to calculate routinely the translational entropy of a solute in water. We also applied the CM formalism to calculate the free volume and translational entropy loss (DeltaS(trsl)) on binding of benzene to a cavity in a mutant T4-lysozyme. Our results agree with previously published estimates of the binding of benzene to this mutant T4-lysozyme. These and other considerations suggest that the cell model is a simple yet efficient theoretical framework to evaluate the translational entropy loss on molecular association in solution.     

Photon and fluorescence correlation spectroscopy and light scattering of eye-lens proteins at moderate concentrations

The bovine eye-lens protein, alpha L-crystallin, has been studied with photon correlation spectroscopy to obtain the mutual diffusion coefficient, Dm, with fluorescence correlation spectroscopy to determine the tracer diffusion coefficient, DT, and with light scattering to get the isothermal osmotic compressibility (delta pi/delta c) P,T. The concentration dependence of Dm, DT, and (delta pi/delta c) P,T up to a volume fraction phi of the protein of 2.5 x 10(-2) has been interpreted on the basis of four different interaction potentials: (a) an extended hard-sphere potential; (b) a shielded Coulomb potential; (c) a shielded Coulomb interaction where the effect of counterions is included; (d) a simple mixed potential. The three parameters Dm, DT, and (delta pi/delta c) P,T have also been combined in the generalized Stokes-Einstein equation, Dm = [(delta pi/delta c)P,T . (1--phi) . (DT)]/(kappa B . T). Our results indicate that, in the case that photon correlation spectroscopy gives the mutual diffusion coefficient Dm, the applicability of the Stokes-Einstein equation can be questioned; or that, when one assumes the Stokes-Einstein equation to be valid, there is significant discrepancy between the result of photon correlation spectroscopy and Dm.     

Detection method for quantifying global DNA methylation by fluorescence correlation spectroscopy

A method for quantifying global DNA methylation using fluorescence correlation spectroscopy (FCS) has been established. The single-molecule methylation assay (SMMA) is based on two methodologies. One methodology, FCS, estimates the translational diffusion coefficient of molecules in solution, whereas the other methodology uses the high affinity of methyl-CpG-binding domain protein 2 (MBD2) to bind specifically to methylated DNA. We studied the specific binding rates of fluorescence-labeled MBD2 and methylated DNA from biological samples using the automated FCS system. Using a standard curve with methylated control DNA, we developed the SMMA index to assess the global DNA methylation level of the biological samples. A marked decrease in the SMMA index was observed when human leukemia cell lines (U937 and K562) were cultured with DNA demethylating agents. Our findings clearly indicate the applicability of SMMA as a simple and rapid tool for quantifying global DNA methylation. SMMA may prove useful for genome-wide comparative methylation analyses of malignancies and as an indicator of the demethylation effects of epigenetic drugs.