Estimation of flattening coefficient for absorption and circular dichroism using simulation

The absorbance and circular dichroism (CD) of suspensions is lower than if the same amount of chromophore were uniformly distributed throughout the medium. Several mathematical treatments of this absorption flattening phenomenon have been presented using various assumptions and approximations. This article demonstrates an alternative simulation approach that allows relaxation of assumptions. On current desktop computers, the algorithm runs quickly with enough particles and light paths considered to get answers that are usually accurate to better than 3%. Results from the simulation agree with the most popular analytical model for 0.01 volume fraction of particles, showing that the extent of flattening depends mainly on the absorbance through a particle diameter. Unlike previous models, the simulation can show that flattening is significantly lower when volume fraction increases to 0.1 but is higher when the particles have a size distribution. The simulation can predict the slope of the nearly linear relationship between flattening of CD and the absorbance of the suspension. This provides a method to correct experimental CD data where volume fraction and particle size are known.     

Band structure of electronic circular dichroism spectra and the born-oppenheimer approximation

Theory is presented for determining the effects of band structure on electronic CD spectra. In this development, the effect of the first-order correction to the Born-Oppenheimer approximation is considered. This removes the unrealistic feature of identical CD and absorbance spectral band structures present in previous models. The predicted order of magnitude of this correction is consistent with experimentally observed differences in CD and absorbance band structure. A Green function formalism is used to determine the contribution of the intrinsic CD to the total CD of an aggregate of chromophores. The intrinsic CD can be determined from the monomeric CD that has been corrected for effects of the intermolecular interactions in the aggregate.     

CD of gels and suspensions: apparent CD in the soret region of sickle hemoglobin gels

CD spectra in the soret region of sickle-cell deoxyhemoglobin (deoxy-HbS) fiber gels are radically different from the CD of deoxy-HbS in solution. An explanation is found using the Stokes–Mueller representation of the interaction of a polarized beam with the instrument optical train and sample to derive expressions for the apparent CD of gels and suspensions of optically active molecules that consist of randomly oriented domains or particles that are linearly dichroic and linearly birefringent. These theoretical considerations show that the apparent CD spectra from such systems have contributions from the LD and birefringence of each domain even if no net linear birefringence and dichroism is apparent in the sample. Thus, the interpretation of the CD from gels and suspensions is problematic, unless it can be demonstrated that each domain or particle has extremely small absorbance or that the LD and birefringence of each is a very small fraction of the total absorbance. As a result, we conclude that the spectra of HbS gels are not due to the CD of the heme per se; rather, they also reflect the randomly oriented domain structure of the gels and the LD and linear birefringence associated with each domain.     

Comparison between histones FV and F2a2 of chicken erythrocyte. II. Interaction with homologous DNA.

The conformation and stability of artificial complexes between chicken erythrocyte DNA and homologous histones FV and F2a2 was studied by circular dichroism (CD) and thermal denaturation followed by both absorbance and CD measurements. The complexes are made after a stepwise potassium fluoride gradient dialysis without urea and studied at low ionic strength (10-minus 3 M). 1) No structural changes of the DNA can be detected up to r equals 0.2 with FV and r equals 0.6 for F2a2. With FV at higher values of r the CD spectrum is altered, indicating the organization of DNA and histones in some kind of aggregate. 2) The conformation of histone molecules inside the complexes is not related to the ionic strength of the medium but to an effective ionic environment close to 0.1 M. This ionic strength would also correspond to the melting temperature of histone-covered DNA. 3) From the analysis of the absorbance melting profile the length of DNA covered with an histone molecule can be estimated. A good agreement is found between the negative charge of this piece of DNA and the net positive charge of the histone. 4) Since the CD transition at 227 nm occurs before the second absorbance transition at 280 nm, the DNA is stabilized no longer by native histone but partially or fully denatured histones. The helical regions of the histone molecule are not involved in the binding process, which appears to be almost purely coulombian and most likely related to some structural fit between the pattern of negative charges in the DNA helix and that of positive charges along the peptide chain.     

Commerical reference shape standards use in the study of particle shape effect on laser diffraction particle size analysis

The purpose of this paper is to describe the use of LGC Promochem AEA 1001 to AEA 1003 monosized fiberanalog shape standards in the study of the effect of particle shape on laser diffraction (LD) particle size analysis (psa). The psa of the AEA standards was conducted using LD psa systems from Beckman Coulter, Horiba, and Malvern Instruments. Flow speed settings, sample refractive index values, and sample cell types were varied to examine the extent to which the shape effect on LD psa results is modified by these variables. The volume and number probability plots resulting from these measurements were each characterized by a spread in the particle size distribution that roughly extended from the breadth to the longest dimension of the particles. For most of the selected sample refractive index values, the volume probability plots were characterized by apparent bimodal distributions. The results, therefore, provide experimental verification of the conclusions from theoretical studies of LD psa system response to monosized elliptical particles in which this apparent bimodality was the predicted result in the case of flow-oriented particles. The data support the findings from previous studies conducted over the past 10 years that have called into question the verity of the tenets of, and therefore the value of the application of, the equivalent spherical volume diameter theory and the random particle orientation model to the interpretation of LD psa results from measurements made on nonspherical particles.     

Commercial reference shape standards use in the study of particle shape effect on laser diffraction particle size analysis

The purpose of this paper is to describe the use of LGC Promochem AEA 1001 to AEA 1003 monosized fiber-analog shape standards in the study of the effect of particle shape on laser diffraction (LD) particle size analysis (psa). The psa of the AEA standards was conducted using LD psa systems from Beckman Coulter, Horiba, and Malvern Instruments. Flow speed settings, sample refractive index values, and sample cell types were varied to examine the extent to which the shape effect on LD psa results is modified by these variables. The volume and number probability plots resulting from these measurements were each characterized by a spread in the particle size distribution that roughly extended from the breadth to the longest dimension of the particles. For most of the selected sample refractive index values, the volume probability plots were characterized by apparent bimodal distributions. The results, therefore, provide experimental verification of the conclusions from theoretical studies of LD psa system response to monosized elliptical particles in which this apparent bimodality was the predicted result in the case of flow-oriented particles. The data support the findings from previous studies conducted over the past 10 years that have called into question the verity of the tenets of, and therefore the value of the application of, the equivalent spherical volume diameter theory and the random particle orientation model to the interpretation of LD psa results from measurements made on nonspherical particles.     

Numerical simulation and PEPT measurements of a 3D conical helical-blade mixer: a high potential solids mixer for solid-state fermentation

Helical-blade solids mixers have a large potential as bioreactors for solid-state fermentation (SSF). Fundamental knowledge of the flow and mixing behavior is required for robust operation of these mixers. In this study predictions of a discrete particle model were compared to experiments with colored wheat grain particles and positron emission particle tracking (PEPT) measurements. In the discrete particle model individual movements of particles were calculated from interaction forces. It was concluded that the predicted overall flow behavior matched well with the PEPT measurements. Differences between the model predictions and the experiments with wheat grains were found to be due to the assumption that substrate particles were spherical, which was in the model. Model simulations and experiments with spherical green peas confirmed this. The mixing in the helical-blade mixer could be attributed to (1) the transport of particles up and down in the interior of the mixer, and (2) dispersion or micro-mixing of particles in the top region of the mixer. It appeared that the mixing rate scaled linearly with the rotation rate of the blade, although the average particle velocity did not scale proportionally. It may be that the flow behavior changes as a function of the rotation rate (e.g., changing thickness of the top region); further study is required to confirm this. To increase the mixing performance of the mixer, a larger blade or a change in the shape of the mixer (larger top surface/volume ratio) is recommended.     

Increased accuracy and speed of absorption cytometric DNA measurements by automatic corrections for nuclear darkness

We have developed a method of calculating the average local absorbance (ALA) of a nucleus from the integrated nuclear absorbance and area. One can use the ALA, along with nuclear areas measured at different point absorbance thresholds, to determine whether a nucleus is stained too lightly or too darkly for accurate absorption measurements; this allows selection of an optimal light wavelength for the performance of these measurements. The ALA can also be used for automatic and instantaneous correction of integrated absorbance values from darkly stained cells. This allows the rapid measurement of the integrated absorbances of a large number of nuclei that are heterogeneous in stain intensity. Coefficients of variation of approximately 3% are obtained for the integrated absorbances of nuclei of nontransformed G0/G1 cells. This correction method can be applied with any image densitometer that generates both integrated absorbance and area values.     

A Monte Carlo simulation of the determination of mean particle volume using the Cavalieri estimator

BACKGROUND: A common morphometric problem is the determination of an estimate of the size of biological particles obtained from measurements made on a sample of profiles observed in sections. Results are reported typically in terms of mean caliper diameter or mean volume of the particle. METHODS: We have investigated the use of the Cavalieri estimator for obtaining estimates of mean particle volume using a Monte Carlo simulation. Samples of spherical and ellipsoidal particles were generated by computer and serially sectioned at a fixed mean thickness with a small, imposed random variation. The area of each profile was determined and the volume of the particle was calculated according to the Cavalieri estimator. The influence on the estimate of the mean particle volume and its 95% confidence interval was evaluated for several variables: the shape of the particles, the standard deviation of the particle volume in the population, the section thickness, and the standard deviation of the section thickness. RESULTS: The results obtained with the Cavalieri estimator correspond favorably with those obtained with previously reported alternative methods. This leads to a recommendation for the strong consideration for the use of the Cavalieri estimator in cases in which it is technically feasible to obtain at least three sections through the individual particles. Graphs are provided, which relate the confidence interval for the mean volume to the number of particles measured.     

An open‐source code for Mie extinction extended multiplicative signal correction for infrared microscopy spectra of cells and tissues

Infrared spectroscopy of single cells and tissue is affected by Mie scattering. During recent years, several methods have been proposed for retrieving pure absorbance spectra from such measurements, while currently no user‐friendly version of the state‐of‐the‐art algorithm is available. In this work, an open‐source code for correcting highly scatter‐distorted absorbance spectra of cells and tissues is presented, as well as several improvements of the latest version of the Mie correction algorithm based on extended multiplicative signal correction (EMSC) published by Konevskikh et al. In order to test the stability of the code, a set of apparent absorbance spectra was simulated. To this purpose, pure absorbance spectra based on a Matrigel spectrum are simulated. Scattering contributions where obtained by mimicking the scattering features observed in a set of experimentally obtained spectra . It can be concluded that the algorithm is not depending strongly on the reference spectrum used for initializing the algorithm and retrieves well the underlying pure absorbance spectrum. The calculation time of the algorithm is considerably improved with respect to the resonant Mie scattering EMSC algorithm used by the community today.      

Structure of human low-density lipoprotein subfractions, determined by X-ray small-angle scattering

The structure of low-density lipoprotein (LDL) particles from three different density ranges (LDL-1: d = 1.006-1.031 g/ml; LDL-3: d = 1.034-1.037 g/ml; LDL-6: d = 1.044-1.063 g/ml) was determined by X-ray small-angle scattering. By using a theoretical particle model, which accounted for the polydispersity of the samples, we were able to obtain fits of the scattering intensity that were inside the noise interval of the measured intensity. The assumption of deviations from radial symmetry is not supported by our data. This implies a spread-out conformation of the apolipoprotein B (apoB) molecule, which appears to be localized in the outer surface shell. A globular structure is not consistent with our data. Furthermore, different models exist concerning the structure of the cholesterol ester core below the phase transition temperature. The electron density data suggest an arrangement in which the steroid moieties are localized at average radii of 3.2 and 6.4 nm. Model calculations show that packing problems can only be avoided if approximately half of the acyl chains of each shell are pointing towards the center of the particle, the other half towards the surface. This arrangement of the acyl chains has never been proposed before. The LDL particles of different density classes differ mainly with respect to the size of the core but also with respect to the width of the surface shells. Model calculations show that the size of different LDL particles can be accurately predicted from the compositional data.     

Circular dichroism studies of subtilisin Carlsberg immobilised on micron sized silica particles

Immobilised enzymes are widely used in industry, but the reasons for loss of activity of such biocatalysts are usually not known. We have used circular dichroism (CD) to investigate the structure of one such system, i.e., subtilisin Carlsberg (SC) immobilised on silica gel particles (60 microm). A number of technical problems have to be overcome in order to obtain appropriate data from which conclusions can be drawn. A rotating cell holder has been developed to avoid sedimentation of the silica particles during the collection of spectra. By moving the cell holder as close as possible to the detector window, the effects of differential scattering can be minimised. However, the effects of absorption flattening limit the extent to which reliable quantitative information on secondary structure content can be obtained from far UV CD studies. We have used an empirical approach based on absorbance units derived from the high-tension voltage to correct for absorption flattening effects. After applying the correction there was satisfactory agreement with the solution spectra. Comparison of the fresh and used (inactive) SC-silica gel spectra in organic media reveals substantial change in the secondary structure. Additional evidence for loss of native conformation is provided by the significant decrease in the near UV CD spectrum. These results for the first time clearly demonstrate the origin of enzyme instability in the immobilised state.     

Analysis and evaluation of channel models: simulations of alamethicin

Alamethicin is an antimicrobial peptide that forms stable channels with well-defined conductance levels. We have used extended molecular dynamics simulations of alamethicin bundles consisting of 4, 5, 6, 7, and 8 helices in a palmitoyl-oleolyl-phosphatidylcholine bilayer to evaluate and analyze channel models and to link the models to the experimentally measured conductance levels. Our results suggest that four helices do not form a stable water-filled channel and might not even form a stable intermediate. The lowest measurable conductance level is likely to correspond to the pentamer. At higher aggregation numbers the bundles become less symmetrical. Water properties inside the different-sized bundles are similar. The hexamer is the most stable model with a stability comparable with simulations based on crystal structures. The simulation was extended from 4 to 20 ns or several times the mean passage time of an ion. Essential dynamics analyses were used to test the hypothesis that correlated motions of the helical bundles account for high-frequency noise observed in open channel measurements. In a 20-ns simulation of a hexameric alamethicin bundle, the main motions are those of individual helices, not of the bundle as a whole. A detailed comparison of simulations using different methods to treat long-range electrostatic interactions (a twin range cutoff, Particle Mesh Ewald, and a twin range cutoff combined with a reaction field correction) shows that water orientation inside the alamethicin channels is sensitive to the algorithms used. In all cases, water ordering due to the protein structure is strong, although the exact profile changes somewhat. Adding an extra 4-nm layer of water only changes the water ordering slightly in the case of particle mesh Ewald, suggesting that periodicity artifacts for this system are not serious.     

Secondary structure in very low density and intermediate density lipoproteins of human serum.

We have studies the secondary structures of the protein moieties of very low density lipoproteins (VLDL) and intermediate density lipoproteins (IDL) of human serum by circular dichroism (CD). Two potential complications in the application of this technique to lipoproteins have been evaluated. First, using chronographic potentiometry in CD measurements of VLDL fractions of different mean particle diameters, we have analyzed statistically the CD signals in order to define the limits imposed by light scattering with respect to both particle diameter and wavelength. We found that CD measurements can be made to as low as 210 nm on particles of 520 A or smaller, and to 194 nm on particles of 450 A and below. Second, we have evaluated the CD contribution of lipid chromophores. Despite the high ratio of lipid to protein, the relative CD effect of the lipids is smaller than for low density lipoproteins (LDL). due to the extremely small ellipticity of natural VLDL triglycerides. Thus, CD measurements can be obtained with confidence on the preponderant bulk of normal VLDL. For the first time we report the CD spectra of human VLDL and IDL. In contrast with human LDL and the lipoproteins of the hypercholesterolemic rabbit, the entire CD SPECTRUM OF HUMAN VLDL shows increased ellipticity with decreasing temperature, which is completely reversible. We have found that the protein moieties of human VLDL and IDL contain substantially more helix (approximately 50%) than does that of human LDL.     

Structure of human low-density lipoprotein subfractions determined by X-ray small-angle scattering

The structure of low-density lipoprotein (LDL) particles from three different density ranges (LDL-1: d = 1.006−1.031 g/ml; LDL-3: d = 1.034−1.037 g/ml; LDL-6: d = 1.044−1.063 g/ml) was determined by X-ray small-angle scattering. By using a theoretical particle model, which accounted for the polydispersity of the samples, we were able to obtain fits of the scattering intensity that were inside the noise interval of the measured intensity. The assumption of deviations from radial symmetry is not supported by our data. This implies a spread-out conformation of the apolipoprotein B (apoB) molecule, which appears to be localized in the outer surface shell. A globular structure is not consistent with our data. Furthermore, different models exist concerning the structure of the cholesterol ester core below the phase transition temperature. The electron density data suggest an arrangmeent in which the steroid moieties are localized at average radii of 3.2 and 6.4 nm. Model calculations show that packing problems can only be avoided if approximately half of the acyl chains of each shell are pointing towards the center of the particle, the other half towards the surface. This arrangement of the acyl chains has never been proposed before. The LDL particles of different density classes differ mainly with respect to the size of the core but also with respect to the width of the surface shells. Model calculations show that the size of different LDL particles can be accurately predicted from the compositional data.     

Integrated stereological and biochemical studies on hepatocytic membranes. II. Correction of section thickness effect on volume and surface density estimates

The basic stereological formulas for estimating volume (Vv) and surface (Sv) densities are strictly valid only for true infinitely thin sections; the use of "ultrathin" sections of finite thickness T introduces systematic errors, mostly in the sense of overestimation of the parameters. These errors depend on the size and shape of the structural elements and on T. Correction factors for this effect of T are derived by considering model structures that simulate the shape and arrangement of subcellular organelles: (a) spherical vesicles, (b) disks as models for rough endoplasmic reticulum (RER) cisternae, (c) cylindrical tublules as models for smooth endoplasmic reticulum (SER) tubules, microvilli, etc. For vesicles, a model of discrete convex spherical particles is assumed; the correction factors consider loss of caps due to grazing sections and size distribution of the vesicles. The disk and tubule models are used in connection with the new integral geometric formulas of R.E. Miles which consider random aggregates of "inter-penetrating" particles so that the resultant structure is non- convex and thus approximates in nature the networks characteristic of endoplasmic reticulum (ER). Some practical examples relative to liver cells show that the errors due to section thickness may be of the order of 20-40% or more. Computation formulas as well as graphs are given for the determination of the correction factors for Vv and Sv.     

Shape effects in elastic scattering by orientationally random ensembles of simple model viruses

Recent theoretical work has shown that the complete set of polarized elastic light scattering studies should yield information about particle structure that has so far hardly been utilized. We present calculations of such light-scattering properties for a number of model structures, exploring particularly the size limit at which the new effects should become visible. The particles are assumed to be randomly oriented in aqueous suspension, and all identical to each other. We compare several particle models of differing geometrical shape, but with identical forward scattering power and identical radii of gyration. We find that one of the ten observables shows particularly desirable properties as a general large-particle characterization parameter: it is nonzero for all structures, it approaches zero as particle size decreases, and it shows an angular dependence that distinguishes among models of different shape. Assuming incident light at 350 nm, it differentiates between different shaped particles with radii of gyration as small as 50 nm. Such particles are well below the optical resolution limit and about the size of many types of viruses.     

External and internal glucose mass transfers in succinic acid fermentation with stirred bed of immobilized Actinobacillus succinogenes under substrate and product inhibitions

This paper is dedicated to the study on the external and internal mass transfers of glucose for succinic acid fermentation under substrate and product inhibitions using a bioreactor with stirred bed of immobilized Actinobacillus succinogenes cells. By means of the substrate mass balance for a single particle of biocatalysts, considering the kinetic model adapted for both inhibitory effects, specific mathematical models were developed for describing the profiles of the substrate concentration in the outer and inner regions of biocatalysts and for estimating the substrate mass flows in the liquid boundary layer surrounding the particle and inside the particle. The values of the mass flows were significantly influenced by the internal diffusion velocity and rate of the biochemical reaction of substrate consumption. These cumulated influences led to the appearance of a biological inactive region near the particle center, its magnitude varying from 0 to 5.3% of the overall volume of particles.     

Perfluorocarbon particle size influences magnetic resonance signal and immunological properties of dendritic cells

The development of cellular tracking by fluorine ((19)F) magnetic resonance imaging (MRI) has introduced a number of advantages for following immune cell therapies in vivo. These include improved signal selectivity and a possibility to correlate cells labeled with fluorine-rich particles with conventional anatomic proton ((1)H) imaging. While the optimization of the cellular labeling method is clearly important, the impact of labeling on cellular dynamics should be kept in mind. We show by (19)F MR spectroscopy (MRS) that the efficiency in labeling cells of the murine immune system (dendritic cells) by perfluoro-15-crown-5-ether (PFCE) particles increases with increasing particle size (560>365>245>130 nm). Dendritic cells (DC) are professional antigen presenting cells and with respect to impact of PFCE particles on DC function, we observed that markers of maturation for these cells (CD80, CD86) were also significantly elevated following labeling with larger PFCE particles (560 nm). When labeled with these larger particles that also gave an optimal signal in MRS, DC presented whole antigen more robustly to CD8+ T cells than control cells. Our data suggest that increasing particle size is one important feature for optimizing cell labeling by PFCE particles, but may also present possible pitfalls such as alteration of the immunological status of these cells. Therefore depending on the clinical scenario in which the (19)F-labeled cellular vaccines will be applied (cancer, autoimmune disease, transplantation), it will be interesting to monitor the fate of these cells in vivo in the relevant preclinical mouse models.