An approach to the isolation of biological particles using sedimentation analysis

A systematic, general approach for the design of an initial purification procedure for any biological particle is described in this communication. A series of centrifugations in fixed angle rotors has been used to obtain information on the sedimentation behavior of particles of interest (Anderson, N.G. (1967) Anal. Biochem. 23, 72-83). Refinements of this technique have facilitated the determination of sedimentation profiles of subcellular organelle markers in suspensions of murine spleen and brain. The degree of homogeneity of several particles with respect to size can be ascertained from the sedimentation profiles. Alterations in these profiles after mechanical disruption and treatment with detergents are readily measurable and have been found to be useful in both the characterization and isolation of subcellular particles. Because fixed angle rotors are used in these studies, the data obtained can be directly applied to the development of a preparatory scheme for purification of a desired particle. These methods for sedimentation analysis are readily applicable to subcellular organelles, macromolecular complexes, viruses, viral-like agents, and a variety of macromolecules.     

Interparticle interactions and structural changes of nucleosome core particles in low-salt solution

The structural behavior of the nucleosome core particles in the range of solvent Na+ concentration from 10.45 to 0.45 mM has been studied by small-angle neutron and synchroton radiation X-ray scattering, sedimentation, atomic absorption spectroscopy, density measurements, and circular dichroism. With decreasing salt concentration, the appearance of a scattering peak that is assignable to interparticle interactions, an intraparticle structural transition, a decrease in the sedimentation velocity of the particle, and a release of bound Na+ ions from the particle are all observed concurrently when the ratio of solvent Na+ ions per particle is below approximately 1000. These observations are interpreted to indicate that a release of bound Na+ ions from the particle brings about structural rearrangements and weakens the electrostatic shielding of the particle, and this introduces long-range repulsive ordering of the particle in low-salt solution. Analyses of the scattering data indicate that the rearrangement within the core particle in low-salt solution is slight, changing the particle's shape slightly from cylindrical to a more spherical form by moving the center of the mass of the DNA somewhat inward with accompanying small decreases in the radii of gyration of both the DNA and the histones.     

Effect of altered G levels on deposition of particulates in the human respiratory tract.

The primary mode of depositon of particles in the respiratory tract in the size range 0.5-10 mum diam (unit density) is sedimentation. The rate of sedimentation is directly proportional to the velocity of settling of the particle. Therefore, the total deposition of particles in the respiratory tract as well as the region of deposition is affected by changes in gravity. Human subjects were exposed to aerosols of 2.02-mum-diam polyvinyltoluene particles at 0, 0.5, 1.0, and 2.0 G. Total deposition was measured at each G level. Results indicate an almost linear increase in total deposition with increasing G levels over the range studied. The deposition measured at 1 G was less than reported in earlier experiments and the deposition at levels less than 1 G was less than had been calculated by Muir and Beeckmans. These data show that although sedimentation plays the major role in depostion of 2.02 mum particles, it is less than previously described.     

Analog modeling of glucagon-induced autophagy in rat liver. II. Evaluation of iron labeling as a means for identifying telolysosome, autophagosome and autolysosome populations.

To evaluate the potential usefulness of iron labeling as a means for identifying the telolysome, autophagosome and autolysosome populations of rat liver, animals treated with Jectofer (iron-citric acid-sorbitol complex), or with Jectofer followed by glucagon, have been studied with a variety of biochemical and morphological methods. Differential centrifugation studies of liver homogenates revealed that the sedimentation velocity and mechanical fragility of acid phosphatase bearing particles increase with the duration of Jectofer treatment and that iron accumulates in the mitochondrial and nuclear fractions. Rate sedimentation studies confirmed the change in sedimentation velocity, which was shown to be due in part to a marked increase in particle density. Quantitative morphological analysis of liver M + L and N + M + L fractions revealed a nearly complete absence of pericanalicular dense bodies after 6–7 days of Jectofer treatment. In these fractions a new type of particle containing fine electron dense granules was seen. The mean volume of these particles was decreased and their number increased when compared to dense bodies but the general morphology and overall size distribution of the two particle classes were similar. In animals given both Jectofer and glucagon, autophagic vacuole formation was similar to that found in animals receiving only glucagon. However, the increase in osmotic fragility of acid phosphatase bearing particles usually seen after glucagon administration occurred at a significantly slower rate. Examination of paniculate fractions revealed the presence of autophagic vacuoles with (autolysosomes) and without (autophagosomes) fine dense granules. The number of autolysosomes and their relative proportion in the autophagic vacuole population were correlated with an increase in the osmotic fragility of the acid phosphatase bearing particles in the same fraction. Organelle degeneration was observed more frequently in autolysosome profiles. These results support the contention that iron labeling can be used to separate the principal particle populations participating in the autophagic response induced by glucagon.     

Isolation of human monocytes according to volume and density

Human peripheral blood monocytes were obtained in very pure preparations by using buoyant density gradient centrifugation followed by velocity sedimentation. We introduced several modifications in the experimental procedure in order to take advantage of the minimal differences in cell density and size between monocytes and lymphocytes. Previous methods used to isolate monocytes based on their physical properties are reviewed, and the theory of velocity sedimentation is discussed with regard to the differences in the methodology used, which account for the different results we obtained.     

Size-separation of yeast mitochondria in the zonal centrifuge

Mitochondria, released from yeast spheroplasts and subjected to rate separation through sorbitol gradients in the zonal centrifuge, migrated in a wide symmetrical zone. Electron micrographs showed that the mitochondria had been resolved within the zone according to size. The mean mitochondrial diameter at the leading edge was approximately twice that at the trailing edge of the particle zone. Activities of the enzymes cytochrome oxidase, malate dehydrogenase, and reduced nicotinamide adenine dinucleotide- and d-lactate cytochrome c reductases were essentially uniform throughout the mitochondrial zone. Mitochondria from a vegetative-petite mutant had almost the same size distribution as the isogenic wild type, but with somewhat larger mean diameter and either absent or markedly reduced enzyme activities. Mixtures of wild-type and petite mitochondria produced sedimentation profiles showing overlap of particle populations with respect to mean sedimentation rates and mitochondrial diameters, as well as intermediate levels of enzyme activities. Both cristate and noncristate organelles were present throughout the mitochondrial zone from these mixtures. Mitochondria centrifuged in sorbitol density gradients were well-preserved and yielded consistent sedimentation profiles, whereas particles in sucrose density gradients migrated more slowly, produced varied sedimentation profiles, and often showed spurious peaks, presumably due to particle aggregations.     

Settling of fixed erythrocyte suspension droplets

The fractionation of micron-size particles according to physical properties of size, density and surface characteristics by centrifugation and electrophoresis is hindered when the particles behave collectively rather than individually. The formation and sedimentation of droplets containing particles is an extreme example of collective behavior and a major problem for these separation methods when large quantities of particles need to be fractionated. In this paper, experiments that measured droplet sizes and settling rates for a variety of particles and droplets are described. Expressions are developed relating the particle concentration in a drop to measurable quantities of the fluids and particles. The number of particles in each droplet was then estimated along with the effective droplet density and certain trends are noted. Since a major application of this work is the purification of biological cells in the range of 10 microns, for which monodisperse inert particles are not available, red blood cells from different animals fixed in glutaraldehyde provided model particle groups with the necessary size range, visibility and stability for these fluid dynamical studies.     

Diffusion of the Reaction Boundary of Rapidly Interacting Macromolecules in Sedimentation Velocity

Sedimentation velocity analytical ultracentrifugation combines relatively high hydrodynamic resolution of macromolecular species with the ability to study macromolecular interactions, which has great potential for studying dynamically assembled multiprotein complexes. Complicated sedimentation boundary shapes appear in multicomponent mixtures when the timescale of the chemical reaction is short relative to the timescale of sedimentation. Although the Lamm partial differential equation rigorously predicts the evolution of concentration profiles for given reaction schemes and parameter sets, this approach is often not directly applicable to data analysis due to experimental and sample imperfections, and/or due to unknown reaction pathways. Recently, we have introduced the effective particle theory, which explains quantitatively and in a simple physical picture the sedimentation boundary patterns arising in the sedimentation of rapidly interacting systems. However, it does not address the diffusional spread of the reaction boundary from the cosedimentation of interacting macromolecules, which also has been of long-standing interest in the theory of sedimentation velocity analytical ultracentrifugation. Here, effective particle theory is exploited to approximate the concentration gradients during the sedimentation process, and to predict the overall, gradient-average diffusion coefficient of the reaction boundary. The analysis of the heterogeneity of the sedimentation and diffusion coefficients across the reaction boundary shows that both are relatively uniform. These results support the application of diffusion-deconvoluting sedimentation coefficient distributions c(s) to the analysis of rapidly interacting systems, and provide a framework for the quantitative interpretation of the diffusional broadening and the apparent molar mass values of the effective sedimenting particle in dynamically associating systems.     

Physical properties of nucleoprotein cores from adenovirus type 5.

Analytical ultracentrifugation, thermal denaturation, and electron microscopy have been used to study nucleoprotein core particles, obtained from disrupted type 5 adenovirus and partially purified on glycerol density gradients. Electron microscopy at low salt concentrations has shown that the cores are homogeneous particles with characteristic structures, which vary with conditions of observation from a fairly loose network of fibers to a highly condensed, compact particle. Sedimentation measurements in the analytical ultracentrifuge, both by boundary and by band techniques, show that the cores are relatively homogeneous in solution and have sedimentation coefficients near 185 S at low salt concentrations, about 243 S in 1 or 2 M NaCl, and 376 S in 1 mM MgCl2. Correlation of sedimentation data with electron microscopic observations suggests that the 185 S particle has a loose, fibrous structure, while the faster species are more highly condensed particles. The melting temperature of the cores in 5 mM Tris/HCl is 79 degrees C, which is 10 degrees C higher than the Tm for purified, viral DNA. This indicates that the protein enhances the stability of DNA in the nucleoprotein complex.     

Particle retention in the forestomach of a browsing ruminant, the roe deerCapreolus capreolus

A combination of a flotation/sedimentation experiment and sieve analysis for the reticulorumen (RR) contents of roe deerCapreolus capreolus Linnaeus, 1758, a browsing ruminant, showed that there was no correlation between particle size and particle density. Large particles were present in both the sedimented and the buoyant fraction, which is in accord with the reported absence of stratification of RR contents in browsing ruminants. Comparative sieve analysis of roe deer RR and caecal/rectal material demonstrated that there must be some selective particle retention in the browsing ruminant as well, as a certain fraction of large particles in RR contents does not occur in the caecal/rectal material. These results lead to the explanatory dilemma that, while selective particle retention is observed, it cannot be due to the mechanisms known to work in grazing ruminants.     

Size transformations of intermediate and low density lipoproteins induced by unesterified fatty acids

Plasma from individual human subjects is known to contain multiple discrete subpopulations of low (LDL) and intermediate (IDL) density lipoproteins that differ in particle size and density. The metabolic origins of these subpopulations are unknown. Transformation of IDL and larger LDL to smaller, denser LDL particles had been postulated to occur as a result of the combined effects of triglyceride hydrolysis and lipid transfer. However, the presence of multiple small LDL subspecies has been described in patients lacking cholesteryl ester transfer protein. We have characterized an alternative pathway in which size decrements in IDL or LDL are produced in the presence of unesterified fatty acids and a source of apolipoprotein (apo) A-I. Incubation of IDL or LDL subfractions with palmitic acid and either high density lipoproteins (HDL), apoHDL, or purified apoA-I gives rise to apoA-I, apoB-containing complexes that can dissociate into two particles, an apoB-containing lipoprotein with particle diameter 10-30 A smaller than the starting material, and a still smaller species (apparent peak particle diameter 140-190 A) containing lipid and apoA-I but no apoB. The newly formed IDL or LDL are depleted in phospholipid and free cholesterol with no change in apoB-100 as assessed by SDS gel electrophoresis. We hypothesize that this reaction may contribute to the formation of discrete IDL and LDL subpopulations of varying size during the course of hydrolysis of triglyceride-rich lipoproteins in plasma.     

SEDIMENTATION IN THE ANGLE CENTRIFUGE

1. Using hemocyanin from Limulus polyphemus as a test material, the process of sedimentation in the angle centrifuge, operating both in vacuum and in the open air, has been investigated. 2. Sedimentation in a given field of force was found less efficient when centrifugation was conducted in the open air, because of thermal convection. 3. Correlations have been made with results obtained in the analytical ultracentrifuge, and a theory of sedimentation in inclined tubes has been presented to explain the experimental results. 4. It has been shown that under proper conditions the angle centrifuge may be used for approximate determinations of particle size. 5. Recommendations, based mostly on experimental evidence, have been made for improving sedimentation and interpreting results. 6. To counteract convective disturbances of either thermal or inertial origin, a satisfactory method has been developed which consists of furnishing the fluid under study with a synthetic density gradient, formed with sucrose or some other non-sedimentable material.     

Gravitational and magnetic activation methods applied to cultured cells (LK 35.2)

Monoclonal antibody 10.2-16 is directed toward the mouse class II major histocompatibility complex gene product 1-Ak expressed on the cell line LK35.2. Instead of activating cells by fluorophor we used (acrylamide-coated) heavy and magnetic microspheres of 0.6 micron in radius. These microspheres are chemically coupled (carbodiimide method) with the antibody toward the surface antigen. The cells are observed through a microscope with horizontal alignment, as they sediment in a (temperature controlled) tube with square cross-section. Stokes Law allows the determination of the density of cells (first alone) using viscosity and density of Dulbecco's modified Eagle's Medium together with the observed mean sedimentation velocity (66 microns/min) and a mean diameter of 10 microns. We found a density of 1.0558 +/- 0.0028 g/cm3 at 10 degrees C. Independently, thinly coated, heavy (and magnetizable) microspheres with the cited antibody are attached to cells and observed likewise. The increased sedimentation velocity permits us to show that the cells were fully covered with microspheres (290 per cell). A magnetic field gradient opposing gravity moved these cells against gravity with two different mean velocities, 340 microns/min and 850 microns/min. The higher velocity resulted in 290 particles per cell, the lower one in 130 particles per cell. The limits for the expansion of this method to smaller particle sizes (down to 10 nm) are evaluated.     

Some Properties of the PBP1 Transduction System in Bacillus pumilus

Bacteriophage PBP1 is a flagella-specific virus that performs generalized transduction in strains of Bacillus pumilus. PBP1 is morphologically and serologically distinct from two other flagella-specific phages, PBS1 and SP-15, which perform generalized transduction in certain Bacillus species. The DNA extracted from PBP1 particles has a buoyant density of 1.690 g/cm(3) in cesium chloride gradients, a melting temperature of 86.1 C, and a sedimentation velocity of 47S in neutral sucrose gradients. Assuming the molecule is a linear duplex, PBP1 DNA has a molecular weight of approximately 76 x 10(6). In two strains of B. pumilus which are sensitive to both PBP1 and PBS1, co-transducible genetic markers are more tightly linked by PBS1 transduction than by PBP1 transduction. The size of the fragment of bacterial DNA carried by PBP1-transducing particles, inferred from transduction studies and sedimentation analysis of viral DNA, suggests that PBP1 may be useful for genetic studies of extrachromosomal DNA elements present in two strains of B. pumilus. Genetic exchange of chromosomally located genes between the plasmid(+) and plasmid(-)B. pumilus strains NRS 576 and NRRL B-3275 has been demonstrated by PBP1 transduction.     

Analytical model of hygroscopic particle behavior in human airways

A model is developed to calculate the deposition of hygroscopic aerosols in the human tracheobronchial (TB) tree. The TB airflow pattern assumed is consistent with experimental observations and accounts for anatomical features such as the larynx and cartilaginous rings in large airways. Some original deposition efficiency formulae are presented for laminar and turbulent airstreams. Stepwise growth is simulated by changes in particle size and density at each TB generation. The dose distribution of NaCl aerosols is studied as a function of inhaled particle size and flow rate. Two NaCl growth rate curves are used which differ in the mode of aerosol-air mixing in the trachea. The initial rate of aerosol mixing in the human due to the laryngeal jet is shown to be an important factor affecting the deposition of hygroscopic aerosols. Total TB deposition of NaCl exceeds that for nonhygroscopic particles of the same inhaled aerodynamic size. Hygroscopic growth can also influence the regional TB distribution of dose when submicron NaCl particles grow rapidly enough to deposit by impaction and sedimentation.     

The higher order repeat structure of chromatin is built up of globular particles containing eight nucleosomes

Mild nuclease digestion of rat liver chromatin generates particles with sedimentation coefficients of about 33S, 60S, and 90S (in 50 mM NaCl). The kinetics of appearance and disappearance of these particles with progressive digestion suggest that they are produced by cleavage from a higher order repeat structure, the 33S particle representing the monomer. At an intermediate stage of digestion, about 75 % of the nuclear chromatin can be recovered as monomers to trimers of this higher order structure. Sedimentation profiles indicate that monomer particles containing 7–8 nucleosomes occur at the highest frequency. The DNA fragments in monomers have a size corresponding to hepta- and octanucleosomes, and those in dimers have a size corresponding to chains of sixteen nucleosomes. The higher order repeat structure is only stable between 30 and 200 mM NaCl; the particles unfold below 30 and above 200 mM NaCl. When examined by electron microscopy, monomers and dimers appear as compact globular structures. Relaxation by lowering the salt concentration results in the appearance of polynucleosomes with a chain length of eight beads in the monomer and sixteen in the dimer particle. These results indicate that the unit particle of the higher order repeat structure of rat liver chromatin contains eight nucleosomes.     

The construction and analysis of sucrose gradients for use with zonal rotors.

The rate of sedimentation of a particle in a sucrose solution depends on the viscosity and density of the medium. These two variables are related to the sucrose concentration and the temperature of the medium by new simple equations. These equations were used in a rapid iterative procedure that relates the distance moved by a zone in a continuous sucrose gradient to its sedimentation coefficient. It is shown by comparison with experiment that this iterative method allows the distance moved by a zone to be calculated rapidly. The method may therefore be used to optimize the separation of particles in a sucrose-gradient-centrifugation experiment. The method also allows the unknown sedimentation coefficients of several zones to be measured from a single sucrose-gradient-centrifugation experiment.     

Assembly and characterization of nucleosomal cores on B- vs. Z-form DNA

The ability of right- vs. left-handed alternating purine/pyrimidine copolymers to support the formation of nucleosomes has been examined by using a trout testis assembly factor. The protein, which is thermostable, has a molecular weight of 29000 and will assemble nucleosomes onto both SV40 and calf thymus DNA. This assembly factor has been used to assemble nucleosomes onto the B and Z conformations of poly[d(Gm5C)] and the B conformation of poly[d(GC)]. The isolated B-form particles, which sediment at approximately 11 S in a sucrose density gradient, contain DNA of 140-200 bases in length and the four core histones. The isolated Z-form particles, which also sediment at approximately 11 S, contain the four core histones and DNA of 170-250 bases in length. Physical analysis of the particles by absorbance and circular dichroic spectroscopy indicates that the DNA remains in the original conformation throughout the isolation procedure. Further, the particles reconstituted onto left-handed DNA compete effectively for an anti-Z DNA antibody, while the corresponding right-handed particles do not. Analytical sedimentation velocity determinations indicate that the B-form poly[d(Gm5C)] and poly[d(GC)] particles sediment at 11.2 and 11.1 S, respectively. In contrast, the poly[d(Gm5C)] Z-form particles have an S20,w of 10.6 S. The differences in the sedimentation velocity and the density of the cores, and in the lengths of DNA associated with the particles, suggest that the conformation of the DNA affects the manner in which it associates with the histone octamer.     

Dispersion of 0.5- to 2-micron aerosol in microG and hypergravity as a probe of convective inhomogeneity in the lung.

We used aerosol boluses to study convective gas mixing in the lung of four healthy subjects on the ground (1 G) and during short periods of microgravity (microG) and hypergravity ( approximately 1. 6 G). Boluses of 0.5-, 1-, and 2-micron-diameter particles were inhaled at different points in an inspiration from residual volume to 1 liter above functional residual capacity. The volume of air inhaled after the bolus [the penetration volume (Vp)] ranged from 150 to 1,500 ml. Aerosol concentration and flow rate were continuously measured at the mouth. The dispersion, deposition, and position of the bolus in the expired gas were calculated from these data. For each particle size, both bolus dispersion and deposition increased with Vp and were gravity dependent, with the largest dispersion and deposition occurring for the largest G level. Whereas intrinsic particle motions (diffusion, sedimentation, inertia) did not influence dispersion at shallow depths, we found that sedimentation significantly affected dispersion in the distal part of the lung (Vp >500 ml). For 0.5-micron-diameter particles for which sedimentation velocity is low, the differences between dispersion in microG and 1 G likely reflect the differences in gravitational convective inhomogeneity of ventilation between microG and 1 G.