Sedimentation behavior of chloroplast ribosomes from Chlamydomonas reinhardtii.

The identity of peaks generated by chloroplast ribosomes of Chlamydomonas reinhardtii were determined by zone velocity sedimentation on sucrose density gradients, and analysis of distribution of ribosomal RNAs in the gradients. The sedimentagion coefficient of the principal peak was 66-70 S (usually 69 S), in good agreement with previously reported values for chloroplast ribosomes of C. reinhardtii, and other organisms. The fast sedimenting side of the 69 S peak contained an excess of chloroplast large subunit. When ribosome dissociation was prevented by sedimentation at low velocity, by aldehyde fixation, or by the presence of nascent polypeptide chains, the principal peak had a sedimentation coefficient of about 75 S. Thus the 69 S peak was an artifact caused by dissociation during centrifugation. Peaks that contained chloroplast ribosomal RNAs were also observed at '60 S' and '45 S' when chloroplast ribosomes were centrifuged unfixed at high velocity. The amounts of '60 S' and '45 S' components were decreased by centrifugation at low speed, or fixation, but sedimentation coefficients remained unchanged. The '60 S', and '45 S' components were identified as large, and small subunits of chloroplast ribosomes, respectively. The artifacts produced by centrifugation of chloroplast ribosomes, are similar to the artifacts produced by centrifuging ribosomes of Escherichia coli. Similar explanations appear to apply to both. We concluded that the 69 S chloroplast ribosome peak occurs because of dissociation of 'tight' couples, and incomplete separation of subunits. Subunit peaks (60 S and 45 S) arise from free subunits, and/or from dissociation of 'loose' couples.     

Properties of various rotors used for zone centrifugation

The following results have been obtained from a quantitative study of zone centrifugation: (1) it is shown that the sedimentation velocity of all kinds of macromolecules is constant in 5–20% constant sucrose gradients, whatever swinging bucket or zonal rotor is being used, and at any usual temperature. (2) The proportionality constants between time of centrifugation and sedimented distance have been calculated for several rotors. They allow an estimate of relative centrifugation times. (3) An equation of the resolving power of zone centrifugation in isokinetic density gradients is used to compare the resolution of various rotors. (4) An equation of Vinograd and Bruner and Spragg and Rankin is discussed and used for the calculation of the maximum macromolecular load of the rotors. A summary of these results is presented in a table, which should help in the choice of the rotor best suited for a particular experiment.     

Polysome disassembly in cell extracts of cricket male accessory gland during sucrose gradient centrifugation

The stability of polysomes in cell extracts of cricket (Acheta domesticus) male accessory gland has been examined by sedimentation through a variety of step and linear sucrose gradients. After prolonged centrifugation there is a considerable decline in polysome content with a concurrent increase in monosomes. The extent of the reduction is more severe in step gradients, although the polysomes that remain show a typical profile on linear gradients.Evidence is presented which indicates that the reduction in polysome content is not due to nuclease action. The presence of detergents can affect the extent of disassembly but is not the principal cause. Comparison of [³H]leucine pulse-labelled gluteraldehyde-fixed and unfixed polysomes subjected to extended centrifugation reveals a release of nascent label near the top of the gradients in unfixed preparations. At least part of this displaced material is present as peptidyl-tRNA, suggesting that forced dissociation of polysomes rather than premature termination of nascent chains occurs as a consequence of sedimentation pressures. Comparison of the distribution of polyadenylic acid (poly(A)) sequences in sucrose gradients following short- and long-term centrifugation shows a shift of poly(A) containing RNA out of the polysome and into the pre-monomer region. It is concluded that sucrose gradient sedimentation results in the disassembly of a portion of the polysome population in the tissue examined. The implications with regard to the study of nonpolysomal messenger ribonucleoprotein and monomeric ribosomes are discussed.     

Gradient design to optimize rate zonal separations

An approach to the design of gradients which maximize resolution is developed by analyzing the sedimentation of particles in linear sucrose gradients. Our analysis establishes the fundamental principles of rate separations. These principles can assist in the successful design of preparative centrifugation procedures. Rate separations are always optimal in homogeneous media or very shallow gradients of low density. In homogeneous media, resolution of particles which differ only in sedimentation coefficients is determined by the ratio of their sedimentation coefficients. Particles whose sedimentation properties oppose each other can, under certain conditions, not separate or barely separate unless conditions are carefully selected. Particle populations which differ more in density than in sedimentation coefficients clearly separate better by rate than by isopycnic banding. Rate separations in gradients are considerably improved in a type of gradient where the viscosity decreased as the density increased.     

A New Procedure for Quantitative Measurements of Virus Particles in Crude Preparations

A new method is described for the quantitative measurement of virus concentration in crude preparations by density gradient centrifugation and electron microscopy. The centrifugation is carried out in a specially designed centrifuge tube which permits separation and sedimentation of virus particles at different levels according to their sedimentation velocity. The gradient of a mixture of heavy and normal water (D(2)O-H(2)O) is designed to sediment the virus particles with constant velocity so that the optimal time of centrifugation can easily be calculated. The virus particles are collected on carbon-coated nickel grids floating on mercury at the bottom of the centrifuge tube and are counted by means of electron microscopy. The efficiency of the method is demonstrated with a crude plant extract of tobacco mosaic virus.     

Effect of large refractive index gradients on the performance of absorption optics in the Beckman XL-A/I analytical ultracentrifuge: an experimental study

An analytical centrifuge cell was modified to detect refraction of light transmitted through the cell caused by refractive index gradients formed by sedimenting solute during centrifugation. Sedimentation velocity and sedimentation equilibrium experiments were carried out in this cell on solutions containing high concentrations of protein and polysaccharide in a Beckman-Coulter XLA analytical ultracentrifuge. Analysis of the results indicates that in the absence of an optical artifact easily recognized as a "black band," the dependence of apparent absorbance upon radial position reported by the instrument may be considered a reliable measure of the solute concentration gradient.     

Subcellular fractionation of striatum: Sedimentation properties of dopaminergic synaptosomes

Linear sucrose density gradient centrifugation of a crude synaptosomal-mitochondrial preparation of rat striatum was performed at 82, 500g for 7.5, 15 and 30 min and 1, 4 and 20 h. After centrifugation various marker enzyme activities were measured throughout the gradients, viz. tyrosine hydroxylase (TH) and DOPA decarboxylase (DD) as markers of dopaminergic synaptosomes, lactate dehydrogenase (LDH) as a general synaptosomal marker and monoamine oxidase (MAO) as a mitochondrial marker. At all centrifugation times the distribution patterns of TH and DD activity coincided almost perfectly. Notable differences were found between the sedimentation properties of these TH/DD-containing particles and LDH-containing particles: TH and DD were symmetrically distributed in the gradient much sooner than LDH, at all centrifugation times the top of the TH and DD curves was lying deeper in the gradient than the highest LDH activity, and Th and DD became enriched in the gradients to a much greater extent than LDH. It is concluded that rat striatal dopaminergic synaptosomes form a relatively homogenous population of particles sedimenting faster into the gradients than the bulk of striatal synaptosomes does. This distinct sedimentation behaviour of the dopaminergic synaptosomes can be usefully applied for analytical purposes.     

Size of infectious DNA from human and murine cytomegaloviruses.

Viral DNA was isolated from human and murine cytomegalovirus by equilibrium centrifugation in cesium chloride gradients. The size of the DNA was measured relative to T4 DNA by velocity sedimentation in neutral glycerol gradients, and fractions were assayed for infectious DNA. Infectious murine cytomegalovirus DNA sedimented as a single peak with an estimated molecular weight of 136 X 10(6). Infectious human cytomegalovirus DNA was detected in two peaks with molecular weights of 130 X 10(6) and 150 X 10(6).     

SEDIMENTATION PROPERTIES OF RAT LIVER MITOCHONDRIA : Effects of Cortisone Treatment

A prediction of the velocity of sedimentation of rat liver mitochondria in sucrose gradients is made on the basis of recent measurements of the size of isolated mitochondria suspended in sucrose medium and the model proposed by Bentzel and Solomon to describe the osmotic behavior of mitochondria. The experimentally observed velocity is extremely close to the predicted value and confirms by a different approach the estimate of mitochondrial volume made by Baudhuin and Berthet on the basis of electron microscopic measurements. Because cortisone treatment of rats is known to result in a marked increase in mitochondrial size as observed under the electron microscope, mitochondria were co-isolated from livers of control and cortisone-treated animals, and the sedimentation behavior of the mixtures was examined by sucrose density gradient centrifugation. Mitochondria from cortisone-treated animals were found to sediment 1.4 times as rapidly as those from control animals, indicating that their increased size cannot entirely be due to an increased imbibition of fluid from the surrounding sucrose medium, and that the change in size must at least in part be due to a change in content of nondiffusible mitochondrial components. Although the increase in sedimentation velocity of mitochondria from cortisone-treated animals is striking, it is less than that predicted solely on the basis of their size relative to that of control mitochondria. It is concluded that the increases in mitochondrial size and content of nondiffusible components produced by cortisone treatment are accompanied by alterations in mitochondrial composition as well.     

Molecular weight determination of glyoxalated RNA by sedimentation centrifugation

A rapid, reliable sedimentation centrifugation technique has been developed to measure the molecular weights of rather large glyoxalated RNAs. A distinctive feature of this method is that the glyoxalated RNAs can be analyzed in sucrose gradients containing no denaturant. This feature allowed us to compute the sedimentation coefficients of glyoxalated RNAs by a comparison with those of native, untreated RNA markers. These values then were used to obtain accurate molecular weight estimates by applying the linear log-log relation between the molecular weight of an RNA and its sedimentation coefficient.     

Simultaneous determination of the individual concentration gradients of two solute species in a centrifuged mixture: application to analytical ultracentrifugation

A procedure for determining the absolute activity of 14C-labeled and 3H-labeled solutes in a mixture from the measured counts per minute in two scintillation energy windows is described. It is shown that the method described here provides a substantially more accurate determination of 3H activity in the presence of a larger 14C activity, and a more accurate determination of 14C activity in the presence of a larger 3H activity, than does the standard dual label analysis implemented in a Beckman LS 3801 scintillation counter. The new dual label procedure is combined with the automated fractionation procedure of Attri and Minton [(1986) Anal. Biochem. 152, 319-328] to permit the gradients of each of two differently radiolabeled solute species in a mixture to be individually determined following centrifugation. It is shown that the sedimentation coefficients of each of two differently labeled noninteracting proteins in a mixture may be readily determined in a sedimentation velocity experiment, and that the molecular weights of each of two such proteins in a mixture may be readily determined in a sedimentation equilibrium experiment.     

Separation of haemopoietic cells for biochemical investigation. Preparation of erythroid and myeloid cells from human and laboratory-animal bone marrow and the separation of erythroblasts according to their state of maturation.

The separation of haemopoietic bone-marrow cells by centrifugation through discontinuous density gradients of Percoll is described. This method was used to prepare fractions enriched in erythroblasts, myeloid blast cells or reticulocytes from bone marrow of anaemic and non-anaemic rabbits, from the marrow of other anaemic laboratory animals and from human samples. It is a simple, rapid, reproducible and inexpensive technique that can be readily adapted to suit individual requirements. Secondly, a convenient method is presented for the separation of large quantities of bone-marrow cells into fractions enriched in erythroblasts at different stages of maturation, by velocity sedimentation through a linear gradient of 1-2% sucrose at unit gravity. In vitro, erythroblasts adhere together strongly via a mechanism almost certainly involving a beta-galactoside-specific surface lectin termed erythroid developmental agglutinin. Since the efficiency of cell-separation techniques depends heavily on the maintenance of a single cell suspension in which each unit can move independently, the presence of an adhesive molecule at the cell surface is of considerable significance. The effect of washing the marrow with a lactose-containing medium, which has been shown to remove the agglutinin, was therefore investigated in relation to both methods. The separation on Percoll gradients is considerably enhanced by this treatment. In addition, the unit-gravity sedimentation gradient can be loaded with 5-10 times more cells after lactose extraction in comparison with intact marrow. Although enrichment is less, a useful fractionation according to maturation is still obtained.     

Synaptophysin is sorted from endocytotic markers in neuroendocrine PC12 cells but not transfected fibroblasts

The targeting of synaptophysin, a major synaptic vesicle protein, in transfected nonneuronal cells has important implications for synaptic vesicle biogenesis, but has proved controversial. We have analyzed four transfected cell types by differential centrifugation and velocity gradient sedimentation to determine whether synaptophysin is targeted to endosomes or to synaptic vesicle-like structures. Synaptophysin was recovered only in vesicles that sedimented more rapidly than synaptic vesicles. The synaptophysin-containing vesicles were labeled if a surface-labeled cell was warmed to 37 degrees C, comigrated with transferrin receptor-containing vesicles on velocity and density gradients, and could be completely immunoadsorbed by anti-LDL receptor tail antibodies. These data demonstrate that synaptophysin was targeted to the early endocytotic pathway in the transfected cells and are inconsistent with the suggestion that synaptophysin expression induces a novel population of vesicles. Targeting of synaptophysin to early endosomes implicates their role in synaptic vesicle biogenesis.     

The evaluation of AKR leukemia virus purity: the requirement for both velocity and isopycnic centrifugation methods.

The purity of AKR murine leukemia virus obtained by isopycnic centrifugation was compared with the purity obtained by combining velocity sedimentation and isopycnic centrifugation methods. Evaluation of AKR and Rauscher viral purity by electron microscopy and by analysis of [³H]uridine-labeled viral RNA demonstrated that the velocity centrifugation step is essential for the removal of contaminants banding in the viral density region (1.19 – 1.15 g/ml). For studies requiring relatively pure oncornavirus preparations, a combination of both velocity sedimentation and isopycnic centrifugation steps are suggested. Viral recovery of about 50% was obtained by the method described.     

Characterization by sedimentation analysis of kinetoplast DNA from Trypanosoma cruzi at different stages of culture.

The kinetoplast DNA networks of Trypanosoma cruzi exist under two forms which have been studied by equilibrium density centrifugation in CsCl gradients containing ethidium bromide and by band sedimentation analysis. The relative proportion of the two forms has been measured and varies significantly between the exponential and stationary phase of growth, suggesting that one of these forms is a replicative intermediate. Both forms exhibit very high sedimentation coefficients. The sedimentation velocity ethidium titration was used to measure the superhelix density of the kinetoplast DNA after having established the validity of the method with in vitro closed DNA networks. The superhelix density of the native form of the kinetoplast DNA minicircles is very low and varies according to the physiological state of the trypanosomes. Furthermore, we observed a significant increase of the superhelix density of the kinetoplast DNA of trypanosomes grown in the presence of ethidium.     

Isolation and purification of a granulosis virus from infected larvae of the Indian meal moth, Plodia interpunctella.

A procedure was developed for purification of a granulosis virus inclusion body produced in vivo in the Indian meal moth, Plodia interpunctella (Hübner). Purification was accomplished by differential centrifugation, treatment with sodium deoxycholate, and velocity sedimentation in sucrose gradients. The adequacy of the procedure was confirmed by mixing experiments in which uninfected, radioactively labeled larvae were mixed with infected, unlabeled larvae. After purification, the virus was shown to be free of host tissue, to retain its physical integrity, and to be highly infectious per os. Preparations of purified virus consisted of homogeneous populations of intact inclusion bodies (210 by 380 nm) whose buoyant density was 1.271 g/cm3 when centrifuged to equilibrium in sucrose gradients. Electron microscopy of thin-sectioned virus or of virus sequentially disrupted on electron microscope grids demonstrated three components: protein matrix, envelope, and nucleocapsid.     

Isolation and purification of a granulosis virus from infected larvae of the Indian meal moth, Plodia interpunctella.

A procedure was developed for purification of a granulosis virus inclusion body produced in vivo in the Indian meal moth, Plodia interpunctella (Hübner). Purification was accomplished by differential centrifugation, treatment with sodium deoxycholate, and velocity sedimentation in sucrose gradients. The adequacy of the procedure was confirmed by mixing experiments in which uninfected, radioactively labeled larvae were mixed with infected, unlabeled larvae. After purification, the virus was shown to be free of host tissue, to retain its physical integrity, and to be highly infectious per os. Preparations of purified virus consisted of homogeneous populations of intact inclusion bodies (210 by 380 nm) whose buoyant density was 1.271 g/cm3 when centrifuged to equilibrium in sucrose gradients. Electron microscopy of thin-sectioned virus or of virus sequentially disrupted on electron microscope grids demonstrated three components: protein matrix, envelope, and nucleocapsid.     

Mass isolation of pole cells from Drosophila melanogaster.

Crude cell suspensions were obtained from 3 × 10⁶ pregastrula staged embryos. These cells fractionated into three bands on Renografin density gradients. Using ultrastructural characteristics for identification, pole cells were localized in the two denser bands. EM analyses also revealed a striking difference in the frequency of lipid vacuoles found in the pole-cell cytoplasm versus the cytoplasm of other embryonic cells. This difference has enabled us to identify pole cells by light microscopy using a neutral lipid stain. Through detailed analyses of the Renografin fractions with this stain, we have shown that pole cells resolve into two to three density classes. Evidence is presented which suggests that these density classes reflect different developmental age classes. The size differences between the pole cells and other embryonic cells contained in the enriched pole-cell fractions from the density gradients has enabled us to use sedimentation velocity centrifugation for additional enrichment. A distinct lower band of cells was obtained which consisted of 80% pole cells. Using these procedures, 1–2 × 10⁷ pole cells can be obtained daily.     

DNA damage, DNA repair and chromosome aberrations of xeroderma pigmentosum cells and controls following exposure to nitrosation products of methylguanidine

Nitrosation of methylguanidine (MG) led to products that caused DNA fragmentation (shift in sedimentation profiles of velocity centrifugation through alkaline sucrose gradients), a DNA repair synthesis (unscheduled uptake of (³H]TdR), chromosome aberrations and a lethal effect of cultured human fibroblasts. The response of repair-deficient xeroderma pigmentosum cells did not differ from that of controls. The nitrosation of MG must be carried out at a pH level below 3, in order to obtain products that react with cellular DNA. The results show that a DNA repair synthesis of human fibroblasts appear to be a sensitive assay for carcinogenic and mutagenic nitrosation products which may be formed within an organism from non-carcinogenic compounds.     

Two detergent-insoluble proteins of the human lymphocyte membrane are enriched in an isolated membrane fraction

Human lymphocytes isolated from peripheral blood on Ficoll/Paque density gradients were surface-labelled by 125I/lactoperoxidase or 3H/reductive alkylation and lysed in buffer solutions containing non-ionic or amphoteric detergents (octylphenylpolyoxyethylenes, octylglucoside, cholylamidopropyldimethylammoniopropane sulfonate) under a variety of conditions. The cell lysate was fractionated by sedimentation or by density gradient centrifugation. The large majority of the labelled proteins is solubilized by the detergents. Two proteins of 45 000 and 30 000 molecular weight are the main detergent-insoluble, surface-labelled components. They can be fractionated from detergent lysates of cells in relatively pure form from the other membrane proteins and from nuclear material on density gradients. The same two proteins are specifically enriched in a membrane fraction isolated from a detergent-free cell homogenate by density gradient centrifugation. Cytoskeletal and other intracellular proteins remain associated with these two proteins when fractionated by either of these two independent methods.