Basal-lateral membranes from rabbit renal cortex prepared on a large scale in a zonal rotor

Basal-lateral membranes from the renal cortex of the rabbit were isolated by sucrose gradient centrifugation in a zonal rotor which allows for a large-scale preparation of these membranes. A heterogeneous population of membranes (P4) which contained 29% of the (Na+ + K+)-ATPase found in the homogenate of renal cortex was prepared by differential centrifugation. When pellet P4 was subjected to centrifugation in a sucrose gradient the activity of (Na+ + K+)-ATPase, a marker for basal-lateral membranes, could be separated from enzymatic markers of other organelles. The specific activity of (Na+ + K+)-ATPase was enriched 12-fold at a density of 1.141 g/cm3. Membranes (P alpha) contained in the (Na+ + K+)-ATPase-rich fractions consisted primarily of closed vesicles which exhibited probenecid inhibitable transport of rho-aminohippurate. These membranes did not exhibit Na+-dependent, phlorizin-inhibitable D-glucose transport. Sodium dodecyl sulfate polyacrylamide gel electrophoresis of proteins from P alpha revealed at least six major protein bands with molecular weights of 91000, 81000, 73000, 65000, 47000 and 38000. A small fraction of total alkaline phosphatase found in the homogenate was found in pellet P4. Membranes containing this alkaline phosphatase activity were distributed widely over the gradient, with peak activity found at a density of 1.141 g/cm3. In contrast, when brush borders were subjected to gradient centrifugation under the same conditions as P4, alkaline phosphatase was found in a narrow distribution, with peak activity at a density of 1.158 g/cm3. The principle subcellular localization of the alkaline phosphatase found in P4 could not be determined unambiguously from the data, but the activity did not seem to be primarily associated with classical brush borders.     

Separation of plant cell organelles by zonal centrifugation in reorienting density gradients

Preparative separations of plant cell organelles (glyoxysomes, proplastids, mitochondria, and endoplasmic reticulum) in an ordinary refrigerated centrifuge were obtained by sucrose density gradient centrifugation in a zonal rotor loaded and unloaded in the static manner. The quality of the separation which was monitored by marker enzymes and electron microscopy compares to analytical separations in swinging-bucket rotors. Membrane alterations observed in glyoxysomes and mitochondria are traced back to sucrose as a major component of the homogenization and density gradient medium.     

Characterization of zonal fractions of calf thymus DNA

DNA isolated from calf thymus nuclei is fractionated by zonal centrifugation into 40 sedimentation-rate classes and the reduced viscosity profile determined. This profile is divided into four fractions, I–IV, IV being the fastest sedimenting. The relative concentrations of repetitive DNA sequences in these is determined by hybridization on membrane filters and also hypochromicity by reannealing at 60 °. Repetitive sequences are found in all fractions, although they are slightly more abundant in the order III > II > I. Moreover, fractions I, II, III, act as good competitors in hybridization experiments with each other, implying that a high degree of complementarity exists between repetitive sequences in each of the fractions. Fraction IV had peculiar hydrodynamic properties which have provoked observations on DNA purification.     

A study of nucleated erythrocytes by density-gradient centrifugation in a zonal rotor

1. Several substances of high molecular weight were examined for their suitability as suspension media in the formation of density gradients for the zonal centrifugation of avian erythrocytes. None proved satisfactory. 2. The behaviour of pigeon erythrocytes in rate-sedimentation experiments in a type A zonal rotor with density gradients of sucrose was examined. The mature cells sediment more rapidly than the younger cells and have a lower RNA/DNA ratio. Maturation is accompanied by a greater loss of RNA from the nucleus than from the cytoplasm. 3. The base composition of the nuclear RNA and of the two species of cytoplasmic ribosomal RNA is reported. 4. The RNA of erythrocytes may be labelled in vivo by injection of inorganic [(32)P]phosphate. The cells most active in the synthesis of RNA sediment less rapidly than the bulk of the cells. 5. Reticulocyte nuclei sediment more slowly than those from erythrocytes. Reticulocyte nuclei have a mean volume of 35mu(3) and are isopycnic with sucrose of density 1.2871 (measured at 20 degrees ). Maturation of the nuclei causes them to shrink to a volume of 25mu(3) and the density to increase to 1.2944.     

The purification of cell nuclei from calf uterus by zonal centrifugation in reorienting density gradients

A method is described for isolation of substantial amounts of pure and enzymatically active nuclei from whole calf uterus. The technique involves a multistep sequential homogenization of the tissue and a zonal centrifugation of the crude nuclear preparation in a reorienting density gradient rotor. Electron and phase contrast microscopic observations show that the nuclei are intact and practically free from cytoplasmic contamination. Based on DNA recovery, the purified fraction contains 9% of the nuclei of the total tissue and more than 19% of the filtered homogenate. The pure nuclear fraction consists of 29% DNA, 7% RNA, and 64% protein, which parallels the composition of purified nuclei from other mammalian tissues.     

Large-scale preparation of synaptosomes from bovine brain using a zonal rotor technique

A zonal rotor technique for the preparation of synaptosomes in bulk from bovine brain frontal cortex based on an empirical transformation of a small-volume discontinuous surcrose density gradient arrangement is presented in detail. The procedure yields new information concerning synaptosomes prepared in sucrose gradients. Cerebroside analysis and electron microscopy show myelin contamination to be restricted to the leading, less dense edge of the synaptosomal profile, free mitochondria to the trailing, more dense edge. Exclusion of fringe areas yields a highly purified synaptosome preparation which entirely enters the next dense layer beyond the 0.81.2 M sucrose interface. This interface collects most of the oubain-sensitive (Na⁺, K⁺) adenosine triphosphatase activity. The purified synaptosomes display very high intrinsic sialidase activity and are rich in di-, tri-, and tetrasialogangliosides, the preferred substrates for the enzyme. Up to 90% of the cholinesterase activity in the zonal rotor synaptosome preparation is specific acetylcholinesterase.     

Fractionation of rat fibroblasts in a zonal rotor by means of a viscosity barrier.

Cell fractionation procedures involving differential sedimentation followed by resuspension of pellets and isopycnic centrifugation are very difficult to apply to the small amounts of material available from tissue culture cells. We have explored the possibility of successive differential and isopycnic sedimentation in a zonal rotor using a short viscosity barrier for the differential sedimentation. The marker enzymes used were cytochrome oxidase, acid phosphatase, catalase, and 5′-nucleotidase. The results of these procedures are compared to the results of one-step isopycnic separations in gradients of sucrose and Stractan. The Stractan gradient was much more effective than the sucrose gradient in separating the marker enzymes from the proteins of a postnuclear supernatant, but neither type of gradient could significantly purify the marker enzymes one from another. A two-step procedure using a viscosity barrier was effective in separating particles carrying catalase from the other marker enzymes assayed and from most of the protein. A three-step procedure resulted in similar purification of mitochondria. Modification of barrier composition and centrifugation times would probably result in further improvement of separations according to individual requirements for yield, purification, and freedom from specific contamination by other subcellular particles.     

Use of alkaline sucrose gradients in a zonal rotor to detect integrated and unintegrated avian sarcoma virus-specific DNA in cells.

We have attempted to distinguish integrated and unintegrated forms of avian sarcoma virus-specific DNA in cells by sedimentaton through an alkaline sucrose gradient in a slowly reorienting zonal rotor. Results obtained with this procedure are similar to those obtained by the more convenient analysis of networks of high-molecular-weight cell DNA. Most, if not all, viral DNA appears completely integrated into the host cell genome in an avian sarcoma virus-transformed mammalian cell and in normal chicken cells (in which viral DNA is genetically transmitted). Fully transformed duck cells and duck embryo fibroblasts infected for 20 to 72 h contain both integrated and unintegrated viral DNA; up to one copy per cell is integrated within 20 h after infection, and four to eight copies are integrated in fully transformed cells. The amount of unintegrated DNA varies but may comprise over 75% of the viral DNA in acutely infected cells and from 20 to 70% of the viral DNA in fully transformed cells. The unintegrated DNA in either case consists principally of duplexes with "minus" strands the length of a subunit of the viral genome (2.5 X 10(6) to 3 X 10(6) daltons) and relatively short "plus" strands (0.5 X 10(6) to 1.0 X 10(6) daltons).     

The repair of large DNA adducts in mammalian cells.

This paper describes experiments involving the measurement of DNA damage and repair after treatment with 4-nitroquinoline 1-oxide (4NQO) or aflatoxin B1 (AFB1) epoxide in a number of mammalian cell cultures primarily associated with defects in the excision repair of UV-induced DNA damage. The results with transformed derivatives of XP cells belonging to different complementation groups showed that the extent of repair of 4NQO adducts at the N2 or C8 of guanosine did not correlate to the extent of repair reported by others after UV-irradiation. An examination of 4NQO repair in rodent UV-sensitive cell lines from different ERCC groups indicated that again there was little correlation between the extent of 4NQO and UV repair. However, regardless of complementation group those mutants that were defective in the repair of pyrimidine dimers and 6,4-photoproducts did exhibit a reduced ability to repair the 4NQO N2 guanosine adduct, whereas those mutants defective in pyrimidine dimer repair alone were able to repair this lesion as normal. In all of these cell lines there was a normal capacity to repair the 4NQO C8 guanosine adduct. Less extensive experiments involving AFB1 epoxide showed an XPC-transformed cell line was able to repair 40% of lesions after 6 h, whereas only 20% of repair is seen after UV. The rodent mutant V-C4 which belongs to the same ionising radiation group as irs2, was partially defective in repairing AFB1-induced damage. These experiments highlight the fact that although there are many commonalities between the repair of UV damages and lesions classed as large DNA adducts differences clearly exist, the most striking example here being the repair of the C8 guanosine 4NQO adduct which rarely correlates with a defect in UV repair.     

Subnuclear redistribution of DNA species in confluent and growing mammalian cells

About 20 to 25 percent of the nuclear DNA from cultured cells of the African green monkey, Cercopithecus aethiops, consists of a homogeneous, highly repetitive fraction designated C. aethiops component DNA. Use of in situ hybridization techniques reveals component at the centromeres of chromosomes from both diploid and heteroploid African green monkey kidney (AGMK) tissue culture cells. — Component DNA comprises 47 percent of the nucleolar DNA in actively growing primary AGMK cells, but only 31 percent of the nucleolar DNA in confluent cells which show density-dependent growth inhibition. Further, there is a pronounced shift of both main band and component DNA from euchromatin to heterochromatin when growing cells attain confluency. Thus, the relative subnuclear distributions of component and main band DNA's are different in growing and confluent cells. — In situ hybridization techniques indicate that component sequences aggregate in clumps in nuclei of growing cells and show a diffuse distribution in nuclei of confluent cells. This suggests that centromeric regions of the various chromosomes or groups of chromosomes aggregate and disaggregate reversibly as the culture changes from density-dependent growth inhibition to active cell division. — Hypotonic citrate treatment of primary AGMK cells causes nucleoli of confluent cells to disperse: this dispersion following citrate treatment was not seen in growing AGMK cells or in confluent or growing heteroploid cells. Similarly, this nucleolar dispersion was seen in confluent diploid mouse and human cells but not in growing diploid cells or in confluent or growing heteroploid cells.     

Condensation by DNA looping facilitates transfer of large DNA molecules into mammalian cells

Experimental studies of complete mammalian genes and other genetic domains are impeded by the difficulty of introducing large DNA molecules into cells in culture. Previously we have shown that GST–Z2, a protein that contains three zinc fingers and a proline-rich multimerization domain from the polydactyl zinc finger protein RIP60 fused to glutathione S-transferase (GST), mediates DNA binding and looping in vitro. Atomic force microscopy showed that GST–Z2 is able to condense 130–150 kb bacterial artificial chromosomes (BACs) into protein–DNA complexes containing multiple DNA loops. Condensation of the DNA loops onto the Z2 protein–BAC DNA core complexes with cationic lipid resulted in particles that were readily transferred into multiple cell types in culture. Transfer of total genomic linear DNA containing amplified DHFR genes into DHFR^– cells by GST–Z2 resulted in a 10-fold higher transformation rate than calcium phosphate co-precipitation. Chinese hamster ovarian cells transfected with a BAC containing the human TP53 gene locus expressed p53, showing native promoter elements are active after GST–Z2-mediated gene transfer. Because DNA condensation by GST–Z2 does not require the introduction of specific recognition sequences into the DNA substrate, condensation by the Z2 domain of RIP60 may be used in conjunction with a variety of other agents to provide a flexible and efficient non-viral platform for the delivery of large genes into mammalian cells.     

Characterization of DNA from three bee species

DNA was isolated from three species of bees: the common honey-bee (Apis mellifera), the Indian honey-bee (Apis cerana), and the leaf-cutting bee (Megachile rotundata). The guanine-cytosine distribution of the two honey-bee DNAs is relatively broad and skewed toward lower values; leaf-cutting bee DNA shows a narrow distribution. No distinct satellite bands are present in any of the species. Renaturation kinetics indicate that the genome sizes of the two honey-bee species are identical to one another and somewhat smaller than that of the leaf-cutting bee. About 89 per cent of the genome of all three species renatures slowly; this fraction presumably comprises the single-copy (unique) sequence portion of the genome.

Sufficient DNA was isolated from the dwarf honey-bee (Apis florea) to determine a guanine-cytosine distribution. Like the other honey-bee species, the distribution is relatively broad.     

Germ tube formation from zonal rotor fractions of Candida albicans.

Homogenous cell populations of increasing cell volume may have been isolated from exponential and stationary culture of Candida albicans by centrifugation on a sucrose gradient. Observations of the yeast-mycelial transition using these populations showed the following. (i) No fraction from early logarithmic phase cells was unable to undergo morphological transition. (ii) The time of initiation of germ tube production was correlated with cell size in stationary-phase cultures. (iii) The rate of appearance of germ tubes was nearly identical in all fractions measured. (iv) Addition of N-acetyl-D-glucosamine to homogeneous cell populations decreased the time of initial appearance of germ tubes but did not affect the rate of appearance after initiation.