A rapidly-banding component of animal DNA preparations that interferes with buoyant density studies

Rapidly-banding components of purified animal cell DNA's have been observed which have abnormal buoyant densities and show anomalous band profiles when centrifuged to equilibrium in cesium salts. These components interfere with the separation of animal DNA fractions and with the analysis of animal cell DNA's by buoyant density techniques. They can be detected by examining photographs of analytical buoyant-density ultracentrifugations before equilibrium has been reached. These rapidly-banding components are removed by phenol treatment.     

Defective Virions in Human Adenovirus Type 12

Purified preparations of human adenovirus type 12 showed two bands when subjected to isopycnic centrifugation in a density gradient of cesium chloride. Their density difference was about 0.003 g/ml, suggesting a small difference in their deoxyribonucleic acid to protein ratio. Virions with a lighter density can kill human KB cells and induce T antigen as efficiently as the heavy virions. However, they appeared incapable to form plaques. Two passages of the heavy infectious virions at low multiplicity of infection did not produce significant amounts of light virions; however, when it was passed at high multiplicity of infection, the light band became visible in a cesium chloride density gradient.     

Purification and characterization of a simple ribonucleoprotein particle containing small nucleoplasmic RNAs (snRNP) as a subset of RNP containing heterogenous nuclear RNA (hnRNP) from HeLa cells.

A ribonucleoprotein complex whose RNA complement consists exclusively of small nuclear RNA species (snRNA) has been purified from particles containing heterogenous nuclear RNA (hnRNP) from HeLa cells. This was accomplished by taking advantage of their ability to band at a density of about 1.43 g/cm3 in plain cesium chloride as well as in cesium chloride gradients containing 0.5% sarkosyl without prior aldehyde fixation. After these two steps of equilibrium density centrifugation, these snRNPs were still largely contaminated by free proteins (and especially phosphoproteins). A final step of purification by velocity sedimentation in a sucrose gradient containing 0.5 M cesium chloride and 0.5% sarkosyl was efficient in completely eliminating all free proteins. U1, U2, U4, U5 and U6 species according to the nomenclature of Lerner et al. (Nature, (1980) 283, 220-224) were found in these purified snRNPs, while a significant part of U6 and a small amount of U2 were found in the bottom fraction. 5S species behaved entirely as free RNA and is presumably a contaminant of cytoplasmic origin. Electrophoresis of proteins from snRNP labeled in vivo with (35S) methionine, revealed four bands with migrations corresponding to molecular weights ranging between 10,000 and 14,000 daltons.     

Biophysical Properties of Frog Virus and Its Deoxyribonucleic Acid: Fate of Radioactive Virus in the Early Stage of Infection

Frog virus (FV-3) was banded by isopycnic centrifugation in cesium chloride, sucrose, or potassium tartrate. Two bands of infectivity were regularly found at positions in cesium chloride corresponding to densities of 1.26 and 1.30 g/cm(3), respectively. Deoxyribonucleic acid from either band had the following characteristics: double-stranded; a T(m) of 76.3 C in 0.1 SSC (0.015 m NaCl plus 0.015 m sodium citrate) and a buoyant density of 1.720 g/cm(3) in cesium chloride, corresponding to a guanine plus cytosine content of 56 to 58% and a molecular weight of 130 x 10(6) daltons, determined by velocity sedimentation. These data, together with electron micrographs of sections of cells infected with material from either band suggest that two types of infectious frog virus particles exists, rather than a second virus in the frog virus stocks. The composition of frog virus was determined. It was found that highly purified preparations of frog virus were composed of 55.8% protein, 30.1% deoxyribonucleic acid, and 14.2% lipid. The kinetics of adsorption and uncoating of FV-3 was studied with radioactive virus. Uncoating is comparatively rapid and in contrast to poxvirus is unaffected by inhibitors of protein synthesis.     

Repetitious DNA in some Anemone Species

The DNA from several Anemone species, which contain different amounts of heterochromatin as revealed by Giemsa staining, was analysed by ultra-centrifugation and renaturation. No satellite band was observed in any of the samples centrifuged in cesium chloride gradients. Renaturation studies showed the presence of repetitive sequences. The proportion of repetitive DNA per genome varied from 53% to 67% and did not correlate with either the DNA content per cell or the relative amount of heterochromatin.     

A physical explanation for multiple-cell classes after centrifugation in colloidal silica gradients.

When cells of Dictyostelium discoideum were centrifuged to density equilibrium in linear gradients of colloidal silica (Ludox), approximately 40 discrete bands appeared. This suggested that there could be at least 40 different cell types. A similar result was found for formalinized red blood cells and plastic bends. Isolated bands of cells rebanded faithfully in new gradients and band spacing depended upon gradient steepness. However, the cell bands resulted from microscopic modifications in the linear gradients of Ludox caused by centrifugation. When the gradients were analyzed in the analytical ultracentrifuge, absorbance scans revealed that cell bands coincided with “bands” of Ludox, which formed even without cells. Evidence ruling out other possible causes for cell bands is presented. Additionally, procedures which avoid this condition are described.     

The Study of Ionizing Radiation Effects on Escherichia coli by Density Gradient Sedimentation

Density gradient sedimentation of bacterial cells in cesium chloride has been used to separate cells which have been irradiated with ⁶⁰Co gamma rays and have lost an appreciable amount of their DNA by subsequent degradation. Irradiated cells are found to band mainly at two characteristic densities, one corresponding to normal unirradiated cells and the other at a considerably lower density. The region corresponding to normal density cells is the only one that contains cells which will form colonies. Cells capable of synthesizing DNA following irradiation are found mainly at the region of normal density cells with some spreading into the lower density region. Cells in the lower density region contain less DNA than normal density cells. From an analysis of the relative numbers of cells in the two regions, it is suggested that the process of DNA degradation either takes place to a considerable extent in the genome or not at all. Analysis of the data in terms of numbers of cells having intact DNA and those having degraded DNA indicates a strong correlation between DNA degradation and cell death in this strain, JG151, and suggests that DNA degradation is a major but not the only cause of cell death.     

Motoneurons purified by cell sorting respond to two distinct activities in myotube-conditioned medium

Spinal motoneurons from chick embryos were purified by retrograde transport and fluorescence-activated cell sorting. Growth conditions for motoneurons were studied, with experiments focused on the effects of conditioned media from chick myotubes, fibroblasts, and spinal cord dividing cells. Motoneurons rapidly extended neurites when plated onto polylysine-coated dishes that had been exposed to these conditioned media. Enzymatic analysis of the substratum-binding, neurite outgrowth-promoting activity from myotube-conditioned medium indicated that it contained heparan sulfate and protein. The neurite outgrowth-promoting activity sedimented as a peak centered at a density of 1.34 in associative cesium chloride gradients, and eluted near the void volume of a Sepharose CL-6B column. Inclusion of myotube conditioned medium in the culture medium of motoneurons also enhanced their survival over periods greater than 2 days in culture. This enhancement of survival could not be explained by myotube-conditioned medium providing motoneurons with a continuous supply of the neurite outgrowth-promoting activity. Media conditioned by spinal cord dividing cells and fibroblasts supported motoneuron survival to some extent, but this effect was not as great as that of myotube-conditioned medium.     

Equilibrium Density Gradient Studies on Simian Virus 40-Yielding Variants of the Adenovirus Type 2-Simian Virus 40 Hybrid Population

The simian virus 40 (SV40)-yielding variants of the adenovirus type 2 (Ad.2)-SV40 hybrid (Ad.2(++)) population were studied by means of fixed-angle equilibrium density gradient centrifugation in cesium chloride. The hybrid virions of the Ad.2(++) high-efficiency yielder population banded at densities of 0.004 g/cm(3) lighter than the nonhybrid Ad.2 virions. The degree of separation of the hybrid particles was sufficient to permit greater than 100-fold relative purification by two cycles of centrifugation. Hybrid particles that produce adenovirus plaques in African green monkey kidney cells by two-hit kinetics (one-hit kinetics when assayed on lawns of nonhybrid adenovirus) were not separable from the particles that yield SV40 virus. The hybrid particle in the Ad.2(++) low-efficiency yielder population was not separable from the nonhybrid Ad.2 virions.     

Chlamydia trachomatis in cell culture. II. Susceptibility of seven established mammalian cell types in vitro. Adaptation of trachoma organisms to McCoy and BHK-21 cells

Trachoma organisms of serotype B were grown serially in irradiated cells (McCoy, BHK-21, Microbiological Associates, and BHK-21, Lister) and tested for infectivity in monolayers of five mammalian cell lines (BHK-21, CHO, HeLa S3, McCoy and OWMK) and two diploid strains (ST/BTL and WI-38). All cell types had low susceptibility to chlamydial infection but the number of inclusions increased when the inoculum was centrifuged onto the monolayers, or when the cells were irradiated. Infection was higher in non-irradiated CHO than in irradiated CHO in three out of a total of six experiments. Inclusion number was increased 300 times in HeLa S3 and up to three times in the other cell types after treatment with diethylaminoethyl-dextran (DEAE-D). Serial passage of Chlamydia trachomatis serotype B (strain Har-36) in CO60 McCoy and CO60 BHK-21 Lister resulted in partial adaptation of the strain to the host cell. The phenomenon of adaptation of serotype B to McCoy compensated for the lower susceptibility of this cell revealed when McCoy cells were inoculated with trachoma elementary bodies grown in BHK-21 Lister or in chick embryo yolk sac. Trachoma organisms of immunotypes A, B and C prepared in yolk sac produced more inclusion-forming units per ml in CO60 BHK-21 Lister than in CO60 McCoy.     

Fractionation of the differentiated types of cells constituting the pseudoplasmodia of the cellular slime molds

The observation of Milleret al. (1969) that the two types of cells (the prestalk and prespore cells) constituting the slug ofDictyostelium are separated by isopicnic centrifugation was reexamined by using more reliable methods both for dissociation of the slug and for identification of the cell type. Dissociated cells of slugs which had been grown on a standard culture medium formed two distinct bands after centrifugation through a Urografin density gradient. Contrary to Miller's findings, however, the light band consisted of the prestalk cells and the heavy band of the prespore cells. When the culture medium was modified, a population of spores of different buoyant density newly appeared during the subculture. Slug cells derived from such a spore had different buoyant densities and formed extra bands in a Urografin gradient. However, the prespore fraction was always heavier than the prestalk fraction derived from the same type of spores.     

A comparison of the effects of different substrata on chondrocyte morphology and the synthesis of collagen types IX and X

Summary Embryonic chick sternal chondrocytes were cultured either within three dimensional gels of type I collagen, type II collagen or agar, or as monolayers on plastic dishes coated with air-dried films of these matrix macromolecules. It was observed that cell shape and cell growth varied markedly between the different culture conditions. Flattened monolayers of cells on plastic or films of type I or type II collagen, proliferated more rapidly and reached a higher final cell density per culture than the more rounded cells found in the cultures on agar films or within three-dimensional gels. Biosynthetic studies demonstrated that in addition to the synthesis of type II collagen, all the cultures were producing collagen types IX and X. Chondrocytes cultured on plastic or films of the different matrix macromolecules all showed a similar expression of types IX and X collagen, independent of whether they displayed a flattened or round cell morphology. In contrast, marked variations in the proportions of the minor collagens, particularly type X collagen, were observed when the cells were cultured within three-dimensional gels. The data suggest that direct interaction of the cell surface with matrix constituents displaying a particular spatial array could be an important aspect in the control of type IX and X collagen expression by chondrocytes. The financial support of the Arthritis & Rheumatism Council and the Medical Research Council is gratefully acknowledged.     

Defective Virions of Reovirus

When purified preparations of stock reovirus, type 3, were digested with chymotrypsin, the virions were converted into two different types of particle. These new particles could be separated from each other by isopycnic centrifugation in cesium chloride gradients. One particle banded at a buoyant density of 1.43 g/cm(3), the other at a density of 1.415 g/cm(3). The former particle is termed the heavy (H) particle, the latter is the light (L) particle. The ratio of H/L particles varied between 0.5 and 0.25 in various purified preparations of virus. In electron micrographs, both H and L particles had the appearance and dimensions of viral cores. H particles were infectious for L cells. When plaques formed by stock virus, or by H particles, were picked and propagated in L cells, the majority of the clones gave rise only to H particles on chymotrypsin digestion. On continued serial passage of the clones, virions containing L particles again appeared in the progeny. The simplest explanation of these results was that stock virus was comprised of two populations of virions. One type of virion which contained H particles was infectious, whereas the other, which contained L particles, was not itself infectious and could replicate only in cells coinfected with an H particle virion. Added weight was given to this hypothesis by two observations. First, a small but definite separation of H and L virions could be achieved by isopycnic centrifugation in a gradient of cesium chloride. Second, L particles and virions containing L particles were both shown to lack the largest of the ten segments of double-stranded ribonucleic acid genome. Thus, L particle virions have defective genomes.     

Technique for the Isolation of Ribonucleic Acid-Rich Mutants from Escherichia coli

A technique for the isolation of ribonucleic acid (RNA)-rich mutants of Escherichia coli is described. Mutagenized cells were centrifuged to isopycnic equilibrium on potassium tartrate or cesium sulfate gradients. Samples from the region of the gradients slightly denser than the majority of the cells were spread on agar plates, and the resulting clones were tested for increased RNA to protein ratios.     

The involvement of RNA in the initiation of DNA synthesis in mammalian cells. Artifacts arising during caesium-salt density-gradient centrifugation which simulate a covalent attachment of RNA to newly synthesized DNA.

Artifacts were encountered during caesium salt density gradient centrifugation which simulated results expected if newly synthesized DNA is covalently attached to RNA. Newly synthesized DNA (in baby hamster kidney cells, BHK-21/C13), pulse-labelled with [3H]thymidine for 10 min at temperatures below 25 degrees C, banded at a greater buoyant density than mature [14C]DNA (heat-denatured nucleic acids) when centrifuged to equilibrium in caesium chloride gradients. Some of the newly synthesized RNA, labelled with [3H]uridine, banded at a buoyant density slightly greater than DNA in caesium sulphate gradients. These results were not obtained when nucleic acids were pulse-labelled at 37 degrees C, nor when samples were heat-denatured in the presence of formaldehyde. This suggests that nucleic acids can aggregate during centrifugation; this is discussed in relation to the molecular size of the DNA.     

Physicochemical properties of kinetoplast DNA from Crithidia acanthocephali. Crithidia luciliae, and Trypanosoma lewisi

The protozoa Crithidia and Trypanosoma contain within a mitochondrion a mass of DNA known as kinetoplast DNA (kDNA) which consists mainly of an association of thousands of small circular molecules of similar size held together by topological interlocking. Using kDNA from Crithidia acanthocephali, Crithidia luciliae, and Trypanosoma lewisi, physicochemical studies have been carried out with intact associations and with fractions of covalently closed single circular molecules, and of open single circular and unit length linear molecules obtained from kDNA associations by sonication, sucrose sedimentation, and cesium chloride-ethidium bromide equilibrium centrifugation. Buoyant density analyses failed to provide evidence for base composition heterogeneity among kDNA molecules within a species. The complementary nucleotide strands of kDNA molecules of all three species had distinct buoyant densities in both alkaline and neutral cesium chloride. For C. acanthocephali kDNA, these buoyant density differences were shown to be a reflection of differences in base composition between the complementary nucleotide strands. The molar ratios of adenine: thymine:guanine:cytosine, obtained from deoxyribonucleotide analyses were 16.8:41.0:28.1:14.1 for the heavy strand and 41.6:16.6:12.8:29.0 for the light strand. Covalently closed single circular molecules of C. acanthocephali (as well as intact kDNA associations of C. acanthocephali and T. lewisi) formed a single band in alkaline cesium chloride gradients, indicating their component nucleotide strands to be alkaline insensitive. Data from buoyant density, base composition, and thermal melting analyses suggested that minor bases are either rare or absent in Crithidia kDNA. The kinetics of renaturation of 32P labeled C. acanthocephali kDNA measured using hydroxyapatite chromatography were consistent with at least 70% of the circular molecules of this DNA having the same nucleotide sequence. Evidence for sequence homologies among the kDNAs of all three species was obtained from buoyant density analyses of DNA in annealed mixtures containing one component kDNA strand from each of two species.     

Autocrine signals enable chondrocytes to survive in culture

We recently proposed that most mammalian cells other than blastomeres may be programmed to kill themselves unless continuously signaled by other cells not to. Many observations indicate that some mammalian cells are programmed in this way, but is it the case for most mammalian cells? As it is impractical to test all of the hundreds of types of mammalian cells, we have focused on two tissues--lens and cartilage-- which each contain only a single cell type: if there are cells that do not require signals from other cells to avoid programmed cell death (PCD), lens epithelial cells and cartilage cells (chondrocytes) might be expected to be among them. We have previously shown that rat lens epithelial cells can survive in serum-free culture without signals from other cell types but seem to require signals from other lens epithelial cells to survive: without such signals they undergo PCD. We show here that the same is true for rat (and chick) chondrocytes. They can survive for weeks in culture at high cell density in the absence of other cell types, serum, or exogenous proteins or signaling molecules, but they die with the morphological features of apoptosis in these conditions at low cell density. Medium from high density cultures, FCS, or a combination of known growth factors, all support prolonged chondrocyte survival in low density cultures, as long as antioxidants are also present. Moreover, medium from high density chondrocyte cultures promotes the survival of lens epithelial cells in low density cultures and vice versa. Chondrocytes isolated from adult rats behave similarly to those isolated from developing rats. These findings support the hypothesis that most mammalian cells require signals from other cells to avoid PCD, although the signals can sometimes be provided by cells of the same type, at least in tissues that contain only one cell type.     

Replication of kinetoplast DNA of Crithidia acanthocephali. I. Density shift experiments using deuterium oxide

The protozoan Crithidia acanthocephali contains, within a modified region of a mitochondrion, a mass of DNA known as kinetoplast DNA (kDNA). This DNA consists mainly of an association of approximately 27,000 covalently closed 0.8-mum circular molecules which are apparently held together in a definite ordered manner by topological interlocking. After culturing of C. acanthocephali cells for 25 generations in medium containing 75% deuterium oxide, both nuclear DNA (rhonative, nondeuterated=1.717 g/cm3) and kDNA (rhonative, nondeuterated=1.702 g/cm3) increased in buoyant density by 0.012 g/cm3. The replication of the two DNAs was studied by cesium chloride buoyant density analysis of DNAs from exponentially growing cells taken at 1.0, 1.4, 2.0, 3.0, and 4.0 cell doublings after transfer of cells from D2O- containing medium into medium containing only normal water. The results obtained from analysis of both native and denatured nuclear DNAs indicate that this DNA replicates semiconservatively. From an analysis of intact associations of kDNA, it appears that this DNA doubles once per generation and that the newly synthesized DNA does not segregate from parental DNA. Fractions of covalently closed single circular molecules and of open circular and unit length linear molecules were obtained from associations of kDNA by sonication, sucrose sedimentation, and cesium chloride-ethidium bromide equilibrium gradient centrifugation. Buoyant density profiles obtained from these fractions indicate that: (a) doubling of the kDNA results from the replication of each circular molecule rather than from repeated replication of a small fraction of the circular molecules; (b) replication of kDNA is semiconservative rather than conservative, but there is recombination between the circles at an undefined time during the cell cycle.