Fractionation of somatic and sperm chromatin during spermatogenesis in fish

A new approach is suggested for studying changes in the interactions of protein with DNA in the cells. Measurements of the buoyant density of chromatin were performed in somatic cells and in cells undergoing meiosis in fish. During the process of spermatogenesis some of the somatic histones on the DNA are replaced by a new class of proteins; consequently, the mature sperm contains a unique type of protein having a low mol. wt and a high proportion of arginine.The chromatin obtained from mature sperm is composed of a single component with a density of 1.48–1.49 g/cm³ as measured by CsCl equilibrium sedimentation. On the other hand, somatic cells contain chromatin with lower densities. Chromatin obtained from erythrocytes contains a single component with a density of 1.41–1.42 g/cm³ while liver chromatin shows two components; a main component with a density of 1.45–1.46 and a more heterogeneous component with a lighter density (1.32–1.35). There is a correlation between the buoyant density of the chromatin, the type of its basic proteins and the level of biosynthetic activity in the cells.     

Scanning Electron Microscopic Observation of Differentiation from the Reproductive Short Form to the Infectious Long Form of Holospora obtusa

To identify the surface features of Holospora obtusa during its differentiation from the reproductive short form to the infectious long form, bacteria of four different buoyant densities were isolated by Percoll density gradient centrifugation of homogenates of host cells or isolated macronuclei, and examined with a scanning electron microscope. Bacteria of buoyant density 1.09 g/ml were reproductive short forms as well as cells at various stages in the elongation process including fully elongated ones. Bacteria of buoyant densities 1.11 g/ml and 1.13 g/ml were premature long forms and those of 1.16 g/ml were mature infectious long forms. Bacteria of buoyant density 1.09 g/ml had an entirely rough surface while those of buoyant densities 1.11 g/ml and 1.13 g/ml were smooth and had wale-like stripes on their surface. A small tapered tip was observed at one end of the bacteria of buoyant density 1.13 g/ml. Bacteria of buoyant density 1.16 g/ml had an entirely smooth surface, but one end always showed a rough surface; this locally differentiated surface of the special tip of the infectious long form may be responsible for both the nuclear and species specificities of the infectivity of H. obtusa. These observations indicate that the surface of H. obtusa changes during differentiation and the special tip develops in bacteria of buoyant density 1.13 g/ml.     

Sea urchin embryo chromatin and nuclear ribonucleoproteins fractionated by anion exchange chromatography.

Chromatin and ribonucleoproteins released from sea urchin embryo nuclei were characterized on the basis of sedimentation properties, buoyant densities and fractionation by anion exchange chromatography. DEAE- and ECTEOLA-cellulose chromatography was used to assay nuclear purity, insofar as ribosomes and polyribosomes could be readily distinguished from ribonucleoproteins released from nuclei. This chromatography was used to separate chromatin fragments on the basis of DNA size, to prepare chromatin fragments substantially enriched in nonhistone proteins, and to analyze nuclear ribonucleoproteins. Solubilized chromatin is fractionated into major and minor components by ECTEOLA-cellulose chromatography. The DNA of these chromatin fractions was analyzed with respect to buoyant density and hybridization with nuclear RNA.     

Characteristic low density and shear sensitivity of cross-linked chromatin containing polycomb complexes

Chromatin cross-linking is widely used for mapping the distribution of chromosomal proteins by immunoprecipitation, but our knowledge of the physical properties of chromatin complexes remains rudimentary. Density gradients have been long used to separate fragments of cross-linked chromatin with their bound proteins from free protein or free DNA. We find that the association of DNA fragments with very-high-molecular-weight protein complexes shifts their buoyant density to values much lower then that of bulk chromatin. We show that in a CsCl gradient, Polycomb response elements, promoters of active genes, and insulator or boundary elements are found at buoyant densities similar to those of free protein and are depleted from the bulk chromatin fractions. In these regions, the low density is associated with the presence of large protein complexes and with high sensitivity to sonication. Our results suggest that separation of different chromatin regions according to their buoyant density may bias chromatin immunoprecipitation results. Density centrifugation of cross-linked chromatin may provide a simple approach to investigate the properties of large chromatin complexes in vivo.     

Buoyant density of Escherichia coli is determined solely by the osmolarity of the culture medium

In previous studies, we had shown that the buoyant density ofEscherichia coli is determined by the osmolarity of the growth medium by varying the osmolarity of the medium with NaCl or sucrose. However, the buoyant density of the cells always exceeded that of the growth medium. Here we determined the effect of medium with a buoyant density greater than the expected buoyant density of cells by adding Nycodenz to Luria broth. Percoll gradients of cells were analyzed by laser light scattering. The buoyant density for 125- and 375-mOsM-grown cells was 0.002 g/ml and 0.003 g/ml more, respectively, for cells grown in the presence of Nycodenz than those grown without Nycodenz, while the buoyant density of 250-mOsM-grown cells was 0.005 g/ml less for cells grown in the presence of Nycodenz than those grown without Nycodenz. Cells grown in 500-mOsM medium with or without Nycodenz had the same buoyant density. the buoyant density of cultures grown in defined medium was the same as those grown in rich medium, with only the medium osmolarity correlating to buoyant density. We conclude from these experiments that neither buoyant density nor chemical make-up of the medium determines the buoyant density of cells grown in that medium. Only the medium osmolarity determines cell buoyant density, suggesting thatE. coli has no mechanisms to sense buoyant density.     

The possible role of endogenous nucleases in the structural organization of chromatin]

Two fractions of rat liver nuclei with different buoyant density have been obtained. The electrophoretic analysis of the oligonucleosome patterns of DNA out of nuclei of these two fractions revealed different levels of activity in endonucleases. In case of inhibition during the extraction of activity in Ca, Mg-dependent endonucleases, the average size of high polymeric DNA is larger for nuclei with bigger buoyant density (fraction I) than for nuclei with smaller ones (fraction II). This finding is evidence of in situ existence of two pools of liver nuclei with different endogenic nuclease activities. In nuclear chromatin fraction I DNA is torsionally stressed; in fraction II it is relaxed that correlates with larger activity of endonucleases and smaller buoyant density of this fraction. A hypothesis on a possible role of endonucleases in chromatin structure organization has been put forward. According to this hypothesis a modulation of activity in nuclear endonucleases can determine different packaging and activity of chromatin from different pools of cellular nuclei.     

Buoyant density centrifugation of sea urchin embryo chromatin on sucrose-glucose gradient

Unsheard chromatin isolated from sea urchin embryos was submitted to buoyant density centrifugation in sucrose-glucose gradients. The main peak of blastula chromatin was at a density position of 1.299±0.028±0.009 g ml^-1 whereas at gastrula stage a shift to a lower buoyant density position of (1.276±0.021±0.007 g ml^-1) was observed. Besides the main peak, a small band with a density of 1.18 g ml^-1 was noticed. The lighter fraction differed from the heavy one in a higher histone to DNA ratio, a lower proportion of the F-1 histone, and a lower nonhistone to DNA ratio. The most pronounced developmental alterations of proteins were observed at the level of nonhistone protein patterns of the light fractions.     

Effect of inclusion bodies on the buoyant density of recombinant Escherichia coli

Summary During batch culture, buoyant density of recombinant E. coli cells increased linearly as inclusion body per cell increased. This indicated that buoyant density can be used to follow inclusion body formation. This will be helpful to optimize product formation because inclusion bodies are mostly composed of foreign poteins produced by recombinant microorganisms.     

Buoyant and potentiometric titrations of synthetic polypeptides. I. Six ionizable homopolypeptides in CsCl solutions

The buoyant density and potentiometric titrations of six ionizable homopolypeptides in concentrated CsCI solutions have been studied. These six homopolypeptides were chosen as models of the behavior of ionizable residues in proteins. Their buoyant and potentiometric results will be of value in interpreting the buoyant and potentiometric results observed for proteins. The buoyant densities for all six homopolypeptides were found to increase sigmoidally as the pH is increased. These density changes are interpreted in terms of changes in the hydrations and ion binding which are associated with the titration of the residues. Preferential hydrations for the homopolypeptides are calculated. The buoyant density titrations are combined with the potentiometric titrations to determine the relationship between the buoyant density and the degree of ionization. A better method of computing buoyant densities of proteins is described. The slope of β(ρ) has been computed for CsCl using least-squares curve fitting and this is used in calculating the isoconcentration position. This method has been found to be more accurate than calculating the isoconcentration position from the normalized isoconcentration ratio, which is known only under limited conditions.     

Cesium chloride gradients of chromatin after treatment with micrococcal nuclease

Cesium chloride equilibrium density centrifugation shows that treatment of rat liver nuclei with low concetrations of micrococcal nuclease for extremely short periods of time results in the appearance of chromatin fractions of low protein/DNA ratio and even free DNA. The DNA of these chromatin fractions is shorter than the DNA moiety of one chromatin subunit. The amount of high buoyant density material is decreased with increasing digestion time. We conclude that this material belongs to the minor chromatin fraction which is not organized according to the subunit model.     

Instability of brain synaptosomal membrane preparations to repeated ultracentrifugation in isoosmotic density gradients

Synaptosomal membranes from rat brain were found to be remarkably unstable, from the criterion of buoyant density, to repeated density gradient ultracentrifugation. These membranes underwent progressive changes in buoyant density through at least three cycles of fractionation on density gradients generating large proportions of material of both higher and lower buoyant density than the original fraction. The observed density changes were not due to osmotic effects of the various gradient density zones, clumping due to the influence of divalent cations, age of the membrane preparation, length of centrifugation time, intermediate processing steps or a variety of other factors. In addition, the method of homogenization including duration and rate of homogenization had only minimal effects on this property of buoyant density instability.     

Effect of salts and chromatin concentrations on the buoyant density of chromatin in metrizamide gradient.

Using isopycnic centrifugation in metrizamide gradient, effect of ions and chromatin concentration on the buoyant density of chromatin was quantitatively examined. An elevation followed by gradual decline and secondary increase of the density occurred in accordance with increase in MgCl2 or NaCl concentration. Maximum density was observed at a concentration of these salts known to result in the condensation of chromatin. Release of protein occurred during the phase of density decline. The second increase in density is mainly due to the density increment of DNA in the chromatin. The density was dependent upon the concentration of chromatin in a band formed in the metrizamide gradient, while the density of free DNA and protein was not so greatly affected by their concentration. The density of chromatin in the presence of 0.14 M NaCl was less affected by the chromatin concentration than that in the absence of salt. Calculation of results indicates that grade of hydration of chromatin at concentrations lower than 400 microgram/ml in 1 mM Tris-HCl (pH 8.0) is higher than that expected from its DNA and protein components.     

On the hydration of DNA. I. Preferential hydration and stability of DNA in concentrated trifluoroacetate solution

The hydration of DNA is an important factor in the stability of its secondary structure. Methods for measuring the hydration of DNA in solution and the results of various techniques are compared and discussed critically. The buoyant density of native and denatured T-7 bacteriophage DNA in potassium trifluoroacetate (KTFA) solution has been measured as a function of temperature between 5 and 50°C. The buoyant density of native DNA increased linearly with temperature, with a dependence of (2.3 ± 0.5) × 10^?4 g/cc-°C. DNA which has been heat denatured and quenched at 0°C in the salt solution shows a similar dependence of buoyant density on temperature at temperatures far below the T_m, and above the T_m. However, there is an inflection region in the buoyant density versus T curve over a wide range of temperatures below the T_m. Optical density versus temperature studies showed that this is due to the. inhibition by KTFA of recovery of secondary structure on quenching. If the partial specific volume is assumed to be the same for native and denatured DNA, the loss of water of hydration on denaturation is calculated to be about 20% in KTFA at a water activity of 0.7 at 25°C. By treating the denaturation of DNA as a phase transition, an equation has immmi derived relating the destabilizing effect of trifluoroacetate to the loss of hydration on denaturation. The hydration of native DNA is abnormally high in the presence of this anion, and the loss of hydration on denaturation is greater than in CsCl. In addition, trifluoroacetate appears to decrease the ΔHof denaturation.     

Ontogeny of body density and the swimbladder in yellowtail kingfish Seriola lalandi larvae

The ontogeny of larval body density and the morphological and histological events during swimbladder development were investigated in two cohorts of yellowtail kingfish Seriola lalandi larvae to understand the relationship between larval morphology and body density. Larvae <3 days post hatch (dph) were positively buoyant with a mean ± s.d . body density of 1·023 ± 0·001 g cm^?3. Histological evidence demonstrated that S. lalandi larvae are initially transient physostomes with the primordial swimbladder derived from the evagination of the gut ventral to the notochord and seen at 2 dph. A pneumatic duct connected the swimbladder to the oesophagus, but degenerated after 5 dph. Initial swimbladder (SB) inflation occurred on 3 dph, and the inflation window was 3–5 dph when the pneumatic duct was still connected to the gut. The swimbladder volume increased with larval age and the epithelial lining on the swimbladder became flattened squamous cells after initial inflation. Seriola lalandi developed into a physoclist with the formation of the rete mirabile and the gas‐secreting gland comprised low‐columnar epithelial cells. Larvae with successfully inflated swimbladders remained positively buoyant, whereas larvae without SB inflation became negatively buoyant and their body density gradually reached 1·030 ± 0·001 g cm^?3 by 10 dph. Diel density changes were observed after 5 dph, owing to day time deflation and night‐time inflation of the swimbladder. These results show that SB inflation has a direct effect on body density in larval S. lalandi and environmental factors should be further investigated to enhance the rate of SB inflation to prevent the sinking death syndrome in the early life stage of the fish larvae.     

Effect of mercuric and silver ions on cesium sulfate equilibrium buoyant densities of synthetic polydeoxyribonucleotides.

The effect of Hg2+ and Ag+ on the buoyant density (rho) of four synthetic DNA polymers, poly[d(A-T)]; poly(dA) - poly(dT); oikt[d(G-C)]; and poly(dG) - poly(dC), was investigated. The buoyant density of poly[d(A-T)] in Cs2SO4 increased dramatically after complexing with Hg2+, but little change in the buoyant density of other polymers resulted except at very high molar ratios of Hg2+/DNA-P (rf). Hg2+ raised the thermal transition temperature (Tm) of alternating polymers and lowered the Tm of homopolymers. Measurements in the preparative ultracentrifuge indicated that lowered Tm correlated with Hg2+-induced strand separation of one homopolymer [poly(dA) - poly(dT)], but strand separation was not observed with another homopolymer [poly(dG) - poly(dC)] complexed with Hg2+. When Ag+ was mixed with the polymers, the buoyant density of poly(dG) - poly(dC) increased most markedly. A substantial increase in the buoyant density of poly[d(A-T)] and a small increase in the buoyant density of poly[d(G-C)] were also observed. The Tm changes induced by Ag+ were not related in any obvious way to buoyant density changes. These findings indicate that nucleotide sequence as well as overall base composition is of importance in understanding the buoyant density changes induced by metal ions. Although these data do not allow construction of a detailed molecular model of polymer-metal ion interactions, they may be used to explain much of the behavior of naturally occurring DNA sequences, such as heterochromatic satellite sequences and 5 S and rRNA sequences, in Hg2+/Cs2SO4 and Ag+/Cs2SO4 gradients.     

The small RNP acceptor of glucocorticoids bound to chromatin in liver cell nuclei

The buoyant density in the CsCl gradient of the small nuclear RNP tightly bound to chromatin has been studied. It was shown that the buoyant density of alpha-RNP is characteristic for ribonucleoproteins (p = 1.36-1.50 g/cm3). The alpha-particles are of extraordinary stability. These RNP were shown to remain stable under drastic conditions (high ionic strength, SDS, 6 M urea) and resist unfixed caesium chloride density centrifugation. The alpha-RNA hybridizes with total rat liver DNA at C0t1/2 = 10(3). The oligonucleotide analysis of the alpha-RNA shows that the alpha-RNA is heterogeneous.     

Metrizamide density gradients of sea urchin chromatin: fractions rich and poor in nascent DNA.

A crude, lightly sheared chromatin preparation obtained from a mixture of [methyl-3H] thymidine pulse and [2-14C] thymidine long-labeled sea urchin embryos (swimming blastulae), was centrifuged in metrizamide to form an isopycnic gradient. The buoyant density of the 3H pulse labeled chromatin was slightly higher than that of the 14C labeled bulk chromatin. The 3H/14C ratios in the higher and lower density regions of the overlapping radioactivity peaks, indicated the presence of fractions rich and poor in nascent DNA in these two density regions. After 15 min chase, the difference disappeared, indicating that the chromatin fractions with nascent DNA have a half-life shorter than 15 min.     

The control of fruiting body formation in the ascomycete Sordaria macrospora Auersw. by arginine and biotin: a two-factor analysis

Summary The distribution of glyoxylate-cycle enzymes between microbodies and mitochondria was examined in ethanol-grown Aspergillus tamarii Kita. Particulate activities of catalase and the two glyoxylate by-pass enzymes, malate synthase and isocitrate lyase, were localized in the microbodies. The microbodies had a buoyant density of about 1.23 g cm^-3 after isopycnic centrifugation in linear sucrose gradients. Particulate activities of the other two glyoxycitrate synthase, together with that of succinate dehydrogenase were restricted to the mitochondria, which had a buoyant density of about 1.20 g cm^-3. Catalase also appeared to be localized in a second particle, perhaps the microbody inclusions or the Woronin bodies, having a buoyant density of about 1.26 g cm^-3.     

THE EFFECT OF ETHIDIUM BROMIDE ON MITOCHONDRIAL DNA SYNTHESIS AND MITOCHONDRIAL DNA STRUCTURE IN HELA CELLS

The synthesis of mitochondrial DNA (mDNA) in HeLa cells is selectively inhibited by relatively low concentrations of ethidium bromide. After exposure of cells to strongly inhibitory concentrations of the drug, the apparent superhelix density of mDNA is rapidly increased, as judged by its buoyant density in CsCl in the presence of ethidium bromide. Mitochondrial DNA synthesized in the presence of partially inhibitory concentrations of ethidium bromide is also altered in its buoyant density in the presence of the dye, but is more heterogeneous in this respect. However, the change in buoyant density of newly synthesized mDNA may be explained by changes in structure other than a change in superhelix density, as indicated by its increased resistance to digestion by pancreatic DNase.     

Metabolically stable ribonucleoproteins in the chromatin of pigeon bone marrow cells

Ribonucleoproteins with buoyant density 1.4 carrying metabolically stable RNA species with sedimentation coefficients up to 28S have been detected in the 0.35M NaCl extracts from pigeon bone marrow chromatin. It is suggested that they correspond to the slowly metabolizing interchromatin particles.