Nuclear DNA in normal and refed Amoeba proteus

Amoeba proteus synthesizes DNA in G2 phase of the cell cycle upon feeding after starvation. The characteristics of the DNA synthesized in G2 have been studied by microscope photometry of individual Feulgen-stained nuclei and by buoyant density centrifugation of nuclear DNA in CsCl. Amoeba nuclei were found to contain 42.8 pg of DNA. This DNA bands in CsCl at a density of 1.693 g/cm³ with a satellite at 1.714 g/cm³ which makes up 24% of nuclear DNA. DNA from whole cells has an additional non-nuclear satellite at 1.726 g/cm³. When cells are starved and re-fed with food labeled with [³H]thymidine, the DNA synthesized is predominantly the 1.714 satellite. The amount of DNA synthesized in G2 is small since there is no measurable difference in Feulgen dye binding to nuclei of starved vs starved and re-fed cells. The data suggest that refeeding induces a resumption of late S phase DNA synthesis, or the preferential synthesis of specific DNA sequences such as rRNA genes.     

Cytoplasmic streaming in Amoeba proteus is inhibited by the actinspecific drug phalloidin

Phalloidin, applied by microinjection into Amoeba proteus inhibits specifically, in a concentration dependent manner, the process of cytoplasmic streaming. Preliminary ultrastructural analysis of phalloidin-injected amoebas shows that extensive arrays of microfilaments are formed. These results are discussed in relation to the specific interaction of phalloidin with actin known to occur in vitro, which involve promotion of actin polymerization and stabilization of F-actin structures.     

Purification and Characterization of the GroESLx Chaperonins from the Symbiotic X-Bacteria in Amoeba proteus

GroELx and GroESx proteins of symbiotic X-bacteria from Amoeba proteus were overproduced in Escherichia coli transformed with pAJX91 and pUXGPRM, respectively, and their chaperonin functions were assayed. We utilized σ⁷⁰-dependent specific promoters of groEx in the expression vectors and grew recombinant cells at 37°C to minimize coexpression of host groE of E. coli. For purifying the proteins, we applied the principle of heat stability for GroELx and pI difference for GroESx to minimize copurification with the hosts GroEL and GroES, respectively. After ultracentrifugation in a sucrose density gradient, the yield and purity of GroELx were 56 and 89%, respectively. The yield and purity of GroESx after anion-exchange chromatography were 62 and 91%, respectively. Purified GroELx had an ATPase activity of 53.2 nmol Pi released/min/mg protein at 37°C. The GroESx protein inhibited ATPase activity of GroELx to 60% of the control at a ratio of 1 for GroESx-7mer/GroELx-14mer. GroESLx helped refolding of urea-unfolded rhodanese up to 80% of the native activity at 37°C. By chemical cross-linking analysis, oligomeric properties of GroESx and GroELx were confirmed as GroESx₇ and GroELx₁₄ in two stacks of GroELx₇. In this study, we developed a method for the purification of GroESLx and demonstrated that their chaperonin function is homologous to GroESL of E. coli.     

Correlation between membrane potential, cell shape, and motile activity in Amoeba proteus

The various motile activities and cell shapes of Amoeba proteus grown in Chalkley's solution are correlated with definitive electrical membrane potentials. The same correlations were found when definitive motile activities and cell shapes were experimentally induced by changing the pH of the culture medium. The highest values of membrane potential (−70 mV) were measured in monopodial amebae during active locomotion. In resting cells, which prevail in acid or basic media, the membrane potential decreases to −5 mV. In those resting cells, which also stop internal cytoplasmic movement at basic pH, the membrane potential turns positive (+9 mV − +30 mV).     

Protein migration from transplanted nuclei in Amoeba proteus. II. An electrophoretic study

Recently, we showed that protein migration from a nucleus transplanted into a host amoeba involved two classes of nuclear proteins. The chemical character of these proteins has now been investigated using isoelectric focusing and SDS gel electrophoresis. The proteins which migrated into the host cytoplasm from the transplanted nucleus have a range of isoelectric points (pI) between 7.0 and 7.6, and a molecular weight (MW) range of 9 000–110 000 D. This class is likely to be involved with the nucleocytoplasmic transfer of RNA. The second class of migratory proteins had a lower MW and pI range; the majority were between 11 000 and 45 000 D, with pIs between 5.9 and 7.0. This class of migratory proteins exhibited a shuttling character, possibly functioning as cytoplasmic regulators of nuclear activities.     

Pattern of DNA synthesis in nuclei of feeding and starving Amoeba proteus : A cytofluorometric study

The DNA content in isolated nuclei of Amoeba proteus was determined for each of the three groups of synchronized amoebae over different intervals after division. Several nuclei of each amoeba group were fixed 1 h after division, before the amoebae were fed. About h after division, some amoebae in each group were given food (Tetrahymena pyriformis), while the rest were left starving. Samples of the nuclei of fed and starved amoebae were fixed 24 h and (in different groups) 42–55 h after division. In each group from 22 to 48% of the fed amoebae had divided prior to the last nuclei fixation. Starved amoebae did not undergo division. In all three amoeba groups the nuclear DNA content of fed cells by the end of interphase had increased to 280–300% the value for 1 h amoebae. The nuclear DNA content of starved amoebae of all three groups was also increased, and in two groups it exceeded the initial level more than two-fold. However, in all three groups, it was lower than that of fed amoebae. In all the groups the nuclear DNA content in fed amoebae grew after 24 h, i.e. during the second half of interphase, the increase accounting for from 11 to 48% of the total increase. The hypothesis is put forward that the increase in the nuclear DNA content during the cell cycle of Amoeba proteus is the result of two processes: (1) one-time replication of the DNA of the whole genome; and (2) repeated replication of some part of the DNA. In amoebae the relation of the pattern of nuclear DNA synthesis to the diet is considered.     

Quantitative analysis of changes in cell shape of Amoeba proteus during locomotion and upon responses to salt stimuli

A new parameter expressing the complexity of cell shape defined as (periphery)²/(area) in 2D projection was found useful for a quantitative analysis of changes in the cell shape of Amoeba proteus and potentially of any amoeboid cells. During locomotion the complexity and the motive force of the protoplasmic streaming in amoeba varied periodically, and the Fourier analysis of the two showed a similar pattern in the power spectrum, giving a rather broad peak at about 2.5 × 10⁻³ Hz. The complexity increased mainly due to elongation of the cell as external Ca²⁺ increased. This effect was blocked by La³⁺, half the inhibition being attained at 1/200 amount of the coexisting Ca²⁺. On the other hand, the complexity decreased due to rounding up of the cell as the concentration of other cations, such as Sr²⁺, Mg²⁺, Co²⁺, Ni²⁺, Na⁺, K⁺ etc., increased. Irrespective of the opposite effects of Ca²⁺ and other cations on the cell shape, the ATP concentration in amoeba decreased in both cases with increase of all these cations. The irregularity in amoeboid motility is discussed in terms of a dynamic system theory.     

Electron microscopic localization of hydrogenase genes on the megaplasmid pHG 1 in Alcaligenes eutrophus

Summary Plasmids carrying hydrogenase genes in Alcaligenes eutrophus wild type H 16 and in two transposon Tn5 —induced mutants have been investigated by electron microscopy. Besides the pHG1 megaplasmid (458±27 kb) carrying genes coding for structural and regulatory properties of hydrogenases, small plasmids of unknown significance have been detected. The sizes of EcoRI fragments obtained from pHG1 were measured from electron micrographs. They were significantly different from sizes determined previously by agarose gel electrophoresis.Plasmid pHG1 isolated from the wild type H 16 was shown to contain two inverted repeats (IR 16-1 and IR 16-2) with sizes similar to known transposons.From electron microscopic hybridization studies, it was deduced that the sites of insertion of Tn5 into a regulation gene on pHG1 for both soluble and membrane-bound hydrogenase, and of Tn5-Mob into the gene coding for structural properties of the soluble hydrogenase, are about 67.2 kb apart. One of the inverted repeats (IR 16-1) was localized in between these sites.     

Electron microscopic visualization of the arrangement of the two protein components of (Na + K)-ATPase

The information obtained by electron microscopic examination of highly purified membrane preparations of (Na⁺ + K⁺)-ATPase after freeze-fracturing or negative staining suggests the following conclusions. The catalytic 100 000 dalton protein component penetrates with its greater ‘globular’ mass the plasma membrane and protudes with its smaller mass from the protoplasmic surface by a stalked knob carrying the catalytic centre. The 40 000 dalton glycoprotein component is anchored in the membrane interior by a non-polar ‘fibrous’ side chain, whereas its major polar mass projects from the outer membrane surface forming a surface coat of ill-definable substructure.     

Electron microscopic visualization of DNA single strand breaks

DNA single strand breaks (ssb) have been induced in FLC/C cells in culture. They have been visualized in the electron microscope after decoration with biotin-avidin-ferritin complexes and spreading as monomolecular mixed films. This allowed one to determine the average number of decorated ssbs per unit of DNA length applying straight-forward and simple evaluation methods. This method has been used to investigate the DNA alterations by benzo[a]pyrene (B[a]P) on FLC/C culture cells. Thus a B[a]P-DNA damage curve can be constructed as a regression with a correlation coefficient of r = 0.97, while its isomer benzo[e]pyrene (B[e]P) known to have only low mutagenicity under the same experimental conditions is virtually without effect. The method has further informational potential regarding damage distribution and repair of DNA.     

Electron microscopic visualization of proteoglycans with Alcian Blue.

The intercellular matrices of bovine nasal cartilage, chick embryo perichordal cartilage, and chick embryo mesenchymal cells cultured in vitro have been examined by electron microscopy after staining them with Alcian Blue in salt solutions according to Scott & Dorling (1965). Matrix granules, which are typical components of cartilage at the ultrastructural level, are not visible after Alcian Blue staining and are replaced by alcianophilic rod-like particles, varying in length and width. With tissue cultures, Alcian Blue stains 40-120 A thick filaments which display an orthogonal and longitudinal relationship to collagen fibrils. We assume that cartilage matrix granules represent linear proteoglycans that are coiled as a consequence of the usual glutaraldehyde-osmium fixation. It is thought that Alcian Blue, on the other hand, contributes to the stabilization of the proteoglycans in their original structural arrangement. This stabilizing property presumably also results in the sharp visualization of fine filaments in the tissue culture matrix.     

Electron microscopic visualization of the filament binding mode of actin-binding proteins

A large number of actin-binding proteins (ABPs) regulate various kinds of cellular events in which the superstructure of the actin cytoskeleton is dynamically changed. Thus, to understand the actin dynamics in the cell, the mechanisms of actin regulation by ABPs must be elucidated. Moreover, it is particularly important to identify the side, barbed-end or pointed-end ABP binding sites on the actin filament. However, a simple, reliable method to determine the ABP binding sites on the actin filament is missing. Here, a novel electron microscopic method for determining the ABP binding sites is presented. This approach uses a gold nanoparticle that recognizes a histidine tag on an ABP and an image analysis procedure that can determine the polarity of the actin filament. This method will facilitate future study of ABPs.     

Electron microscopic visualization of the outer membrane permeability of Bacteroides fragilis

Abstract Electron microscopy of negatively stained Bacteroides fragilis cells treated with hypertonic solutions of di- or trisaccharides showed the shrinkage of whole cells, whereas the pentose- or hexose-treated cells shrank less significantly. Electron microscopy of thin sections of the monosaccharide-treated cells showed plasmolysis. Determination of the diffusion rate by the liposome-swelling method suggested that the apparent exclusion limit of the outer membrane pore is close to the size of uncharged saccharides of approx. M _r 250. These results suggested that the outer membrane of B. fragilis contains small diffusion pores.     

Electron microscopic localization of replication origins in Oenothera chloroplast DNA

Summary The origins of chloroplast DNA (cpDNA) replication were mapped in two plastome types of Oenothera in order to determine whether variation in the origin of cpDNA replication could account for the different transmission abilities associated with these plastomes. Two pairs of displacement loop (D-loop) initiation sites were observed on closed circular cpDNA molecules by electron microscopy. Each pair of D-loops was mapped to the inverted repeats of the Oenothera cpDNA by the analysis of restriction fragments. The starting points of the two adjacent D-loops are approximately 4 kb apart, bracketing the 16S rRNA gene. Although there are small DNA length variations near one of the D-loop initiation sites, no apparent differences in the number and the location of replication origins were observed between plastomes with the highest (type I) and lowest (type IV) transmission efficiencies.     

Electron microscopic examination of the orexin immunoreactivity in the dorsal raphe nucleus

The ultrastructure and the synaptic relationships of the orexin-A-like immunoreactive fibers in the dorsal raphe nucleus were examined with an immunoelectron microscopic method. At the electron microscopic level, most of the immunoreactive fibers, a varicosity appearance at the light microscopic level, were found as axon terminals. The large dense-cored vesicles contained in the immunoreactive axon terminals were the most intensely immunostained organellae. These axon terminals were often found to make synapses. While the axo-dendritic synapses were usually asymmetric in appearance, the axo-somatic synapses were symmetric. Orexin-A-like immunoreactive processes with no synaptic vesicles were also found. These processes often received asymmetric synapses. With less frequency, the synapses were found between the orexin-like immunoreactive processes. The results suggest that the orexin peptides are stored in the large dense-cored vesicles; the orexin-containing fibers may have influences on the physiological activities of the dorsal raphe nucleus through direct synaptic relationships.     

Electron microscopic visualization of restriction sites on DNA molecules.

DNA molecules were adsorbed to a polylysine-treated carbon film and digested directly on the film by restriction enzymes. After washing the film with 1 M NaCl, 0.4% Kodak Photo-Flo and 9% formamide, each cleavage site introduced was visualized as a gap under the electron microscope. By measuring the gapped positions on linear DNA molecules induced by other enzymes, a single EcoRI site on a lambda dv1 molecule and three HinHI sites on an fd1RF molecule were mapped at the positions expected from the cleavage maps, respectively. This electron-microscopic procedure may be useful for the construction of a cleavage map.