Accumulation of the early histone messenger RNAs during the development of Strongylocentrotus purpuratus

The developmental profile of amounts of the mRNAs for the early histones was determined. Sea urchin embryos (Strongylocentrotus purpuratus) were labeled with ³H nucleoside, and the RNA was extracted and fractionated by electrophoresis on polyacrylamide gels. Radioactivity in the resolved mRNA bands was determined and converted to molar quantities by knowledge of the precursor pool-specific activity. Between the 16- and the 200-cell stages 7–10 × 10⁶ molecules of each core histone mRNA, and 2.5 × 10⁵ molecules of H1 mRNA accumulate. During the subsequent few hours of cleavage the accumulated mRNAs disappear with a half-life of 1.5–2 hr. It is argued that mRNA half-life may be regulated during cleavage.     

Characterization of Ehrlich ascites tumor cell messenger RNA specifying ribosomal proteins by translation in vitro

We have examined the messenger RNA which codes for the ribosomal proteins in Ehrlich ascites tumor cells. Poly(A)-containing mRNA was isolated from polysomes and fractionated into 11 size classes whose average molecular weights were between 1.8 × 10⁵ and 24 × 10⁵. These mRNAs were used to direct protein synthesis in a fractionated translational system that was derived completely from Ehrlich ascites tumor cells. More than 90% of the ribosomal proteins which we could identify were coded for by mRNAs averaging in size between Mr = 180 × 10³ and 320 × 10³. The small size of these mRNAs indicates that the cytoplasmic mRNAs which specify the ribosomal proteins are monocistronic. We could detect the synthesis of 36 of 48 ribosomal reference proteins as well as 20 additional polypeptides which had characteristics similar to ribosomal protein. The ribosomal proteins were identified on the basis of their positive charge, small size, electrophoretic properties on two-dimensional polyacrylamide gels and chromatographic characteristics on carboxymethyl-cellulose.     

Isolation and physicochemical characterization of mitochondrial DNA from cultured cells ofPetunia hybrida

Summary Mitochondrial DNA ofPetunia hybrida was purified from cell suspension cultures. Up to 50% of the DNA could be isolated as supercoiled DNA molecules by CsCl-ethidium bromide density gradient centrifugation. The DNA purified from DNase-treated mitochondria bands at a single buoyant density of 1.760 gcm^–3 in neutral density gradients and runs on agarose gels as a single band with an apparent molecular weight exceeding 30 megadaltons (Md). Summing of the restriction endonuclease fragment lengths indicates a mitochondrial genome size of at least 190 Md. Electron microscopic analysis reveals the presence of a heterogeneous population of circular DNA molecules, up to 60 Md in size. Small circular DNA molecules, ranging in size from 2–30 Md are present, but unlike in cultured cells of other plant species they do not form discrete size classes and furthermore, they constitute less than 5% of the total DNA content of the mitochondria. The restriction endonuclease patterns of mitochondrial DNA do not qualitatively alter upon prolonged culture periods (up to at least two years).     

Stoichiometry of chromatin proteins

The stoichiometry of rat liver chromatin proteins has been estimated by quantitative disc electrophoresis. There are about 1.3 × 10⁸ histone and 2.4 × 10⁷ nonhistone polypeptide molecules per haploid genome, an average of one such molecule for every 21 and 117 base pairs of DNA, respectively. Nonhistone proteins have been separated into 115 polypeptide size classes. The total number of molecules represented in distinct size classes ranges from 4.2 × 10³ (limits of sensitivity) to 1.7 × 10⁶ per haploid genome, with a mean of 2.1 × 10⁵.     

Effect of pressure on the sol-gel transition of carrageenans

The effects of pressure on the sol-gel transition of κ- and ι-carrageenans were studied in KCl solutions under high pressures up to 3000 kg/cm². The carrageenan gels were destabilized by pressure: the pressure depression of melting temperature, (dT/dP)_m, was ?5.7 × 10^?3 and ?4.0 × 10^?3 K cm²/kg independent of KCl concentration for κ- and ι-carrageenans, respectively. The enthalpy, entropy and volume changes accompanying the gel formation were calculated from the Eldridge-Ferry's plots and the Clausius-Clapeyron equation. The volume change per unit cross-link (two disaccharide residues) was estimated to be (2.5 ～ 4.9) and (1.7 ～ 3.4) ml/mol for κ- and ι-carrageenans, respectively. The compressibility of both carrageenan molecules appeared to be larger by (1.6 ～ 2.6) × 10^?12 (κ-form) and by (0.8 ～ 1.3) × 10^?12cm²/dyn (i-form) in gel state as compared with in sol state These increases in volume and compressibility on gelation were attributed to a reduction of water of hydration from the carrageenan molecules, which is mainly due to a replacement of the polymer-water hydrogen bond by the polymer-polymer hydrogen bond. These results seemed not inconsistent with the idea that a double helix structure of carrageenan gels may persist in solution as well as in the solid state.     

Characterization of 10S RNA: a new stable rna molecule from Escherichia coli.

Summary When cells of Escherichia coli are labeled with ³²P_i for long periods of time and the cell content is subjected to electrophoresis in polyacrylamide gels, an RNA band appears which is about 10S in size. This band seems to contain three conformers. After treatment with formamide only a single band appears in this region of the gel, which contains 550 nucleotides as determined from its mobility. The complexity of the fingerprint of this material, after digestion with T₁-RNase, is in agreement with the size as determined by the mobility, this confirming that indeed it is a single molecule. Composition of the T₁-oligonucleotides was determined by digesting the T₁-generated oligonucleotides with pancreatic RNase and T₂-RNase. The quantitative and qualitative analysis of these digestions suggests that 10S RNA contains 609 nucleotides. The molecule contains, besides the four regular bases, one copy per molecule of the modified base pseudouridine.10S RNA cannot be processed by cell extracts to tRNA-sized molecules and does not bind significantly to ribosomes, hence it is unlikely to be a tRNA precursor or an mRNA.     

Discrete sizes of replication intermediates in drosophila cells

The size of DNA replication intermediates from Drosophila cells pulse-labeled with ³H-thymidine for 30–120 sec was determined by electrophoresis in formamide-polyacrylamide gels. Replication intermediates were formed in three discrete size classes, with median lengths of 61, 125 and 240 nucleotides. Replication intermediates in the 125 nucleotide size class occurred most frequently. Two of the three size classes may contain discrete species of replication intermediates about 90–400 nucleotides long. The data also suggested that some larger replication intermediates accumulate in pulse-labeled cells. We concluded that 61 nucleotide molecules give rise to 125 and 240 nucleotide molecules, which then form high molecular weight DNA. Mechanisms for forming these replication intermediates are discussed.     

Separation of α- and β-Globin Messenger RNAs

THE 10S RNA fraction of reticulocytes from various species contains the haemoglobin messenger RNA^1–4. When this 10S RNA fraction is added to a cell-free system derived from reticulocytes or Krebs II ascites cells, it directs the synthesis of α and β chains of haemoglobin^5–8. The α and β messenger RNA molecules contained in this fraction, however, have not yet been separated and identified. When reticulocyte. RNA of mouse is subjected to electrophoresis on 6% polyacrylamide gels, the 10S fraction contains two major bands and three minor bands⁹, suggesting that the major lOS RNA bands contain the messenger RNAs for the α- and β-globin chains.     

Extrachromosomal DNA in Bacillus thuringiensis var. kurstaki, var. finitimus, var. sotto, and in Bacillus popilliae

Four entomopathogenic bacteria contained extrachromosomal deoxyribonucleic acid (DNA) molecules of various sizes. Bacillus thuringiensis var. kurstaki contained twelve elements banding on agarose gels that ranged from 0.74 to > 50 × 10⁶ daltons, three of which were giant extrachromosomal DNA elements. B. thuringiensis var. sotto contained one giant extrachromosomal DNA element with a molecular size of about 23.5 × 10⁶ daltons and two lesser elements of 0.80 and 0.62 × 10⁶ daltons. B. thuringiensis var. finitimus harbored two giant DNA elements corresponding to >50 × 10⁶ daltons and two lesser bands with relative small size (0.98 and 0.97 × 10⁶ daltons). B. popilliae contained no giant extrachromosomal DNA elements but did contain two smaller elements corresponding to 4.45 and 0.58 × 10⁶ daltons. The possible use of extrachromosomal DNA elements that prove to be autonomous replicons for recombinant DNA studies is discussed.     

Size distribution and maturation of newly replicated DNA through the S and G2 phases of physarum polycephalum

The size distribution of newly made DNA and the dynamics of size maturation of progeny DNA molecules were studied in the synchronous S and G2 phases of Physarum polycephalum. Pulse labeling of DNA and analysis of the products on alkaline sucrose gradients showed that synthesis of primary replication units (which will also be referred to as “Okazaki” fragments) occurred throughout the S period. Pulse and pulse-chase experiments revealed a distinct pattern of size maturation. An apparently linear increase in molecular weight of progeny DNA molecules during the first hour of the S phase occurred at a rate of approximately 4–5 × 10⁵ daltons per min at 26°C, corresponding to the joining of 6–8 Okazaki fragments. The resulting 35–45S (1.1–2.2 × 10⁷ daltons) DNA molecules may correspond to the Physarum “replicon.” The further size increases of the newly made DNA appear to occur in steps, possibly reflecting a clustering of isochronous replicons along the chromatide. These observations are discussed with regard to mechanisms of DNA replication and size maturation.     

On the size relationship between nuclear and cytoplasmic RNA in sea urchin embryos

The approximate sizes of heterogeneous nuclear (HnRNA) and cytoplasmic RNA of sea urchin embryos were determined by DMSO density gradient centrifugation and acrylamide-formamide gel electrophoresis. The data suggest that the sizes of these molecules are smaller than those estimated under nondenaturing conditions. The size of most of the nuclear RNA ranges from 0.5 to 3 × 10⁶ daltons, while that of the cytoplasmic RNA ranges from 0.1 to 2 × 10⁶ daltons. Both nuclear and cytoplasmic RNA of sea urchin embryos may have a minor fraction (5–10%) of very large species with molecular weights up to 4 to 5 × 10⁶ daltons.The idea that the size of HnRNA may be larger in organisms higher on the evolutionary scale is discussed.     

In vitro synthesis of a 2.1 x 10(6) dalton DNA in the endogenous retrovirus reverse transcriptase reaction.

A discrete, homogeneous population of single-stranded DNA molecules complementary to virion RNA has been synthesized in a modified RNA directed DNA polymerase reaction involving the endogenous retrovirus produced by the mouse cell line JLS V-6. A molecular weight of 2.1 × 10⁶ dalton for the DNA was assigned from the sedimentation coeffecient in alkaline sucrose gradients, the electrophoretic mobility in formamide gels, and the lengths of the molecules in electron micrographs.     

Messenger RNA for isocitrate lyase from Chlorella fusca var. vacuolata

Chlorella fusca cultures growing in the light and adapting to acetate in the dark were labelled with adenine-³H and adenine-¹⁴C, respectively. Poly(A)-containing RNA from the mixed cultures was analysed for ¹⁴C/³H ratio after polyacrylamide gel electrophoresis in 98% formamide. The RNA from acetateadapting C. fusca cells contained excess label migrating in the gels at a position equivalent to about 0.85×10⁶ mol.wt. Partially purified anti-isocitrate lyase serum linked to p-aminobenzoyl-cellulose bound 3.5–13% of polysomes from acetate-adapting C. fusca, containing 5–10% of polysomal poly(A)-containing RNA. The antibody-bound poly(A)-containing RNA fraction showed a unimodal size distribution with a mean size of about 0.85×10⁶ mol.wt. after electrophoresis on 4% polyacrylamide gels in 98% formamide. Cell-free translation assays showed a three-fold enrichment of isocitrate lyase mRNA after antibody selection of polysomes and indicated that isocitrate lyase mRNA was abundant in acetate-adapting C. fusca cells.Abbreviations A ₂₆₀ unit The amount of material in 1.0 ml giving an absorbance of 1.0 at 260 nm in a 1 cm light path - PAB-cellulose p-aminobenzoyl-cellulose - SDS sodium lauryl sulphate To whom offprint requests are to be sent     

Effect of puromycin on cartilage proteoglycan structure and capacity to bind hyaluronic acid

Rat chondrosarcoma chondrocytes were cultured in the presence of puromycin to induce premature termination of core protein precursor. The structure and function of intracellular and extracellular proteoglycans were assessed by molecular sieve chromatography and polyacrylamide gel electrophoresis. [³H]Serine incorporation was maximally inhibited by 3 × 10^?4m puromycin but unaffected by 10 ^?5m puromycin. Proteoglycans synthesized in the presence of puromycin exhibited increased monomer size due to increased chondroitin sulfate chain size, typical of proteoglycans synthesized in the presence of protein synthesis inhibitors, but no loss in ability to bind to hyaluronic acid; and no loss in core protein size was observed after treatment with chondroitinase. These data suggest that chondrocytes select only completed or nearly completed core protein molecules to process into proteoglycans.     

The effects of different thymidine concentrations on DNA replication in pea-root cells synchronized by a protracted 5-fluorodeoxyuridine treatment

Single-cell and DNA fiber autoradiography, cytophotometry and velocity sedimentation in alkaline sucrose gradients were used to analyse DNA replication and nascent replicon maturation in 5-fluorodeoxyuridine (FUdR)-synchronized cells of Pisum sativum. The replicon size was not significantly changed by the protracted FUdR treatment. When the synchronized cells were released from the inhibitor, labeled with [³H]TdR for 30 min, and chased in medium containing 1 × 10⁻⁶ M or lower concentrations of cold thymidine, DNA replication stopped after approx. 25% of the genome had replicated, and the nascent strands failed to grow above 9–12 × 10⁶ D single-stranded (ss) DNA. When the cells were chased in medium with 1 × 10⁻⁵ M cold thymidine, the DNA content of the labeled cells steadily increased with time and the size of the nascent molecules grew continuously until replicon size was achieved; then they were accumulated at replicon size until the cells arrived in late S or G2. When the FUdR-synchronized cells were chased in medium containing 1 × 10⁻⁴ M cold thymidine, the size of the nascent strands increased continuously with time, indicating that some neighbouring nascent replicons were joined as soon as they completed their replication. These observations led us to postulate that in FUdR-synchronized cells the rates of chain elongation, cell progression through the S phase and nascent replicon maturation are controlled by thymidine availability.     

Resolving Power: A Quantitative Measure of Electrophoretic Resolution

Resolving power is a quantitative measure of the ability of an electrophoretic system to separate DNA (and other) molecules of similar size. It is a dimensionless quantity, and hence facilitates comparison of the performance of electrophoretic systems that operate very differently. Resolving power can be determined as a function of molecular length from experimental data consisting of a series of completely resolved bands on a gel or blot; closely spaced bands are not required. We discuss factors such as the mass of DNA in a particular band and the spatial resolution of the system used to image the distribution of DNA on a gel or blot that, while not an intrinsic part of the electrophoretic system, may influence the observed resolving power. We derive an empirical global dispersion function that applies both to images of gels obtained after a fixed time of electrophoresis of all the samples and to images obtained as each species reaches a detector located at a fixed distance from the starting well. We use this dispersion function to show that the improvement in resolving power produced by extending the time or distance of electrophoresis in a static, uniform electric field asymptotically approaches a limiting value that is a function of the length of the DNA. When plotted as a function of molecular length, this limiting value defines an envelope that characterizes the intrinsic limits of performance of a particular electrophoretic system (e.g., electric field strength, gel type and concentration, buffer, temperature). Comparing the resolving power of static field agarose gel electrophoresis as routinely practiced for separating DNA molecules from 10³ to 10⁵ bp long with other electrophoretic schemes suggests that significant improvements should be achievable.     

Bradyrhizobium japonicum Survival in and Soybean Inoculation with Fluid Gels

The utilization of gels, which are used for fluid drilling of seeds, as carriers of Bradyrhizobium japonicum for soybean (Glycine max (L.) Merr.) inoculation was studied. Gels of various chemical composition (magnesium silicate, potassium acrylate-acrylamide, grafted starch, and hydroxyethyl cellulose) were used, although the hydroxyethyl cellulose gels were more extensively investigated. Gel inocula were prepared by mixing gel powder with liquid cultures of B. japonicum (2% [wt/vol]). The population of B. japonicum USDA 110 did not change in each gel type during 8 days of incubation at 28°C. These fluid gels were prepared with late-exponential-growth-phase cells that were washed and suspended in physiological saline. Mid-exponential-growth-phase B. japonicum USDA 110, 123, and 138 grew in cellulose gels prepared with yeast extract-mannitol broth as well as or better than in yeast extract-mannitol broth alone for the first 10 days at 28°C. Populations in these cellulose gels after 35 days were as large as when the gels had originally been prepared, and survival occurred for at least 70 days. Soybeans grown in sand in the greenhouse had greater nodule numbers, nodule weights, and top weights with gel inoculants compared with a peat inoculant. In soil containing 10³ indigenous B. japonicum per g of soil, inoculation resulted in increased soybean nodule numbers, nodule weights, and top weights, but only nodule numbers were greater with gel than with peat inoculation. The gel-treated seeds carried 10² to 10³ more bacteria per seed (10⁷ to 10⁸) than did the peat-treated seeds.