Isolation and properties of isolated nuclei from the Florida red tide dinoflagellate Gymnodinium breve (Davis)

A simple and rapid method is described for the isolation of nuclei from the Florida red tide dinoflagellate Gymnodinium breve. The nuclei are free of cytoplasmic contamination and are active in endogenous RNA synthesis. The ratio of DNA : RNA : acid-soluble protein : acid-insoluble protein is 1:0.39:0.13:0.63, respectively, and each nucleus contains ca. 113 picograms of DNA. Electrophoretic analysis of the acid-soluble proteins reveals the presence of two histone-like proteins with molecular weights of 12,000 and 13,000.     

ISOLATION OF NUCLEI FROM THE UNICELLULAR ALGA OLISTHODISCUS LUTEUS (CHLOROMONADOPHYCEAE)1

Methods are described for the isolation of nuclei from the marine chloromonad Olisthodiscus luteus. For each of the three alternative methods, the ratios to DNA of RNA, acid-soluble and acid-insoluble protein are 0. 17, 1.1 and 2.0, respectively. The nuclear preparations are free of whole cell and organelle contamination, although some membranes are present. The yield is 65–80% based on the recovery of DNA in the nuclear pellet. The nuclei are in DNA-dependent RNA synthesis.     

Cytofluorometric determination of DNA and protein in the nuclei and nucleoli of Physarum polycephalum during the intermitotic period

Summary Cytofluorometric methods were used to study the syntheses of DNA and of some proteins during the second intermitotic period of isolated nuclei and nucleoli of Physarum polycephalum. Interferometric methods were used for the determination of their dry mass.The volume and dry mass of nuclei and nucleoli showed similar behaviour, the nuclei doubling their volume and dry mass, and the nucleoli tripling them.The DNA synthesis began immediately after mitosis; the content nearly doubled after the first 3 hours in the case of the nuclei, after the first 5 hours in the case of the nucleoli. In both cases a slow increase (10%) was registered until the next mitosis.Of all proteins investigated only protein-bound lysine of nuclei and nucleoli did not double in initial content, this is ascribed to the isolation method used. This fact was also reflected by the total protein analysis, as nuclei and nucleoli were very rich in lysine. Protein-bound arginine of the nuclei and nucleoli showed an evolution similar to DNA. The histones showed a synthesis independent of that of DNA. The comparison of total protein content and dry mass suggested that the quicker increase of the latter should be attributed to RNA.     

Assorbimento dopo colorazione al Fast-green di cellule della caliptra di Allium cepa localizzate in differenti regioni istologiche

Abstract

Fast-green absorption of cells localized in different regions of Allium cepa root cap.—The nuclear and cytoplasmic protein content of two cell population (C2 = columella cells; P2 = peripheral cells) has been determined by Barr and Stroud cytophotometer after Fast-green staining (after DNA extraction and without DNA extraction). The collected data seem indicate that: 1) histone content is higher in nuclei of C2 cells than in nuclei of P2 ones; 2) acid proteins content is higher in nuclei of P2 cells than in those of C2 ones; 3) the cytoplasmic proteins of the two cell populations are quite different in their Fast-green reactivity.     

The chemical composition of nuclei and chromosomes isolated by the Langmuir trough technique

The pattern of staining for DNA, histone, and nonhistone protein has been studied in whole cells and in nuclei and chromosomes isolated by surface spreading. In whole interphase cells from bovine kidney tissue culture, nuclear staining for DNA and histones reveals numerous small, intensely stained clumps, surrounded by more diffusely stained material. Nuclei in whole cells stained for nonhistone proteins also contain intensely stained regions surrounded by diffuse stain. These intensely stained regions also stain for RNA, indicating that the regions contain nucleolar material. Electron microscopy of kidney cells confirms that multiple nucleoli are present. Kidney nuclei isolated by surface spreading show an even distribution of stain for DNA, histones, and nonhistone proteins, indicating that the surface forces disperse both condensed chromatin and nucleoli. DNA and protein staining was also studied in metaphase chromosomes from testes of the milkweed bug, Oncopeltus fasciatus. Staining for DNA and histones in metaphase chromosomes is essentially the same in sections of fixed and embedded testes as in preparations isolated by surface spreading. However, striking differences are noted in the distribution of nonhistone proteins. In sections, nonhistone stain is concentrated in extrachromosomal areas; metaphase chromosomes do not stain for nonhistone proteins. Chromosomes isolated by surface spreading, however, stain intensely for nonhistone proteins. This suggests that nonhistone proteins are bound to the chromosomes as a contaminant during the isolation procedure. The relationship of these findings to current work with chromosomes isolated for electron microscopy is discussed.     

Determinants of sperm nuclear shaping in the genus Xenopus

The morphogenesis of sperm nuclei was investigated in six different species or subspecies of the genus Xenopus (Pipidae, Anura). The sequence of nuclear morphogenesis was similar in each species used in this study. Electrophoretic comparison of the basic chromatin proteins from late spermatids and sperm of each species demonstrated that the complements of histones and spermatid-sperm-specific basic proteins were extremely diverse suggesting that shape was not determined by specific basic proteins or mechanisms of histone removal. This conclusion was reinforced by the observation that Xenopus sperm DNA decondensed by 2.0 M NaCl remained contrained in residual structures which resembled intact sperm nuclei. These observations suggested that morphogenesis of sperm nuclei is directed by proteins or RNA molecules which are not directly responsible for chromatin condensation.     

Improved performance of protein‐based recombinant gene therapy vehicles by tuning downstream procedures

Protein engineering offers a robust platform for the design and production in cell factories of a plethora of protein‐based drugs, including nonviral gene therapy vehicles. We have determined here that a protein nanoparticle, formed by highly cationic protein monomers, fails to bind exogenous DNA and to promote detectable gene expression in target cells despite recruiting all the needed functions. Removal of DNA and RNA with nucleases previous to forming complexes with exogenous DNA dramatically enhances the ability of the protein to bind and transfer DNA to target cell nuclei. These data point out contaminant nucleic acids deriving from the cell factory as a major factor impairing the performance of protein‐based artificial viruses and stress the need of a nuclease step in the downstream of proteins whose function is based on cationic domains. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1458–1463, 2013     

An autoradiographic and cytophotometric study of oogenesis in a pulmonate snail,Planorbarius corneus

Summary The spatial and temporal patterns of macromolecular syntheses in oocytes and somatic auxiliary cells of the snail Planorbarius corneus have been investigated by autoradiography and cytophotometry. Oogenesis has been divided into three stages, comprising early meiosis up to diplotene (stage I), previtellogenetic growth phase (stage II), and vitellogenesis (stage III). No DNA synthesis was found in any oocyte stage. In stage-I oocytes, only nucleoli were found labelled with ³H-uridine. Oocyte nuclei of stage II and III actively synthesize RNA in nucleoli and chromosomes. The most intense incorporation of uridine in chromatin probably occurs during the previtellogenesis — vitellogenesis transition period during which cytological findings suggest well developed lampbrush chromosomes. RNA synthesis in amphinucleoli of stage-III oocytes is restricted to basophilic nucleolar parts, whereas acidophilic parts (protein bodies) neither synthesize nor store RNA. During vitellogenesis oocytes incorporate amino acids into yolk platelet proteins. Radioactive proteins are found in yolk platelet precursors 5 h after injection of the tracer and in yolk platelets 3 h thereafter. The labelling pattern suggests that oocytes synthesize certain hitherto unidentified yolk components. No evidence for the participation of follicle cells in synthesis and transport of vitellogenic proteins has been obtained from autoradiography. Cytological findings suggest an important role for these cells in oogenesis. They are highly active in RNA and protein synthesis. Cellular differentiation is accompanied by polyploidization of the nuclei which attain a highest DNA content of 256 c. Polyploidization probably occurs in incremental steps as indicated by complete endomitotic chromosomal cycles. Autoradiographs show that, during vitellogenesis, oocytes do not incorporate significant amounts of glucose, and only certain follicle cells were labelled with glucose, probably indicating the synthesis of glycogen.     

Isolation and Properties of Nuclei from Control and Auxin-treated Soybean Hypocotyl

A quick procedure for the isolation of nuclei with good yield from soybean hypocotyl (Glycine max var. Wayne) was developed. The isolated nuclei appeared to retain their structural integrity. They were typically ellipsoidal with minima and maxima diameter of about 6 and 8 to 10 micrometers. While the nuclei were similar in size, the nucleoli were significantly larger in nuclei from auxin-treated tissue. The DNA content per nucleus was 4 ± 1 picograms for both untreated and auxin-treated tissues. The DNA: RNA: protein ratio of isolated nuclei in untreated and auxin-treated tissues was 1: 3.1: 11 and 1: 5.4: 21.7, respectively. The purified nuclei were active in RNA synthesis; the level of RNA polymerase II activity expressed in the nuclei from untreated tissue was 50 to 60% higher than RNA polymerase. I. The nuclei from auxin-treated tissues contained about 2.5 times as much RNA polymerase I activity as nuclei from untreated tissue. The purified nuclei from both untreated and auxin-treated tissues were also active in the incorporation of ³H-TTP into DNA.     

AN ANALYSIS OF HETEROCHROMATIN IN MAIZE ROOT TIPS

The B chromosomes of maize are condensed in appearance during interphase and are relatively inert genetically; therefore they fulfill the definition of heterochromatin. This heterochromatin was studied in root meristem cells by radioautography following administration of tritiated thymidine and cytidine, and was found to behave in a characteristic way, i.e. it showed asynchronous DNA synthesis and very low, if any, RNA synthesis. A cytochemical comparison of normal maize nuclei with nuclei from isogenic maize stock containing approximately 15–20 B-chromosomes in addition to the normal complement has revealed the following: (a) the DNA and histone contents are greater in nuclei with B chromosomes; (b) the proportion of DNA to histone is identical with that of nuclei containing only normal chromosomes; (c) the amount of nonhistone protein in proportion to DNA in interphase is less in nuclei with B chromosomes than in normal nuclei. In condensed B chromosomes the ratio of nonhistone protein to DNA is similar to that in other condensed chromatin, such as metaphase chromosomes and degenerating nuclei. The B chromosomes appear to have no effect on nucleolar RNA and protein. Replication of B chromosomes is precisely controlled and is comparable to that of the ordinary chromosomes not only in synthesis for mitosis but also in formation of polyploid nuclei of root cap and protoxylem cells.     

Diurnal variations in endogenous RNA polymerase activity and amounts of nuclear non-histone protein, DNA and cytoplasmic protein in rat liver.

From rats fed ad libitum and kept under a 12 + 12 h light/dark regimen, the DNA dependent RNA polymerase activity of liver cell nuclei was determined avery four hours. From identical rats, nuclear non-histone protein and DNA, and cytoplasmic protein was determined by Feulgen-Naphthol Yellow S cytophotometry of isolated liver cells. The minimum: maximum ratio of the RNA polymerase activity is 0.77; the min:max ratio of nuclear non-histone protein is 0.84. These two parameters have identical time courses with a gradual decline during the light period and a sharp rise after the onset of the dark period. The variations in nuclear DNA content, estimated as the amount of Feulgen stain bound, closely parallel those of the RNA polymerase activity and nuclear non-histone protein content (min:max = 0.96). The amount of cytoplasmic protein per cell also varies throughout the day, but its time curve lags behind those of nuclear non-histone content and RNA polymerase activity. These results are consistent with the concept of nuclear non-histone proteins as de-repressors of the DNA template in differentiated, non-proliferating cells, and support the validity of using Feulgen-Naphthol Yellow S cytophotometry of nuclear non-histone proteins as an estimate of gene expression in such cells.     

Diurnal variations in endogenous RNA polymerase activity and amounts of nuclear non-histone protein,DNA and cytoplasmic protein in rat liver

Summary From rats fed ad libitum and kept under a 12+12 h light/dark regimen, the DNA dependent RNA polymerase activity of liver cell nuclei was determined every four hours. From identical rats, nuclear non-histone protein and DNA, and cytoplasmic protein was determined by Feulgen-Naphtol Yellow S cytophotometry of isolated liver cells. The minimum: maximum ratio of the RNA polymerase activity is 0.77; the min:max ratio of nuclear non-histone protein is 0.84. These two parameters have identical time courses with a gradual decline during the light period and a sharp rise after the onset of the dark period. The variations in nuclear DNA content, estimated as the amount of Feulgen stain bound, closely parallel those of the RNA polymerase activity and nuclear non-histone protein content (min:max=0.96). The amount of cytoplasmic protein per cell also varies throughout the day, but its time curve lags behind those of nuclear nonhistone content and RNA polymerase activity. These results are consistent with the concept of nuclear non-histone proteins as de-repressors of the DNA template in differentiated, non-proliferating cells, and support the validity of using Feulgen-Naphthol Yellow S cytophotometry of nuclear non-histone proteins as an estimate of gene expression in such cells.     

Isolation,fractionation and biochemical analysis of the metaphase chromosomes of Microtus agrestis

A method has been developed for isolating metaphase chromosomes from Microtus agrestis fibroblasts in relatively large quantities with recovery of about 50% of the chromosomes present in the metaphase cells. The method employs pressure homogenisation to release the chromosomes from the cells. The average chemical composition of the Microtus chromosome preparations is 24.6% DNA, 19.9% RNA and 55.5% protein. The isolated chromosomes were fractionated by sedimentation velocity in a density gradient into three size groups in one of which 75–80% of the chromosomes were the large sex-chromosomes. The relative composition of this fraction containing most of the heterochromatin of the cell was DNA: 100, RNA: 59, acid-soluble protein: 54, acid-insoluble protein: 178. — Disc electrophoresis studies revealed no significant difference in the histone patterns between the euchromatic and heterochromatic chromosomes of the three chromosome size-groups. Metaphase chromosomes appear to have a lower lysine-rich histone content than interphase nuclei.     

A histological and histochemical study of the cotyledons ofPhaseolus vulgaris L. during germination

Summary The cotyledon ofPhaseolus vulgaris L. comprises four tissues: epidermis, abaxial hypodermis, storage parenchyma, and procambium. A complex intercellular space system is present throughout the storage tissue and comprises about 16% of the cotyledon volume. All the cells contain protein bodies, and the hypodermis and storage parenchyma also contain starch grains. The epidermal cells are at the 2 C level of DNA, those of the hypodermis at the 4 C level, and the storage cells vary from 8 C to 32 C. During germination stomata differentiate in the epidermis. Reserve mobilization begins in the cells furthest from the epidermis and from the vascular tissue. Protein is removed from these cells with little or no coalescence of protein bodies. The DNA content of the nuclei decreases. The cell walls swell and then decrease in thickness as material is removed. Finally the nuclei and cytoplasm disappear and the cells collapse. In the cells near vascular bundles the protein bodies coalesce before losing their protein. The DNA content of the nuclei declines but nuclei and cytoplasm are still present at abscission. These cells do not collapse. Cytoplasmic RNA content is highest near the abaxial surface. Most of the RNA is removed during the first three days of germination.     

Epitope selection for multipeptide proteins: the case of RNA polymerase IV and V

Large multipeptide protein complexes have provided a challenge for epitope selection, which is required for immunological protocols where native conformations are needed. Immunolocalization requires native conformation of the proteins, which is essential for further understanding of biological activity. RNA polymerase IV and V are multisubunit proteins that interact with other factors in the RNA-directed DNA methylation pathway for control of DNA silencing by small interfering RNA and DNA methylation. DNA silencing is an important process during cell differentiation, nuclear structure and viral control among others. RNA polymerase IV and V are yet to be studied in model monocot systems like Oryza sativa, which may provide further data to define if the genetic silencing mechanism has diverged over time as compared to dicots. Here we show an in silico selection process of exposed sequences and their use for obtaining antibodies against native RNA polymerase IV and V in O. sativa.     

Isolation and characterization of nuclei from Neurospora crassa.

A procedure was developed for isolating nuclei from either the conidial or germinated conidial growth phase of Neurospora crassa. A frozen conidial suspension was lysed by passage through a French pressure cell, and the nuclei were freed from the broken cells by repeated homogenization in an Omni-Mixer. Pure nuclei were obtained from the crude nuclear fraction by density banding in a Ludox gradient. The final nuclear yield was 20 to 30%. The nuclei had a deoxyribonucleic acid (DNA):ribonucleic acid (RNA):protein ratio of 1:3.5:7 and were active in RNA synthesis. The nuclei, stained with the DNA stain 4,6-diamidino-2-phenylindole, appeared under fluorescence microscopy as bright blue spheres, 1 micron in diameter, essentially free from cytoplasmic attachments. Chromatin extracted from the nuclei in a 70 to 75% yield by dissociation with 2 M sodium chloride and 5 M urea had a DNA:RNA:protein ratio of 1:1.05:1.7. Chromatin reconstituted from this preparation exhibited a level of RNA polymerase template activity lower than that of pure Neurospora DNA, but the maximum level of reconstitution obtained was only 10%. Fractionation of Neurospora chromatin on hydroxylapatite separated the histones from the chromatin acidic proteins. The normal complement of histone proteins was present in both the reconstituted and dissociated chromatin preparations. The acidic protein fraction exhibited a variety of bands on sodium dodecyl sulfate gel electrophoresis ranging in molecular weight from 15,000 to 70,000. The gel pattern was much more complex for total dissociated chromatin than for reconstituted chromatin.     

Age- and ploidy-related changes in the non-histone proteins of rat liver nuclei

Hepatic nuclei from young, mature and aged rats were separated into 2n, 4n and 8n ploidy classes on sucrose gradients, and characterized in terms of DNA, RNA, histones and non-histone proteins (NHP). The absolute DNA content per nucleus doubled with each increase in ploidy as expected, and the relative proportions of other components remained uniform in all cases. Despite such overall similarity in pattern however, marked electrophoretic heterogeneity was observed among the NHP, both in relation to ploidy and animal age. All nuclei shared a common spectrum of soluble and residual NHP, but discrete variations among several specific proteins were observed. Most prominent was a systematic, age-related decrease in two major polypeptides of about 125 000 and 57 000 mol. wt, respectively. There were no comparable variations in the histone proteins. The results are discussed in terms of possible functional differentiation among hepatocytes of the various ploidy classes.