METHYL GREEN-PYRONIN : I. BASIS OF SELECTIVE STAINING OF NUCLEIC ACIDS

1. Methyl green stains selectively highly polymerized desoxyribonucleic acid, and fails to stain, to any significant extent, depolymerized desoxyribonucleic acid and ribonucleic acid. 2. Pyronin stains preferentially low polymers of nucleic acid. 3. Triphenylmethane dyes with two amino groups appear to share the selectivity of methyl green. Those with three amino groups are not selective. 4. A stereochemical hypothesis is offered to account for these observations.     

The Site of Action of the Crystal Violet Nuclear Stain

Enzymatic treatment of bacterial cells prior to staining revealed that the crystal violet nuclear stain reacts with protein components of the nucleus as contrasted to the desoxyribonucleic acid specificity of some nuclear stains.     

A Differential Stain for Nucleic Acids

An easily used trichrome stain consisting of orange G, methyl green, and toluidine blue is proposed as a method of differentiating desoxyribonucleic acid (DNA) and ribonucleic acid (RNA) in cells. Carnoy's acetic-alcohol is the fixative of choice, though cold acetone is also satisfactory. Photomicrographs taken with ultraviolet and visible light show that the structures containing nucleic acid are exactly those which stain with methyl green and toluidine blue. Studies with nucleases and extraction of nucleic acids with cold and hot perchloric acid further indicate a specificityy of the dyes for DNA and RNA. Present experiments are directed toward using the stain for quantitative estimation of the nucleic acids.     

The behavior of the nucleic acids during the early development of the sea urchin egg (Arbacia)

1. The unfertilized Arbacia egg contains an average of 20gamma x 10(-3) ribonucleic acid and 0.7 to 1gamma x 10(-3) desoxyribonucleic acid. 2. During the first 24 hours of development, the amount of ribonucleic acid per embryo remains practically unchanged whereas that of desoxyribonucleic acid steadily increases. At the end of this period, the amount of desoxyribonucleic acid per embryo is 10 to 15 times larger than that of the unfertilized egg.     

Histone differentiation and nuclear activity

When fast green and eosin are used in combination to stain histones, nuclei display different affinities toward the dyes, some binding fast green exclusively, others binding eosin exclusively, and still others, both stains. In a given tissue, the frequencies of nuclei exhibiting the different colors remain fairly constant over a wide range of staining conditions. Nuclei of cells of the same type may stain differently, but when they are in the same stage of development or state of activity they tend to stain alike. Xenopus erythrocyte nuclei stain bright pink. Condensed mitotic and meiotic chromosomes stain purple. In the grasshopper spermatocyte, the main body of the interphase nucleus stains bright green, but the condensed chromosome stains purple. The mole crab sperm contains several distinct histone-like proteins, that differ in their amino acid compositions, within separate areas of the cell. In these sperms, the lysine-rich histones bind eosin, while the protamine-like protein and arginine-rich histone bind fast green. In general, the eosin and fast green bind preferentially to the lysine and arginine rich histones respectively, when the dyes are permitted to compete with one another. In several systems, including spermiogenesis and erythropoiesis, the aquisition of an eosinophilic component by the nuclei accompanies the slowing of RNA synthesis, and it is suggested that there may be a causal relationship between the two events, the eosinophilic histone effecting RNA synthesis within the nucleus as a whole.     

The properties and the enzymatic degradation of desoxyribonucleoprotein from liver cell nuclei

The isolation and properties of a desoxyribonucleoprotein of the rat liver cell nucleus are described. This material consists of DNA (desoxyribonucleic acid) bound to the residual chromosomal protein by what appear to be covalent linkages. Lipide is present, but can be removed by extraction in lipide solvents prior to isolation of the nucleoprotein, without much change in the physical properties of the latter. The nucleoprotein in question forms elastic, recoilable gels in molar saline at pH 7.0 or in water at pH 8.0 to 10.0 or even higher, which are similar to those that can be obtained from whole nuclei. The effects of x-rays, heat, and enzymes on the nucleoprotein are discussed, and the composition of the protein component is investigated. The latter contains an "occult" protein that can be liberated by heating in 0.1 N HCl. A study of the enzymatic degradation of the desoxyribonucleoprotein has been made, with the aim of attempting the isolation of small polynucleotide fragments attached to amino acids or short peptides that might be useful in characterizing the mode of attachment of the desoxyribonucleic acid to the protein in the desoxyribonucleoprotein. Evidence is presented indicating that such products can be isolated through the use of electrophoresis on paper.     

Tissue culture studies; the relationship of incorporation of radioactive phosphorus in nucleic acid to the growth of cells in vitro

Growing cultures are shown to incorporate more radioactive phosphorus into ribo- and desoxyribonucleic acid than non-growing cultures. Strong indications are found that the incorporation of inorganic phosphorus into desoxyribonucleic acid parallels the mitotic coefficient and serves as a sensitive index of synthesis of new cells. There are indications that the phosphorus compounds from which the DNA molecule was synthesized were in equilibrium with the inorganic phosphorus of the medium. The effect of the implant upon growth of new cells and the assay of growth is discussed. Metabolic turnover was increased in adequate medium.     

Low level sequence variant analysis of recombinant proteins: an optimized approach

Sequence variants in recombinant biopharmaceuticals may have a relevant and unpredictable impact on clinical safety and efficacy. Hence, their sensitive analysis is important throughout bioprocess development. The two stage analytical approach presented here provides a quick multi clone comparison of candidate production cell lines as a first stage, followed by an in-depth analysis including identification and quantitation of aberrant sequence variants of selected clones as a second stage. We show that the differential analysis is a suitable tool for sensitive and fast batch to batch comparison of recombinant proteins. The optimized approach allows for detection of not only single amino acid substitutions in unmodified peptides, but also substitutions in posttranslational modified peptides such as glycopeptides, for detection of truncated or elongated sequence variants as well as double amino acid substitutions or substitution with amino acid structural isomers within one peptide. In two case studies we were able to detect sequence variants of different origin down to a sub percentage level. One of the sequence variants (Thr → Asn) could be correlated to a cytosine to adenine substitution at DNA (desoxyribonucleic acid) level. In the second case we were able to correlate the sub percentage substitution (Phe → Tyr) to amino acid limitation in the chemically defined fermentation medium.     

A comparison of the toxicity of certain dyestuffs to the conidia of Fusarium culmorum

The toxicity of a number of dyestuffs to the spores of Fusarium culmorum and Cercosporella herpotrichoides was determined by the slide-germination technique. No attempt was made to distinguish between fungistatic and fungicidal activity.
The toxicity of basic dyestuffs was unaffected by the acid radicle associated with the dye base.
The high toxicity to Fusarium culmorum of malachite green dye base was reduced weight for weight and mole for mole by substitution of ethyl, propyl or butyl groups for methyl groups.
The reduction of malachite green to malachite green leuco base removed toxicity.
The substitution of amino groups and alkylated amino groups in benzene nuclei of triphenyl methane increased toxicity, whereas acid groups reduced toxicity. Sulphonation and carboxylation reduced toxicity to vanishing point.
Alkylation of amino groups increased, but alkylation of benzene nuclei did not affect toxicity appreciably.
When the central carbon atom of the triphenyl methane dyestuffs was replaced by nitrogen (e.g. Bindschedler's green) the diphenyl ammonium compounds were less toxic than the corresponding triphenyl-methane compounds.
The prevention of rotation of the aminated benzene rings by bridging, in the o -position to central atom, with O or N, and so obtaining a planar molecule only slightly affected toxicity.
Certain acid dyes stimulated fungal growth.
The toxicity of the basic dyestuffs seems to depend not on one specific part but on the molecule as a whole, and within certain limits the structure may be varied without pronounced changes in toxicity.     

A microphotometric study of the syntheses of desoxyribonucleic acid and nuclear histone

1. The fast green stain of Alfert and Geschwind for nuclear basic protein is shown to obey the Beer-Lambert laws when used on purified histone. Interference from acid substances other than nucleic acids as a possible source of error is indicated. 2. Use of this technique after a modified Feulgen stain enables determination of relative amounts of desoxyribonucleic acid and histone in the same individual cells. 3. DNA and histone are shown to have the same distribution in formalin-fixed nuclei. 4. The syntheses of DNA and histone proceed simultaneously resulting in the doubling of both these substances prior to cell division. 5. The standard error for histone values is greater than that for DNA; however, the source of this variability is not known.     

Adenine methylation of Okazaki fragments in Escherichia coli.

In Escherichia coli polA lig-4 bacteria, the moles percent 6-methyladenine content of 10S deoxyribonucleic acid (Okazaki fragments) is 0.96 compared with 1.4 for bulk desoxyribonucleic acid.     

Inhibition of the succinic oxidase system by some structural analogs of succinic and malonic acids

The desoxyribonucleic acid and the ribonucleic acid have been prepared from pneumococcus type VI organism by a new method which has excluded deproteinization and treatment with enzymes. The yields are not high.     

The role of chloroplast-membrane-protein synthesis in the circadian clock. Purification and partial characterization of a polypeptide which is suggested to be involved in the clock.

A polypeptide (polypeptide P39), which is presumed to involved in the photosynthetic circadian rhythm in the green alga Acetabularia, was purified from the EDTA-insoluble chloroplast membrane fraction by means of preparative dodecylsulfate gel electrophoresis and then partially characterized. The purity of the isolated polypeptide P39 was confirmed by a further electrophoresis on an analytical dodecylsulfate gel and further elucidated by amino-terminal analysis which shows that glycine is the only amino-terminal amino acid of the purified polypeptide material. The molecular weight of the polypeptide P39 was found to be about 39,000 on analytical gel electrophoresis and the value was further supported by those obtained from amino acid composition and peptide mapping. The amino acid composition of polypeptide P39 showed that the proportion of intermediate amino acid groups is high while the proportion of hydrophilic amino acid groups is well balanced by that of hydrophobic amino acid groups, a property characteristic of membrane proteins.     

A MICROPHOTOMETRIC STUDY OF THE SYNTHESES OF DESOXYRIBONUCLEIC ACID AND NUCLEAR HISTONE

1. The fast green stain of Alfert and Geschwind for nuclear basic protein is shown to obey the Beer-Lambert laws when used on purified histone. Interference from acid substances other than nucleic acids as a possible source of error is indicated. 2. Use of this technique after a modified Feulgen stain enables determination of relative amounts of desoxyribonucleic acid and histone in the same individual cells. 3. DNA and histone are shown to have the same distribution in formalin-fixed nuclei. 4. The syntheses of DNA and histone proceed simultaneously resulting in the doubling of both these substances prior to cell division. 5. The standard error for histone values is greater than that for DNA; however, the source of this variability is not known.     

The classification of various organisms according to the free amino acid composition change as the result of biological evolution

Summary. The free amino acid compositions in archaeobacteria, eubacteria, protozoa, blue-green alga, green alga, slime mold, plants and mammalian cells were analyzed, to investigate whether changes in their free amino acid compositions reflect biological evolution. Cell homogenates were treated with 80–90% ethanol to separate cellular proteins and free amino acids contained in the cells. Different patterns of the free amino acid compositions were observed in the various organisms. Characteristic differences were observed between plant and mammalian cells, and between archaeobacteria and eubacteria. The patterns of the free amino acid composition in blue-green alga, green alga, protozoa and slime mold differed from each other and from those of eubacteria and archaeobacteria. Rat hepatoma cells (R-Y121B) were cultured in Eagle's minimum essential medium (MEM) containing 5% serum or in a modified MEM lacking arginine, tyrosine and glutamine. No significant difference in the free amino acid composition was observed between the two cell groups cultured under two different conditions. It is suggested that the free amino acid composition reflects apparent biological changes as the result of evolution. Received July 5, 2000 Accepted July 31, 2001     

Rapid test for distinguishing membrane-active antibacterial agents

In the search for antibacterial agents with a novel mode-of-action (MOA) many targeted cellular and cell-free assays are developed and used to screen chemical and natural product libraries. Frequently, hits identified by the primary screens include compounds with nonspecific activities that can affect the integrity and function of bacterial membrane. For a rapid dereplication of membrane-active compounds, a simple method was established using a commercially available Live/Dead(R) Bacterial Viability Kit. This method utilized two fluorescent nucleic acid stains, SYTO9 (stains all cells green) and propidium iodide (stains cells with damaged membrane red) for the drug-treated bacterial cells. The cells were then either examined visually by fluorescence microscopy or their fluorescence emissions were recorded using a multi-label plate reader set to measure emissions at two different wavelengths. The ratio of green versus red was compared to a standard curve indicating the percentage of live versus dead bacteria. Nine known antibiotics and 14 lead compounds from various antibacterial screens were tested with results consistent with their MOA.     

Adaptations of Goldner's Masson Trichrome Stain for the Study of Undecalcified Plastic Embedded Bone

Specialized adaptations for application of Goldner's Masson trichrome stain to plastic embedded undecalcified bone specimens are presented. This stain can be used successfully on methyl-glycol methacrylate, glycol methacrylate and Spurr embedded bones. The stain affords the advantage of good cellular staining due to the hematoxylin component with concomitant sharp discrimination of mature bone matrix which stains green, immature new bone matrix which stains red, and calcified cartilage which stains very pale green. Use of red filters during photomicrography aids in bone-osteoid discrimination in black and white photographs.     

Isolation and study of a bacteriophage of Pseudomonas testosteroni

A virulent phage specific for Pseudomonas testosteroni is described. This phage have a regular icosahedral head (52 nm between opposite angles) and a contractile tail (165 X 8 nm) but no fibers on. The buoyant density is 1,51 +/- 0,01 g/ml. The nucleic acid is an desoxyribonucleic acid with a density of 1,696 +/- 0,03 g/ml and a GC% between 33,7 and 39,7.     

A comparative study of<Emphasis Type="Italic"> bchG</Emphasis> from green photosynthetic bacteria

The gene bchG, coding for bacteriochlorophyll a synthase from a variety of green sulfur bacteria and the filamentous anoxygenic phototrophic bacteria, Chloroflexus aurantiacus, Chloronema sp., and Roseiflexus castenholzii HL08, was partially sequenced and compared. The deduced amino acid consensus sequences for green sulfur bacteria and green filamentous anoxygenic phototrophic bacteria were found to belong to the UbiA enzyme family of polyprenyltransferases with the most similar sequences being those of photosynthetic organisms. All deduced amino acid sequences showed a highly conserved region, which includes the motif DRXXD, characteristic of polyprenyltransferases, which was extended to DREVDAINEP for green sulfur bacteria. Neighbor-joining analysis of a protein similitude matrix displayed a relatively high distance between green sulfur bacteria and the other groups. Sequences from green sulfur bacteria were more closely related to those of purple bacteria than to those of filamentous anoxygenic phototrophic bacteria. In addition, internal grouping within green sulfur bacteria was congruent regarding taxonomic features including cell shape, presence of gas vacuoles and NaCl requirement. In addition to bchlG, another gene encoding for a second chlorophyll synthetase, previously tentatively identified as chlG, was also found in Chlorobium tepidum, showing the highest similarities with polyprenyltransferases from chlorophyll- a-containing organisms.     

Spectrophotometric Characteristics and Assay of Biological Stains IV. the Phenyl Methane Dyes

This paper continues the investigation of the assay and spectral properties of biological stains. The phenyl methane dyes, auramine O, basic and acid fuchsins, methyl violet, crystal violet, methyl green, and anilin blue W. S., may all be assayed by the spectrophotometric method. Of these, methyl green has been found unstable both in solid form and in solution, hence color densities of this dye must be measured promptly after preparation.