Isolation and separation of nucleic acids from Streptomyces hydrogenans (author's transl)]

Different methods for homogenization of cells of Streptomyces hydrogenans, for extraction of nucleic acids and for fractionation of the RNA and DNA obtained were critically examined. The only way to prepare high molecular weight rapidly labelled RNA and polysomes was to grind freeze-dried cells together with kieselguhr with a mortar and pestle. The best results for extraction of nucleic acids from the cell homogenate were obtained in the presence of diethyl pyrocarbonate (diethyl oxydiformate), yielding nucleic acids of considerable purity in a minimal amount of time. The best resolution of extracted nucleic acids was achieved by electrophoresis in 2% agarose acrylamide gels. This technique proved that during the cell homogenization and extraction procedure the bulk of nucliec acids was not degraded to low molecular weight material. An improved device for the registration of the profile of the absorption after gel electrophoresis is described.     

Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil

A universally adaptable protocol for quantitative extraction of high-purity nucleic acids from soil is presented. A major problem regarding the extraction of nucleic acids from soil is the presence of humic substances, which interfere with the extraction process itself and in subsequent analytical manipulations. By the approach described here, the humic compounds are precipitated prior to cell lysis with Al(2)(SO(4))(3), and thus eliminated prior to the nucleic acid extraction. The protocol allows for removing of a considerable content and range of humic acids and should therefore be applicable for a wide spectrum of soil types. Accordingly, reproducible results in analyses of different soil types are made possible, inclusively for quantitative comparisons.     

Experiments with lysis of living cells of Eremothecium ashbyii and of Methanomonas by microbial enzymes

The possibility to use microorganisms as human food is limited by several factors. The intact cell is resistant to digestion, the cell wall is unbalanced in essential amino acids, and the nucleic acids are said to be harmful. For using single cell protein as food it may thus be necessary to disrupt the cell wall and separate the protein from nucleic acid. This paper is concerned with the production and properties of extracellular enzymes able to lyse cell walls of microorganisms. Soil bacteria and actinomycetes have been cultivated and lytic enzymes from these organisms have been used to lyse living cells of the yeast like organism E. ashbyii. Efforts were also made to use these enzymes for lysing cell of a Methanomonas sp.     

Chemical and Serological Relationships Between the Heteropolysaccharides of Mycobacterium tuberculosis and Mycobacterium kansasii

The identity of a heteropolysaccharide from cell walls of Mycobacterium tuberculosis H37Ra with Seibert's tuberculopolysaccharide I was demonstrated by thin-layer chromatography, chemical analysis, and antigenic tests. The polysaccharide of M. kansasii was shown to be identical with that of M. tuberculosis. Defatted cells were disintegrated by ultrasonic treatment in the presence of glass beads; cell walls were obtained by differential ultracentrifugation. Ethyl alcohol-precipitated carbohydrate extracts were analyzed for protein and nucleic acid; these impurities were removed. Tuberculopolysaccharide I from the mycobacterial culture filtrate is probably derived from a lipopolysaccharide of the cell wall, which is partially removed by chloroform in the intact state. Alkaline extraction releases additional polysaccharide, in varying degrees of association with cell wall murein.     

Stable carbon isotope analysis of nucleic acids to trace sources of dissolved substrates used by estuarine bacteria.

The natural abundance of stable carbon isotopes measured in bacterial nucleic acids extracted from estuarine bacterial concentrates was used to trace sources of organic matter for bacteria in aquatic environments. The stable carbon isotope ratios of Pseudomonas aeruginosa and nucleic acids extracted from cultures resembled those of the carbon source on which bacteria were grown. The carbon isotope discrimination between the substrate and total cell carbon from bacterial cultures averaged 2.3% +/- 0.6% (n = 13). Furthermore, the isotope discrimination between the substrate and nucleic acids extracted from bacterial cultures was 2.4% +/- 0.4% (n = 10), not significantly different from the discrimination between bacteria and the substrate. Estuarine water samples were prefiltered through 1-micron-pore-size cartridge filters. Bacterium-sized particles in the filtrates were concentrated with tangential-flow filtration and centrifugation, and nucleic acids were then extracted from these concentrates. Hybridization with 16S rRNA probes showed that approximately 90% of the nucleic acids extracted on two sample dates were of eubacterial origin. Bacteria and nucleic acids from incubation experiments using estuarine water samples enriched with dissolved organic matter from Spartina alterniflora and Cyclotella caspia had stable carbon isotope values similar to those of the substrate sources. In a survey that compared diverse estuarine environments, stable carbon isotopes of bacteria grown in incubation experiments ranged from -31.9 to -20.5%. The range in isotope values of nucleic acids extracted from indigenous bacteria from the same waters was similar, -27.9 to -20.2%. Generally, the lack of isotope discrimination between bacteria and nucleic acids that was noted in the laboratory was observed in the field.(ABSTRACT TRUNCATED AT 250 WORDS)     

A solid-phase extraction procedure for DNA purification

The preparation and use of particulate materials for the removal of proteins from nucleic acid samples by solid-phase extraction procedures are described. The solid-phase extraction procedure is analogous to the classical phenol extraction for DNA purification, with the exception that the phenol is replaced with insoluble particulate materials that are chemically similar to phenol and thus function in an analogous manner. These particulate materials have a very high affinity for proteins and a very low affinity for nucleic acids. With these materials, it is possible to remove large quantities of proteins (i.e., tens of milligrams) from minute quantities (submicrogram) of nucleic acid and quantitatively recover the latter in a biologically active state. Compared to other procedures that are currently used to purify nucleic acids, the protocols using these materials offer the advantages of speed, quantitative DNA recovery, safety, and convenience.     

Stable carbon isotope analysis of nucleic acids to trace sources of dissolved substrates used by estuarine bacteria

The natural abundance of stable carbon isotopes measured in bacterial nucleic acids extracted from estuarine bacterial concentrates was used to trace sources of organic matter for bacteria in aquatic environments. The stable carbon isotope ratios of Pseudomonas aeruginosa and nucleic acids extracted from cultures resembled those of the carbon source on which bacteria were grown. The carbon isotope discrimination between the substrate and total cell carbon from bacterial cultures averaged 2.3% +/- 0.6% (n = 13). Furthermore, the isotope discrimination between the substrate and nucleic acids extracted from bacterial cultures was 2.4% +/- 0.4% (n = 10), not significantly different from the discrimination between bacteria and the substrate. Estuarine water samples were prefiltered through 1-micron-pore-size cartridge filters. Bacterium-sized particles in the filtrates were concentrated with tangential-flow filtration and centrifugation, and nucleic acids were then extracted from these concentrates. Hybridization with 16S rRNA probes showed that approximately 90% of the nucleic acids extracted on two sample dates were of eubacterial origin. Bacteria and nucleic acids from incubation experiments using estuarine water samples enriched with dissolved organic matter from Spartina alterniflora and Cyclotella caspia had stable carbon isotope values similar to those of the substrate sources. In a survey that compared diverse estuarine environments, stable carbon isotopes of bacteria grown in incubation experiments ranged from -31.9 to -20.5%. The range in isotope values of nucleic acids extracted from indigenous bacteria from the same waters was similar, -27.9 to -20.2%. Generally, the lack of isotope discrimination between bacteria and nucleic acids that was noted in the laboratory was observed in the field.(ABSTRACT TRUNCATED AT 250 WORDS)     

Improved protocol for high-quality Co-extraction of DNA and RNA from rumen digesta

We report an improved method for total nucleic acids extraction from rumen content samples. The method employs bead beating, and phenol-chloroform extraction followed by saline-alcohol precipitation. Total nucleic acids and RNA yield and purity were assessed by spectrophotometric measurements; RNA integrity was estimated using Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer. The method provided total nucleic acids and RNA extracts of good quantity and quality. The extraction is not time consuming and it is valuable for ecological studies of rumen microbial community structure and gene expression.     

Some methods for processing of single-cell protein

Methods for the production of protein concentrates, with a low content of nucleic acid, in kilogram quantities from yeast have been studied with the aid of equipment designed for operation on pilot-plant scale. The influence of drum drying and mechanical disintegration on the nutritive value of the yeast was also investigated. Drum drying and mechanical disintegration improved the nutritive value of the yeast but high extractability of protein and nucleic acid was only obtained after mechanical disintegration. Protein concentrates without and with cell walls were produced from mechanically disintegrated yeast. The different fractions which were obtained when separating cell walls and precipitating protein by heating at alkaline pH, were analyzed. After protein precipitation, about 90% of the RNA could be precipitated from the supernatant by addition of acid, giving a product containing 50% RNA of the dry weight. The protein precipitate obtained after cell wall separation had an RNA content of less than 2% and contained 70–l75% of the amino acids in the starting yeast material. Protein concentrates containing cell walls were produced by precipitating protein by heating at alkaline pH directly after mechanical disintegration. The content of RNA was about 2% and the yield of amino acids was 70–80%. It was found that the nutritive value of the protein concentrate was higher than that of the starting yeast material. To produce such a protein concentrate on a large scale, the process described can probably be employed.     

Chloroplast and cytoplasmic low-molecular-weight ribonucleic acid components of the leaf of Vicia faba L

1. A method for the extraction of plant nucleic acids and their separation on methylated-serum-albumin-kieselguhr columns is described. It is demonstrated that the characteristics of the elution profiles of material from the same source are consistently reproducible. 2. Major dissimilarities were found in the elution profiles of nucleic acids from root and from leaves of Vicia faba L. These dissimilarities were confirmed by polyacrylamide-gel electrophoresis. 3. Four distinct types of low-molecular-weight RNA were demonstrated to be present in leaves, clearly distinguished by their behaviour when chromatographed on methylated-serum-albumin-kieselguhr columns. (a) Both cytoplasmic and chloroplast ribosomes contained a low-molecular-weight RNA, and these components were distinct from each other. (b) The chloroplast possessed a unique ;soluble' RNA (i.e. RNA that is not precipitated by centrifugal forces that sediment ribosomes) which was not present in the rest of the cell. (c) A soluble component, probably transfer RNA, was found in both the chloroplasts and in the cytoplasm. 4. The components distinguishable by methylated-serum-albumin-kieselguhr column chromatography could not be distinguished by sucrose-density-gradient centrifugation.     

Nucleic acid interaction with VERO cells. A temperature barrier in the interaction pattern.

The interaction of VERO cell monolayers with spin (nitroxide)-(labeled polynucleotides (1(N)n) was examined by electron spin resonance (ESR) spectroscopy at various temperatures. Nitroxide labels covalently linked to (A)n, (dUfl)n, (U)n and (A)n . (U)n were used to monitor the interaction. The VERO cells were grown on small quartz plates with a cell viability of 95% or better and then used directly for the ESR studies. The ESR results indicated that the interaction between VERO cells and spin-labeled nucleic acids is temperature dependent. No temperature dependence was found when VERO cells were in contact with nitroxide radicals which were free in solution or covalently bound to Sepharose 4B. The temperature dependence established with nitroxide-labeled nucleic acids indicates that a temperature barrier must exist between 20 and 26 degrees C for the interaction between nucleic acids and VERO cells; namely, at 26 degrees C or above spin-labeled nucleic acids interact significantly with a VERO cell surface; whereas, at 20 degrees C the ESR signal reports no interaction. It is concluded that a temperature-dependent phase transition of membrane components or cell surface products active at 26 degrees C or above play a key role in the nucleic acid cell surface interaction process.     

The lipid content of cell walls obtained from juvenile,yeast-like and filamentous cells ofCandida albicans

Purified cell walls ofCandida albicans obtained from juvenile cells, mature yeast-like cells and filamentous cells were analyzed for their lipid components. Chloroform: methanol (2:1 v v) extraction of the acetone-treated dried cell walls indicated the total lipid content to be 2.1% of the dry weight of the juvenile cell walls, 1.8% of the mature yeast-like cell walls and 4.5% of the filamentous cell walls. Separation of the chloroform: methanol extractable fraction through a silicie acid column and quantitative determination of the fractions showed significant amounts of sterol esters, triglycerides, sterols, free fatty acids, and phospholipids in these extracts. Following acetone extraction sterols were shown to constitute a greater percentage of the cell wall of juvenile cells than mature cells. Thin-layer chromatography separated the acetone-extractable lipids into at least four components. Diethyl ether extracts of the cell walls indicated the presence of small amounts of glycerol phospholipids in the cell walls of juvenile and mature yeast cells. Boiling 95% ethanol also removed a small lipid fraction from the cell walls of both juvenile and mature yeast which could include sphingosine phosphatides or glycosides.     

A comparison of some procedures of salt extraction of nucleic acids from pollen. Elimination of interfering substances from extracts

Some methods were studied which use hot 10% NaCl solution for the extraction of both RNA and DNA from pollen. The raw salt extracts were precipitated with perchloric acid, trichloroacetic acid or ethanol and purified according to the described methods. The nucleic acid hydrolysates were obtained in several ways. In all the samples spectra in the UV-region were measured and the nucleic acid contents were determined according to the absorbance at 260 nm. In order to ascertain the extent of contaminants, the contents of phosphorus, saccharides and proteins were determined. It was found that by the methods studied it is possible to remove some impurities from extracts, but that the extractions of nucleic acids from pollen are not quite quantitative. A part of nucleic acids remained unextracted after the salt extraction in pollen, but it was possible to obtain it only by an additional extraction with 1 N perchloric acid at 75°C.     

Preparation and Chemical Composition of the Cell Walls of Mature Infectious Dense Forms of Meningopneumonitis Organisms

Relatively large-scale production and purification of meningopneumonitis organisms was developed for chemical and immunological studies on cell walls of the infectious dense forms. By disruption of purified organisms with glass beads in a Mickle shaker, highly purified preparations of cell walls were obtained by sucrose density gradient centrifugation, enzyme digestion, and sodium dodecyl sulfate treatment. The dry-weight recovery of purified cell walls from intact organisms was about 13%. When (32)P-labeled preparations of cell walls were fractionated into acid-soluble, lipid, ribonucleic acid (RNA), deoxyribonucleic (DNA), and residual fractions, about 80% of the (32)P in cell wall preparations was recovered in the phospholipid fraction, which corresponded to about 3% of the total phospholipid in the intact organisms. About 7% of the (32)P in purified cell walls was recovered in the RNA and DNA fractions respectively, but this corresponds to only about 0.4% of the (32)P found in those fractions in intact organisms. From dry-weight determinations, it was calculated that the purified cell wall preparations contained only 0.6% total nucleic acids, and these are probably not true cell wall constituents. These cell walls contained 70 to 75% protein, corresponding to about 14% of the protein in intact organisms. Amino acid analysis of these protein showed the existence of all common amino acids, glucosamine, and galactosamine. However, no muramic acid was detected by the methods employed.     

Monoclonal antibodies showing sequence specificity in their interaction with single-stranded DNAs.

Six hybridoma cell lines which secrete monoclonal antibodies binding to nucleic acids were produced from autoimmune NZB/NZW mice. Four of the antibodies were IgG's and the other two were IgM's. Using a solid phase radioimmunoassay (SPRIA) the binding of the antibodies to over thirty different nucleic acids was estimated. All the antibodies were extremely specific. There was no detectable interaction with various RNAs, and single-stranded DNAs bound more antibodies than duplex or multi-stranded DNAs. In every case the antibodies also showed considerable sequence preferences. For example one monoclonal antibody bound to d(TTC)n but not to d(TCC)n while another interacted strongly with D(TG)n and d(CA)n but not with d(TC)n, d(GA)n or homopolymers. In other cases the patterns of sequence specificity were extremely difficult to interpret although it seems clear that monoclonal antibodies have the potential to distinguish between any two nucleic acids however similar.     

The molecular structure of bacterial walls. The size of ribitol teichoic acids and the nature of their linkage to glycosaminopeptides

1. Ribitol teichoic acids prepared by fractional precipitation of trichloroacetic acid extracts of bacterial cell walls are essentially undegraded and have similar chain length to the teichoic acid originally present in the walls. 2. The chain length of teichoic acid can be determined directly, without prior extraction from the wall. Accurate values have been obtained by measurement of the formaldehyde produced by oxidation of walls with periodate. Less accurate values have been derived from the amount of inorganic phosphate formed by heating walls at pH4. 3. The relative amounts of N-acetylglucosaminylribitol and its mono- and di-phosphates produced by heating walls of Staphylococcus aureus with alkali agree with the amounts calculated for the hydrolysis of teichoic acid having the chain length determined by other methods. 4. Chemical considerations indicate that the linkage between teichoic acid and the wall may involve a phosphoramidate bond between the terminal phosphate of the teichoic acid and one of the amino groups in the glycosaminopeptide.     

Factors influencing the extraction and determination of nucleic acids in plant material: Length of homogenization and precipitation from sodium chloride extracts

When studying the determination of nucleic acids in pollen based on extraction with hot 10% NaCl, further factors influencing the results were observed. Prolongation of the homogenization from 3 to 5 or 7 min caused considerable loss of DNA in extracts. On using trichloracetic acid to precipitate nucleic acids from the NaCl extracts, higher final values for the sum of nucleic acids were obtained than by precipitating with perchloric acid.     

Method for automated extraction and purification of nucleic acids and its implementation in microfluidic system

A method and a microfluidic device for automated extraction and purification of nucleic acids from biological samples have been developed. The method involves disruption of bacterial cells and/or viral particles by combining enzymatic and chemical lysis procedures followed by solid-phase sorbent extraction and purification of nucleic acids. The procedure is carried out in an automated mode in a microfluidic module isolated from the outside environment, which minimizes contact of the researcher with potentially infectious samples and, consequently, decreases the risk of laboratory-acquired infections. The module includes reservoirs with lyophilized components for lysis and washing buffers; a microcolumn with a solid-phase sorbent; reservoirs containing water, ethanol, and water-ethanol buffer solutions for dissolving freeze-dried buffer components, rinsing the microcolumn, and eluting of nucleic acids; and microchannels and valves needed for directing fluids inside the module. The microfluidic module is placed into the control unit that delivers pressure, heats, mixes reagents, and flows solutions within the microfluidic module. The microfluidic system performs extraction and purification of nucleic acids with high efficiency in 40 min, and nucleic acids extracted can be directly used in PCR reaction and microarray assays.