Preparation of cytochrome c peroxidase from baker's yeast.

A simple and readily reproducible procedure is presented for the preparation and purification of cytochrome c peroxidase from baker's yeast. Following autolysis of the yeast and extraction, the enzyme is collected on DEAE-cellulose at moderately high ionic strength, cluted, concentrated, and subjected to gel filtration in 0.1 m sodium acetate buffer, pH 5.0. The properties of the crude preparation make gel filtration in this buffer suitable for near-final purification of the heme protein. The enzyme is then easily crystallized by dialysis.     

Improved method for expression and isolation of the Mycoplasma hominis arginine deiminase from the recombinant strain of Escherichia coli

Arginine deiminase is a promising anticancer drug active against melanoma, hepatocarcinoma and other tumors. Recombinant strains of Escherichia coli that express arginine deiminase from pathogenic bacteria Mycoplasma have been developed. However, production costs of heterologous arginine deiminase are high due to use of an expensive inducer and extraction buffer, as well as using diluted culture for enzyme induction. We report on a new advanced protocol for Mycoplasma hominis arginine deiminase expression, extraction and renaturation. The main improvements include manipulation with dense suspensions of E. coli, use of lactose instead of isopropyl β-d-1-thiogalactopyranoside as an inducer and a cheaper but not less efficient buffer for solubilization of arginine deiminase inclusion bodies. In addition, supplementation of the storage culture medium with glucose and substrate (arginine) significantly stabilized the recombinant arginine deiminase producer. Homogenous preparations of recombinant arginine deiminase were obtained using anion-exchange and hydrophobic chromatography. The purified enzyme retained a specific activity of 30–34 U/mg for 12 months when stored at 4 °C in 20 mM sodium phosphate buffer pH 7.2 containing 1 M NaCl.     

Isolation of high quality RNA and construction of a suppression subtractive hybridization library from ramie (Boehmeria nivea L. Gaud.)

Isolation of high quality RNA from ramie (Boehmeria nivea L. Gaud.) is difficult due to its high levels of polyphenols, polysaccharides, pectin, fat, wax and other secondary metabolites. A modified procedure based on guanidinium isothiocyanate for RNA preparation of ramie was developed in this study. High concentrations (5%, v/v) of guanidinium isothiocyanate, PVP-4000, sodium citrate and sodium lauryl sarcosinate and β-mercaptoethanol were used in the extraction buffer, together with a low pH sodium acetate (pH 4.0) added to improve the RNA quality. The average yield was about 400 μg RNAg^?1 fresh leaves. One SSH library which was induced by ramie anthracnose was constructed by utilizing the RNA extracted through the present method. These results showed that our protocol was applicable for RNA isolation from recalcitrant ramie tissues.     

Rapid and efficient extraction of soluble proteins from Gram-negative microorganisms without disruption of cell walls

The ability of buffer solutions containing low concentrations of nonionic detergents (Triton X-100, Tween 20, Brij 58, and Lubrol PX) and the anionic detergent sodium deoxycholate, as well as mixtures of these detergents with chaeotropes (urea and guanidine hydrochloride), to extract intracellular proteins of Gram-negative microorganisms (Escherichia coli and Pseudomonas aeruginosa) was studied. It was established that the solutions containing Triton X-100 and sodium deoxycholate and the mixtures of these detergents with urea are the most effective. It was shown that the extraction of proteins from bacterial cells under the studied conditions is not accompanied by a release of DNA into solution but is associated with extraction of low-molecular RNAs. The level of protein extraction reaches 80%. No disruption of the bacterial cell wall occurs during the extraction, and proteins probably penetrate through meshes of the murein network. The efficiencies of our buffer mixtures are close to or higher than that of the commercial reagent CelLytic B (Sigma, United States). The practical uses of the chaeotropic mixtures developed are discussed.     

In vitro stability of nitrate reductase from barley leaves

Barley seedling nitrate reductase was stabilized in vitro without the use of extraneous protein by optimizing the buffer components. The extraction buffer (NRT 8.5) consists of 0.25 M Tris-HCl, pH 8.5, 3 mM DTT, 5 μM FAD, 1 μ M sodium molybdate and 1 mM EDTA. This buffer stabilizes the extracted nitrate reductase at O° and 30°, whereas the addition of extraneous protein to standard extraction buffers stabilizes the enzyme only at 0°.     

High-performance liquid chromatographic assay for 3′-amino-3′-deoxythymidine in plasma,with 9-fluorenyl methyl chloroformate as the derivatization agent

We have developed a sensitive high-performance liquid chromatographic assay for the determination of the zidovudine metabolite 3′-amino-3′-deoxythimidine (AMT) using fluorescence detection and sensitivity in the picomolar range. Plasma was diluted with 0.05 M sodium phosphate buffer pH 7.2 and subsequently prepared for analysis using solid-phase extraction. AMT was derivatized with 9-fluorenyl methylchloroformate and chromatographed using a reversed-phase system. The mobile phase consisted of acetonitrile-0.01 M potassium phosphate buffer (pH 7) (32:68, v/v). The fluorescence of the column effluent was monitored at 262 nm (excitation) and 306 nm (emission). Good resolution of AMT from endogenous plasma components was obtained. Within- and between-day variability was less than 10%. The limit of quantitation was 0.9 μg/l. The assay was successfully applied to the determination of AMT in human plasma and plasma of mice treated with zidovudine.     

Delignification and hemicellulose extraction of cell walls of Lolium perenne and Trifolium pratense

The rates of delignification of samples of Lolium perenne at four different stages of maturity and a sample of Trifolium pratense by the action of sodium chlorite-acetic acid have been determined. For samples with lignin contents of < 8%, delignification was essentially complete within 30 min. The yield and composition of hemicelluloses obtained by alkaline extraction of cell walls was dependent on the duration of the delignification reaction.     

Elimination of artifactual immunogold labeling from secondary walls of woody stem sections

Preliminary in situ transmission electron microscopy immunogold localization of a 24-kDa dehydrin-like protein in red-osier dogwood (Cornus sericea L.) stem cross-sections was contaminated with extensive background labeling of secondary cell walls in both positive and negative control samples. Alterations in antibody dilution, buffer salt concentration and stringency of the washing solutions failed to eliminate background cell-wall labeling. A procedure was developed in which lyophilized cold-acclimated C. sericea xylem tissue was pulverized and boiled with sodium dodecyl sulfate (SDS)-protein extraction buffer to remove soluble proteins and to inactivate proteases. Wood powder, treated with SDS-protein extraction buffer, was used to pre-absorb chicken immune serum specific for a 24-kDa dehydrin-like protein prior to immunolocalization assays. Pre-incubation of primary antibodies did not compromise the recognition of the 24-kDa protein, and this technique effectively eliminated background cell-wall labeling.     

Degradation of ribonucleic acid in Candida lipolytica: extraction of ribonucleic acid degrading enzymes

We developed an efficient and simple method for RNase extraction from Candida lipolytica cells which consists of predrying the cells with solvents and incubating them for 8 to 15 hr at 37 to 45°C in a slightly acid buffer which contains EDTA or salts. This method is called Solvent Dehydration Buffer Extraction (SDBE) procedure. Predrying with acetone or ethanol, or by lyophilization, followed by washing with acetone or ethylacetate gives the most efficient RNase extraction. The yield and specific activity obtained by this extraction procedure are higher than by any other method examined. An apparent 1.5- to 2.0-fold activation of RNase occurred during the SDBE process. Activation of RNase in homogenates obtained by grinding fresh cells is also observed with EDTA or acetate buffer. The SDBE procedure works efficiently regardless of growth phase for Candida lipolytica, and works also with other Candida yeasts.     

Improved Method for Purification of Bacterial DNA from Bovine Milk for Detection of Brucella spp. by PCR

Different methods of extraction of bacterial DNA from bovine milk to improve the direct detection of Brucella by PCR were evaluated. We found that the use of a lysis buffer with high concentrations of Tris, EDTA, and NaCl, high concentrations of sodium dodecyl sulfate and proteinase K, and high temperatures of incubation was necessary for the efficient extraction of Brucella DNA. The limit of detection by PCR was 5 to 50 Brucella CFU/ml of milk.     

Regulation of the activity of Phosphoenolpyruvate carboxylase isolated from germinating maize (Zea mays L.) seeds by some metabolites

Phosphoenolpyruvate carboxylase (PEPC) was isolated from maize seeds which were germinated for 20 h, using a procedure which included extraction of seed homogenate with Tris-HCl or sodium phosphate buffer, precipitation of the extract with ammonium sulphate, chromatography on DEAE cellulose, and gel filtration on Sephadex G-200. Phosphate buffer was found to be less suitable than Tris-HCl buffer both for maize seed extraction and for further PEPC purification steps. The enzyme preparation obtained was electrophretically homogenous. PEPC activity was inhibited by both phosphate and malate. It values obtained at pH 8.1 which is the pH optimum of the reaction equelled to 42 mmoll^-1 for phosphate and to 13 mmoll^-1 for malate. PEPC isolated from germinating maize seeds was activated by glucose-6-phosphate, glucose-1-phosphate, ribulose-l,5-bisphosphate, fructose-1,6-bisphosphate, and fructose-2,6-bisphosphate. The authors intend to elucidate the mechanism of PEPC activation by sugars by means of the application of a number of derivatives of the sugar phosphates, among which for example 2-deoxy-2-fluoro glucosephosphate also activated PEPC. Sugar phosphates activated PEPC isolated from germinating maize seeds in this order, with increasing effect: fructose-l,6-bisphosphate, glucose-1-phosphate, glucose-6-phosphate, 2-deoxy-2-fluoro glucosephosphate, ribulose-l,5-bisphos-phate, fructose-2-6-bisphosphate.     

Purification and hydrophobic properties of the δ-endotoxin in the parasporal crystal produced by Bacillus thuringiensis var. entomocidus

Parasporal crystals of Bacillus thuringiensis var. entomocidus were separated from spores and other cell debris by the water-chloroform biphase procedure. The solubilization and fractionation were carried out under mild conditions at 4°C. Crystals were solubilized in 0.01 M dithiothreitol and 0.2 M glycine NaOH buffer at pH 10.0. The solution was treated overnight with 0.01 M Tris-HCl buffer, pH 5.5, containing 0.1% Triton N-101 and 0.1% sodium cholate, and then placed on a Sepharose 6B column, equilibrated, and later developed with the same buffer. Under these conditions, four fractions were obtained, one of which had a molecular weight ranging from 60,000 to 70,000, and demonstrated a high insecticidal activity on second instar larvae of Spodoptera litioralis. The LC₅₀ value of this fraction was a half of that of the solubilized crystals. The other three fractions had a lower activity. The active fraction was further fractionated on an octyl-Sepharose 4B resin. Elution of this column with the same buffer separated the proteins into two fractions. The first eluted fraction was highly active, while the second demonstrated a very low activity. The active fraction was further purified by loading on a short column of octyl-Sepharose 4B and eluted with a linear gradient of the same detergents. Under these conditions, the highly active fraction gave a sharp and symmetrical peak that revealed five close bands at the pH range of 6.1–6.5 on isoelectric focusing gel electrophoresis.     

Rapid isolation of RNA using proteinase K and sodium perchlorate.

A simple, efficient procedure for the isolation of cellular nucleic acids is described. It combines the use of sodium dodecyl sulfate, proteinase K, sodium perchlorate, and isopropanol precipitation. The yields and purity of RNA extracted from a variety of sources are comparable or superior to those obtained by phenol extraction. High molecular weight RNA (ribosomal as well as nonribosomal) is recovered intact and in high yield. Fibroin messenger RNA (M_r 5.8 × 10⁶) isolated by this procedure is biologically active.     

An Efficient and Reliable Method of DNA Extraction from Meyna spinosa — A Traditional Medicinal Plant from North-East India

A simple, efficient and reliable CTAB method is standardized for genomic DNA isolation from fresh young leaves of a traditional medicinal plant Meyna spinosa. Key steps in the modified procedure include additional chloroform: isoamyl alcohol (24:1, v/v) extraction, addition of 4% PVP in the extraction buffer and an overnight isopropanol precipitation at room temperature. This procedure yields a high amount (46 μg DNA g^?1 fresh leaf tissue) of good quality DNA free from contaminants. The isolated DNA is suitable for digestion with EcoRI and HindIII restriction enzymes and can be used in other DNA manipulation techniques.     

Microsomal flavonoid 3'-monooxygenase from maize seedlings

Identification of flavonoid 3′-monooxygenase establishes another reaction in the biosynthesis of flavonoid compounds in maize (Zea mays L.). The flavonoid 3′-hydroxylase was obtained as a microsomal enzyme preparation by buffer extraction of 5 day old maize seedlings and ultracentrifugation. Seedlings were exposed to light 24 hours prior to enzyme extraction. The extraction buffer required the addition of sucrose or glycerin and dithiothreitol to obtain an active hydroxylase that retained its activity on storage at −70°C. Enzymic activity required O₂ and NADPH, was optimum at pH 8.5 and 30°C, and could be inhibited 79% by carbon monoxide. Carbon monoxide inhibition could be reduced to 21% by irradiation of the samples with 450 nanometer light during incubation. Kaempferol, a flavonol; naringenin, a flavanone; and apigenin, a flavone, all served as substrates for the hydroxylase. Treatment of the microsomal enzyme preparation, previously reduced with sodium dithionite, with carbon monoxide gave a 455 nanometer absorption peak which disappeared on oxidation of the preparation with the formation of a 420 nanometer peak. These results suggest a cytochrome P-450 type monooxygenase enzyme. The concentration of cytochrome P-450 was 0.21 nanomoles per milligram protein. Identification of the monooxygenase provides further biochemical information about a biosynthetic sequence for which the genetics have been studied intensely.     

A simple method for the extraction and quantification of photopigments from Symbiodinium spp.

We have developed a simple, mild extraction procedure using methanol which, when coupled with HPLC analysis and diode array detection (DAD), can be used to quantify the major photopigments found in cultured Symbiodinium spp. Extracts were prepared by suspending, fresh or frozen (− 70 °C), wet cell pellets in methanol and sonicating or not sonicating the cell suspensions before soaking the cells for 2 h in an ice bath. To assist the soaking process, cell suspensions were vortex mixed at 30 min intervals. After soaking, 0.5 M ammonium acetate buffer was added (1 part buffer to 9 parts methanol) before suspensions were stored over night at − 20 °C. Greater than 92% the recoverable pigment was obtained in the initial extraction of the four major photopigments, chlorophyll c, peridinin, diadinoxanthin, and chlorophyll a. Neither sonication nor freezing substantially increased the recovery of photopigments extracted with methanol. Extraction by other commonly used solvents such as acetone or acetone:water with or without freezing and sonication were less effective.     

THE EFFECT OF ACETATE BUFFER MIXTURES,ACETIC ACID,AND SODIUM ACETATE,ON THE PROTOPLASM,AS INFLUENCING THE RATE OF PENETRATION OF CRESYL BLUE INTO THE VACUOLE OF NITELLA

When living cells of Nitella are exposed to a solution of sodium acetate and are then placed in a solution of brilliant cresyl blue made up with a borate buffer mixture at pH 7.85, a decrease in the rate of penetration of dye is found, without any change in the pH value of the sap. It is assumed that this inhibiting effect is caused by the action of sodium on the protoplasm. This effect is not manifest if the dye solution is made up with phosphate buffer mixture at pH 7.85. It is assumed that this is due to the presence of a greater concentration of base cations in the phosphate buffer mixture. In the case of cells previously exposed to solutions of acetic acid the rate of penetration of dye decreases with the lowering of the pH value of the sap. This inhibiting effect is assumed to be due chiefly to the action of acetic acid on the protoplasm, provided the pH value of the external acetic acid is not so low as to involve an inhibiting effect on the protoplasm by hydrogen ions as well. It is assumed that the acetic acid either has a specific effect on the protoplasm or enters as undissociated molecules and by subsequent dissociation lowers the pH value of the protoplasm. With acetate buffer mixture the inhibiting effect is due to the action of sodium and acetic acid on the protoplasm. The inhibiting effect of acetic acid and acetate buffer mixture is manifested whether the dye solution is made up with borate or phosphate buffer mixture at pH 7.85. It is assumed that acetic acid in the vacuole serves as a reservoir so that during the experiment the inhibiting effect still persists.     

Technical note: Bone DNA extraction and purification using silica-coated paramagnetic beads

The goal of this study was to develop a simple method to improve DNA recovery from challenging bone samples. To this end, an optimized procedure was developed that combined the demineralization and DNA extraction into a single step, followed by DNA purification using an automated silica-coated paramagnetic bead procedure. This method replaced a previous silica-membrane-based procedure, which was able to recover sufficient DNA to obtain full autosomal and Y chromosome STR profiles from greater than 90% of the samples, including samples greater than 20 years old. The development process began with the evaluation of buffer and demineralization systems to determine the best reagent combination. During the developmental process, we observed that the addition of EDTA and DTT affected silica-based DNA purification methods by raising the pH of the digest buffer. The protocols with buffer ATL, PK, EDTA, and DTT followed by lowering the pH with sodium acetate just before purification resulted in the best yields. The method reduced the extraction volume from 10 to 1.5 ml and used commercially available reagents already being utilized in forensic DNA casework. Because of the simplicity and small volume needed for the procedure, many steps where contamination could be introduced have been eliminated or minimized. This study demonstrated a new method of recovering DNA from bone samples capable of extracting trace quantities of DNA, removing potential inhibitors, and minimizing the potential for exogenous DNA contamination.     

Considerations in the isolation of rat liver nuclear matrix,nuclear envelope,and pore complex lamina

A number of recent studies have demonstrated a salt-, nuclease, and detergent-resistant subnuclear structure termed the nuclear protein matrix which consists of a fibrogranular intranuclear network, residual components of the nucleolus, and a peripheral lamina. Other workers, however, have shown that somewhat similar methods result in the isolation of the peripheral lamina devoid of the intranuclear components. In this report we demonstrate that seemingly slight changes in the isolation procedure cause major changes in the morphology of the residual structures obtained. When freshly purified rat liver nuclei were digested with DNase I and RNase A and then extracted with buffers of low magnesium ion concentration (LS buffer) and high ionic strength (HS buffer), the resulting structures isolated prior to or after Triton X-100 extraction lacked the extensive intranuclear network and the easily identifiable residual nucleoli present in the nuclear protein matrix. Systematic modification of this extraction procedure revealed that morphologically identifiable residual nucleoli were present when digestion with RNase A followed extraction with HS buffer but were absent when the order of these steps was reversed. The removal of the nucleolus by RNase A and HS buffer correlated with the removal of nuclear RNA by the same treatments. These coordinate events could not be prevented by treatment with protease inhibitors but were prevented by treatment of the RNase A with diethylpyrocarbonate, an RNase inhibitor. The extensive intranuclear network seen in the nuclear protein matrix was sparse or absent when residual structures were prepared from DNase- and RNase-treated nuclei under conditions which minimized the oxidation of protein sulfhydryl groups. In contrast, an extensive non-chromatin intranuclear network was seen if the formation of intermolecular protein disulfide bonds was promoted by extraction of nuclei with cationic detergents, by overnight incubation, or by treatment with oxidizing agents like sodium tetrathionate prior to nuclease digestion and subsequent extraction. By varying the order of extraction steps and the extent of disulfide cross-linking, it is possible to isolate from a single batch of nuclei residual structures with a wide range of morphologies and compositions.     

Purification and identification of inactive forms of repressible and constitutive acid phosphatase in yeast

Acid phosphatase (EC 3.1.3.2, orthophosphoric-monoester phosphohydrolase, (acid optimum)) from the budding yeast Saccharomyces cerevisiae was purified from repressed and depressed cells. Without Triton X-100 in the extraction buffer only the constitutive or repressible active enzyme eluted from a Sepharose CL-6B column, the last step of the purification procedure. When Triton X-100 was included in the extraction buffer, an additional protein peak eluted prior to the active acid phosphatase. The material from this new peak, a glycoprotein, had no acid phosphatase activity but cross-reacted with antibodies raised against repressible acid phosphatase. The tryptic fingerprints of the inactive proteins are very similar to the ones of the corresponding active enzymes. We conclude that this new glycoprotein represents an inactive form of repressible and constitutive acid phosphatase. The fact that inactive acid phosphatase can be recovered only in the presence of Triton X-100 indicates that it is membrane-bound.