Source and avoidance of the "nothing dehydrogenase" effect, a spurious band produced during polyacrylamide gel electrophoresis of dehydrogenase enzymes from yeasts

During a study of the distribution of several NAD-linked dehydrogenase enzymes in various yeasts, in which polyacrylamide gel electrophoresis, followed by activity staining with phenazine methosulfate and a tetrazolium was used, a band was frequently detected, the production of which appeared to be independent of any added substrate (the "nothing dehydrogenase" effect). It has been shown that this effect is caused by alcohol dehydrogenase acting on traces of ethanol inadvertently introduced into the system. Two sources of ethanol were identified. They were (i) the enzyme extracts, which could be freed from ethanol by gel filtration, and (ii) the acrylamide used to prepare the gel, which could be freed from ethanol by recrystallization from ethanol-free chloroform. It is suggested that the use of commercial chloroform (stabilized with ethanol) as a recrystallizing solvent is the source of ethanol contamination in commercial preparations of acrylamide.     

New reactive oxidizing species causes formation of carbon-centered radical adducts in organic extracts of blood following liver transplantation

-(4-pyridyl-1-oxide)-N-t-butylnitrone (4-POBN) radical adducts from Folch (chloroform:methanol) extraction of blood of transplanted livers exhibited a large 6-line electron paramagnetic resonance (EPR) spectrum. Slow EPR sample preparation involving freezing and thawing prior to extraction over 15 min yielded a spectrum assigned as a lipid-derived free radical species, whereas rapid (< min) extraction without a freeze-thaw cycle yielded a mixture of radicals, one with coupling constants similar to the -hydroxymethyl-4-POBN adduct (4-POBN/^.CH₂OH). Extraction with purified chloroform, however, yielded a much weaker, probably lipid-derived signal. Use of ¹³C-methanol in the Folch extracting solution yielded a 12-line EPR spectrum, indicating that a new, highly reactive oxidant species from blood following liver transplantation can convert organic solvents used in tissue extractions to free radicals. This hypothesis was supported by simulation of EPR spectra of free radicals extracted rapidly with Folch, which indicated that the spectrum contained two carbon-centered species, one with hyperfine coupling constants similar to the -methylhydroxyl-4-POBN adduct, the other probably lipid-derived. Because the former originates from methanol in the Folch, extraction of samples with alcohol-free organic solvent is most likely superior when the potential for formation of stable oxidant species exists, such as after liver transplantation.     

Purification and properties of the adenosine triphosphatase released from the liver mitochondrial membrane by chloroform

1. Soluble ATPase (adenosine triphosphatase) activity is released when rat liver submitochondrial particles are shaken with chloroform, provided that ATP or glycerol is present in the suspending medium. The extraction is very rapid and appears to be complete. 2. The ATPase of the chloroform extract is about 50% pure and can be readily purified to a specific activity of 60-70mumol/min per mg of protein by (NH(4))(2)SO(4) fractionation and column chromatography on Sephadex G-200. 3. The particulate and soluble ATPases have many similar properties, including their K(m) values for ATP, activation by various metal ions, hydrolytic activity with other nucleotides and stimulation by bicarbonate ions. 4. Unlike the particulate enzyme, the soluble enzyme is cold-labile and insensitive to oligomycin. 5. The molecular weight indicated by the mobility of the soluble ATPase on Sepharose 6B is 360000. 6. The soluble ATPase combines very readily with liver submitochondrial particles depleted of ATPase by salt extraction, and oligomycin-sensitivity is restored. Very little recombination of the enzyme occurs with chloroform-extracted particles. 7. The soluble enzyme contains orcinol-reactive material, suggesting that it may be a glycoprotein. The carbohydrate content was estimated to be 1-2% by weight. 8. It is concluded that the liver ATPase obtained by the chloroform extraction method of Beechey, Hubbard, Linnett, Mitchell & Munn [(1975) Biochem. J.148, 533-537] is similar to other preparations described previously and that this method is superior in simplicity and speed.     

利用改进的酚-氯仿法从猪毛囊中提取基因组DNA

为提高从猪毛囊组织中提取基因组DNA的效率, 文章在借鉴从其他组织提取基因组DNA方法的基础上, 对经典的酚-氯仿法的反应体系和步骤进行了改进。利用改进的酚－氯仿抽提法, 从猪的毛囊组织中快速、高效地提取了高质量基因组DNA。利用该方法从1~6根猪毛囊中提取的基因组DNA可满足基于PCR技术的相关分子生物学实验需要。     

Fungal Transformation of the Tricyclic Antidepressant Amoxapine: Identification of N-Carbomethoxy Compounds Formed as Artifacts by Phosgene in Chloroform used for the Extraction of Metabolites

The biotransformation of the antidepressant drug amoxapine by Cunninghamella elegans formed three metabolites, 7-hydroxyamoxapine, N-formyl-7-hydroxyamoxapine, and N-formylamoxapine; two other compounds were only present when chloroform was used in the extraction process. All five of the compounds were separated by reversed-phase HPLC, then analyzed by ¹H NMR and mass spectrometry, and by ¹³C NMR when sample quantities permitted. The artifacts were identified as N-carbomethoxy-7-hydroxyamoxapine and N-carbomethoxyamoxapine. Phosgene is a decomposition product of chloroform that can form carbomethoxy compounds at the secondary nitrogen of a piperazine ring in an alcoholic solution. Since N-carbomethoxy compounds were not observed when ethyl acetate was used for extraction of the culture medium, they were considered artifacts and not metabolites. These findings suggest that chloroform should be tested for the formation of phosgene before using it to extract any compound with a piperazine ring or any other amine-containing structure.     

Studies on tropane alkaloid extraction by volatile organic solvents: dichloromethane vs. chloroform

In order to investigate the production of tropane alkaloids by hairy roots of Atropa baetica, transgenic for the gene h6h encoding the enzyme hyoscyamine 6beta-hydroxylase, solvent extraction with chloroform and with dichloromethane of the metabolites present in the liquid medium and in the root tissue was compared. The extraction of scopolamine from the liquid medium was equally effective with either solvent, giving maximum values of around 850 microg/flask. For the roots, three different extraction methods were employed: A, employing chloroform:methanol: (25%) ammonia (15:5:1) for initial extraction, followed by treatment with sulfuric acid and ammonia, and using chloroform for the final extraction and washes; B, as A but using dichloromethane for extraction and washes; and C, as B but substituting chloroform for dichloromethane in the extraction cocktail. Scopolamine was the most abundant metabolite (present in amounts of 3250-3525 microg/g dry weight) and presented similar extraction efficiencies with all of the extraction methods employed. The highest amounts of hyoscyamine and the intermediate 6beta-hydxoxyhyoscyamine were present on day 31 (800 and 975 microg/g dry weight, respectively) and no statistical differences between the three extraction methods employed were detected. This study confirms that, for the extraction of tropane alkaloids, dichloromethane can replace the commonly employed chloroform, the use of which incurs major health, security and regulation problems.     

A simple method for extraction of fungal genomic DNA

We have developed a new, simple and effective method for extraction of fungal genomic DNA. The initial steps involved suspension of freeze-dried mycelium in buffer containing sodium dodecyl sulphate, detachment of DNA from polysaccharides by mild shearing, NaCl precipitation of polysaccharides and protein, chloroform extraction and ethanol precipitation. The ethanol precipitate was then subjected to a second round of mild shearing, NaCl precipitation, chloroform extraction and ethanol precipitation. The procedure required approximately 1 h to perform. The method yielded 8-32 microg of high molecular weight DNA per 30 mg of freeze-dried mycelium when tested on six fungal species: Aspergillus niger, A. flavus, Fusarium graminarum, Neotyphodium lolii, Penicillium citrinum and Rhizopus nigricanes. The DNA was digestible with EcoRI, HindIII, SalI and BamHI. For the slow-growing N. lolii, a modification of the method was developed that removed the agar residue from colonies grown on agar plates by centrifugation at 13 000 rev min(-1) in the presence of CsCl. The modified method yielded 1.5-2 microg of high molecular weight DNA per colony.     

Molecular diagnosis of Eimeria species affecting naturally infected Gallus gallus

We used PCR to test various protocols and define a technique for DNA extraction directly from chicken-shed stool samples for the identification of Eimeria species that parasitize birds. It was possible to extract and amplify DNA of seven Eimeria species from field stool samples, using both protocols tested; extractions made with phenol/chloroform protocols gave the best results. The primers were specific and sensitive, allowing amplification of samples containing as few as 20 oocysts, both in individual and in a multiplex PCR. Individualized PCR with the phenol/chloroform DNA extraction protocol detected a larger number of Eimeria species. Molecular diagnosis was found to be practical and precise, and can be used for monitoring and epidemiological studies of Eimeria.     

Comparison of different procedures for the lipid extraction from HL-60 cells: a MALDI-TOF mass spectrometric study

A human leukaemia cell line--HL-60--can be differentiated into neutrophils or macrophages and both differentiation processes are accompanied by changes of the lipid composition. Various methods were described for the extraction of lipids from cellular systems, but only two of them were applied to the HL-60 cell line so far. In this study we compared five selected extraction methods for the lipid extraction from HL-60 cells with regard to their qualitative analysis by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS): chloroform/methanol at volume ratios 2:1 and 1:2, isopropanol/ chloroform, isopropanol/hexane and butanol. In addition, the cholesterol and phospholipid concentrations in organic extracts were measured by colorimetric assays. Results can be summarized as follows: For the analysis of polar phospholipids obtained from HL-60 cells by MALDI-TOF MS, a chlorofom/methanol (1:2) or isopropanol/chloroform mixture or butanol can be applied as extraction systems On the other hand, if one would like to analyze changes in triacylglycerols, then chloroform/methanol (2:1) would be the method of choice.     

An evaluation of lipid extraction techniques for interpretation of carbon and nitrogen isotope values in bottlenose dolphin (Tursiops truncatus) skin tissue

We studied the effects of two common chemical extraction techniques on bottlenose dolphin (Tursiops truncatus) skin tissues with the intent to develop a mathematical lipid correction for dolphin skin δ¹³C. One method employs a hot solvent mixture (chloroform and methanol) while the other method requires washing the samples with cold solvent followed by water. The water wash method resulted in significant alteration of tissue δ¹⁵N. We found no correlation between change in sample mass and C/N or between change in sample mass and the change in δ¹³C (Δδ¹³C) following lipid extraction. Although Δδ¹³C was positive following lipid extraction (mean = 1.6‰ and 1.2‰, for the two methods), there was no correlation between C/N and Δδ¹³C for either method. Cumulatively, these results prevented us from applying a mathematical lipid normalization. Based on our findings and consideration of previously reported results, we suggest that applying these extraction techniques to dolphin skin with C/N < 4.5 introduces greater uncertainty than is warranted. We recommend against lipid correction for dolphin skins with C/N < 4.5, but stress that the resulting uncertainty in δ¹³C needs to be accounted for when implementing isotope mixing models to assess diet or organic matter sources.     

Efficacy of extraction methods for lipid and fatty acid composition from fungal cultures

The efficacy of three extraction methods for determining the lipid and fatty acid composition of six fungal cultures was studied. The extraction methods were: chloroform/methanol (2:1), hexane/isopropanol (3:2) and Soxhlet extraction by using hexane. The total lipid and fatty acid composition varied in fungal cultures depending on the extraction conditions. Of the three methods, chloroform/methanol (2:1) was found to be the best for extraction of lipid and fatty acids from fungal cultures.     

Extraction of steroidal glucosiduronic acids from aqueous solutions by anionic liquid ion-exchangers

A pilot study on the extraction of three steroidal glucosiduronic acids from water into organic solutions of liquid ion-exchangers is reported. A single extraction of a 0.5mm aqueous solution of either 11-deoxycorticosterone 21-glucosiduronic acid or cortisone 21-glucosiduronic acid with 0.1m-tetraheptylammonium chloride in chloroform took more than 99% of the conjugate into the organic phase; under the same conditions, the very polar conjugate, beta-cortol 3-glucosiduronic acid, was extracted to the extent of 43%. The presence of a small amount of chloride, acetate, or sulphate ion in the aqueous phase inhibited extraction, but making the aqueous phase 4.0m with ammonium sulphate promoted extraction strongly. An increase in the concentration of ion-exchanger in the organic phase also promoted extraction. The amount of cortisone 21-glucosiduronic acid extracted by tetraheptylammonium chloride over the pH range of 3.9 to 10.7 was essentially constant. Chloroform solutions of a tertiary, a secondary, or a primary amine hydrochloride also will extract cortisone 21-glucosiduronic acid from water. The various liquid ion exchangers will extract steroidal glucosiduronic acid methyl esters from water into chloroform, although less completely than the corresponding free acids. The extraction of the glucosiduronic acids from water by tetraheptylammonium chloride occurs by an ion-exchange process; extraction of the esters does not involve ion exchange.     

Association of fallout radiocesium with soil constituents: effect of sterilization of forest soils by fumigation with chloroform

The effect of soil sterilization by chloroform fumigation on the release of fallout radiocesium incorporated in the fungal biomass of the organic layer of two forest soils was investigated by applying a sequential extraction procedure for radiocesium. The amount of the biomass in all soil samples was estimated by determination of the dissolved organic carbon (DOC) before and after fumigation, and qualitatively also by the ergosterol test. The five fractions obtained by sequential extraction (modified Tessier procedure) were: (I) easily exchangeable, (II) bound to oxides, (III) bound to organic matter, (IV) persistently bound, (V) residual. For the samples from the soil under spruce trees, no significant effects were apparent in any of these five fractions as a result of chloroform fumigation, indicating that the amount of radiocesium in the biomass of this soil was obviously negligibly small compared with the radiocesium associated with other soil constituents. The results obtained for the soil samples from the beech stand, however, reveal that the destruction of the biomass by chloroform fumigation modified considerably the extent of the association (i.e., binding) of radiocesium with the various other soil constituents (especially the clay minerals). As a result of this rapid redistribution of radiocesium released by the fungal biomass, it is not possible, in general, to attribute the observed increase of radiocesium in fraction I (easily exchangeable) after soil sterilization quantitatively to radiocesium released by the biomass. A reliable method to determine the amount of radiocesium incorporated in the fungal biomass of the soil samples which also contain clay minerals has, therefore, still to be developed. Received: 12 February 1996 / Accepted in revised form: 30 April 1996     

The use of real-time PCR technology to assess the effectiveness of methods of DNA extraction from cultures of acidophilic chemolithotrophic microorganisms

Comparative evaluation of efficiency of several methods of DNA extraction from storage cultures of acidophilic chemolithotrophic microorganism communities isolated from sulfide ores of Shanuch ore deposit (Kamchatka peninsula) was conducted. DNA extraction methods in various combinations of physical (heating to 65–98°C, grinding with SiO₂ particles), enzymatic (treatment with lysozyme and proteinase K), and chemical (GuSCN, CTAB and KOH) treatments were tested. The evaluation of efficiency was performed using Real-time PCR. The best result was obtained for the combined method based on GuSCN lysis activity (lysis at 65°C) followed by purification with phenol and chloroform.     

Brain proteolipids. Isolation, purification and effect on ionic permeability of membranes

Proteolipid apoproteins have been isolated from a whole bovine brain homogenate by chloroform/methanol extraction, and fractionated by chromatography on modified (lipophilic) Sephadex, followed by ion-exchange chromatography on CM-Trisacryl. The various final, highly hydrophobic, fractions are homogeneous (sodium dodecyl sulfate/polyacrylamide gel electrophoresis). Transmembrane ion transfers were studied by 22Na + flux and electrical conductance measurements. Single channel events were observed at low protein concentrations, in particular with one of the final homogeneous apoproteolipids of molecular mass 24 kDa.     

Solvent effect on the synergic extraction of thulium(III) with acetylacetone and 1,10-phenanthroline

The synergic extraction equilibrium of Tm(III) with acetylacetone (Hacac) and 1,10-phenanthroline (phen) in various organic solvents has been studied. The adduct formation constants, β_s, for Tm(acac)₃^? phen, were determined in heptane, cyclohexane, carbon tetrachloride, benzene and chloroform. The solvent effect on β_s is explained in connection with the activity coefficients of the neutral ligand, the chelate, and the adduct in the organic solvent. The activity coefficients can be calculated from the corresponding solubility parameters on the basis of the regular solution theory, and the solubility parameters of the solutes were estimated from their two-phase partition coefficients. It is demonstrated that β_s in different organic solvents except those having a specific interaction with the solute, such as chloroform, can be calculated by the present approach.     

千年桐种子油提取工艺研究及其主要脂肪酸成分分析

本文以氯仿、石油醚和正己烷-异丙醇(3:2,v/v)三种不同溶剂对千年桐种子油进行提取,比较了不同溶剂对种子出油率的影响,结果表明以氯仿为溶剂时出油率最高,达到了35％;并考查了提取时间和提取溶剂体积对出油率的影响.最终优化的提取工艺为:以氯仿为溶剂,液料比为12:1(v/w),提取时间6h,出油率达到了37％.提取的种子油经转酯化后,GC-MS分析其主要脂肪酸组分,结果表明千年桐种子油中总脂肪酸占总油酯的90.55％,其中棕榈酸3.87％,硬脂酸4.11％,亚油酸12.15％,油酸13.31％,亚麻酸12.09％,共轭亚麻酸51.20％和EPA(二十碳五烯酸)3.30％.千年桐种子油中富含不饱和脂肪酸,是一种良好的干性油.     

Recovery and purification of intracellular polyhydroxyalkanoates from recombinant Cupriavidus necator using water and ethanol

A new halogen-free and environmental-friendly method using water and ethanol is developed as an alternative for the recovery of polyhydroxyalkanoates (PHA) from recombinant Cupriavidus necator in comparison to the established chloroform extraction method. After optimisation, our results showed that the halogen-free method produced a PHA with 81% purity and 96% recovery yield, in comparison to the chloroform extraction system which resulted in a highly pure PHA with 95% yield. Although the purity of the PHA using the new method is lower, the molecular weight of the extracted PHA is not compromised. This new method can be further developed as an alternative and more environmental-friendly method for industrial application.     

Genomic DNA extraction from medicinal plants available in Malaysia using a TriOmic(TM) improved extraction kit

DNA extraction was carried out on 32 medicinal plant samples available in Malaysia using the TriOmic(TM) extraction kit. Amounts of 0.1 g flowers or young leaves were ground with liquid nitrogen, lysed at 65°C in RY1(plus) buffer and followed by RNAse treatment. Then, RY2 buffer was added to the samples and mixed completely by vortexing before removal of cell debris by centrifugation. Supernatants were transferred to fresh microcentrifuge tubes and 0.1 volume RY3 buffer was added to each of the transferred supernatant. The mixtures were applied to spin columns followed by a centrifugation step to remove buffers and other residues. Washing step was carried out twice by applying 70% ethanol to the spin columns. Genomic DNA of the samples was recovered by applying 50 μL TE buffer to the membrane of each spin column, followed by a centrifugation step at room temperature. A modification of the TriOmic(TM) extraction procedure was carried out by adding chloroform:isoamyl alcohol (24:1) steps in the extraction procedure. The genomic DNA extracted from most of the 32 samples showed an increase of total yield when chloroform:isoamyl alcohol (24:1) steps were applied in the TriOmicTM extraction procedure. This preliminary study is very important for molecular studies of medicinal plants available in Malaysia since the DNA extraction can be completed in a shorter period of time (within 1 h) compared to manual extraction, which entails applying phenol, chloroform and ethanol precipitation, and requires 1-2 days to complete.     

Isolation of genomic DNA from medicinal plants without liquid nitrogen

Genomic DNA was extracted from eight medicinal plants using the present DNA extraction protocols (CTAB extraction method) with some modifications. Leaves were fixed in different fixing solutions containing absolute alcohol (99.99%), chloroform and EDTA, but without liquid nitrogen. DNA quality and quantity obtained were comparable to those isolated with liquid nitrogen, as the lambda260/lambda280 ratio with liquid nitrogen was in range 1.3-1.7 and with other fixing solutions it was 1.1-1.5. Absolute alcohol showed best results as fixing solution. Good quality of DNA was isolated without using liquid nitrogen from different medicinal plant species. DNA isolated by this method was suitable for various molecular biology applications.