Determination of low bacterial concentrations in hyperarid Atacama soils: comparison of biochemical and microscopy methods with real-time quantitative PCR

Hyperarid Atacama soils are reported to contain significantly reduced numbers of microbes per gram of soil relative to soils from other environments. Molecular methods have been used to evaluate microbial populations in hyperarid Atacama soils; however, conflicting results across the various studies, possibly caused by this low number of microorganisms and consequent biomass, suggest that knowledge of expected DNA concentrations in these soils becomes important to interpreting data from any method regarding microbial concentrations and diversity. In this paper we compare the number of bacteria per gram of Atacama Desert soils determined by real-time quantitative polymerase chain reaction with the number of bacteria estimated by the standard methods of phospholipids fatty acid analysis, adenine composition (determined by liquid chromatography - time-of-flight mass spectrometry), and SYBR-green microscopy. The number determined by real-time quantitative polymerase chain reaction as implemented in this study was several orders of magnitude lower than that determined by the other three methods and probably underestimates the concentrations of soil bacteria, most likely because of soil binding during the DNA extraction methods. However, the other methods very possibly overestimate the bacteria concentrations owing to desiccated, intact organisms, which would stain positive in microscopy and preserve both adenine and phospholipid fatty acid for the other methods.     

Synthesis of chromophoric, spin label enzyme substrates useful for cryoenzymology.

The spin label nitroxide derivative 3-(2,2,5,5-tetramethylpyrroline-1-oxyl)-propen-2-oic acid has been synthesized and characterized by chemical methods. It is a useful intermediate in the preparation of a new class of chromophoric spin label substrates for enzyme studies, as shown by the synthesis of O-3-(2,2,5,5-tetramethylpyrroline-1-oxyl)-propen-2-oyl-L-beta-phenyllactic acid, a specific ester substrate of bovine pancreatic carboxypeptidase A (peptidyl-L-amino acid hydrolase; EC 3.4.12.2). Kinetic parameters of the esterolytic reaction are conveniently determined by UV spectrophotometric methods, and a reaction intermediate can be stabilized in fluid cryosolvent mixtures at subzero temperatures. Results are presented of preliminary electron spin resonance studies to demonstrate that structural relationships of the spin label substrate in a catalytically active configuration to active site residues can be determined for this low temperature-stabilized reaction intermediate. This substrate thus demonstrates the utility of this new class of spin label derivatives for characterization of enzyme reaction intermediates stabilized by cryoenzymologic techniques.     

Investigation of catalytic reaction with spectrofluorimetric method

Numerous derivatives of nicotinic acid hydrazids are suitable for sensitive fluorescence determination of metal ions. The reaction proceeds upon ultraviolet illumination in the presence of an oxidizing agent and catalyst forming a fluorescent product. Therefore, the catalyst metal ion can be quantitatively determined by fluorescence methods. We have studied the reaction of nicotinic acid (di-pyridin-2-yl-methylene)-hydrazide (NADPMH), catalyzed by Mn(II)ion, and determined the optimal parameters of metal ion method.     

Determination of total copper and zinc contents of Egyptian soils using three different methods

Summary To compare chemical methods for determining total contents of Cu and Zn in Egyptian soils, surface samples of two groups of soils from Egypt namely the alluvial and the calcareous were chosen. The samples were analyzed for the total Cu and Zn using three chemical methods namely, aqua regia, hydrofluoric acid and fusion methods. The mean values of total Cu determined by aqua regia, hydrofluoric acid and fusion methods were 58.7, 69.2, 69.4 ppm for the alluvial soils and 11.8, 13.0, 12.8 ppm for the calcareous soils respectively. The corresponding values of Zn were 138.6, 189.4, 189.8 ppm for the alluvial soils and 58.6, 89.7, 90.3 ppm for the calcareous soils. The Cu and Zn contents in the alluvial and calcareous soils, determined by the aqua regia method was lower as compared with those determined by the fusion or hydrofluoric methods.An attempt was made to use the etching of soil with aqua regia and the linear relationship, to quantitavely evaluate the total content of Cu and Zn determined with hydrofluoric acid or fusion methods.     

Screening and optimization of the derivatization of polar herbicides with trimethylanilinium hydroxide for GC-MS analysis

In the present study, a derivatization method for the determination of acidic herbicides has been investigated. This procedure involves the methylation with the quaternary ammonium salt trimethylanilinium hydroxide (TMAH) directly in the gas chromatographic auto-sampler vial for analysis by gas chromatography combined with mass spectrometry. The derivatization reaction has been screened for influential factors and statistically significant parameters. The identified factors, reaction time, temperature and hold-up time were optimized by a complete factorial response surface design and optimal reaction conditions were generated. Finally, the optimized methylation procedure was compared to different alkylation methods and obtained results demonstrated the applicability of derivatization with trimethylanilinium hydroxide. Acidic herbicides used in the study consist of several families of compounds like derivatives of acetic acid (2,4-D and 2,4,5-T), butanoic acid (MCPB), benzoic acid (chloramben, dicamba), phenol (dinoseb and dinoterb), propanoic acid (mecoprop) and other miscellaneous acids such as pyridinecarboxlyic acid (picloram). A reliably working, rapid method for the preparation of methyl compounds is generated with respect to automation for routine analysis.     

Comparative thermodynamic analysis of DNA--protein interactions using surface plasmon resonance and fluorescence correlation spectroscopy

We report a kinetic and thermodynamic analysis of interactions between ssDNA and replication protein A (RPA) using surface plasmon resonance (SPR) and fluorescence correlation spectroscopy (FCS) at variable temperature. The two methods yield different values for the Gibbs free energy but nearly the same value for the reaction enthalpy of ssDNA-RPA complex formation. The Gibbs free energy was determined by SPR and FCS to be -62.6 and -54.7 kJ/mol, respectively. The values for the reaction enthalpy are -64.4 and -66.5 kJ/mol. It is concluded that the difference in Gibbs free energy measured by the two methods is due to different reaction entropies. The entropic contribution to the free energy at 25 degrees C is -1.8 kJ/mol for SPR and -11.8 kJ/mol for FCS. In SPR, the reaction is restricted to two dimensions because of immobilization of the DNA molecules to the sensor surface. In contrast, FCS is able to follow complex formation without spatial restrictions. In consequence, the reaction entropy determined from SPR experiments is lower than for FCS experiments.     

Monitoring biotransformations in polyamide fibres

The enzymatic hydrolysis of polyamide fibres yields amino and carboxylic groups. These groups can be found in solution treatments as polyamide monomers and soluble oligomers. The amino groups can also be found at the surface of the fibres as end group chains. In this paper we report two methods to quantify the formation of these groups as a result of the enzymatic action. Soluble amino groups can be quantified with 2,4,6-trinitrobenzenesulfonic acid (TNBS), which yields a coloured complex which can be determined spectrophotometrically. The amino groups on the fibre surface can be quantified by reaction with a wool reactive dye and determination of colour intensities after a dyeing procedure below the glass transition temperature of polyamide.     

Lipase-catalyzed dimethyl adipate synthesis: Response surface modeling and kinetics

Dimethyl adipate (DMA) was synthesized by immobilized Candida antarctica lipase B-catalyzed esterification of adipic acid and methanol. To optimize the reaction conditions of ester production, response surface methodology was applied, and the effects of four factors namely, time, temperature, enzyme concentration, and molar ratio of substrates on product synthesis were determined. A statistical model predicted that the maximum conversion yield would be 97.6%, at the optimal conditions of 58.5°C, 54.0 mg enzyme, 358.0 min, and 12:1 molar ratio of methanol to adipic acid. The R² (0.9769) shows a high correlation between predicted and experimental values. The kinetics of the reaction was also investigated in this study. The reaction was found to obey the ping-pong bi-bi mechanism with methanol inhibition. The kinetic parameters were determined and used to simulate the experimental results. A good quality of fit was observed between the simulated and experimental initial rates.     

Kinetic studies on the reaction between Trametes villosa laccase and dioxygen

A laccase from the fungus Trametes villosa (TviL) was investigated in order to elucidate the reaction mechanism of the reduction of dioxygen to water performed by this blue multi-copper oxidase. The ability of TviL to activate dioxygen was studied by stopped-flow experiments and under steady-state conditions. In the stopped-flow experiments TviL was reduced with a small excess of 4-hydroxyphenylacetic acid and afterwards the re-oxidation process was monitored by stopped-flow techniques by mixing with excess dioxygen. The reaction between reduced TviL and dioxygen was studied in the temperature range 10-35 degrees Celsius and with the concentration of dioxygen between 30 and 240microM. The observed rate constant k(obs) is found to be linear dependent on the dioxygen concentration and the observed second-order rate constant for the re-oxidation of reduced TviL is, at 25 degrees Celsius, determined to be 1.14x10(6)M(-1)s(-1). The activation energy, E(a), is from the same data determined to be 22kJmol(-1). Oxidation of different phenols (4-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, guaiacolsulfonic acid and hydroquinone) under steady state conditions was investigated at concentrations of dioxygen ranging from 60 to 250microM. This line of experiments showed that TviL follows a ping-pong mechanism, and an observed second-order rate constant for the reaction with dioxygen of 7.1x10(5)M(-1)s(-1) at 25 degrees Celsius was found with 4-hydroxyphenylacetic acid as reducing substrate. The two kinetic methods resulted in observed rate constants of equal magnitudes for the reaction with dioxygen, which suggests that the rate limiting step(s) is (are) included in both the reactions studied by the two different techniques.     

Flow cytoenzymology of intracellular tartrate-resistant acid phosphatase.

Tartrate-resistant acid phosphatase (TRACP) is a cytochemical marker for hairy cell leukemia, macrophages, dendritic cells, and osteoclasts. Our purpose was to develop multicolor cytofluorometric methods to evaluate intracellular TRACP enzymic activity using a fluorogenic cytochemical reaction in combination with immunochemical stains for distinct surface membrane antigens. Monocyte-derived dendritic cells (DCs) were the model TRACP-expressing cells studied. Intracellular TRACP activity was disclosed using naphthol-ASBI phosphate as substrate with fast red-violet LB salt as coupler for the reaction product. Before the TRACP enzymic reaction, surface antigens, CD86 and CD11c of DCs, were bound with specific fluorescent antibodies to test compatibility of surface labeling and intracellular staining. TRACP activity varied in DCs from donor to donor but was reproducible on repeated examinations of each sample. Samples could be stained for simultaneous analysis of surface antigens and intracellular TRACP activity, provided certain technical details were observed. The TRACP reaction time should not exceed 9 min and the cell number should not exceed 2 x 10(5)/100 micro l test. Fluorescent surface labels did not affect the intensity of the TRACP stain, but the intensity of some surface labels may be diminished by elution of low-affinity antibodies during the TRACP reaction. Readjustment of the threshold settings in triple-labeled cells is needed to compensate for this phenomenon. Intracellular TRACP activity can be quantitated in subpopulations of cells within mixed cell populations by flow cytofluorometry using simple cytochemical methods in combination with fluorescent antibodies to cell-surface and other differentiation antigens. The cytochemical method should be useful for basic investigations of differentiation, maturation, and function of macrophages, DCs, and osteoclasts, and for diagnosis and management of hairy cell leukemia.     

The fractionation of phosphatidylinositol into molecular species by thin-layer chromatography on silver nitrate-impregnated silica gel

1. Two methods for the fractionation of phosphatidylinositol into molecular species were developed. In addition to preserving the fatty acid moiety of the molecule, the first method preserves the phosphorus, and the second preserves both the phosphorus and inositol ring. 2. In the first method, phosphatidylinositol was oxidized with periodate and the products reacted with diazomethane. I.r. examination showed that the main product was identical with dimethylphosphatidic acid. Fractionation to molecular species was carried out on thin layers impregnated with silver nitrate. The fatty acid composition of the species was determined by gas-liquid chromatography, and their distribution in lamb liver phosphatidylinositol was studied by a method using [(3)H]methanol. 3. In the second method, phosphatidylinositol was acetylated under mild reaction conditions. The major product was the triacetylated derivative of this phospholipid. This was reacted with diazomethane and the methylated-triacetylated phosphatidylinositol was fractionated into molecular species on silver nitrate-impregnated thin layers. Solvent mixtures containing acetone and distilled chloroform were found most suitable for this purpose. The fatty acid composition of the molecular species was determined by g.l.c., and their distribution in lamb liver phosphatidylinositol was studied by a method using [1-(14)C]acetic anhydride during the acetylation reaction. 4. Results from both methods agree fairly well. The most predominant species of lamb liver phosphatidylinositol is the monoenoic (60%) followed by the tetraenoic (17%). The di- and tri-enoic species existed as minor components.     

Hydrogen fluoride saccharification of wood: lignin fluoride content, isolation of alpha-D-glucopyranosyl fluoride and posthydrolysis of reversion products

Wood chips from bigtooth aspen (Populus grandidentata Michx.) were saccharified by reaction with liquid hydrogen fluoride either anhydrous or containing up to 10% v/v water. The reaction products were separated into a solid lignin fraction and a water-soluble saccharide fraction. The fluoride content of the lignin (determined after alkaline fusion) was initially about 1 mg/g wood, but was lowered to 0.1 mg/g wood by grinding and washing. Thus little or no chemical binding of fluoride to lignin occurred during hydrogen fluoride (HF) solvolysis. Analysis of the water-soluble fraction by gel filtration on Biogel P2 columns showed a range of low-molecular-weight oligosaccharides and only 10-20% sugar monomers. Thus considerable reversion occurred during HF evacuation. Posthydrolysis conditions were optimized for these reversion products by varying temperature and acid concentration. Optimal conditions at 1 h were 140 degrees C with 100mN sulfuric acid or 225mN Hydrofluoric acid resulting in monomer yields of > 90% for 0.5% sugar solutions and > 80% for 10% sugar solutions. After reaction of pure cellulose (Filter paper) with hydrogen fluoride in the absence of water, and terminating the reaction with calcium carbonate, the reaction intermediate alpha-D-glucopyranosylfluoride was isolated with a maximal yield of 0.2 g/g paper. Upon purification via paper chromatography glucosylfluoride was identified by its specific rotation and also by gas chromatography-mass spectrometry of its tetra-O-trimethylsilyl derivative.     

Optimization of microwave-assisted transesterification of dry algal biomass using response surface methodology

The effect of microwave irradiation on the simultaneous extraction and transesterification (in situ transesterification) of dry algal biomass to biodiesel was investigated. A high degree of oil/lipid extraction from dry algal biomass and an efficient conversion of the oils/lipids to biodiesel were demonstrated in a set of well-designed experimental runs. A response surface methodology (RSM) was used to analyze the influence of the process variables (dry algae to methanol (wt/vol) ratio, catalyst concentration, and reaction time) on the fatty acid methyl ester conversion. Based on the experimental results and RSM analysis, the optimal conditions for this process were determined as: dry algae to methanol (wt/vol) ratio of around 1:12, catalyst concentration about 2 wt.%, and reaction time of 4 min. The algal biodiesel samples were analyzed with GC-MS and thin layer chromatography (TLC) methods. Transmission electron microscopy (TEM) images of the algal biomass samples before and after the extraction/transesterification reaction are also presented.     

Activity of some lysosomal enzymes in peripheral blood lymphocytes of patients with lung cancer. A cytochemical study

In 33 patients with lung cancer (6 women and 27 men, aged at average 61.2 years) the activity and intracellular localization of acid phosphatase, beta-glucuronidase and N-acetyl-beta-glucosaminidase in peripheral blood lymphocytes were determined by means of semiquantitative cytochemical methods. In comparison to the control group of healthy subjects, the patients with lung cancer showed increased counts of acid phosphatase-positive lymphocytes with granular-diffuse cytochemical reaction, increased counts of beta-glucuronidase-positive lymphocytes with solely granular type of reaction and increased numbers of N-acetyl-beta-glucosaminidase-positive cells showing the granular, granular-diffuse and diffuse type of reaction. The total count of beta-glucuronidase-positive and N-acetyl-beta-glucosaminidase-positive lymphocytes was significantly elevated in these patients. The authors discuss the significance of their observations for evaluating lymphocyte response in patients with lung cancer.     

Reaction of colloidal silica with membranes of intact mammalian cells

Colloidal silical particles were produced at a size that permitted reaction with human erythrocytes and rat macrophages without affecting cell integrity. Binding of colloid was shown by increased electrophoretic mobility of red cells and also resulted in changes in the surface topography of red cells as seen with scanning electron microscopy. The degree to which colloid binds to red cells was determined by microprobe analysis of single intact cells. Furthermore, the capacity of red cells to bind silica was increased if sialic acid residues were removed enzymatically from the cell surface.     

Reaction of S-(2-amino-2-carboxyethylsulfonyl)-L-cysteine with thiosulfate: synthesis of L-alanine sulfodisulfane and application to the determination of thiosulfate

A new reaction of S-(2-amino-2-carboxyethylsulfonyl)-L-cysteine (ACESC) with thiosulfate is described. The reaction proceeded quantitatively in formic or acetic acid solutions, yielding equimolar amounts of L-alanine sulfodisulfane (2-amino-2-carboxyethyl sulfodisulfane) and L-alanine 3-sulfinic acid. L-Alanine sulfodisulfane was obtained as pure monosodium salt; the yield was 92% of the theoretical. A new method is described for the determination of thiosulfate. The method is based on the quantitative reaction between ACESC and thiosulfate, and L-alanine sulfodisulfane, one of the reaction products, was determined using acid ninhydrin reagent 2 of M. K. Gaitonde (1967, Biochem. J. 104, 627-633). The recovery was over 95%. When samples contained sulfite in addition to thiosulfate, S-sulfo-L-cysteine (T. Ubuka et al., 1982, Anal. Biochem. 126, 273-277) was produced in addition to L-alanine sulfodisulfane by the treatment with ACESC. Both products were separated by a small Dowex 1 column and determined with the acid ninhydrin reagent 2. The recoveries were over 95%. The new method was applied to the thiosulfate sulfurtransferase reaction, in which thiosulfate, a substrate, and sulfite, a product, were determined separately.     

Surface modification of chitosan films. Effects of hydrophobicity on protein adsorption

The surface of chitosan films was modified using acid chloride and acid anhydrides. Chemical composition at the film surface was analyzed by attenuated total reflectance Fourier-transform infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS). ATR-FTIR data verified that the substitution took place at the amino groups of chitosan, thus forming amide linkages, and the modification proceeded to the depth at least 1 microm. Choices of molecules substituted at the amino groups of the glucosamine units did affect the hydrophobicity of the film surface, as indicated by air-water contact angle analysis. The surface became more hydrophobic than that of non-modified film when a stearoyl group (C(17)H(35)CO-) was attached to the films. The reaction of chitosan films with succinic anhydride or phthalic anhydride, however, produced more hydrophilic films. Selected modified films were subjected to protein adsorption study. The amount of protein adsorbed, determined by bicinchoninic acid (BCA) assay, related to the types of attached molecules. The improved surface hydrophobicity affected by the stearoyl groups promoted protein adsorption. In contrast, selective adsorption behavior was observed in the case of the chitosan films modified with anhydride derivatives. Lysozyme adsorption was enhanced by H-bonding and charge attraction with the hydrophilic surface. While the amount of albumin adsorbed was decreased possibly due to negative charges that gave rise to repulsion between the modified surface and albumin. This study has demonstrated that it is conceivable to fine-tune surface properties which influence its response to bio-macromolecules by heterogeneous chemical modification.     

Reaction of S-(2-amino-2-carboxyethylsulfonyl)- -cysteine with thiosulfate: Synthesis of -alanine sulfodisulfane and application to the determination of thiosulfate

A new reaction of S-(2-amino-2-carboxyethylsulfonyl)- -cysteine (ACESC) with thiosulfate is described. The reaction proceeded quantitatively in formic or acetic acid solutions, yielding equimolar amounts of -alanine sulfodisulfane (2-amino-2-carboxyethyl sulfodisulfane) and -alanine 3-sulfinic acid. -Alanine sulfodisulfane was obtained as pure monosodium salt; the yield was 92% of the theoretical. A new method is described for the determination of thiosulfate. The method is based on the quantitative reaction between ACESC and thiosulfate, and -alanine sulfodisulfane, one of the reaction products, was determined using acid ninhydrin reagent 2 of [7.]. The recovery was over 95%. When samples contained sulfite in addition to thiosulfate, S-sulfo- -cysteine ([6.]) was produced in addition to -alanine sulfodisulfane by the treatment with ACESC. Both products were separated by a small Dowex 1 column and determined with the acid ninhydrin reagent 2. The recoveries were over 95%. The new method was applied to the thiosulfate sulfurtransferase reaction, in which thiosulfate, a substrate, and sulfite, a product, were determined separately.     

反应条件下苯丙氨酸解氨酶的活力稳定性

在苯丙氨酸解氨酶(PAL)的作用下由肉桂酸和氨合成L-苯丙氨酸(L-Phe)是酶法合成该氨基酸的重要途径,国外已利用该途径进行L-苯丙氨酸的工业生产,但是该过程仍存在着转化率低和酶活力稳定性差的问题。为解决这些问题,有必要在现有基础上开展提高酶活力稳定性的研究。