Association of Fe-S center(s) with the large subunit(s) of photosystem I particles

Treatment of photosystem I particles from spinach (Spinacia oleracea) with dodecyl sulfate destroyed the protein-bound Fe-S centers and converted some of the acid-labile sulfide to zero-valence sulfur which remained covalently bound to the proteins. When the proteins were resolved by gel-permeation chromatography or by polyacrylamide gel electrophoresis in the presence of dodecyl sulfate, a considerable amount of zero-valence sulfur was associated with the large molecular weight polypeptide(s) (63,000 and 59,000). The results strongly suggest that an intact two-peptide P700 chlorophyll a-protein is an Fe-S protein.     

Spectrophotometric Characteristics and Assay of Biological Stains

I. The chemical and spectrophotometric methods adopted in the Stain Commission laboratories for the certification of stains are described. Spectrophotometric examination is by the Beckman spectrophotometer in which the color density at the absorption maximum is determined as well as a ratio of color densities designed to detect abnormal symmetry of the absorption curve. A somewhat modified titanous chloride assay is described; eerie sulfate is used to determine the normality of the unstable titanous chloride, and the oxidant solution, which is stable, is standardized against Bureau of Standards arsenious oxide. The general approach used for re-study of the stains by these methods and the criteria necessary for adoption of the spectrophotometric method of assay are described.

II. This report gives the details of the spectrophotometric examination and assay of the individual stains in the thiazin group, namely methylene blue, thionin, methylene violet, toluidine blue O, and azures A, B, and C. The spectrophotometric method of assay was adopted for the first three named; the others showed too large a variation among samples to permit adoption of this simpler type of assay. In the case of methylene violet it was necessary to do nitrogen analyses to relate purity of the dye and color density. Complete absorption curves for typical samples of each of the above stains are presented.     

Measurement and biological significance of the volatile sulfur compounds hydrogen sulfide,methanethiol and dimethyl sulfide in various biological matrices

This review deals with the measurement of the volatile sulfur compounds hydrogen sulfide, methanethiol and dimethyl sulfide in various biological matrices of rats and humans (blood, serum, tissues, urine, breath, feces and flatus). Hydrogen sulfide and methanethiol both contain the active thiol (–SH) group and appear in the free gaseous form, in the acid-labile form and in the dithiothreitol-labile form. Dimethyl sulfide is a neutral molecule and exists only in the free form. The foul odor of these sulfur volatiles is a striking characteristic and plays a major role in bad breath, feces and flatus. Because sulfur is a biologically active element, the biological significance of the sulfur volatiles are also highlighted. Despite its highly toxic properties, hydrogen sulfide has been lately recommended to become the third gasotransmitter, next to nitric oxide and carbon monoxide, based on high concentration found in healthy tissues, such as blood and brain. However, there is much doubt about the reliability of the assay methods used. Many artifacts in the sulfide assays exist. The methods to detect the various forms of hydrogen sulfide are critically reviewed and compared with findings of our group. Recent findings that free gaseous hydrogen sulfide is absent in whole blood urged the need to revisit its role as a blood-borne signaling molecule.     

Assay methods and biological roles of labile sulfur in animal tissues

Sulfur is a chemically and biologically active element. Sulfur compounds in animal tissues can be present in two forms, namely stable and labile forms. Compounds such as methionine, cysteine, taurine and sulfuric acid are stable sulfur compounds. On the other hand, acid-labile sulfur and sulfane sulfur compounds are labile sulfur compounds. The sulfur atoms of labile sulfur compounds are liberated as inorganic sulfide by acid treatment or reduction. Therefore, the determination of sulfide is the basis for the determination of labile sulfur. Determination of sulfide has been performed by various methods, including spectrophotometry after derivatization, ion chromatography, high-performance liquid chromatography after derivatization, gas chromatography, and potentiometry with a sulfide ion-specific electrode. These methods were originally developed for the determination of sulfide in air and water samples and were then applied to biological samples. The metabolic origin of labile sulfur in animal tissues is cysteine. The pathways of cysteine metabolism leading to the formation of sulfane sulfur are discussed. Finally, reports on the physiological roles and pathological considerations of labile sulfur are reviewed.     

Sulfide Intrusion and Detoxification in the Seagrass Zostera marina

Gaseous sulfide intrusion into seagrasses growing in sulfidic sediments causes little or no harm to the plant, indicating the presence of an unknown sulfide tolerance or detoxification mechanism. We assessed such mechanism in the seagrass Zostera marina in the laboratory and in the field with scanning electron microscopy coupled to energy dispersive X-ray spectroscopy, chromatographic and spectrophotometric methods, and stable isotope tracing coupled with a mass balance of sulfur compounds. We found that Z. marina detoxified gaseous sediment-derived sulfide through incorporation and that most of the detoxification occurred in underground tissues, where sulfide intrusion was greatest. Elemental sulfur was a major detoxification compound, precipitating on the inner wall of the aerenchyma of underground tissues. Sulfide was metabolized into thiols and entered the plant sulfur metabolism as well as being stored as sulfate throughout the plant. We conclude that avoidance of sulfide exposure by reoxidation of sulfide in the rhizosphere or aerenchyma and tolerance of sulfide intrusion by incorporation of sulfur in the plant are likely major survival strategies of seagrasses in sulfidic sediments.     

Colorimetric broth microdilution method for the antifungal screening of plant extracts against yeasts

Screening plant extracts for antifungal activity is increasing due to demand for new antifungal agents, but the testing methods present many challenges. Standard broth microdilution methods for antifungal susceptibility testing of available antifungal agents are available now, but these methods are optimised for single compounds instead of crude plant extracts. In this study we evaluated the standard NCCLS method as well as a modification which uses spectrophotometric determination of the end-points with a plate reader. We also evaluated another standard method, the EUCAST method, which is a similar microdilution assay to the NCCLS method, but uses a larger inoculum size and a higher glucose concentration in the medium as well as spectrophotometric end-point determination. The results showed that all three methods had some drawbacks for testing plant extracts and thus we modified the NCCLS broth microdilution method by including a colorimetric indicator-resazurin for end-point determination. This modified method showed good reproducibility and clear-cut end-point, plus the end-point determination needed no instruments. It enabled us to evaluate the activity of a selection of extracts from six Combretaceous plants against three Candida spp. and thus provided pharmacological evidence for some traditional uses of these plants while assisting the identification of the active ingredients.     

Analytical measurement of discrete hydrogen sulfide pools in biological specimens

Hydrogen sulfide (H₂S) is a ubiquitous gaseous signaling molecule that plays a vital role in numerous cellular functions and has become the focus of many research endeavors, including pharmacotherapeutic manipulation. Among the challenges facing the field is the accurate measurement of biologically active H₂S. We have recently reported that the typically used methylene blue method and its associated results are invalid and do not measure bona fide H₂S. The complexity of analytical H₂S measurement reflects the fact that hydrogen sulfide is a volatile gas and exists in the body in various forms, including a free form, an acid-labile pool, and bound as sulfane sulfur. Here we describe a new protocol to discretely measure specific H₂S pools using the monobromobimane method coupled with RP-HPLC. This new protocol involves selective liberation, trapping, and derivatization of H₂S. Acid-labile H₂S is released by incubating the sample in an acidic solution (pH 2.6) of 100 mM phosphate buffer with 0.1 mM diethylenetriaminepentaacetic acid (DTPA), in an enclosed system to contain volatilized H₂S. Volatilized H₂S is then trapped in 100 mM Tris–HCl (pH 9.5, 0.1 mM DTPA) and then reacted with excess monobromobimane. In a separate aliquot, the contribution of the bound sulfane sulfur pool was measured by incubating the sample with 1 mM TCEP (tris(2-carboxyethyl)phosphine hydrochloride), a reducing agent, to reduce disulfide bonds, in 100 mM phosphate buffer (pH 2.6, 0.1 mM DTPA), and H₂S measurement was performed in a manner analogous to the one described above. The acid-labile pool was determined by subtracting the free hydrogen sulfide value from the value obtained by the acid-liberation protocol. The bound sulfane sulfur pool was determined by subtracting the H₂S measurement from the acid-liberation protocol alone compared to that of TCEP plus acidic conditions. In summary, our new method allows very sensitive and accurate measurement of the three primary biological pools of H₂S, including free, acid-labile, and bound sulfane sulfur, in various biological specimens.     

Determination of hydrogen sulfide and acid-labile sulfur in animal tissues by gas chromatography and ion chromatography

A sensitive and reliable method was developed for the determination of hydrogen sulfide and acid-labile sulfur (ALS) in animal tissues using gas chromatography with flame photometric detector (GC-FPD) and ion chromatography (IC). Hydrogen sulfide trapped in alkaline solution was determined by GC-FPD as hydrogen sulfide or by IC as sulfate after oxidation with hydrogen peroxide. Sodium sulfide used as a source of hydrogen sulfide was standardized by IC. Fresh rat liver and heart tissues contained 112.2±23.0 and 274.1±34.6 nmol/g of ALS respectively. Free hydrogen sulfide was not detected.     

Quantitation of labile sulfide content and P700 photochemistry in spinach photosystem I particles

Treatment of spinach photosystem I particles with 2 or 4 M urea containing 5 mM ferricyanide produces a time-dependent conversion of labile sulfide to zero-valence sulfur in the membrane-bound iron-sulfur proteins. The integrity of the primary electron donor, P700, remains intact when measured as a chemical oxidized-minus-reduced difference spectrum. The effect on the light-induced oxidation of P700 is complex; the extent of the normally-fast P700 photooxidation correlates directly with the amount of labile sulfide remaining in the particle but a slow phase of photooxidation only becomes evident in increasingly depleted particles and shows no relationship with the amount of remaining labile sulfide. The data is taken as evidence for the participation of an iron-sulfur protein in the primary photochemistry of photosystem I in green plants.     

Spectrophotometric measurement of carotenes, xanthophylls, and chlorophylls in extracts from plant seeds

The method of spectrophotometric measurement of carotenoid and chlorophyll content in extracts from plant seeds was modified. The pigments were extracted with a mixture of petroleum ether (PE) and tetrahydrofuran (THF) (PE to THF ratio 4: 1). Equations for calculations of β-carotene, lutein, chlorophyll a and b content in PE: THF mixture were obtained using specific absorption coefficients of solutions of particular pigments. It was shown that subtraction of chlorophyll contribution from the absorption spectrum of seed extracts yields spectra, which could be used in some cases for calculation of carotene and xanthophyll contents.     

A Proposal for the Use of Standardized Methods for Chlorophyll Determinations in Ecological and Eco-physiological Investigations

The various methods for chlorophyll determination, found in the literature, may give chlorophyll values differing by as much as 20%. Not only the choice of solvent and equations but also the routines and conditions for processing of samples can be large sources of errors. In the present paper some recommendations are given concerning sampling and storage of plant material, extraction and determination of chlorophylls. A simple and fast method for chlorophyll determinations is described and recommended as a suitable method for most ecological and eco-physiological investigations in which chlorophylls are determined. The principle of the method is that the total amount of chlorophylls is determined in a colorimeter calibrated for chlorophyll measurements. Results from a prototype of the “Chlorophyllometer” are presented and compared with spectrophotometric determinations.     

Measurement of lipoxygenase activity in crude and partially purified potato extracts

Two assay systems, one a spectrophotometric assay at 234 nm, the other based on the oxygen electrode, were compared as methods for the routine analysis of lipoxygonase activity in crude and partially purified potato extracts. The spectrophotometric assay was unsuitable for the analysis of crude extracts and only gave meaningful results under very restricted reaction conditions. The oxygen electrode provided a reliable method for routine analysis of lipoxygenase activity.     

A sensitive fluorometric assay for measuring xanthine dehydrogenase and oxidase in tissues

The conversion of xanthine dehydrogenase to a free radical producing oxidase is an important component of oxygen-mediated tissue injury. Current assays for these enzymes are of limited sensitivity, making it difficult to analyze activities in organ biopsies or cultured cells. The xanthine oxidase-catalyzed conversion of pterin (2-amino-4-hydroxypteridine) to isoxanthopterin provides the basis for a fluorometric assay which is 100-500 times more sensitive than the traditional spectrophotometric assay of urate formation from xanthine. Enzyme activity as low as 0.1 pmol min-1 ml-1 can be measured with the fluorometric pterin assay. Xanthine oxidase is assayed in the presence of pterin only, while combined xanthine dehydrogenase plus oxidase activity is determined with methylene blue which replaces NAD+ as an electron acceptor. The relative proportions and specific activities of xanthine oxidase and dehydrogenase determined by the fluorometric pterin assay are comparable with the spectrophotometric measurement of activities present in rat liver, intestine, kidney, and plasma. The assay has been successfully applied to brain, human kidney, and cultured mammalian cells, where xanthine dehydrogenase and oxidase activities are too low to detect spectrophotometrically.     

Purification and properties of paramagnetic protein from Clostridium pasteurianum W5.

The purification to homogeneity of the non-heme iron protein, sometimes referred to as either "red protein" or "paramagnetic protein", from Clostridium pasteurianum W5 extracts is described and its physicochemical properties studied. This paramagnetic protein (g= 1.94) has a molecular weight of about 25000 and contains two iron and two acid-labile sulfur atoms per mol of protein. Its midpoint potential at pH 7.5, as determined by electron paramagnetic resonance titration, is -300 mV. Optical circular dichroism and electron paramagnetic resonance spectra of the paramagnetic protein are similar to those of two iron-two acid-labile sulfur ferredoxins. The biochemical reduction of the purified protein was also studied.     

Repair of damaged DNA by Arabidopsis cell extract

All living organisms have to protect the integrity of their genomes from a wide range of genotoxic stresses to which they are inevitably exposed. However, understanding of DNA repair in plants lags far behind such knowledge in bacteria, yeast, and mammals, partially as a result of the absence of efficient in vitro systems. Here, we report the experimental setup for an Arabidopsis in vitro repair synthesis assay. The repair of plasmid DNA treated with three different DNA-damaging agents, UV light, cisplatin, and methylene blue, after incubation with whole-cell extract was monitored. To validate the reliability of our assay, we analyzed the repair proficiency of plants depleted in AtRAD1 activity. The reduced repair of UV light- and cisplatin-damaged DNA confirmed the deficiency of these plants in nucleotide excision repair. Decreased repair of methylene blue-induced oxidative lesions, which are believed to be processed by the base excision repair machinery in mammalian cells, may indicate a possible involvement of AtRAD1 in the repair of oxidative damage. Differences in sensitivity to DNA polymerase inhibitors (aphidicolin and dideoxy TTP) between plant and human cell extracts were observed with this assay.     

Euglena gracilis cadmium-binding protein-II contains sulfide ion

Sulfide ions are a constituent of the cadmium-binding protein-II in the alga Euglena gracilis. Their presence was demonstrated by the methylene blue assay, by acid labilization induced reductions in the Cd-S charge transfer band at 254 nm and by reactions with the thiol reagent, 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB). Direct reduction of DTNB by sulfide and precipitation of CdS yield a complex stoichiometry for the DTNB reaction. The S2-/Cd2+ ratios determined, 1.25 +/- 0.10 (methylene blue) and 1.37 +/- 0.16 (DTNB), are in good agreement.     

The biosynthesis of cysteine and homocysteine in Methanococcus jannaschii

The pathway for the biosynthesis of cysteine and homocysteine in Methanococcus jannaschii has been examined using a gas chromatography-mass spectrometry (GC-MS) stable isotope dilution method to identify and quantitate the intermediates in the pathways. The first step in the pathway, and the one responsible for incorporation of sulfur into both cysteine and methionine, is the reaction between O-phosphohomoserine and a presently unidentified sulfur source present in cell extracts, to produce L-homocysteine. This sulfur source was shown not to be sulfide. The resulting L-homocysteine then reacts with O-phosphoserine to form L-cystathionine, which is cleaved to L-cysteine. The pathway has elements of both the plant and mammalian pathways in that the sulfur is first incorporated into homocysteine using O-phosphohomoserine as the acceptor and the resulting homocysteine, via transsulfuration, supplies the sulfur for cysteine formation. The pathway leading to these two amino acids represents an example of metabolic thrift where the preexisting cellular metabolites O-phosphohomoserine and O-phosphoserine are used as the ultimate source of the carbon framework for the biosynthesis of these amino acids. These findings explain the absence of identifiable genes in the genome of this organism for the biosynthesis of cysteine and homocysteine.     

The 110-kDa reaction center protein of photosystem I, P700-chlorophyll a-protein 1, is an iron-sulfur protein

Germination and growth of barley (Hordeum vulgare L.) in the presence of 59Fe2+ or 35SO4(2-) allows heavy incorporation of both isotopes into the thylakoid membranes and into isolated photosystem I particles. Analysis of 59Fe-labeled preparations by sodium dodecyl sulfate-polyacrylamide gel electrophoresis under mild conditions demonstrates that a minimum of four iron atoms/P700 is carried on P700-chlorophyll a-protein 1. When isolated from 35S-labeled preparations, P700-chlorophyll a-protein 1 binds zero valence 35S, which is converted into acid-labile [35S]sulfide by dithiothreitol reduction. Isolated photosystem I particles contain 14 acid-labile sulfide atoms and 10 iron atoms for each molecule of P700 and are composed of polypeptides of 110, 18, 15, 10, and 8 kDa of which the 10-kDa component is loosely bound. Under the electrophoretic conditions used, none of the low molecular weight polypeptides could be shown to be specifically associated with iron or acid-labile sulfide. Carboxymethylation of cysteine residues shows a high cysteine content in the 8-kDa polypeptide and an intermediate content in the 110- and 18-kDa polypeptides, whereas the 15-kDa polypeptide is devoid of sulfur amino acids. The experiments with the 59Fe-labeled thylakoids reveal other labeled polypeptides not associated with photosystem I, namely cytochrome f and possibly cytochromes b6 and b559.     

Characterization of the catalyzed phosphate assay.

A detailed analysis of the catalyzed phosphate assay is presented. This assay uses polyvinylpyrrolidone as a catalyst to form phosphomolybdate complex in a relatively weak acid and hydroxylamine as a reductant to form molybdenum blue. It was found that this assay, which is useful in determining inorganic phosphate in the presence of acid-labile phosphates such as ATP and phosphocreatine, has the following advantages: The assay (a) forms phosphomolybdate at a relatively high pH (pH 1.9–2.1; in some cases even at pH 4.0), (b) is relatively insensitive to interfering reagents, and (c) does not require deproteinization. Conditions are described which make the present assay more sensitive than the Fiske-SubbaRow method.     

On the limits of applicability of spectrophotometric and spectrofluorimetric methods for the determination of chlorophyll a/b ratio

The concentration limits for spectrophotometric and spectrofluorimetric determinations of the chlorophyll (Chl) a/b ratio in barley leaves were studied using 80% acetone extracts at room temperature. The optimum sample absorbances (at 663.2 nm – maximum of the Q_Y) band of Chl a) for the Chl a/b determination were determined. For given spectrometers and sample positions, these absorbances ranged between 0.2 and 1.0 and 0.008–0.1 for the absorption and fluorescence methods, respectively. Precision of the measurements and the distorting effects are discussed. The lower limits of both absorption and fluorescence methods depend on sensitivity of the spectrometers for the Chl b detection. The spectrophotometric determination of Chl a/b ratio at higher Chl concentrations can be distorted by the chlorophyll fluorescence signal. The extent of this distortion depends on sample-detector geometry in any given type of the spectrometer. The effect of inner filter of Chl molecules and the detection instrumental function affect the value of the upper limit for the spectrofluorimetric method. Both methods were applied to estimate the Chl a/b ratio in pigment extracts from greening barley leaves, which are characterized by a low Chl concentration and a high Chl a/b ratio at the beginning of greening process.