Processing samples of benthic marine diatoms from Mediterranean oligotrophic areas

The processing of benthic diatoms is tedious and involves several potentially damaging steps for cells. Although the preservation of siliceous frustules is of paramount importance in the implementation of biotic indices, only few studies quantified treatment-induced cell losses. We assumed that commonly used treatments may lead to mechanical (centrifugation, sedimentation, boiling, sonication and mounting in Naphrax) and chemical (cold H₂O₂ digestion) damages on diatoms. We analysed the potential adverse effects of these treatments and the cleaning efficiency of H₂O₂ and incineration in order to find out the most suitable technique to process lightly silicified Mediterranean populations. Results showed that successive resuspensions of material after each concentration treatment (sedimentation and centrifugation) and low speed centrifugation did not alter the physical integrity of frustules. In contrast, boiling and sonication exhibited adverse effects especially on the preservation of large frustules and Naphrax mounting proved to be the most damaging step whatever the size of diatoms. For cleaning treatments, incineration provided the most satisfactory results and acted on a non-selective way as opposed to hydrogen peroxide which led to either a large number of non-cleaned frustules or dissolved valves. Our recommendations for processing samples of lightly silicified Mediterranean benthic diatoms include the use of low-speed centrifugations, dehydration at room temperature, incineration and dry mounting.     

Improved operational stability of chloroperoxidase through use of antioxidants

Chloroperoxidase (CPO) from Caldariomyces fumago is a potentially very useful enzyme due to its ability to catalyze a large variety of stereoselective oxidation reactions, but poor operational stability is a main limitation for commercial use. In the present study, the possibility of increasing the operational stability by use of antioxidants was investigated using the oxidation of indole as model reaction. Caffeic acid was the antioxidant showing the strongest positive effects, reaching a total turnover number (TTN) of 135,000 at pH 4 and 4 mM hydrogen peroxide, compared to 28,700 in the absence of antioxidant. Portion-wise addition of hydrogen peroxide in the presence of caffeic acid caused a further increase in TTN to 171,000. An alternative way to reach high TTN was to use tert-butyl hydroperoxide as oxidant instead of hydrogen peroxide: a TTN of 600,000 was achieved although the reaction was quite slow. In this case, antioxidants did not have any positive effect. Possible mechanisms for the observed inactivation of CPO are discussed.     

Cereal genome analysis using rice as a model

Researchers are eagerly waiting for the physical map of rice to become completed and available for use as a model for all cereals. The most significant advances of the past year have been the progress toward positional cloning of genes and the identification of quantitative trait loci (QTL) from detailed restriction fragment length polymorphism maps. Future focus will be: first, the enhanced dissemination and integration of the available data in World Wide Web accessible databases for easy comparison of genetic and physical mapping data across various species; second, the expanded distribution of a wide variety of DNA materials (cDNA clones, yeast artificial chromosomes, bacterial artificial chromosomes and other probes) for use in other cereals on the basis of the rice model map; and third, the applied breeding by locating and isolating sequences corresponding to important agronomic traits, often correlating with QTL.     

The Action of Nine Chelators on Iron-Dependent Radical Damage

Nine iron chelators were tested in five systems for their effects on radical-generation and conversion at chelator: iron molar ratios from 0.1 to 10. Stimulatory actions might distinguish toxic from safer chelators. Radical-generating reactions which represent different aspects of iron (ferrous and ferric) availability were studied: a) the reaction with hydrogen peroxide to hydroxylate benzoate; b) the oxidation of ascorbate; c) the reaction with hydrogen peroxide to fragment proteins; d) the reaction with hydrogen peroxide to permit amplified chemiluminescence; and e) the induction of peroxidation of mitochondrial membrane lipids. The compounds used were HBED, CP130, Desferal, EDTA, pyridine-hydrazone (CGP 43'902B), Ferrozine, CP 94 (CGP 46'700), LI (CGP 37 391) and rhodotorulic acid (CGP 45 274). Only the hexadentate compounds HBED, CP130 and Desferal were uniformly inhibitory (“protective”). The protective compounds were also apparently more stable during radical fluxes than the other chelators.     

Recognition of neutral species with synthetic receptors

The design of synthetic receptors for neutral molecules is an area of intense current interest. The area has grown from early work on cyclodextrin or single crown ether complexation to encompass a wide array of receptor shapes and structures. Furthermore, the range of substrate selectivities has increased from simple aromatic or metal ion substrates to include key biological components such as peptides and carbohydrates. Recent advances have included the application of split bead combinatorial methods for the identification of receptors for oligopeptides, the design of self-assembling spherical receptors, the use of multiple hydrogen bonding groups for carboxylic acid and carbohydrate recognition and the achievement of impressive catalytic effects with synthetic receptors.     

Prostaglandins attenuate cardiac contractile dysfunction produced by free radical generation but not by hydrogen peroxide

The aim of this study was to examine and compare the potential influence of cyclooxygenase or lipoxygenase derived metabolises of arachidonic acid on myocardial injury produced either by a free radical generating system consisting of purine plus xanthine oxidase or that produced by hydrogen peroxide. A free radical generating system consisting of purine (2.3 mM) and xanthine oxidase (10 U/L) as well as hydrogen peroxide (75 µM) produced significant functional changes in the absence of either significant deficits in high energy phosphates or ultrastructural damage. Prostaglandin F2; (30 nM) significantly attenuated both the negative inotropic effect of purine plus xanthine oxidase as well as the ability of the free radical generator to elevate resting tension. An identical concentration of prostaglandin I2 (prostacyclin) significantly reduced resting tension elevation only and had no effect on contractile depression. The salutary effects of the two PGs occurred in the absence of any inhibitory influence on superoxide anion generation produced by the purine and xanthine oxidase reaction. None of prostaglandins modulated the response to hydrogen peroxide. In addition, neither prostaglandin E2 nor leukotrienes exerted any effect on changes produced by either type of oxidative stress. A 5 fold elevation in the concentrations of free radical generators or hydrogen peroxide produced extensive injury as characterized by a virtual total loss in contractility, 400% elevation in resting tension, ultrastructural damage and significant depletions in high energy phosphate content. None of these effects were modulated by eicosanoid treatment. Our results therefore demonstrate a selective ability of both prostaglandin F2; and to a lesser extent prostacyclin, to attenuate dysfunction produced by purine plus xanthine oxidase but not hydrogen peroxide. It is possible that these eicosanoids may represent endogenous protective factors under conditions of enhanced oxidative stress associated with superoxide anion generation.     

Decolorization of melanin by lignin peroxidase from<Emphasis Type="Italic">Phanerochaete chrysosporium</Emphasis>

Melanin was decolorized by lignin peroxidase fromPhanerochaete chrysosporium. This decolorization reaction showed a Michaelis-Mentens type relationship between the decolorization rate and concentration of two substrates: melanin and hydrogen peroxide. Kinetic constants of the decolorization reaction were 0.1 OD₄₇₅/min (V _max) and 99.7 mg/L (K _m) for melanin and 0.08 OD₄₇₅/min (V _max) and 504.9 μM (K _m) for hydrogen peroxide, respectively. Depletion of hydrogen peroxide interrupted the decolorization reaction, indicating the essential requirement of hydrogen peroxide. Pulsewise feeding of hydrogen peroxide continued the decolorizing reaction catalyzed by lignin peroxidase. These results indicate that enzymatic decolorization of melanin has applications in the development of new cosmetic whitening agents.     

Pattern of shift rota modulates oral temperature circadian rhythm and sleep-wakefulness profiles in shift workers

Twenty four shift workers (8 from a steel industry and 16 from a Government hospital) participated in the study. The subjects were instructed to self-measure oral temperature, 4 6 times a day for about three weeks. Sleep quantity and quality for each subject were analysed with the help of an appropriate inventory. The data were analysed by cosinor and power spectrum methods. The frequency of circadian rhythm detection was in the order of 48% in senior nurses, 29% in steel plant workers and 14% in junior nurses. These were also complemented by the results of power spectrum analysis. Present results suggest that rhythms of subjective fatigue and subjective drowsiness are governed neither by oral temperature oscillator nor by the sleep/wake cycle oscillator. The results show that shift rotation pattern chiefly modulates the circadian time structure of shift workers. It is also suggested that the phenomenon of circadian rhythm desynchronization in oral temperature appears to be independent of per day total sleep length.     

Within- and among-population variation in oviposition preference for urea-supplemented food inDrosophila melanogaster

Oviposition preference for ureasupplemented food was assayed by simultaneous choice trials on five pairs of closely related laboratory populations of Drosophila melanogaster.Each pair of populations had been derived from a separate ancestral population about 85 generations prior to this study. One population in each pair had been subjected to selection for larval tolerance to the toxic effects of urea; the other population served as a control. Considerable variation in oviposition preference was seen both within and among populations, with four of the ten populations showing a significant mean preference for ureasupplemented food. The degree of specificity shown by individual females was surprisingly high, leading to a bimodal distribution of oviposition preference in some populations. Overall, selection for larval tolerance to urea did not significantly affect oviposition preference. However, the data indicated that pairwise comparisons between randomly selected populations from the two larval selection regimes would lead to a range of possible outcomes, suggesting, in several cases, that selection for larval urea tolerance had led to significant differentiation of adult oviposition preference for urea in one or the other direction. The results, therefore, highlight the importance of population level replication and caution against the practice, common in ecological studies, of assaying oviposition preference in two populations that utilize different hosts in nature, and then drawing broad evolutionary inferences from the results.     

Desmin detection in FNAB samples of rhabdomyosarcoma: an immunocytochemical study

We performed immunocytochemical (ICC) staining for desmin on 65 fine needle aspiration biopsies from 45 patients with rhabdomyosarcoma, using the avidin-biotin-peroxidase complex method (ABC), and two types of antibodies, D33 and DE-R-11. The material was fixed either in ether-alcohol or in Delaunay's solution. The ABC method was applied to Papanicolaou stained slides, without destaining. We compared the quality of staining on fresh, routinely prepared slides vs archival material and the quality of staining on smears vs cytospins. In 20 cases, D33 and DE-R-II were applied to a pair of slides from the same tumour sample in order to see if there was any difference in their ability to recognize desmin. Desmin was positive in all 18 cases in which ICC staining was performed at the same time diagnoses were given. Among the 27 cases where ICC staining was carried out on archival material, seven were negative. Slides from four of these cases were 20 or more years old and negative reaction could be attributed to heating of slides before coversliping and/or to uneven distribution of desmin immunoreactivity in tumours. The second reason was probably the cause of negative reactions in cases from 1985 and 87. The type of slide preparation had no influence on the quality of staining. However, results were easier to read on cytospins because cells were more evenly distributed. Finally, our results proved that there was no significant difference between D33 and DE-R-11 in their ability to recognize desmin.     

Hydrogen peroxide-induced chlorophyll a bleaching in the cytochrome b 6 f complex: a simple and effective assay for stability of the complex in detergent solutions

The instability of cytochrome b ₆ f complex in detergent solutions is a well-known problem that has been studied extensively, but without finding a satisfactory solution. One of the important reasons can be short of the useful method to verify whether the complex suspended in different detergent is in an intact state or not. In this article, a simple and effective assay for stability of the complex was proposed based on the investigation on the different effects of the two detergents, n-octyl-β-d-glucopyranoside (OG) and dodecyl-β-d-maltoside (DDM), on the properties of the complex. DDM stabilizes the complex preparation more effectively whereas OG denatures the interactions of the heme groups and pigment molecules with the protein environment, leading to the bleaching of chlorophyll a induced by addition of hydrogen peroxide. The assay of the use of hydrogen peroxide to characterize the complex by studying the bleaching of chlorophyll induced by hydrogen peroxide and the peroxidase activity of the complex was discussed. This simple method will probably be useful to study the stability of the complex. Xiao-Bo Chen and Xiao-Hui Zhao contributed equally to this work.     

Redox regulation of proliferation of lens epithelial cells in culture

Both oxidants and antioxidants have been shown to modulate cell proliferation. We studied the effects of hydrogen peroxide and two antioxidants on the rate of proliferation of lens epithelial cells in culture. Hydrogen peroxide at concentrations higher than 32 microM caused a significant inhibition of proliferation. However, in the concentration range of 0.01-0.5 microM, hydrogen peroxide stimulated the rate of proliferation. The effect of hydrogen peroxide was dependent on the amount of cells in an individual culture well, indicating decomposition of hydrogen peroxide by cellular enzymes. In order to eliminate the possibility of decomposition of the dose of hydrogen peroxide given as a bolus, we induced continual production of hydrogen peroxide by adding glucose oxidase to the incubation medium. We found that hydrogen peroxide, generated by 1-50 microU x ml(-1) of glucose oxidase significantly increased the rate of cell proliferation. This effect was most apparent at the beginning of the exponential phase of cellular growth. Glucose oxidase alone (100-500 microU x ml(-1)) did not produce any effect. The effects of pro-oxidative hydrogen peroxide were compared with the effects of two biologically important antioxidants, alpha-tocopherol and retinol. Both antioxidants completely inhibited proliferation at concentrations of 30 microM and higher. In contrast to retinol, the effect of alpha-tocopherol was dependent on the amount of cells, indicating cellular decomposition of alpha-tocopherol. The results document the possibility of redox regulation of cellular proliferation at physiologically relevant reactant concentrations.     

A relation between G-, C-, and N-band patterns as revealed by progressive oxidation of chromosomes and a note on the nature of N-bands

Near-ultraviolet irradiation of chromosome preparations mounted in a hydrogen peroxide solution resulted in an oxidative disintegration of the structure of fixed metaphase chromosomes with concomitant production of various band patterns appearing after staining with Giemsa. Neither irradiation nor hydrogen peroxide alone could produce banding. After irradiation in the presence of hydrogen peroxide the gradually increasing effect of oxidation on the chromosomes along the gradient of light intensities from the periphery of the slide towards the radiation focus in the centre of the slide became visible as G-, C-, and N-banding, respectively. Close to the centre only contours of chromosomes were left after this treatment. Although G-banding and differential DNA-extraction often went together, extraction of DNA was not an absolute requirement to obtain a G-band pattern. N-bands appeared to be the chromosomal regions that were most resistant to destruction. Staining methods specific for DNA failed to demonstrate these bands, although with Giemsa an intense staining reaction occurred. On the analogy of the staining behaviour of model protein preparations with Giemsa a phosphoprotein nature is suggested for the N-band material in the chromosomes.     

A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas

Microdissection has been used for the examination of tissues at DNA, RNA, and protein levels for over a decade. Laser capture microscopy (LCM) is the most common microdissection technique used today. In this technique, a laser is used to focally melt a thermoplastic membrane that overlies a dehydrated tissue section¹. The tissue section composite is then lifted and separated from the membrane. Although this technique can be used successfully for tissue examination, it is time consuming and expensive. Furthermore, the successful completion of procedures using this technique requires the use of a laser, thus limiting its use. A new more affordable and practical microdissection approach called mesodissection is a possible solution to the pitfalls of LCM. This technique employs the MESO-1/MeSectr system to mill the desired tissue from a slide mounted tissue sample while concurrently dispensing and aspirating fluid to recover the desired tissue sample into a consumable mill bit. Before the dissection process begins, the user aligns the formalin fixed paraffin embedded (FFPE) slide with a hematoxylin and eosin stained (H&E) reference slide. Thereafter, the operator annotates the desired dissection area and proceeds to dissect the appropriate segment. The program generates an archived image of the dissection. The main advantage of mesodissection is the short duration needed to dissect a slide, taking an average of ten minutes from set up to sample generation in this experiment. Additionally, the system is significantly more cost effective and user friendly. A slight disadvantage is that it is not as precise as laser capture microscopy. In this article we demonstrate how mesodissection can be used to extract RNA from slides from FFPE granulomas caused by Mycobacterium tuberculosis (Mtb).     

Structural Evidence that Peroxiredoxin Catalytic Power Is Based on Transition-State Stabilization

Peroxiredoxins (Prxs) are important peroxidases associated with both antioxidant protection and redox signaling. They use a conserved Cys residue to reduce peroxide substrates. The Prxs have a remarkably high catalytic efficiency that makes them a dominant player in cell-wide peroxide reduction, but the origins of their high activity have been mysterious. We present here a novel structure of human PrxV at 1.45 Å resolution that has a dithiothreitol bound in the active site with its diol moiety mimicking the two oxygens of a peroxide substrate. This suggests diols and similar di-oxygen compounds as a novel class of competitive inhibitors for the Prxs. Common features of this and other structures containing peroxide, peroxide-mimicking ligands, or peroxide-mimicking water molecules reveal hydrogen bonding and steric factors that promote its high reactivity by creating an oxygen track along which the peroxide oxygens move as the reaction proceeds. Key insights include how the active-site microenvironment activates both the peroxidatic cysteine side chain and the peroxide substrate and how it is exquisitely well suited to stabilize the transition state of the in-line S_N2 substitution reaction that is peroxidation.     

Reactions of Peroxynitrite and Nitrite with Organic Molecules and Hemoglobin

In this work, the reactions of nitrite (NO2-) and peroxynitrite (ONOO-) with organic molecules as well as with hemoglobin (Hb) were examined and the potential interference with the detection of hydrogen peroxide and Hb was investigated. ONOO- at low concentrations (35-140 microM) induced a concentration-dependent oxidation of o-phenylenediamine and guaiacol, and this process can be improved by the addition of Hb in a concentration-dependent manner. This enhancing effect of Hb was possibly due to the formation of such highly reactive species as ferrylHb during the reaction of ONOO- and Hb. NO2- also oxidized the aromatic amine o-phenylenediamine, but its efficiency was much lower than that of ONOO-. A 300-fold excess of NO2- over hydrogen peroxide inhibited the oxidation of Pyrogallol Red mediated by hydrogen peroxide and Hb, which was due in part to the reaction of NO2- with Hb ferryl species compound I and compound II and the phenoxyl radical. These data suggest that ONOO- and NO2- can interfere with the detection of hydrogen peroxide. The overestimation or underestimation of the hydrogen peroxide detected is dependent upon the organic molecule utilized for detection and the relative rate of NO2-, superoxide, and ONOO- generation.     

不同纤维桩表面处理方式对牙根修复后抗折裂强度的影响

目的:探讨不同纤维桩表面处理方式对牙根修复后抗折裂强度的影响。方法:收集行正畸拔除的前磨牙120颗作为本研究样本,随机将120个纤维桩分为对照组、喷砂组和过氧化氢酸蚀组,每组40例。对照组纤维桩表明不给予任何处理,喷砂组给予氧化铝砂粒持续喷砂粗化处理,过氧化氢酸蚀组给予10%过氧化氢溶液处理,均包埋于纤维桩道预备好的离体牙内,采用相同树脂制备成核,行全冠修复与黏固,再模拟口腔内部环境给予样本牙冷热循环处理,经相同环境加载后,置于电子万能实验机获取样本牙抗折裂强度数据。对比三组离体牙样本体型数据、离体牙断裂方式、抗折裂强度,对三组进行为期24个月的定期随访,统计三组修复体断裂率,并采用Kaplan-Meier曲线和Log Rank法分析三组的生存状况。结果:三组的离体牙样本关于牙齿长度、牙根长度、颈部颊舌径及颈部近远中径对比差异无统计学意义(P0.05);喷砂组和过氧化氢酸蚀组的离体牙抗折裂强度显著强于对照组(P0.05);喷砂组和过氧化氢酸蚀组的牙齿折裂总发生率分别为20.00%和22.50%,均显著低于对照组的70.00%(P0.05)。但两组间比较差异无统计学意义(P0.05)。喷砂组、过氧化氢酸蚀组的生存状况显著优于对照组。结论:前磨牙修复过程中,对纤维桩表面进行喷砂或过氧化氢酸蚀处理均能提高牙根修复后抗折裂强度,改善修复体修复效果生存状况,且两种纤维桩表面处理方式对离体牙样本的断裂方式和抗折裂强度影响相当。     

Remediation of a Diesel-Contaminated Soil Using a Fenton-Like Advanced Oxidation Process: Optimization by Response Surface Methodology

Magnetite, a naturally occurring mineral of iron oxide, and zero-valent iron (ZVI) were used to catalyze hydrogen peroxide and initiate a dark Fenton-like reaction of diesel-contaminated loamy sand in a batch system at circumneutral pH. The effects of hydrogen peroxide concentration and catalyst content on the removal efficiency of total petroleum hydrocarbons (TPHs) were studied. A central composite rotatable design was applied and the derived equation for magnetite and ZVI were linear and quadratic, respectively. In both equations, the factor of hydrogen peroxide concentration was more significant than catalyst content. At optimum conditions (4.27 wt% of catalyst content and 2.17 mol/L of hydrogen peroxide), 57% and 67% of TPH removal were achieved by magnetite and ZVI, respectively. The obtained results suggest the potential of ZVI and magnetite to catalyze a heterogeneous Fenton-like reaction at circumneutral pH. It seems that using ZVI, rather than magnetite, as a catalyst may result in slightly more TPH mineralization; however, since magnetite is a naturally occurring mineral, it may be able to compete economically with ZVI.     

A possible origin of chemiluminescence in phagocytosing neutrophils. Reaction between chloramines and H2O2

A mixture of chloramines and hydrogen peroxide emits light. It was found that the reaction between taurine monochloramine and hydrogen peroxide is very slow. The stoichiometry of the reaction is 1:1 and taurine is detected as one of the products. The chlorinated proteins and bacteria, containing N-Cl groups, when reacting with hydrogen peroxide, are more effective in emitting light than low-molecular chloramines. Luminol enhances considerably light yield of the chloramine-hydrogen peroxide reaction. The chloramine-H2O2 reaction may account for light emitted by neutrophils during phagocytosis.     

Biosynthetic systems for nonribosomal peptide antibiotic assembly

Modular peptide synthetases, which act as the protein templates for the synthesis of a large number of peptide antibiotics and siderophores, hold great potential for the development of novel compounds. Recently, significant progress has been made towards understanding their molecular architecture and substrate specificity. The first crystal structure of a peptide synthetase has been solved, and the enzymes responsible for post-translational modification of peptide synthetases have recently been discovered. These will allow addressing important yet poorly understood mechanistic aspects.